• Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features

    Finkel Y., Schmiedel D., Tai-Schmiedel J. et al., Nachshon A., Winkler R., Dobesova M., Schwartz M., Mandelboim O., Stern-Ginossar N. (2020), eLife. 9, 50960   |  All authors
  • The NADH Dehydrogenase Nde1 Executes Cell Death after Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface

    Saladi S., Boos F., Poglitsch M. et al., Meyer H., Sommer F., Muehlhaus T., Schroda M., Schuldiner M., Madeo F., Herrmann J. M. (2020), Molecular Cell. 77, 1, p. 189-202   |  All authors
  • Systematic Detection of Amino Acid Substitutions in Proteomes Reveals Mechanistic Basis of Ribosome Errors and Selection for Translation Fidelity

    Mordret E., Dahan O., Asraf O. et al., Rak R., Yehonadav A., Barnabas G. D., Cox J., Geiger T., Lindner A. B., Pilpel Y. (2019), Molecular Cell. 75, 3, p. 427-441   |  All authors
  • Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

    Jaitin D. A., Adlung L., Thaiss C. A. et al., Weiner A., Li B., Descamps H., Lundgren P., Bleriot C., Liu Z., Deczkowska A., Keren-Shaul H., David E., Zmora N., Eldar S. M., Lubezky N., Shibolet O., Hill D. A., Lazar M. A., Colonna M., Ginhoux F., Shapiro H., Elinav E., Amit I. (2019), Cell. 178, 3, p. 686-698.e14   |  All authors
  • Spatial heterogeneity in the mammalian liver

  • Cooperativity between stromal cytokines drives the invasive migration of human breast cancer cells

    Elisha Y., Sagi Y., Klein G. et al., Straussman R., Geiger B. (2019), Philosophical Transactions of the Royal Society B: Biological Sciences. 374, 1779, 20180231   |  All authors
  • No guts, no research glory

  • Conversion of Escherichia coli to Generate All Biomass Carbon from CO2

    Gleizer S., Ben-Nissan R., Bar-On Y. M. et al., Antonovsky N., Noor E., Zohar Y., Jona G., Krieger E., Shamshoum M., Bar-Even A., Milo R. (2019), Cell. 179, 6, p. 1255-1263   |  All authors
  • The mitochondrial intermembrane space-facing proteins Mcp2 and Tgl2 are involved in yeast lipid metabolism

    Odendall F., Backes S., Tatsuta T. et al., Weill U., Schuldiner M., Langer T., Herrmann J. M., Rapaport D., Dimmer K. S. (2019), Molecular Biology of the Cell. 30, 21, p. 2681-2694   |  All authors
  • Tumor diversity and the trade-off between universal cancer tasks

    Hausser J., Szekely P., Bar N. et al., Zimmer A., Sheftel H., Caldas C., Alon U. (2019), Nature Communications. 10, 5423   |  All authors
  • Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

    Zviran A., Mor N., Rais Y. et al., Gingold H., Peles S., Chomsky E., Viukov S., Buenrostro J. D., Scognamiglio R., Weinberger L., Manor Y. S., Krupalnik V., Zerbib M., Hezroni H., Jaitin D. A., Larastiaso D., Gilad S., Benjamin S., Gafni O., Mousa A., Ayyash M., Sheban D., Bayerl J., Aguilera-Castrejon A., Massarwa R., Maza I., Hanna S., Stelzer Y., Ulitsky I., Greenleaf W. J., Tanay A., Trumpp A., Amit I., Pilpel Y., Novershtern N., Hanna J. H. (2019), Cell Stem Cell. 24, 2, p. 328-341.e9   |  All authors
  • A niche-dependent myeloid transcriptome signature defines dormant myeloma cells

    Khoo W. H., Ledergor G., Weiner A. et al., Roden D. L., Terry R. L., McDonald M. M., Chai R. C., De Veirman K., Owen K. L., Opperman K. S., Vandyke K., Clark J. R., Seckinger A., Kovacic N., Nguyen A., Mohanty S. T., Pettitt J. A., Xiao Y., Corr A. P., Seeliger C., Novotny M., Lasken R. S., Nguyen T., Oyajobi B. O., Aftab D., Swarbrick A., Parker B., Hewett D. R., Hose D., Vanderkerken K., Zannettino A. C. W., Amit I., Phan T. G., Croucher P. (2019), Blood. 134, 1, p. 30-43   |  All authors
  • Widespread Utilization of Peptide Communication in Phages Infecting Soil and Pathogenic Bacteria

    Stokar-Avihail A., Tal N., Erez Z. et al., Lopatina A., Sorek R. (2019), Cell Host & Microbe. 25, 5, p. 746-755.e5   |  All authors
  • Potential roles of gut microbiome and metabolites in modulating ALS in mice

    Blacher E., Bashiardes S., Shapiro H. et al., Rothschild D., Mor U., Dori-Bachash M., Kleimeyer C., Moresi C., Harnik Y., Zur M., Zabari M., Brik R. B., Kviatcovsky D., Zmora N., Cohen Y., Bar N., Levi I., Amar N., Mehlman T., Brandis A., Biton I., Kuperman Y., Tsoory M., Alfahel L., Harmelin A., Schwartz M., Israelson A., Arike L., Johansson M. E. V., Hansson G. C., Gotkine M., Segal E., Elinav E. (2019), Nature. 572, 7770, p. 474-480   |  All authors
  • Long Noncoding RNA MALAT1 Regulates Cancer Glucose Metabolism by Enhancing mTOR-Mediated Translation of TCF7L2

    Malakar P., Stein I., Saragovi A. et al., Winkler R., Stern-Ginossar N., Berger M., Pikarsky E., Karni R. (2019), Cancer Research. 79, 10, p. 2480-2493   |  All authors
  • Sybil-Resilient Conductance-Based Community Growth

    Poupko O., Shahaf G., Shapiro E. et al., Talmon N. (2019), COMPUTER SCIENCE - THEORY AND APPLICATIONS. Springer Basel AG, p. 359-371 (Lecture Notes in Computer Science).   |  All authors
  • MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

    Baran Y., Bercovich A., Sebe-Pedros A. et al., Lubling Y., Giladi A., Chomsky E., Meir Z., Hoichman M., Lifshitz A., Tanay A. (2019), GENOME BIOLOGY. 20, 1, 206   |  All authors
  • The global mass and average rate of rubisco

  • The cancer microbiome

    Elinav E., Garrett W. S., Trinchieri G. et al., Wargo J. (2019), Nature Reviews Cancer. 19, 7, p. 371-376   |  All authors
  • A rhlI 5 ' UTR-Derived sRNA Regulates RhlR-Dependent Quorum Sensing in Pseudomonas aeruginosa

    Thomason M. K., Voichek M., Dar D. et al., Addis V., Fitzgerald D., Gottesman S., Sorek R., Greenberga E. P. (2019), mBio. 10, 5, ARTN e0225   |  All authors
  • Evolthon: A community endeavor to evolve lab evolution

    Kaminski Strauss S., Schirman D., Jona G. et al., Brooks A. N., Kunjapur A. M., Ba A. N. N., Flint A., Solt A., Mershin A., Dixit A., Yona A. H., Csorgo B., Busby B. P., Hennig B. P., Pal C., Schraivogel D., Schultz D., Wernick D. G., Agashe D., Levi D., Zabezhinsky D., Russ D., Sass E., Tamar E., Herz E., Levy E. D., Church G. M., Yelin I., Nachman I., Gerst J. E., Georgeson J. M., Adamala K. P., Steinmetz L. M., Ruebsam M., Ralser M., Klutstein M., Desai M. M., Walunjkar N., Yin N., Hefetz N. A., Jakimo N., Snitser O., Adini O., Kumar P., Smith R. S. H., Zeidan R., Hazan R., Rak R., Kishony R., Johnson S., Nouriel S., Vonesch S. C., Foster S., Dagan T., Wein T., Karydis T., Wannier T. M., Stiles T., Olin-Sandoval V., Mueller W. F., Bar-On Y. M., Dahan O., Pilpel Y. (2019), PLoS Biology. 17, 3, p. e3000182, 3000182   |  All authors
  • PD-1/PD-L1 checkpoint blockade harnesses monocyte-derived macrophages to combat cognitive impairment in a tauopathy mouse model

    Rosenzweig N., Dvir-Szternfeld R., Tsitsou-Kampeli A. et al., Keren-Shaul H., Ben-Yehuda H., Weill-Raynal P., Cahalon L., Kertser A., Baruch K., Amit I., Weiner A., Schwartz M. (2019), Nature Communications. 10, 465   |  All authors
  • Noise-precision tradeoff in predicting combinations of mutations and drugs

    Tendler A., Zimmer A., Mayo A. et al., Alon U. (2019), PLoS Computational Biology. 15, 5, 1006956   |  All authors
  • Leukocyte-specific siRNA delivery revealing IRF8 as a potential anti-inflammatory target

    Veiga N., Goldsmith M., Diesendruck Y. et al., Ramishetti S., Rosenblum D., Elinav E., Behlke M. A., Benhar I., Peer D. (2019), Journal of Controlled Release. 313, p. 33-41   |  All authors
  • Transcriptional Heterogeneity of Beta Cells in the Intact Pancreas

    Farack L., Golan M., Egozi A. et al., Dezorella N., Halpern K. B., Ben-Moshe S., Garzilli I., Toth B., Roitman L., Krizhanovsky V., Itzkovitz S. (2019), Developmental Cell. 48, 1, p. 115-125.e4   |  All authors
  • Infinite Assembly of Folded Proteins in Evolution, Disease, and Engineering

    Garcia-Seisdedos H., Villegas J. A., Levy E. D. (2019), Angewandte Chemie - International Edition. 58, 17, p. 5514-5531
  • Central dogma rates and the trade-off between precision and economy in gene expression

    Hausser J., Mayo A., Keren L. et al., Alon U. (2019), Nature Communications. 10, 68   |  All authors
  • Successful Brincidofovir Treatment of Metagenomics-detected Adenovirus Infection in a Severely Ill Signal Transducer and Activator of Transcription-1-deficient Patient

    Averbuch D., Safadi R., Dar D. et al., Wolf D., Cherniak M., Sorek R., Amit S. (2019), Pediatric Infectious Disease Journal. 38, 3, p. 297-299   |  All authors
  • Systematic interrogation of human promoters

    Weingarten-Gabbay S., Nir R., Lubliner S. et al., Sharon E., Kalma Y., Weinberger A., Segal E. (2019), Genome Research. 29, 2, p. 171-183   |  All authors
  • Revisiting Trade-offs between Rubisco Kinetic Parameters

    Flamholz A., Prywes N., Moran U. et al., David D., Bar-On Y. M., Oltrogge L. M., Alves R., Savage D., Milo R. (2019), Biochemistry. 58, 31, p. 3365-3376   |  All authors
  • Coming together to define membrane contact sites

    Scorrano L., De Matteis M. A., Emr S. et al., Giordano F., Hajnoczky G., Kornmann B., Lackner L. L., Levine T. P., Pellegrini L., Reinisch K., Rizzuto R., Simmen T., Stenmark H., Ungermann C., Schuldiner M. (2019), Nature Communications. 10, 1287   |  All authors
  • Identity domains capture individual differences from across the behavioral repertoire

    Forkosh O., Karamihalev S., Roeh S. et al., Alon U., Anpilov S., Touma C., Nussbaumer M., Flachskamm C., Kaplick P. M., Shemesh Y., Chen A. (2019), Nature Neuroscience. 22, 12, p. 2023-2028   |  All authors
  • Senescent cell turnover slows with age providing an explanation for the Gompertz law

    Karin O., Agrawal A., Porat Z. et al., Krizhanovsky V., Alon U. (2019), Nature Communications. 10, 5495   |  All authors
  • Overexpression of branched-chain amino acid aminotransferases rescues the growth defects of cells lacking the Barth syndrome-related gene TAZ1

    Antunes D., Chowdhury A., Aich A. et al., Saladi S., Harpaz N., Stahl M., Schuldiner M., Herrmann J. M., Rehling P., Rapaport D. (2019), Journal Of Molecular Medicine-Jmm. 97, 2, p. 269-279   |  All authors
  • The role of the microbiome in NAFLD and NASH

    Kolodziejczyk A. A., Zheng D., Shibolet O. et al., Elinav E. (2019), EMBO Molecular Medicine. 11, 2, e9302   |  All authors
  • Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

    Li H., van der Leun A. M., Yofe I. et al., Lubling Y., Gelbard-Solodkin D., van Akkooi A. C. J., van den Braber M., Rozeman E. A., Haanen J. B. A. G., Blank C. U., Horlings H. M., David E., Baran Y., Bercovich A., Lifshitz A., Schumacher T. N., Tanay A., Amit I. (2019), Cell. 176, 4, p. 775-789.e18   |  All authors
  • Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds

    Sas-Chen A., Schwartz S. (2019), Methods. 156, p. 53-59
  • The rationale and design of the personal diet study, a randomized clinical trial evaluating a personalized approach to weight loss in individuals with pre-diabetes and early-stage type 2 diabetes

    Popp C. J., St-Jules D. E., Hu L. et al., Ganguzza L., Illiano P., Curran M., Li H., Schoenthaler A., Bergman M., Schmidt A. M., Segal E., Godneva A., Sevick M. A. (2019), Contemporary Clinical Trials. 79, p. 80-88   |  All authors
  • Disease-causing mutations in subunits of OXPHOS complex I affect certain physical interactions

    Barshad G., Zlotnikov-Poznianski N., Gal L. et al., Schuldiner M., Mishmar D. (2019), Scientific Reports. 9, 1, 9987   |  All authors
  • YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries

    Dubreuil B., Sass E., Nadav Y. et al., Heidenreich M., Georgeson J. M., Weill U., Duan Y., Meurer M., Schuldiner M., Knop M., Levy E. D. (2019), Nucleic Acids Research. 47, D1, p. D1245-D1249   |  All authors
  • Deciphering the "m6A Code" via Antibody-Independent Quantitative Profiling

    Garcia-Campos M. A., Edelheit S., Toth U. et al., Safra M., Shachar R., Viukov S., Winkler R., Nir R., Lasman L., Brandis A., Hanna J. H., Rossmanith W., Schwartz S. (2019), Cell. 178, 3, p. 731-747   |  All authors
  • c-Met activation leads to the establishment of a TGF beta-receptor regulatory network in bladder cancer progression

    Sim W. J., Iyengar P. V., Lama D. et al., Lui S. K. L., Ng H. C., Haviv-Shapira L., Domany E., Kappei D., Tan T. Z., Saie A., Jaynes P. W., Verma C. S., Kumar A. P., Rouanne M., Ha H. K., Radulescu C., ten Dijke P., Eichhorn P. J. A., Thiery J. P. (2019), Nature Communications. 10, 4349   |  All authors
  • Cytotoxicity of 1-deoxysphingolipid unraveled by genome-wide genetic screens and lipidomics in Saccharomyces cerevisiae

    Haribowo A. G., Hannich J. T., Michel A. H. et al., Megyeri M., Schuldiner M., Kornmann B., Riezman H. (2019), Molecular Biology of the Cell. 30, 22, p. 2814-2826   |  All authors
  • Generation of Human Primordial Germ Cell-like Cells at the Surface of Embryoid Bodies from Primed-pluripotency Induced Pluripotent Stem Cells

    Mitsunaga S., Shioda K., Isselbacher K. J. et al., Hanna J. H., Shioda T. (2019), Jove-Journal Of Visualized Experiments. 143, e58297   |  All authors
  • Pro-inflammatory Cytokines Alter the Immunopeptidome Landscape by Modulation of HLA-B Expression

    Javitt A., Barnea E., Kramer M. P. et al., Wolf-Levy H., Levin Y., Admon A., Merbl Y. (2019), Frontiers in Immunology. 10, 141   |  All authors
  • Structural variation in the gut microbiome associates with host health

    Zeevi D., Korem T., Godneva A. et al., Bar N., Kurilshikov A., Lotan-Pompan M., Weinberger A., Fu J., Wijmenga C., Zhernakova A., Segal E. (2019), Nature. 568, p. 43-48   |  All authors
  • Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries

    Mikl M., Hamburg A., Pilpel Y. et al., Segal E. (2019), Nature Communications. 10, 4572   |  All authors
  • Transfer of the Septin Ring to Cytokinetic Remnants in ER Stress Directs Age-Sensitive Cell-Cycle Re-entry

    Chao J. T., Pina F., Onishi M. et al., Cohen Y., Lai Y., Schuldiner M., Niwa M. (2019), Developmental Cell. 51, 2, p. 173-191   |  All authors
  • High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding

    Bykov Y. S., Cohen N., Gabrielli N. et al., Manenschijn H., Welsch S., Chlanda P., Kukulski W., Patil K. R., Schuldiner M., Briggs J. A. G. (2019), Journal of Cell Biology. 218, 8, p. 2797-2811   |  All authors
  • Citrobacter rodentium induces rapid and unique metabolic and inflammatory responses in mice suffering from severe disease

    Carson D., Barry R., Hopkins E. G. D. et al., Roumeliotis T., Garcia-Weber D., Mullineaux-Sanders C., Elinav E., Arrieumerlou C., Choudhary J. S., Frankel G. (2019), Cellular Microbiology. 13126   |  All authors
  • Dynamic lineage priming is driven via direct enhancer regulation by ERK

    Hamilton W. B., Mosesson Y., Monteiro R. S. et al., Emdal K. B., Knudsen T. E., Francavilla C., Barkai N., Olsen J. V., Brickman J. M. (2019), Nature. 575, 7782, p. 355-360   |  All authors
  • Vaginal microbiome transplantation in women with intractable bacterial vaginosis

    Lev-Sagie A., Goldman-Wohl D., Cohen Y. et al., Dori-Bachash M., Leshem A., Mor U., Strahilevitz J., Moses A. E., Shapiro H., Yagel S., Elinav E. (2019), Nature Medicine. 25, 10, p. 1500-+   |  All authors
  • Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis

    Betin V., Penaranda C., Bandyopadhyay N. et al., Yang R., Abitua A., Bhattacharyya R. P., Fan A., Avraham R., Livny J., Shoresh N., Hung D. T. (2019), Scientific Reports. 9, 19244   |  All authors
  • MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing

    Keren-Shaul H., Kenigsberg E., Jaitin D. A. et al., David E., Paul F., Tanay A., Amit I. (2019), NATURE PROTOCOLS. 14, 6, p. 1841-1862   |  All authors
  • Compartmentalized Synthesis of Triacylglycerol at the Inner Nuclear Membrane Regulates Nuclear Organization

    Barbosa A. D., Lim K., Mari M. et al., Edgar J. R., Gal L., Sterk P., Jenkins B. J., Koulman A., Savage D. B., Schuldiner M., Reggiori F., Wigge P. A., Siniossoglou S. (2019), Developmental Cell. 50, 6, p. 755-766   |  All authors
  • Global views of proteasome-mediated degradation by mass spectrometry

  • Plasmacytoid dendritic cells develop from Ly6D(+) lymphoid progenitors distinct from the myeloid lineage

    Dress R. J., Dutertre C., Giladi A. et al., Schlitzer A., Low I., Shadan N. B., Tay A., Lum J., Kairi M. F. B. M., Hwang Y. Y., Becht E., Cheng Y., Chevrier M., Larbi A., Newell E. W., Amit I., Chen J., Ginhoux F. (2019), Nature Immunology. 20, p. 852-864   |  All authors
  • Deep microbial analysis of multiple placentas shows no evidence for a placental microbiome

    Kuperman A. A., Zimmerman A., Hamadia S. et al., Ziv O., Gurevich V., Fichtman B., Gavert N., Straussman R., Rechnitzer H., Barzilay M., Shvalb S., Bornstein J., Ben-Shachar I., Yagel S., Haviv I., Koren O. (2019), BJOG: An International Journal of Obstetrics and Gynaecology.   |  All authors
  • The Transcriptome of Latent Human Cytomegalovirus

    Schwartz M., Stern-Ginossar N. (2019), Journal of Virology. 93, 11, ARTN e0004
  • Geometric description of self-interaction potential in symmetric protein complexes

    Empereur-Mot C., Garcia-Seisdedos H., Elad N. et al., Dey S., Levy E. D. (2019), Scientific data. 6, 64   |  All authors
  • Embrace the fat when getting old

    Adlung L., Amit I., Elinav E. (2019), AGING-US. 11, 20, p. 8730-8732
  • Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells

    Ben-Moshe N. B., Hen-Avivi S., Levitin N. et al., Yehezkel D., Oosting M., Joosten L. A. B., Netea M. G., Avraham R. (2019), Nature Communications. 10, 3266   |  All authors
  • Genuine Personal Identifiers and Mutual Sureties for Sybil-Resilient Community Formation

    Shahaf G., Shapiro E., Talmon N. (2019), arXiv.
  • DC Respond to Cognate T Cell Interaction in the Antigen-Challenged Lymph Node

    Curato C., Bernshtein B., Zupancic E. et al., Dufner A., Jaitin D., Giladi A., David E., Chappell-Maor L., Leshkowitz D., Knobeloch K., Amit I., Florindo H. F., Jung S. (2019), Frontiers in Immunology. 10, 863   |  All authors
  • Diet-microbiota interactions and personalized nutrition

    Kolodziejczyk A. A., Zheng D., Elinav E. (2019), Nature Reviews Microbiology. 17, 12, p. 742-753
  • A Significant Expansion of Our Understanding of the Composition of the Human Microbiome

    Leviatan S., Segal E. (2019), mSystems. 4, 1, ARTN e0001
  • Toward unrestricted use of public genomic data: Publication interests should not limit access to public data

    Amann R. I., Baichoo S., Blencowe B. J. et al., Bork P., Borodovsky M., Brooksbank C., Chain P. S. G., Colwell R. R., Daffonchio D. G., Danchin A., de Lorenzo V., Dorrestein P. C., Finn R. D., Fraser C. M., Gilbert J. A., Hallam S. J., Hugenholtz P., Ioannidis J. P. A., Jansson J. K., Kim J. F., Klenk H., Klotz M. G., Knight R., Konstantinidis K. T., Kyrpides N. C., Mason C. E., McHardy A. C., Meyer F., Ouzounis C. A., Patrinos A. A. N., Podar M., Pollard K. S., Ravel J., Munoz A. R., Roberts R. J., Rossello-Mora R., Sansone S., Schloss P. D., Schriml L. M., Setubal J. C., Sorek R., Stevens R. L., Tiedje J. M., Turjanski A., Tyson G. W., Ussery D. W., Weinstock G. M., White O., Whitman W. B., Xenarios I. (2019), Science. 363, 6425, p. 350-352   |  All authors
  • Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program

    Geirsdottir L., David E., Keren-Shaul H. et al., Weiner A., Bohlen S. C., Neuber J., Balic A., Giladi A., Sheban F., Dutertre C., Pfeifle C., Peri F., Raffo-Romero A., Vizioli J., Matiasek K., Scheiwe C., Meckel S., Maetz-Rensing K., van der Meer F., Thormodsson F. R., Stadelmann C., Zilkha N., Kimchi T., Ginhoux F., Ulitsky I., Erny D., Amit I., Prinz M. (2019), Cell. 179, 7, p. 1609-1622.e16   |  All authors
  • Microbiome diurnal rhythmicity and its impact on host physiology and disease risk

    Nobs S. P., Tuganbaev T., Elinav E. (2019), EMBO Reports. 20, 4, 47129
  • Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer

    Shee K., Jiang A., Varn F. S. et al., Liu S., Traphagen N. A., Owens P., Ma C. X., Hoog J., Cheng C., Golub T. R., Straussman R., Miller T. W. (2019), FASEB Journal. 33, 2, p. 1644-1657   |  All authors
  • Stem Cell-Derived Human Gametes: The Public Engagement Imperative

    Adashi E. Y., Cohen I. G., Hanna J. H. et al., Surani A. M., Hayashi K. (2019), Trends in Molecular Medicine. 25, 3, p. 165-167   |  All authors
  • Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability

    Rom A., Melamed L., Gil N. et al., Goldrich M. J., Kadir R., Golan M., Biton I., Perry R. B., Ulitsky I. (2019), Nature Communications. 10, 5092   |  All authors
  • Towards a quantitative view of the global ubiquity of biofilms

    Bar-On Y. M., Milo R. (2019),
  • Stage-specific requirement for Mettl3-dependent m(6)A mRNA methylation during haematopoietic stem cell differentiation

    Lee H., Bao S., Qian Y. et al., Geula S., Leslie J., Zhang C., Hanna J. H., Ding L. (2019), Nature Cell Biology. 21, p. 700-709   |  All authors
  • The pros, cons, and many unknowns of probiotics

    Suez J., Zmora N., Segal E. et al., Elinav E. (2019), Nature Medicine. 25, 5, p. 716-729   |  All authors
  • When Cultures Meet: The Landscape of "Social" Interactions between the Host and Its Indigenous Microbes

    Geva-Zatorsky N., Elinav E., Pettersson S. (2019), BioEssays. 1900002
  • IL-23-producing IL-10Rα-deficient gut macrophages elicit an IL-22-driven proinflammatory epithelial cell response

    Bernshtein B., Curato C., Ioannou M. et al., Thaiss C. A., Gross-Vered M., Kolesnikov M., Wang Q., David E., Chappell-Maor L., Harmelin A., Elinav E., Thakker P., Papayannopoulos V., Jung S. (2019), Science immunology. 4, 36, 6571   |  All authors
  • Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome

    Leshem A., Horesh N., Elinav E. (2019), Frontiers in Immunology. 10, 1341
  • The Biomass Composition of the Oceans: A Blueprint of Our Blue Planet

    Bar-On Y. M., Milo R. (2019), Cell. 179, 7, p. 1451-1454
  • Dynamics of Spaetzle morphogen shuttling in the Drosophila embryo shapes gastrulation patterning

    Rahimi N., Averbukh I., Carmon S. et al., Schejter E. D., Barkai N., Shilo B. (2019), Development. 146, 21, 181487   |  All authors
  • m6A modification controls the innate immune response to infection by targeting type I interferons

    Winkler R., Gillis E., Lasman L. et al., Safra M., Geula S., Soyris C., Nachshon A., Tai-Schmiedel J., Friedman N., Le-Trilling V. T. K., Trilling M., Mandelboim M., Hanna J. H., Schwartz S., Stern-Ginossar N. (2019), Nature Immunology. 20, 2, p. 173-182   |  All authors
  • An iPSC-Derived Myeloid Lineage Model of Herpes Virus Latency and Reactivation

    Poole E., Huang C. J. Z., Forbester J. et al., Shnayder M., Nachshon A., Kweider B., Basaj A., Smith D., Jackson S. E., Liu B., Shih J., Kiskin F. N., Roche K., Murphy E., Wills M. R., Morrell N. W., Dougan G., Stern-Ginossar N., Rana A. A., Sinclair J. (2019), Frontiers in Microbiology. 10, 2233   |  All authors
  • You are what you eat: diet, health and the gut microbiota

  • Children's Object Structure Perspective-Taking: Training and Assessment

  • Transmissible inflammation-induced colorectal cancer in inflammasome-deficient mice

    Hu B., Friedman G., Elinav E. et al., Flavell R. A. (2019), OncoImmunology. 8, 10, 981995   |  All authors
  • The N-6-Methyladenosine mRNA Methylase METTL3 Controls Cardiac Homeostasis and Hypertrophy

    Dorn L. E., Lasman L., Chen J. et al., Xu X., Hund T. J., Medvedovic M., Hanna J. H., van Berlo J. H., Accornero F. (2019), Circulation. 139, 4, p. 533-545   |  All authors
  • Corticosteroid signaling at the brain-immune interface impedes coping with severe psychological stress

    Kertser A., Baruch K., Deczkowska A. et al., Weiner A., Croese T., Kenigsbuch M., Cooper I., Tsoory M., Ben-Hamo S., Amit I., Schwartz M. (2019), Science advances. 5, 5, aav4111   |  All authors
  • Translational Control in Virus-Infected Cells

    Stern-Ginossar N., Thompson S. R., Mathews M. B. et al., Mohr I. (2019), Cold Spring Harbor perspectives in biology. 11, 3, a033001   |  All authors
  • Yeast ceramide synthases, Lag1 and Lac1, have distinct substrate specificity

    Megyeri M., Prasad R., Volpert G. et al., Sliwa-Gonzalez A., Haribowo A. G., Aguilera-Romero A., Riezman H., Barral Y., Futerman A. H., Schuldiner M. (2019), Journal of Cell Science. 132, 12, jcs228411   |  All authors
  • Mutual interplay between IL-17-producing γδT (gamma delta T) cells and microbiota orchestrates oral mucosal homeostasis

    Wilharm A., Tabib Y., Nassar M. et al., Reinhardt A., Mizraji G., Sandrock I., Heyman O., Barros-Martins J., Aizenbud Y., Khalaileh A., Eli-Berchoer L., Elinav E., Wilensky A., Foerster R., Bercovier H., Prinz I., Hovav A. (2019), Proceedings Of The National Academy Of Sciences Of The United States Of America-Physical Sciences. 116, 7, p. 2652-2661   |  All authors
  • Germline NPM1 mutations lead to altered rRNA 2 '-O-methylation and cause dyskeratosis congenita

    Nachmani D., Bothmer A. H., Grisendi S. et al., Mele A., Bothmer D., Lee J. D., Monteleone E., Cheng K., Zhang Y., Bester A. C., Guzzetti A., Mitchell C. A., Mendez L. M., Pozdnyakova O., Sportoletti P., Martelli M., Vulliamy T. J., Safra M., Schwartz S., Luzzatto L., Bluteau O., Soulier J., Darnell R. B., Falini B., Dokal I., Ito K., Clohessy J. G., Pandolfi P. P. (2019), Nature Genetics. 51, 10, p. 1518-1529   |  All authors
  • Protein Topology Prediction Algorithms Systematically Investigated in the Yeast Saccharomyces cerevisiae

    Weill U., Cohen N., Fadel A. et al., Ben-Dor S., Schuldiner M. (2019), BioEssays. 1800252   |  All authors
  • Harnessing the microbiota for therapeutic purposes

    Liwinski T., Elinav E. (2019), American Journal of Transplantation.
  • Cyclic GMP-AMP signalling protects bacteria against viral infection

    Cohen D., Melamed S., Millman A. et al., Shulman G., Oppenheimer-Shaanan Y., Kacen A., Doron S., Amitai G., Sorek R. (2019), Nature. 574, 7780, p. 691-695   |  All authors
  • Accurate detection of m6A RNA modifications in native RNA sequences

    Liu H., Begik O., Lucas M. C. et al., Ramirez J. M., Mason C. E., Wiener D., Schwartz S., Mattick J. S., Smith M. A., Novoa E. M. (2019), Nature Communications. 10, 1, 4079   |  All authors
  • ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma

    Srivastava S., Nataraj N. B., Sekar A. et al., Ghosh S., Bornstein C., Drago-Garcia D., Roth L., Romaniello D., Marrocco I., David E., Gilad Y., Lauriola M., Rotkopf R., Kimchi A., Haga Y., Tsutsumi Y., Mirabeau O., Surdez D., Zinovyev A., Delattre O., Kovar H., Amit I., Yarden Y. (2019), Cell Reports. 29, 1, p. 104-117   |  All authors
  • Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms

    Frumkin I., Yofe I., Bar-Ziv R. et al., Gurvich Y., Lu Y., Voichek Y., Towers R., Schirman D., Krebber H., Pilpel Y. (2019), PLoS Biology. 17, 8, 3000423   |  All authors
  • Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

    Riquelme E., Zhang Y., Zhang L. et al., Montiel M., Zoltan M., Dong W., Quesada P., Sahin I., Chandra V., San Lucas A., Scheet P., Xu H., Hanash S. M., Feng L., Burks J. K., Do K., Peterson C. B., Nejman D., Tzeng C. D., Kim M. P., Sears C. L., Ajami N., Petrosino J., Wood L. D., Maitra A., Straussman R., Katz M., White J. R., Jenq R., Wargo J., McAllister F. (2019), Cell. 178, 4, p. 795-806.e12   |  All authors
  • Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations

    Rojo R., Raper A., Ozdemir D. D. et al., Lefevre L., Grabert K., Wollscheid-Lengeling E., Bradford B., Caruso M., Gazova I., Sanchez A., Lisowski Z. M., Alves J., Molina-Gonzalez I., Davtyan H., Lodge R. J., Glover J. D., Wallace R., Munro D. A. D., David E., Amit I., Miron V. E., Priller J., Jenkins S. J., Hardingham G. E., Blurton-Jones M., Mabbott N. A., Summers K. M., Hohenstein P., Hume D. A., Pridans C. (2019), Nature Communications. 10, 3215   |  All authors
  • Universally non-immunogenic iPSCs

    Shani T., Hanna J. H. (2019), Nature Biomedical Engineering. 3, 5, p. 337-338
  • Sequence determinants of polyadenylation-mediated regulation

    Slutskin I. V., Weinberger A., Segal E. (2019), Genome Research. 29, 10, p. 1635-1647
  • Spatial sorting enables comprehensive characterization of liver zonation

    Ben-Moshe S., Shapira Y., Moor A. E. et al., Manco R., Veg T., Halpern K. B., Itzkovitz S. (2019), Nature metabolism. 1, p. 899-911   |  All authors
  • A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle

    Teufel L., Tummler K., Floettmann M. et al., Herrmann A., Barkai N., Klipp E. (2019), Scientific Reports. 9, 3343   |  All authors
  • Promethin Is a Conserved Seipin Partner Protein

    Castro I. G., Eisenberg-Bord M., Persiani E. et al., Rochford J. J., Schuldiner M., Bohnert M. (2019), Cells. 8, 3, 268   |  All authors
  • Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity

    Blecher-Gonen R., Bost P., Hilligan K. L. et al., David E., Salame T. M., Roussel E., Connor L. M., Mayer J. U., Halpern K. B., Toth B., Itzkovitz S., Schwikowski B., Ronchese F., Amit I. (2019), Cell Systems. 8, 2, p. 109-121.e6   |  All authors
  • The integrated stress response promotes B7H6 expression

    Obiedat A., Charpak-Amikam Y., Tai-Schmiedel J. et al., Seidel E., Mahameed M., Avril T., Stern-Ginossar N., Springuel L., Bolsee J., Gilham D. E., Dipta P., Shmuel M., Chevet E., Mandelboim O., Tirosh B. (2019), Journal Of Molecular Medicine-Jmm. p. 135-148   |  All authors
  • Assessment of GFP Tag Position on Protein Localization and Growth Fitness in Yeast

    Weill U., Krieger G., Avihou Z. et al., Milo R., Schuldiner M., Davidi D. (2019), Journal of Molecular Biology. 431, 3, p. 636-641   |  All authors
  • Transforming medicine with the microbiome

    Zmora N., Soffer E., Elinav E. (2019), Science Translational Medicine. 11, 477, eaaw1815
  • Resolving noise-control conflict by gene duplication

    Chapal M., Mintzer S., Brodsky S. et al., Carmi M., Barkai N. (2019), PLoS Biology. 17, 11, 3000289   |  All authors
  • The EXPANDER Integrated Platform for Transcriptome Analysis

    Hait T. A., Maron-Katz A., Sagir D. et al., Amar D., Ulitsky I., Linhart C., Tanay A., Sharan R., Shiloh Y., Elkon R., Shamir R. (2019), Journal of Molecular Biology. 431, 13, p. 2398-2406   |  All authors
  • Cell composition analysis of bulk genomics using single-cell data

    Frishberg A., Peshes-Yaloz N., Cohn O. et al., Rosentul D., Steuerman Y., Valadarsky L., Yankovitz G., Mandelboim M., Iraqi F. A., Amit I., Mayo L., Bacharach E., Gat-Viks I. (2019), Nature Methods. 16, 4, p. 327-332   |  All authors
  • Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

    Dietz S., Lifshitz A., Kazdal D. et al., Harms A., Endris V., Winter H., Stenzinger A., Warth A., Sill M., Tanay A., Sueltmann H. (2019), International Journal of Cancer. 144, 5, p. 1061-1072   |  All authors
  • The gut microbiota regulates white adipose tissue inflammation and obesity via a family of microRNAs

    Virtue A. T., McCright S. J., Wright J. M. et al., Jimenez M. T., Mowel W. K., Kotzin J. J., Joannas L., Basavappa M. G., Spencer S. P., Clark M. L., Eisennagel S. H., Williams A., Levy M., Manne S., Henrickson S. E., Wherry E. J., Thaiss C. A., Elinav E., Henao-Mejia J. (2019), Science Translational Medicine. 11, 496, 1892   |  All authors
  • A secretion-enhancing cis regulatory targeting element (SECReTE) involved in mRNA localization and protein synthesis

    Cohen-Zontag O., Baez C., Lim L. Q. J. et al., Olender T., Schirman D., Dahary D., Pilpel Y., Gerst J. E. (2019), PLoS Genetics. 15, 7, 1008248   |  All authors
  • Acid-Induced Downregulation of ASS1 Contributes to the Maintenance of Intracellular pH in Cancer

    Silberman A., Goldman O., Assayag O. B. et al., Jacob A., Rabinovich S., Adler L., Lee J. S., Keshet R., Sarver A., Frug J., Stettner N., Galai S., Persi E., Halpern K. B., Zaltsman-Amir Y., Pode-Shakked B., Eilam R., Anikster Y., Nagamani S. C. S., Ulitsky I., Ruppin E., Erez A. (2019), Cancer Research. 79, 3, p. 518-533   |  All authors
  • Short tandem repeat stutter model inferred from direct measurement of in vitro stutter noise

    Raz O., Biezuner T., Spiro A. et al., Amir S., Milo L., Titelman A., Onn A., Chapal-Ilani N., Tao L., Marx T., Feige U., Shapiro E. (2019), Nucleic Acids Research. 47, 5, p. 2436-2445   |  All authors
  • Prediction of ultra-high-order antibiotic combinations based on pairwise interactions

    Katzir I., Cokol M., Aldridge B. B. et al., Alon U. (2019), PLoS Computational Biology. 15, 1, 1006774   |  All authors
  • Walk on the wildling side

    Nobs S. P., Elinav E. (2019), Science. 365, 6452, p. 444-445
  • Continuum of Gene-Expression Profiles Provides Spatial Division of Labor within a Differentiated Cell Type

    Adler M., Kohanim Y. K., Tendler A. et al., Mayo A., Alon U. (2019), Cell Systems. 8, 1, p. 43-52.e5   |  All authors
  • Phenotypic Screen Identifies JAK2 as a Major Regulator of FAT10 Expression

    Reznik N., Kozer N., Eisenberg-Lerner A. et al., Barr H., Merbl Y., London N. (2019), ACS Chemical Biology. 14, 12, p. 2538-2545   |  All authors
  • Rho-Associated Coiled-Coil Kinase 1 Translocates to the Nucleus and Inhibits Human Cytomegalovirus Propagation

    Eliyahu E., Tirosh O., Dobesova M. et al., Nachshon A., Schwartz M., Stern-Ginossar N. (2019), Journal of Virology. 93, 19, 00453-19   |  All authors
  • Peer power - A women's peer-mentoring program at the workplace:: example from the academia

    Levy-Tzedek S., Moran G. S., Alon U. et al., Sal-Man N. (2018), EMBO Reports. 19, 12, 47246   |  All authors
  • Design principles of the paradoxical feedback between pancreatic alpha and beta cells

    Garzilli I., Itzkovitz S. (2018), Scientific Reports. 8, 10694
  • Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma

    Ledergor G., Weiner A., Zada M. et al., Wang S., Cohen Y. C., Gatt M. E., Snir N., Magen H., Koren-Michowitz M., Herzog-Tzarfati K., Keren-Shaul H., Bornstein C., Rotkopf R., Yofe I., David E., Yellapantula V., Kay S., Salai M., Ben Yehuda D., Nagler A., Shvidel L., Orr-Urtreger A., Halpern K. B., Itzkovitz S., Landgren O., San-Miguel J., Paiva B., Keats J. J., Papaemmanuil E., Avivi I., Barbash G. I., Tanay A., Amit I. (2018), Nature Medicine. 24, 12, p. 1867-+   |  All authors
  • Microglial immune checkpoint mechanisms

    Deczkowska A., Amit I., Schwartz M. (2018), Nature Neuroscience. 21, 6, p. 779-786
  • Revealing the cellular degradome by mass soectrometry analysis of proteasome-cleaved peptides

    Wolf-Levy H., Javitt A., Eisenberg-Lerner A. et al., Kacenl A., Ulman A., Sheban D., Dassa B., Fishbain-Yoskovitz V., Carmona-Rivera C., Kramer M. P., Nudel N., Regevl I., Zahavi L., Elinger D., Kaplan M. J., Morgenstern D., Levin Y., Merbl Y. (2018), Nature Biotechnology. 36, 11, p. 1110-1116   |  All authors
  • Environment dominates over host genetics in shaping human gut microbiota

    Rothschild D., Weissbrod O., Barkan E. et al., Kurilshikov A., Korem T., Zeevi D., Costea P. I., Godneva A., Kalka I. N., Bar N., Shilo S., Lador D., Vila A. V., Zmora N., Pevsner-Fischer M., Israeli D., Kosower N., Malka G., Wolf B. C., Avnit-Sagi T., Lotan-Pompan M., Weinberger A., Halpern Z., Carmi S., Fu J., Wijmenga C., Zhernakova A., Elinav E., Segal E. (2018), Nature. 555, 7695, p. 210-215   |  All authors
  • Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies

    Haimon Z., Volaski A., Orthgiess J. et al., Boura-Halfon S., Varol D., Shemer A., Yona S., Zuckerman B., David E., Chappell-Maor L., Bechmann I., Gericke M., Ulitsky I., Jung S. (2018), Nature Immunology. 19, 6, p. 636-+   |  All authors
  • Hypercalcemia: a consultant's approach

    Auron A., Alon U. S. (2018), Pediatric Nephrology. 33, 9, p. 1475-1488
  • Contemporary Phage Biology: From Classic Models to New Insights

    Ofir G., Sorek R. (2018), Cell. 172, 6, p. 1260-1270
  • Viruses cooperate to defeat bacteria

    Bernheim A., Sorek R. (2018), Nature. 559, 7715, p. 482-484
  • Endocytosis as a stabilizing mechanism for tissue homeostasis

    Adler M., Mayo A., Zhou X. et al., Franklin R. A., Jacox J. B., Medzhitov R., Alon U. (2018), Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115, 8, p. E1926-E1935   |  All authors
  • mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues

    Ben-Moshe N. B., Gilad S., Perry G. et al., Benjamin S., Balint-Lahat N., Pavlovsky A., Halperin S., Markus B., Yosepovich A., Barshack I., Gal-Yam E. N., Domany E., Kaufman B., Dadiani M. (2018), BMC Genomics. 19, 419   |  All authors
  • Loss of MicroRNA-21 Influences the Gut Microbiota, Causing Reduced Susceptibility in a Murine Model of Colitis

    Johnston D. G. W., Williams M. A., Thaiss C. A. et al., Cabrera-Rubio R., Raverdeau M., McEntee C., Cotter P. D., Elinav E., O'Neill L. A. J., Corr S. C. (2018), Journal of Crohn's and Colitis. 12, 7, p. 835-848   |  All authors
  • Sequential BMP7/TGF-beta 1 signaling and microbiota instruct mucosal Langerhans cell differentiation

    Capucha T., Koren N., Nassar M. et al., Heyman O., Nir T., Levy M., Zilberman-Schapira G., Zelentova K., Eli-Berchoer L., Zenke M., Hieronymus T., Wilensky A., Bercovier H., Elinav E., Clausen B. E., Hovav A. (2018), Journal of Experimental Medicine. 215, 2, p. 481-500   |  All authors
  • Salient experiences are represented by unique transcriptional signatures in the mouse brain

    Mukherjee D., Ignatowska-Jankowska B. M., Itskovits E. et al., Gonzales B. J., Turm H., Izakson L., Haritan D., Bleistein N., Cohen C., Amit I., Shay T., Grueter B., Zaslaver A., Citri A. (2018), eLife. 7, 31220   |  All authors
  • point:: Foundations of Internet-enabled Democracy

  • RAS Regulates the Transition from Naive to Primed Pluripotent Stem Cells

    Altshuler A., Verbuk M., Bhattacharya S. et al., Abramovich I., Haklai R., Hanna J. H., Kloog Y., Gottlieb E., Shalom-Feuerstein R. (2018), Stem Cell Reports. 10, 3, p. 1088-1101   |  All authors
  • DISARM is a widespread bacterial defence system with broad anti-phage activities

    Ofir G., Melamed S., Sberro H. et al., Mukamel Z., Silverman S., Yaakov G., Doron S., Sorek R. (2018), Nature Microbiology. 3, 1   |  All authors
  • Systematic mapping of contact sites reveals tethers and a function for the peroxisome-mitochondria contact

    Shai N., Yifrach E., van Roermund C. W. T. et al., Cohen N., Bibi C., Ijlst L., Cavellini L., Meurisse J., Schuster R., Zada L., Mari M. C., Reggiori F. M., Hughes A. L., Escobar-Henriques M., Cohen M. M., Waterham H. R., Wanders R. J. A., Schuldiner M., Zalckvar E. (2018), Nature Communications. 9, 1761   |  All authors
  • Programming cells and tissues New toolkits of biological parts allow powerful cell programming by synthetic biologists

    Glass D. S., Alon U. (2018), Science. 361, 6408, p. 1199-1200
  • PDB-wide identification of biological assemblies from conserved quaternary structure geometry

    Dey S., Ritchie D. W., Levy E. D. (2018), Nature Methods. 15, 1, p. 67-+
  • Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit

    Shammai A., Petreikov M., Yeselson Y. et al., Faigenboim A., Moy-Komemi M., Cohen S., Cohen D., Besaulov E., Efrati A., Houminer N., Bar M., Ast T., Schuldiner M., Klemens P. A. W., Neuhaus E., Baxter C. J., Rickett D., Bonnet J., White R., Giovannoni J. J., Levin I., Schaffer A. (2018), Plant Journal. 96, 2, p. 343-357   |  All authors
  • Meiotic Recombination: Genetics' Good Old Scalpel

    Slomka S., Pilpel Y. (2018), Cell. 172, 3, p. 391-392
  • Noise-Seeded Developmental Pattern Formation in Filamentous Cyanobacteria

    Arbel-Goren R., Di Patti F., Fanelli D. et al., Stavans J. (2018), Life-Basel. 8, 4, 58   |  All authors
  • Translational control of ERK signaling through miRNA/4EHP-directed silencing

    Jafarnejad S. M., Chapat C., Matta-Camacho E. et al., Gelbart I. A., Hesketh G. G., Arguello M., Garzia A., Kim S., Attig J., Shapiro M., Morita M., Khoutorsky A., Alain T., Christos G. G., Stern-Ginossar N., Tuschl T., Gingras A., Duchaine T. F., Sonenberg N. (2018), eLife. 7, 35034   |  All authors
  • The biomass distribution on Earth

  • An ER surface retrieval pathway safeguards the import of mitochondrial membrane proteins in yeast

    Hansen K. G., Aviram N., Laborenz J. et al., Bibi C., Meyer M., Spang A., Schuldiner M., Herrmann J. M. (2018), Science. 361, 6407, p. 1118-1122   |  All authors
  • Variants in PUS7 Cause Intellectual Disability with Speech Delay, Microcephaly, Short Stature, and Aggressive Behavior

    De Brouwer A. P. M., Abou Jamra R., Koertel N. et al., Soyris C., Polla D. L., Safra M., Zisso A., Powell C. A., Rebelo-Guiomar P., Dinges N., Morin V., Stock M., Hussain M., Shahzad M., Riazuddin S., Ahmed Z. M., Pfundt R., Schwarz F., de Boer L., Reis A., Grozeva D., Raymond F. L., Riazuddin S., Koolen D. A., Minczuk M., Roignant J., van Bokhoven H., Schwartz S. (2018), American Journal of Human Genetics. 103, 6, p. 1045-1052   |  All authors
  • A repressor-decay timer for robust temporal patterning in embryonic Drosophila neuroblast lineages

    Averbukh I., Lai S., Doe C. Q. et al., Barkai N. (2018), eLife. 7, 38631   |  All authors
  • Inferring and using protein quaternary structure information from crystallographic data

  • Evolutionary trade-offs and the structure of polymorphisms

    Sheftel H., Szekely P., Mayo A. et al., Sella G., Alon U. (2018), Philosophical Transactions of the Royal Society B: Biological Sciences. 373, 1747, 20170105   |  All authors
  • Dramatic action: A theater-based paradigm for analyzing human interactions

    Liron Y., Raindel N., Alon U. (2018), PLoS One. 13, 3, e0193404
  • Pax6 regulation of Sox9 in the mouse retinal pigmented epithelium controls its timely differentiation and choroid vasculature development

    Cohen-Tayar Y., Cohen H., Mitiagin Y. et al., Abravanel Z., Levy C., Idelson M., Reubinoff B., Itzkovitz S., Raviv S., Kaestner K. H., Blinder P., Elkon R., Ashery-Padan R. (2018), Development. 145, 15, dev163691   |  All authors
  • Sybil-Resilient Reality-Aware Social Choice

    Shahaf G., Shapiro E., Talmon N. (2018), arXiv.
  • Incorporating Reality into Social Choice

  • Repertoires of tRNAs: The Couplers of Genomics and Proteomics

  • Bile acids in glucose metabolism in health and disease

    Shapiro H., Kolodziejczyk A. A., Halstuch D. et al., Elinav E. (2018), Journal of Experimental Medicine. 215, 2, p. 383-396   |  All authors
  • Therapeutically targeting tumor microenvironment-mediated drug resistance in estrogen receptor-positive breast cancer

    Shee K., Yang W., Hinds J. W. et al., Hampsch R. A., Varn F. S., Traphagen N. A., Patel K., Cheng C., Jenkins N. P., Kettenbach A. N., Demidenko E., Owens P., Faber A. C., Golub T. R., Straussman R., Miller T. W. (2018), Journal of Experimental Medicine. 215, 3, p. 895-910   |  All authors
  • Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

    Mor N., Rais Y., Sheban D. et al., Peles S., Aguilera-Castrejon A., Zviran A., Elinger D., Viukov S., Geula S., Krupalnik V., Zerbib M., Chomsky E., Lasman L., Shani T., Bayerl J., Gafni O., Hanna S., Buenrostro J. D., Hagai T., Masika H., Vainorius G., Bergman Y., Greenleaf W. J., Esteban M. A., Elling U., Levin Y., Massarwa R., Merbl Y., Novershtern N., Hanna J. H. (2018), Cell Stem Cell. 23, 3, p. 412-425.e10   |  All authors
  • Role of the gut microbiota in nutrition and health

    Valdes A. M., Walter L., Segal E. et al., Spector T. D. (2018), British Medical Journal. 361, 2179   |  All authors
  • Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

    Giladi A., Amit I. (2018), Cell. 172, 1-2, p. 14-21
  • Temporal Stability of the Healthy Human Skin Microbiome Following Dead Sea Climatotherapy

    Brandwein M., Fuks G., Israel A. et al., Al-Ashhab A., Nejman D., Straussman R., Hodak E., Harari M., Steinberg D., Bentwich Z., Shental N., Meshner S. (2018), Acta Dermato-Venereologica. 98, 2, p. 256-261   |  All authors
  • MTCH2-mediated mitochondrial fusion drives exit from naive pluripotency in embryonic stem cells

    Bahat A., Goldman A., Zaltsman Y. et al., Khan D. H., Halperin C., Amzallag E., Krupalnik V., Mullokandov M., Silberman A., Erez A., Schimmer A. D., Hanna J. H., Gross A. (2018), Nature Communications. 9, 5132   |  All authors
  • NKp46 Receptor-Mediated Interferon-gamma Production by Natural Killer Cells Increases Fibronectin 1 to Alter Tumor Architecture and Control Metastasis

    Glasner A., Levi A., Enk J. et al., Isaacson B., Viukov S., Orlanski S., Scope A., Neuman T., Enk C. D., Hanna J. H., Sexl V., Jonjic S., Seliger B., Zitvogel L., Mandelboim O. (2018), Immunity. 48, 1, p. 107-+   |  All authors
  • The Helix Twist: Damage and Repair Follows the DNA Minor Groove

    Kotler E., Segal E. (2018), Cell. 175, 4, p. 902-904
  • Aggregation over Metric Spaces: Proposing and Voting in Elections, Budgeting, and Legislation

    Shahaf G., Shapiro E., Talmon N. (2018), arXiv.
  • Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration

    Tomic G., Morrissey E., Kozar S. et al., Ben-Moshe S., Hoyle A., Azzarelli R., Kemp R., Chilamakuri C. S. R., Itzkovitz S., Philpott A., Winton D. J. (2018), Cell Stem Cell. 23, 3, p. 436-+   |  All authors
  • Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

    Dar D., Sorek R. (2018), mBio. 9, 5, ARTN e0173
  • Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

    Suez J., Zmora N., Zilberman-Schapira G. et al., Mor U., Dori-Bachash M., Bashiardes S., Zur M., Regev-Lehavi D., Brik R. B., Federici S., Horn M., Cohen Y., Moor A. E., Zeevi D., Korem T., Kotler E., Harmelin A., Itzkovitz S., Maharshak N., Shibolet O., Pevsner-Fischer M., Shapiro H., Sharon I., Halpern Z., Segal E., Elinav E. (2018), Cell. 174, 6, p. 1406-1423.e16   |  All authors
  • Virus-Induced Changes in mRNA Secondary Structure Uncover cis-Regulatory Elements that Directly Control Gene Expression

    Mizrahi O., Nachshon A., Shitrit A. et al., Gelbart I. A., Dobesova M., Brenner S., Kahana C., Stern-Ginossar N. (2018), Molecular Cell. 72, 5, p. 862-874   |  All authors
  • Immune cell type 'fingerprints' at the basis of outcome diversity of human infection

    Hen-Avivi S., Avraham R. (2018), Current Opinion in Microbiology. 42, p. 31-39
  • Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

    Cohen M., Giladi A., Gorki A. et al., Galbard Solodkin D., Zada M., Hladik A., Miklosi A., Salame T., Halpern K. B., David E., Itzkovitz S., Harkany T., Knapp S., Amit I. (2018), Cell. 175, 4, p. 1031-+   |  All authors
  • A model for 'sustainable' US beef production

    Eshel G., Shepon A., Shaket T. et al., Cotler B. D., Gilutz S., Giddings D., Raymo M. E., Milo R. (2018), Nature Ecology and Evolution. 2, 1, p. 81-85   |  All authors
  • Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity

    Gil N., Ulitsky I. (2018), Cell Systems. 7, 5, p. Pages 537-547.e3
  • Robust stochastic Turing patterns in the development of a one-dimensional cyanobacterial organism

    Di Patti F., Lavacchi L., Arbel-Goren R. et al., Schein-Lubomirsky L., Fanelli D., Stavans J. (2018), PLoS Biology. 16, 5, e2004877   |  All authors
  • Regulation of Neuroregeneration by Long Noncoding RNAs

    Perry R. B., Hezroni H., Goldrich M. J. et al., Ulitsky I. (2018), Molecular Cell. 72, 3, p. 553-+, 5   |  All authors
  • Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

    Sebe-Pedros A., Saudemont B., Chomsky E. et al., Plessier F., Mailhe M., Renno J., Loe-Mie Y., Lifshitz A., Mukamel Z., Schmutz S., Novault S., Steinmetz P. R. H., Spitz F., Tanay A., Marlow H. (2018), Cell. 173, 6, p. 1520-+   |  All authors
  • Epigenetic Control of Expression Homeostasis during Replication Is Stabilized by the Replication Checkpoint

    Voichek Y., Mittelman K., Gordon Y. et al., Bar-Ziv R., Smit D. L., Shenhav R., Barkai N. (2018), Molecular Cell. 70, 6, p. 1121-+   |  All authors
  • Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

    Steuerman Y., Cohen M., Peshes-Yaloz N. et al., Valadarsky L., Cohn O., David E., Frishberg A., Mayo L., Bacharach E., Amit I., Gat-Viks I. (2018), Cell Systems. 6, 6, p. 679-+   |  All authors
  • Probiotics administration following sleeve gastrectomy surgery: a randomized double-blind trial

    Sherf-Dagan S., Zelber-Sagi S., Zilberman-Schapira G. et al., Webb M., Buch A., Keidar A., Raziel A., Sakran N., Goitein D., Goldenberg N., Mahdi J. A., Pevsner-Fischer M., Zmora N., Dori-Bachash M., Segal E., Elinav E., Shibolet O. (2018), International Journal of Obesity. 42, 2, p. 147-155   |  All authors
  • Extensive reshaping of bacterial operons by programmed mRNA decay

    Dar D., Sorek R. (2018), PLoS Genetics. 14, 4, 1007354
  • Prediction of acute myeloid leukaemia risk in healthy individuals

    Abelson S., Collord G., Ng S. W. K. et al., Weissbrod O., Mendelson Cohen N., Niemeyer E., Barda N., Zuzarte P. C., Heisler L., Sundaravadanam Y., Luben R., Hayat S., Wang T. T., Zhao Z., Cirlan I., Pugh T. J., Soave D., Ng K., Latimer C., Hardy C., Raine K., Jones D., Hoult D., Britten A., McPherson J. D., Johansson M., Mbabaali F., Eagles J., Miller J. K., Pasternack D., Timms L., Krzyzanowski P., Awadalla P., Costa R., Segal E., Bratman S. V., Beer P., Behjati S., Martincorena I., Wang J. C. Y., Bowles K. M., Quirós J. R., Karakatsani A., La Vecchia C., Trichopoulou A., Salamanca-Fernández E., Huerta J. M., Barricarte A., Travis R. C., Tumino R., Masala G., Boeing H., Panico S., Kaaks R., Krämer A., Sieri S., Riboli E., Vineis P., Foll M., McKay J., Polidoro S., Sala N., Khaw K., Vermeulen R., Campbell P. J., Papaemmanuil E., Minden M. D., Tanay A., Balicer R. D., Wareham N. J., Gerstung M., Dick J. E., Brennan P., Vassiliou G. S., Shlush L. I. (2018), Nature. 559, 7714, p. 400-404   |  All authors
  • The opportunity cost of animal based diets exceeds all food losses

  • Interactions between short and long noncoding RNAs

  • RNA editing in bacteria: occurrence, regulation and significance

    Bar-Yaacov D., Pilpel Y., Dahan O. (2018), RNA Biology. 15, 7, p. 863-867
  • Defining the Transcriptional Landscape during Cytomegalovirus Latency with Single-Cell RNA Sequencing

    Shnayder M., Nachshon A., Krishn B. et al., Poole E., Boshkov A., Binyamin A., Maza I., Sinclair J., Schwartz M., Stern-Ginossar N. (2018), mBio. 9, 2, ARTN e0001   |  All authors
  • Human brain organoids on a chip reveal the physics of folding

    Karzbrun E., Kshirsagar A., Cohen S. R. et al., Hanna J. H., Reiner O. (2018), Nature Physics. 14, 5, p. 515-522   |  All authors
  • Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

    Halpern K. B., Shenhav R., Massalha H. et al., Toth B., Egozi A., Massasa E. E., Medgalia C., David E., Giladi A., Moor A. E., Porat Z., Amit I., Itzkovitz S. (2018), Nature Biotechnology. 36, 10, p. 962-+   |  All authors
  • Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner

    Thion M. S., Low D., Silvin A. et al., Chen J., Grisel P., Schulte-Schrepping J., Blecher R., Ulas T., Squarzoni P., Hoeffel G., Coulpier F., Siopi E., David F. S., Scholz C., Shihui F., Lum J., Amoyo A. A., Larbi A., Poidinger M., Buttgereit A., Lledo P., Greter M., Chan J. K. Y., Amit I., Beyer M., Schultze J. L., Schlitzer A., Pettersson S., Ginhoux F., Garel S. (2018), Cell. 172, 3, p. 500-516.e16   |  All authors
  • Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures

    Lee J. S., Adler L., Karathia H. et al., Carmel N., Rabinovich S., Auslander N., Keshet R., Stettner N., Silberman A., Agemy L., Helbling D., Eilam R., Sun Q., Brandis A., Malitsky S., Itkin M., Weiss H., Pinto S., Kalaora S., Levy R., Barnea E., Admon A., Dimmock D., Stern-Ginossar N., Scherz A., Nagamani S. C. S., Unda M., Wilson D. M., Elhasid R., Carracedo A., Samuels Y., Hannenhalli S., Ruppin E., Erez A. (2018), Cell. 174, 6, p. 1559-1570.e22   |  All authors
  • Towards utilization of the human genome and microbiome for personalized nutrition

    Bashiardes S., Godneva A., Elinav E. et al., Segal E. (2018), Current Opinion in Biotechnology. 51, p. 57-63   |  All authors
  • Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection

    Thaiss C. A., Levy M., Grosheva I. et al., Zheng D., Soffer E., Blacher E., Braverman S., Tengeler A. C., Barak O., Elazar M., Ben-Zeev R., Lehavi-Regev D., Katz M. N., Pevsner-Fischer M., Gertler A., Halpern Z., Harmelin A., Aamar S., Serradas P., Grosfeld A., Shapiro H., Geiger B., Elinav E. (2018), Science. 359, 6382, p. 1376-1383   |  All authors
  • Global Cryptodemocracy Is Possible and Desirable

  • Identification of a unique Staphylococcus aureus ribosomal signature in severe atopic dermatitis

    Brandwein M., Fuks G., Israel A. et al., Nejman D., Straussman R., Hodak E., Harari M., Steinberg D., Bentwich Z., Shental N., Meshner S. (2018),   |  All authors
  • Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration

    Deczkowska A., Keren-Shaul H., Weiner A. et al., Colonna M., Schwartz M., Amit I. (2018), Cell. 173, 5, p. 1073-1081   |  All authors
  • Quantitative species-level ecology of reef fish larvae via metabarcoding

    Kimmerling N., Zuqert O., Amitai G. et al., Gurevich T., Armoza-Zvuloni R., Kolesnikov I., Berenshtein I., Melamed S., Gilad S., Benjamin S., Rivlin A., Ohavia M., Paris C. B., Holzman R., Kiflawi M., Sorek R. (2018), Nature ecology & evolution. 2, 2, p. 306-+   |  All authors
  • Subepithelial telocytes are an important source of Wnts that supports intestinal crypts

    Shoshkes-Carmel M., Wang Y. J., Wangensteen K. J. et al., Toth B., Kondo A., Massassa E. E., Itzkovitz S., Kaestner K. H. (2018), Nature. 557, 7704, p. 242-+   |  All authors
  • Genome-wide SWAp-Tag yeast libraries for proteome exploration

    Weill U., Yofe I., Sass E. et al., Stynen B., Davidi D., Natarajan J., Ben-Menachem R., Avihou Z., Goldman O., Harpaz N., Chuartzman S., Kniazev K., Knoblach B., Laborenz J., Boos F., Kowarzyk J., Ben-Dor S., Zalckvar E., Herrmann J. M., Rachubinski R. A., Pines O., Rapaport D., Michnick S. W., Levy E. D., Schuldiner M. (2018), Nature Methods. 15, 8, p. 617-622   |  All authors
  • The GET pathway can increase the risk of mitochondrial outer membrane proteins to be mistargeted to the ER

    Vitali D. G., Sinzel M., Bulthuis E. P. et al., Kolb A., Zabel S., Mehlhorn D. G., Costa B. F., Farkas A., Clancy A., Schuldiner M., Grefen C., Schwappach B., Borgese N., Rapaport D. (2018), Journal of Cell Science. 131, 10, jcs211110   |  All authors
  • A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

    Kotler E., Shani O., Goldfeld G. et al., Lotan-Pompan M., Tarcic O., Gershoni A., Hopf T. A., Marks D. S., Oren M., Segal E. (2018), Molecular Cell. 71, 1, p. 178-190.e8   |  All authors
  • Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment

    Lauridsen F. K. B., Jensen T. L., Rapin N. et al., Aslan D., Wilhelmson A. S., Pundhir S., Rehn M., Paul F., Giladi A., Hasemann M. S., Serup P., Amit I., Porse B. T. (2018), Cell Reports. 24, 3, p. 766-780   |  All authors
  • Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

    Bornstein C., Nevo S., Giladi A. et al., Kadouri N., Pouzolles M., Gerbe F., David E., Machado A., Chuprin A., Toth B., Goldberg O., Itzkovitz S., Taylor N., Jay P., Zimmermann V. S., Abramson J., Amit I. (2018), Nature. 559, 7715, p. 622-626   |  All authors
  • m(1)A within cytoplasmic mRNAs at single nucleotide resolution: a reconciled transcriptome-wide map

  • A biological-computational human cell lineage discovery platform based on duplex molecular inversion probes

    Tao L., Raz O., Marx Z. et al., Biezuner T., Amir S., Milo L., Adar R., Onn A., Chapal-Ilani N., Berman V., Levy R., Oron B., Halaban R., Shapiro E. (2018), BioRxiv.   |  All authors
  • Fold-change Response of Photosynthesis to Step Increases of Light Level

    Tendler A., Wolf B. C., Tiwari V. et al., Alon U., Danon A. (2018), iScience. 8, p. 126-137   |  All authors
  • Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

    Moor A. E., Harnik Y., Ben-Moshe S. et al., Massasa E. E., Rozenberg M., Eilam R., Halpern K. B., Itzkovitz S. (2018), Cell. 175, 4, p. 1156-1167   |  All authors
  • Viral Short ORFs and Their Possible Functions

    Finkel Y., Stern-Ginossar N., Schwartz M. (2018), Proteomics. 18, 10, 1700255
  • Decay of the Stress-Induced Ligand MICA Is Controlled by the Expression of an Alternative 3 ' Untranslated Region

    Toledano T., Vitenshtein A., Stern-Ginossar N. et al., Seidel E., Mandelboim O. (2018), Journal of Immunology. 200, 8, p. 2819-2825   |  All authors
  • From the Human Cell Atlas to dynamic immune maps in human disease

  • The bone marrow is patrolled by NK cells that are primed and expand in response to systemic viral activation

    Milo I., Blecher-Gonen R., Barnett-Itzhaki Z. et al., Bar-Ziv R., Tal O., Gurevich I., Feferman T., Drexler I., Amit I., Bousso P., Shakhar G. (2018), European Journal of Immunology. 48, 7, p. 1137-1152   |  All authors
  • Functional characterization of the p53 "mutome"

    Kotler E., Segal E., Oren M. (2018), Molecular & cellular oncology. 5, 6, 1511207
  • Application of Algebraic Topology to homologous recombination of DNA

    Braslavsky I., Stavans J. (2018), iScience. 4, p. 64-67
  • The Citrobacter rodentium type III secretion system effector EspO affects mucosal damage repair and antimicrobial responses

    Berger C. N., Crepin V. F., Roumeliotis T. I. et al., Wright J. C., Serafini N., Pevsner-Fischer M., Yu L., Elinav E., Di Santo J. P., Choudhary J. S., Frankel G. (2018), PLoS Pathogens. 14, 10, 1007406   |  All authors
  • High-resolution RNA 3 '-ends mapping of bacterial Rho-dependent transcripts

  • Host genetics and microbiome associations through the lens of genome wide association studies

    Weissbrod O., Rothschild D., Barkan E. et al., Segal E. (2018), Current Opinion in Microbiology. 44, p. 9-19   |  All authors
  • A Bird's-Eye View of Enzyme Evolution: Chemical, Physicochemical, and Physiological Considerations

    Davidi D., Longo L. M., Jablonska J. et al., Milo R., Tawfik D. S. (2018), Chemical Reviews. 118, 18, p. 8786-8797   |  All authors
  • Positioning Europe for the EPITRANSCRIPTOMICS challenge

    Jantsch M., Quattrone A., O'Connell M. et al., Helm M., Frye M., Macias-Gonzales M., Ohman M., Ameres S., Willems L., Fuks F., Oulas A., Vanacova S., Nielsen H., Bousquet-Antonelli C., Motorin Y., Roignant J., Balatsos N., Dinnyes A., Baranov P., Kelly V., Lamm A., Rechavi G., Pelizzola M., Liepins J., Holodnuka Kholodnyuk I., Zammit V., Ayers D., Drablos F., Dahl J. A., Bujnicki J., Jeronimo C., Almeida R., Neagu M., Costache M., Bankovic J., Banovic B., Kyselovic J., Valor L. M., Selbert S., Pir P., Demircan T., Cowling V., Schäfer M., Rossmanith W., Lafontaine D., David A., Carre C., Lyko F., Schaffrath R., Schwartz S. (2018),   |  All authors
  • Trained Memory of Human Uterine NK Cells Enhances Their Function in Subsequent Pregnancies

    Gamliel M., Goldman-Wohl D., Isaacson B. et al., Gur C., Stein N., Yamin R., Berger M., Grunewald M., Keshet E., Rais Y., Bornstein C., David E., Jelinski A., Eisenberg I., Greenfield C., Ben-David A., Imbar T., Gilad R., Haimov-Kochman R., Mankuta D., Elami-Suzin M., Amit I., Hanna J. H., Yagel S., Mandelboim O. (2018), Immunity. 48, 5, p. 951-+   |  All authors
  • A General Path-Based Representation for Predicting Program Properties

  • Single molecule approaches for studying gene regulation in metabolic tissues

    Farack L., Egozi A., Itzkovitz S. (2018), Diabetes Obesity & Metabolism. 20, p. 145-156
  • Translating microbiome futures

    Taroncher-Oldenburg G., Jones S., Blaser M. et al., Bonneau R., Christey P., Clemente J. C., Elinav E., Ghedin E., Huttenhower C., Kelly D., Kyle D., Littman D., Maiti A., Maue A., Olle B., Segal L., Vlieg J. E. T. v. H., Wang J. (2018), Nature Biotechnology. 36, 11, p. 1037-1042   |  All authors
  • Early metazoan cell type diversity and the evolution of multicellular gene regulation

    Sebe-Pedros A., Chomsky E., Pang K. et al., Lara-Astiaso D., Gaiti F., Mukamel Z., Amit I., Hejnol A., Degnan B. M., Tanay A. (2018), Nature ecology & evolution. 2, 7, p. 1176-+   |  All authors
  • Mind the Organelle Gap - Peroxisome Contact Sites in Disease

    Castro I. G., Schuldiner M., Zalckvar E. (2018), Trends in Biochemical Sciences. 43, 3, p. 199-210
  • Genome-wide C-SWAT library for high-throughput yeast genome tagging

    Meurer M., Duan Y., Sass E. et al., Kats I., Herbst K., Buchmuller B. C., Dederer V., Huber F., Kirrmaier D., Stefl M., Van Laer K., Dick T. P., Lemberg M. K., Khmelinskii A., Levy E. D., Knop M. (2018), Nature Methods. 15, 8, p. 598-600   |  All authors
  • The anti-inflammatory IFITM genes ameliorate colitis and partially protect from tumorigenesis by changing immunity and microbiota

    Alteber Z., Sharbi-Yunger A., Pevsner-Fischer M. et al., Blat D., Roitman L., Tzehoval E., Elinav E., Eisenbach L. (2018), Immunology and Cell Biology. 96, 3, p. 284-297   |  All authors
  • Creative exploration as a scale-invariant search on a meaning landscape

    Hart Y., Goldberg H., Striem-Amit E. et al., Mayo A. E., Noy L., Alon U. (2018), Nature Communications. 9, 5411   |  All authors
  • A Visual Framework for Classifying Determinants of Cell Size

    Jonas F., Soifer I., Barkai N. (2018), Cell Reports. 25, 12, p. 3519-3529.e2
  • Circuit Design Features of a Stable Two-Cell System

    Zhou X., Franklin R. A., Adler M. et al., Jacox J. B., Bailis W., Shyer J. A., Flavell R. A., Mayo A., Alon U., Medzhitov R. (2018), Cell. 172, 4, p. 744-757.e17   |  All authors
  • Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast

    Chuartzman S. G., Schuldiner M. (2018), Yeast. 35, 7, p. 477-483
  • Identification of seipin-linked factors that act as determinants of a lipid droplet subpopulation

    Eisenberg-Bord M., Mari M., Weill U. et al., Rosenfeld-Gur E., Moldavski O., Castro I. G., Soni K. G., Harpaz N., Levine T. P., Futerman A. H., Reggiori F., Bankaitis V. A., Schuldiner M., Bohnert M. (2018), Journal of Cell Biology. 217, 1, p. 269-282   |  All authors
  • A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

    Bahr C., von Paleske L., Slu V. V. U. et al., Emeseiro S. R., Takayama N., Ng S. W., Murison A., Langenfeld K., Petretich M., Scognamiglio R., Zeisberger P., Benk A. S., Amit I., Zandstra P. W., Lupien M., Dick J. E., Trumpp A., Spitz F. (2018), Nature. 553, 7689, p. 515-+   |  All authors
  • Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

    Giladi A., Paul F., Herzog Y. et al., Lubling Y., Weiner A., Yofe I., Jaitin D., Cabezas-Wallscheid N., Dress R., Ginhoux F., Trumpp A., Tanay A., Amit I. (2018), Nature Cell Biology. 20, 7, p. 836-+   |  All authors
  • The Role of m(6)A/m-RNA Methylation in Stress Response Regulation

    Engel M., Eggert C., Kaplick P. M. et al., Eder M., Roeh S., Tietze L., Namendorf C., Arloth J., Weber P., Rex-Haffner M., Geula S., Jakovcevski M., Hanna J. H., Leshkowitz D., Uhr M., Wotjak C. T., Schmidt M. V., Deussing J. M., Binder E. B., Chen A. (2018), Neuron. 99, 2, p. 389-403.e9   |  All authors
  • Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

    Zmora N., Zilberman-Schapira G., Suez J. et al., Mor U., Dori-Bachash M., Bashiardes S., Kotler E., Zur M., Regev-Lehavi D., Brik R. B., Federici S., Cohen Y., Linevsky R., Rothschild D., Moor A. E., Ben-Moshe S., Harmelin A., Itzkovitz S., Maharshak N., Shibolet O., Shapiro H., Pevsner-Fischer M., Sharon I., Halpern Z., Segal E., Elinav E. (2018), Cell. 174, 6, p. 1388-1405.e21   |  All authors
  • On the journey from nematode to human, scientists dive by the zebrafish cell lineage tree

    Shapiro E. (2018), Genome Biology. 19, 1, 63
  • Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling

    Alyagor I., Berkun V., Keren-Shaul H. et al., Marmor-Kollet N., David E., Mayseless O., Issman-Zecharya N., Amit I., Schuldiner O. (2018), Developmental Cell. 47, 1, p. 38-52   |  All authors
  • A Bacterial Growth Law out of Steady State

    Korem Kohanim Y., Levi D., Jona G. et al., Towbin B. D., Bren A., Alon U. (2018), Cell Reports. 23, 10, p. 2891-2900   |  All authors
  • Modulating cell state to enhance suspension expansion of human pluripotent stem cells

    Lipsitz Y. Y., Woodford C., Yin T. et al., Hanna J. H., Zandstra P. W. (2018), Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115, 25, p. 6369-6374   |  All authors
  • Codon usage of highly expressed genes affects proteome-wide translation efficiency

    Frumkin I., Lajoie M. J., Gregg C. J. et al., Hornung G., Church G. M., Pilpel Y. (2018), Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115, 21, p. E4940-E4949   |  All authors
  • Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

    Slutskin I. V., Weingarten-Gabbay S., Nir R. et al., Weinberger A., Segal E. (2018), Nature Communications. 9, 529   |  All authors
  • Sieving through gut models of colonization resistance

    Mullineaux-Sanders C., Suez J., Elinav E. et al., Frankel G. (2018), Nature Microbiology. 3, 2, p. 132-140   |  All authors
  • Altered p53 functionality in cancer-associated fibroblasts contributes to their cancer-supporting features

    Arandkar S., Furth N., Elisha Y. et al., Belugali Nataraj N., van der Kuip H., Yarden Y., Aulitzky W., Ulitsky I., Geiger B., Oren M. (2018), Proceedings Of The National Academy Of Sciences Of The United States Of America-Biological Sciences. 115, 25, p. 6410-6415   |  All authors
  • Impaired immune surveillance accelerates accumulation of senescent cells and aging

    Ovadya Y., Landsberger T., Leins H. et al., Vadai E., Gal H., Biran A., Yosef R., Sagiv A., Agrawal A., Shapira A., Windheim J., Tsoory M., Schirmbeck R., Amit I., Geiger H., Krizhanovsky V. (2018), Nature Communications. 9, 5435   |  All authors
  • Dynamic proteomics reveals bimodal protein dynamics of cancer cells in response to HSP90 inhibitor

    Zimmer A., Amar Farkash F. S., Danon T. et al., Alon U. (2017), BMC Systems Biology. 11, 33   |  All authors
  • Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine

    Geller L. T., Barzily-Rokni M., Danino T. et al., Jonas O. H., Shental N., Nejman D., Gavert N., Zwang Y., Cooper Z. A., Shee K., Thaiss C. A., Reuben A., Livny J., Avraham R., Frederick D. T., Ligorio M., Chatman K., Johnston S. E., Mosher C. M., Brandis A., Fuks G., Gurbatri C., Gopalakrishnan V., Kim M., Hurd M. W., Katz M., Fleming J., Maitra A., Smith D. A., Skalak M., Bu J., Michaud M., Trauger S. A., Barshack I., Golan T., Sandbank J., Flaherty K. T., Mandinova A., Garrett W. S., Thayer S. P., Ferrone C. R., Huttenhower C., Bhatia S. N., Gevers D., Wargo J. A., Golub T. R., Straussman R. (2017), Science. 357, 6356, p. 1156-1160   |  All authors
  • Post-translational modification profiling-functional proteomics for the analysis of immune regulation

  • Immunology, one cell at a time

    Giladi A., Amit I. (2017), Nature. 547, 7661, p. 27-29
  • A multiplexed screening method for pluripotency

    Plotnikov A., Kozer N., Krupalnik V. et al., Peles S., Mor N., Rais Y., Hanna J. H., Barr H. M. (2017), Stem Cell Research. 23, p. 158-162   |  All authors
  • Early commitment and robust differentiation in colonic crypts

    Toth B., Ben-Moshe S., Gavish A. et al., Barkai N., Itzkovitz S. (2017), Molecular Systems Biology. 13, 1, 902   |  All authors
  • Prediction of drug cocktail effects when the number of measurements is limited

    Zimmer A., Tendler A., Katzir I. et al., Mayo A., Alon U. (2017), PLoS Biology. 15, 10, e2002518   |  All authors
  • RNA editing in bacteria recodes multiple proteins and regulates an evolutionarily conserved toxin-antitoxin system

    Bar-Yaacov D., Mordret E., Towers R. et al., Biniashvili T., Soyris C., Schwartz S., Dahan O., Pilpel Y. (2017), Genome Research. 27, 10, p. 1696-1703   |  All authors
  • The path towards microbiome-based metabolite treatment

    Suez J., Elinav E. (2017), Nature Microbiology. 2, 6, 17075
  • Coupling phenotypic persistence to DNA damage increases genetic diversity in severe stress

    Yaakov G., Lerner D., Bentele K. et al., Steinberger J., Barkai N. (2017), Nature ecology & evolution. 1, 1, 0016   |  All authors
  • Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence

    Barczak A., Avraham R., Luo S. et al., Zhang W., Bray M., Hinman A., Thompson M., Nietupski R., Golas A., Montgomery P., Fitzgerald M., Smith R., White D., Tischler A., Carpenter A., Hung D., Singh S. (2017), PLoS Pathog. 13, 5   |  All authors
  • Ectopic colonization of oral bacteria in the intestine drives T(H)1 cell induction and inflammation

    Atarashi K., Suda W., Luo C. et al., Kawaguchi T., Motoo I., Narushima S., Kiguchi Y., Yasuma K., Watanabe E., Tanoue T., Thaiss C. A., Sato M., Toyooka K., Said H. S., Yamagami H., Rice S. A., Gevers D., Johnson R. C., Segre J. A., Chen K., Kolls J. K., Elinav E., Morita H., Xavier R. J., Hattori M., Honda K. (2017), Science. 358, 6361, p. 359+   |  All authors
  • Saccharomyces cerevisiae cells lacking Pex3 contain membrane vesicles that harbor a subset of peroxisomal membrane proteins

    Wroblewska J. P., Cruz-Zaragoza L. D., Yuan W. et al., Schummer A., Chuartzman S. G., de Boer B. R., Oeljeklaus S., Schuldiner M., Zalckvar E., Warscheid B., Erdmann R., van der Klei d. K. I. J. (2017), Biochimica Et Biophysica Acta-Molecular Cell Research. 1864, 10, p. 1656-1667   |  All authors
  • Communication between viruses guides lysis-lysogeny decisions

    Erez Z., Steinberger-Levy I., Shamir M. et al., Doron S., Stokar Avihail A. A., Peleg Y., Melamed S., Leavitt A., Savidor A., Albeck S., Amitai G., Sorek R. (2017), Nature. 541, 7638   |  All authors
  • Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation

    Yona S., David E., Kim K. et al., Goldmann T., Amit I., Heikenwalder M., Nedospasov S., Prinz M., Friedman N., Jung S. (2017), Journal of Experimental Medicine. 214, 4, p. 905-917   |  All authors
  • Dynamic zonation of liver polyploidy

    Tanami S., Ben Moshe M. S., Elkayam A. et al., Mayo A., Halpern K. B., Itzkovitz S. (2017), Cell and Tissue Research. 368, 2, p. 405-410   |  All authors
  • Inflammasomes and intestinal inflammation

    Zmora N., Levy M., Pevsner-Fischer M. et al., Elinav E. (2017), Mucosal Immunology. 10, 4, p. 865-883   |  All authors
  • Placebo can enhance creativity

    Rozenkrantz L., Mayo A. E., Ilan T. et al., Hart Y., Noy L., Alon U. (2017), PLoS One. 12, 9, e0182466   |  All authors
  • Increased NK cell immunity in a transgenic mouse model of NKp46 overexpression

    Glasner A., Isaacson B., Viukov S. et al., Neuman T., Friedman N., Mandelboim M., Sexl V., Hanna J. H., Mandelboim O. (2017), Scientific Reports. 7, 13090   |  All authors
  • Genomic Characterization of Murine Monocytes Reveals C/EBP beta Transcription Factor Dependence of Ly6C(-) Cells

    Mildner A., Schoenheit J., Giladi A. et al., David E., Lara Astiaso A. D., Lorenzo Vivas V. E., Paul F., Chappell-Maor L., Priller J., Leutz A., Amit I., Jung S. (2017), Immunity. 46, 5, p. 849-862   |  All authors
  • A Participatory Democratic Budgeting Algorithm

    Shapiro E., Talmon N. (2017), arXiv.
  • Multiscale 3D Genome Rewiring during Mouse Neural Development

    Bonev B., Cohen N. M., Szabo Q. et al., Fritsch L., Papadopoulos G. L., Lubling Y., Xu X., Lv X., Hugnot J., Tanay A., Cavalli G. (2017), Cell. 171, 3, p. 557+   |  All authors
  • p53 is essential for DNA methylation homeostasis in naive embryonic stem cells, and its loss promotes clonal heterogeneity

    Tovy A., Spiro A., McCarthy R. et al., Shipony Z., Aylon Y., Allton K., Ainbinder E., Furth N., Tanay A., Barton M., Oren M. (2017), GENES & DEVELOPMENT. 31, 10, p. 959-972   |  All authors
  • Combining Deep Sequencing, Proteomics, Phosphoproteomics, and Functional Screens To Discover Novel Regulators of Sphingolipid Homeostasis

    Lebesgue N., Megyeri M., Cristobal A. et al., Scholten A., Chuartzman S. G., Voichek Y., Scheltema R. A., Mohammed S., Futerman A. H., Schuldiner M., Heck A. J. R., Lemeer S. (2017), Journal of Proteome Research. 16, 2, p. 571-582   |  All authors
  • Cellular Consequences of Diminished Protein O-Mannosyltransferase Activity in Baker's Yeast

    Zatorska E., Gal L., Schmitt J. et al., Bausewein D., Schuldiner M., Strahl S. (2017), International Journal of Molecular Sciences. 18, 6, 1226   |  All authors
  • Optimal Regulatory Circuit Topologies for Fold-Change Detection

    Adler M., Szekely P., Mayo A. et al., Alon U. (2017), Cell Systems. 4, 2, p. 171-+   |  All authors
  • Chromatin dynamics During DNA replication

    Barkai N. (2017),
  • Buffering Global Variability of Morphogen Gradients

    Shilo B., Barkai N. (2017), Developmental Cell. 40, 5, p. 429-438
  • CD74 is a novel transcription regulator

    Gil-Yarom N., Radomir L., Sever L. et al., Kramer M. P., Lewinsky H., Bornstein C., Blecher-Gonen R., Barnett Itzhaki Z., Mirkin V., Friedlander G., Shvidel L., Herishanu Y., Lolis E. J., Becker Herman S., Amit I., Shachar I. (2017), Proceedings of the National Academy of Sciences of the United States of America. 114, 3, p. 562-567   |  All authors
  • m(6)A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover

    Ke S., Pandya-Jones A., Saito Y. et al., Fak J. J., Vagbo C. B., Geula S., Hanna J. H., Black D. L., Darnell J. E., Darnell R. B. (2017), GENES & DEVELOPMENT. 31, 10, p. 990-1006   |  All authors
  • Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo

    Berger C. N., Crepin V. F., Roumeliotis T. I. et al., Wright J. C., Carson D., Pevsner-Fischer M., Furniss R. C. D., Dougan G., Dori-Bachash M., Yu L., Clements A., Collins J. W., Elinav E., Larrouy-Maumus G. J., Choudhary J. S., Frankel G. (2017), Cell Metabolism. 26, 5, p. 738+   |  All authors
  • Microbiome, metabolites and host immunity

    Levy M., Blacher E., Elinav E. (2017), Current Opinion in Microbiology. 35, p. 8-15
  • Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

    Van Dijk D. D., Sharon E., Lotan-Pompan M. et al., Weinberger A., Segal E., Carey L. (2017), Genome Research. 27, 1, p. 87-94   |  All authors
  • Principles of Systems Biology, No. 14

    Erez Z., Sorek R., Shao S. et al., Hegde R. S., Schweppe D. K., Chavez J. D., Bruce J. E., Mizrachi E., Verbeke L., de Peer P. Y. V., Marchal K., Myburg A. A., Bennett J. A., Klironomos J., Payne G. F., Bentley W. E., Fleming R., Thiele I., Cheng J. K., Alper H. S., Rose J., Maly D., Piraner D., Abedi M., Shapiro M., Cui Z., Mureev S., Alexandrov K. (2017), Cell Systems. 4, 2, p. 140-143   |  All authors
  • Cell-cycle dynamics of chromosomal organization at single-cell resolution

    Nagano T., Lubling Y., Varnai C. et al., Dudley C., Leung W., Baran Y., Cohen N. M., Wingett S., Fraser P., Tanay A. (2017), Nature. 547, 7661, p. 61-+   |  All authors
  • The Genetic Requirements for Pentose Fermentation in Budding Yeast

    Mittelman K., Barkai N. (2017), G3-GENES GENOMES GENETICS. 7, 6, p. 1743-1752
  • MICROBIOLOGY Intracellular signaling in CRISPR-Cas defense

    Amitai G., Sorek R. (2017), Science. 357, 6351, p. 550-551
  • The m(1)A landscape on cytosolic and mitochondrial mRNA at single-base resolution

    Safra M., Sas-Chen A., Nir R. et al., Winkler R., Nachshon A., Bar-Yaacov D., Erlacher M., Rossmanith W., Stern-Ginossar N., Schwartz S. (2017), Nature. 551, 7679, p. 251-255   |  All authors
  • The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element

    Marin-Bejar O., Mas A. M., Gonzalez J. et al., Martinez D., Athie A., Morales X., Galduroz M., Raimondi I., Grossi E., Guo S., Rouzaut A., Ulitsky I., Huarte M. (2017), GENOME BIOLOGY. 18, 202   |  All authors
  • Syp1 regulates the clathrin-mediated and clathrin-independent endocytosis of multiple cargo proteins through a novel sorting motif

    Apel A. R., Hoban K., Chuartzman S. et al., Tonikian R., Sidhu S., Schuldiner M., Wendland B., Prosser D. (2017), Molecular Biology of the Cell. 28, 18, p. 2434-2448   |  All authors
  • Editorial overview: Systems biology for biotechnology

    Heinemann M., Pilpel Y. (2017), Current Opinion in Biotechnology. 46, p. IV-V
  • The microbiome in anti-cancer therapy

    Bashiardes S., Tuganbaev T., Federici S. et al., Elinav E. (2017), Seminars in Immunology. 32, C, SI, p. 74-81   |  All authors
  • NFIL-trating the Host Circadian Rhythm-Microbes Fine-Tune the Epithelial Clock

    Thaiss C. A., Nobs S. P., Elinav E. (2017), Cell Metabolism. 26, 5, p. 699-700
  • OCT4 impedes cell fate redirection by the melanocyte lineage master regulator MITF in mouse ESCs

    Sheinboim D., Maza I., Dror I. et al., Parikh S., Krupalnik V., Bell R. E., Zviran A., Suita Y., Hakim O., Mandel-Gutfreund Y., Khaled M., Hanna J. H., Levy C. (2017), Nature Communications. 8, 1022   |  All authors
  • A different kind of love - lipid droplet contact sites

  • Principles of cellular resource allocation revealed by condition-dependent proteome profiling

    Metzl-Raz E., Kafri M., Yaakov G. et al., Soifer I., Gurvich Y., Barkai N. (2017), eLife. 6, e28034   |  All authors
  • Principles of Systems Biology, No. 21

    Cao J., Packer J., Waterston R. et al., Trapnell C., Shendure J., Rajaram S., Wu L. F., Altschuler S. J., Liang J., O'Brien L. E., Eizenberg-Magar I., Rimer J., Friedman N., Metzl-Raz E., Kafri M., Yaakov G., Soifer I., Gurvich Y., Barkai N., Mardinoglu A., Ponten F., Uhlen M., Rahi S. J., Cross F. R., Baumgart M., Noack S. (2017), Cell Systems. 5, 3, p. 158-160   |  All authors
  • An Endogenously Tagged Fluorescent Fusion Protein Library in Mouse Embryonic Stem Cells

    Harikumar A., Edupuganti R. R., Sorek M. et al., Azad G. K., Markoulaki S., Sehnalova P., Legartova S., Bartova E., Farkash-Amar S., Jaenisch R., Alon U., Meshorer E. (2017), Stem Cell Reports. 9, 4, p. 1304-1314   |  All authors
  • Targeting and translocation of proteins to the endoplasmic reticulum at a glance

    Aviram N., Schuldiner M. (2017), Journal of Cell Science. 130, 24, p. 4079-4085
  • Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress

    Tamarkin Ben Harush B. H. A., Vasseur J., Debart F. et al., Ulitsky I., Dikstein R. (2017), eLife. 6, e21907   |  All authors
  • Lessons on enzyme kinetics from quantitative proteomics

  • Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses

    Lavin Y., Kobayashi S., Leader A. et al., Amir E. D., Elefant N., Bigenwald C., Remark R., Sweeney R., Becker C. D., Levine J. H., Meinhof K., Chow A., Kim-Shulze S., Wolf A., Medaglia C., Li H., Rytlewski J. A., Emerson R. O., Solovyov A., Greenbaum B. D., Sanders C., Vignali M., Beasley M. B., Flores R., Gnjatic S., Pe'er D., Rahman A., Amit I., Merad M. (2017), Cell. 169, 4, p. 750-765   |  All authors
  • Ground control to major TOM: mitochondria-nucleus communication

    Eisenberg-Bord M., Schuldiner M. (2017), FEBS Journal. 284, 2, p. 196-210
  • Pex35 is a regulator of peroxisome abundance

    Yofe I., Soliman K., Chuartzman S. G. et al., Morgan B., Weill U., Yifrach E., Dick T. P., Cooper S. J., Ejsing C. S., Schuldiner M., Zalckvar E., Thoms S. (2017), Journal of Cell Science. 130, 4, p. 791-804   |  All authors
  • Single-cell transcriptome conservation in cryopreserved cells and tissues

    Guillaumet-Adkins A., Rodriguez-Esteban G., Mereu E. et al., Mendez-Lago M., Jaitin D. A., Villanueva A., Vidal A., Martinez-Marti A., Felip E., Vivancos A., Keren-Shaul H., Heath S., Gut M., Amit I., Gut I., Heyn H. (2017), GENOME BIOLOGY. 18, 45   |  All authors
  • Coordinated Pulses of mRNA and of Protein Translation or Degradation Produce EGF-Induced Protein Bursts

    Golan-Lavi R., Giacomelli C., Fuks G. et al., Zeisel A., Sonntag J., Sinha S., Kostler W., Wiemann S., Korf U., Yarden Y., Domany E. (2017), Cell Reports. 18, 13, p. 3129-3142   |  All authors
  • A pathway of targeted autophagy is induced by DNA damage in budding yeast

    Eapen V. V., Waterman D. P., Bernard A. et al., Schiffmann N., Sayas E., Kamber R., Lemos B., Memisoglu G., Ang J., Mazella A., Chuartzman S. G., Loewith R. J., Schuldiner M., Denic V., Klionsky D. J., Haber J. E. (2017), Proceedings of the National Academy of Sciences of the United States of America. 114, 7, p. E1158-E1167   |  All authors
  • RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure

    Solomon O., Di Segni A., Cesarkas K. et al., Porath H. T., Marcu-Malina V., Mizrahi O., Stern-Ginossar N., Kol N., Farage-Barhom S., Glick-Saar E., Lerenthal Y., Levanon E. Y., Amariglio N., Unger R., Goldstein I., Eyal E., Rechavi G. (2017), Nature Communications. 8   |  All authors
  • GAS6 is a key homeostatic immunological regulator of host-commensal interactions in the oral mucosa

    Nassar M., Tabib Y., Capucha T. et al., Mizraji G., Nir T., Pevsner-Fischer M., Zilberman-Schapira G., Heyman O., Nussbaum G., Bercovier H., Wilensky A., Elinav E., Burstyn-Cohen T., Hovav A. (2017), Proceedings of the National Academy of Sciences of the United States of America. 114, 3, p. E337-E346   |  All authors
  • A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease

    Keren-Shaul H., Spinrad A., Weiner A. et al., Matcovitch-Natan O., Dvir-Szternfeld R., Ulland T. K., David E., Baruch K., Lara-Astaiso D., Toth B., Itzkovitz S., Colonna M., Schwartz M., Amit I. (2017), Cell. 169, 7, p. 1276-+   |  All authors
  • Efficient and Accurate Translation Initiation Directed by TISU Involves RPS3 and RPS10e Binding and Differential Eukaryotic Initiation Factor 1A Regulation

    Haimov O., Sinvani H., Martin F. et al., Ulitsky I., Emmanuel R., Tamarkin Ben Harush B. H. A., Vardy A., Dikstein R. (2017), Molecular and Cellular Biology. 37, 15, UNSP e0015   |  All authors
  • Exhaustive search of linear information encoding protein-peptide recognition

    Kelil A., Dubreuil B., Levy E. D. et al., Michnick S. W. (2017), PLoS Computational Biology. 13, 4, e1005499   |  All authors
  • Iron affects Ire1 clustering propensity and the amplitude of endoplasmic reticulum stress signaling

    Cohen N., Breker M., Bakunts A. et al., Pesek K., Chas A., Argemi J., Orsi A., Gal L., Chuartzman S., Wigelman Y., Jonas F., Walter P., Ernst R., Aragon T., van Anken E., Schuldiner M. (2017), Journal of Cell Science. 130, 19, p. 3222-+   |  All authors
  • Engineering carbon fixation in E. coil: from heterologous RuBisCO expression to the Calvin-Benson-Bassham cycle: from heterologous RuBisCO expression to the Calvin-Benson-Bassham cycle

    Antonovsky N., Gleizer S., Milo R. (2017), Current Opinion in Biotechnology. 47, p. 83-91
  • Global mRNA polarization regulates translation efficiency in the intestinal epithelium

    Moor A. E., Golan M., Massasa E. E. et al., Lemze D., Weizman T., Shenhav R., Baydatch S., Mizrahi O., Winkler R., Golani O., Stern-Ginossar N., Itzkovitz S. (2017), Science. 357, 6357, p. 1299-+   |  All authors
  • hSnd2 protein represents an alternative targeting factor to the endoplasmic reticulum in human cells

    Hassdenteufel S., Sicking M., Schorr S. et al., Aviram N., Fecher-Trost C., Schuldiner M., Jung M., Zimmermann R., Lang S. (2017), FEBS Letters. 591, 20, p. 3211-3224   |  All authors
  • Two novel effectors of trafficking and maturation of the yeast plasma membrane H+-ATPase

    Geva Y., Crissman J., Arakel E. C. et al., Gomez-Navarro N., Chuartzman S. G., Stahmer K. R., Schwappach B., Miller E. A., Schuldiner M. (2017), Traffic. 18, 10, p. 672-682   |  All authors
  • Regulation of antibiotic-resistance by non-coding RNAs in bacteria

  • Casein kinase 1-epsilonor1-delta required for Wnt-mediated intestinal stem cell maintenance

    Morgenstern Y., Das Adhikari A. U., Ayyash M. et al., Elyada E., Toth B., Moor A., Itzkovitz S., Ben-Neriah Y. (2017), EMBO Journal. 36, 20, p. 3046-3061   |  All authors
  • Heterosis as a consequence of regulatory incompatibility

    Herbst R. H., Bar-Zvi D., Reikhav S. et al., Soifer I., Breker M., Jona G., Shimoni E., Schuldiner M., Levy A. A., Barkai N. (2017), BMC Biology. 15, 38   |  All authors
  • Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

    Gritsenko A. A., Weingarten-Gabbay S., Elias-Kirma S. et al., Nir R., De Ridder R. D., Segal E. (2017), PLoS Computational Biology. 13, 9, e1005734   |  All authors
  • Mitochatting - If only we could be a fly on the cell wall

  • Design principles of autocatalytic cycles constrain enzyme kinetics and force low substrate saturation at flux branch points

    Barenholz U., Davidi D., Reznik E. et al., Bar-On Y., Antonovsky N., Noor E., Milo R. (2017), eLife. 6, 20667   |  All authors
  • Incredibly close-A newly identified peroxisome-ER contact site in humans

    Schuldiner M., Zalckvar E. (2017), Journal of Cell Biology. 216, 2, p. 287-289
  • Expansion-restriction of Spemann's organizer by an ADMP self-regulatory switch to scale the BMP gradient

    Fainsod A., Leibovich A., Leibovich-Kot H. et al., Ben-Zvi D., Barkai N. (2017),   |  All authors
  • Dual role of starvation signaling in promoting growth and recovery

    Gurvich Y., Leshkowitz D., Barkai N. (2017), PLoS Biology. 15, 12, 2002039
  • Cap-binding protein 4EHP effects translation silencing by microRNAs

    Chapat C., Jafarnejad S. M., Matta-Camacho E. et al., Hesketh G. G., Gelbart I. A., Attig J., Gkogkas C. G., Alain T., Stern-Ginossar N., Fabian M. R., Gingras A., Duchaine T. F., Sonenberg N. (2017), Proceedings of the National Academy of Sciences of the United States of America. 114, 21, p. 5425-5430   |  All authors
  • MicroRNA-142 controls thymocyte proliferation

    Mildner A., Chapnik E., Varol D. et al., Aychek T., Lampl N., Rivkin N., Bringmann A., Paul F., Boura-Halfon S., Hayoun Y. S., Barnett Itzhaki I. Z., Amit I., Hornstein E., Jung S. (2017), European Journal of Immunology. 47, 7, p. 1142-1152   |  All authors
  • scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing

    Avital G., Avraham R., Fan A. et al., Hashimshony T., Hung D. T., Yanai I. (2017), GENOME BIOLOGY. 18, 200   |  All authors
  • Transcriptional programs that control expression of the autoimmune regulator gene Aire

    Herzig Y., Nevo S., Bornstein C. et al., Brezis M. R., Ben-Hur S., Shkedy A., Eisenberg-Bord M., Levi B., Delacher M., Goldfarb Y., David E., Weinberger L., Viukov S., Ben-Dor S., Giraud M., Hanna J. H., Breiling A., Lyko F., Amit I., Feuerer M., Abramson J. (2017), Nature Immunology. 18, 2, p. 161-172   |  All authors
  • TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

    Safra M., Nir R., Farouq D. et al., Slutzkin I. V., Schwartz S. (2017), Genome Research. 27, 3, p. 393-406   |  All authors
  • Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

    Medaglia C., Giladi A., Stoler-Barak L. et al., De Giovanni M., Salame T. M., Biram A., David E., Li H., Iannacone M., Shulman Z., Amit I. (2017), Science. 358, 6370, p. 1622-1626   |  All authors
  • Analysis of blood-based gene expression in idiopathic Parkinson disease

    Shamir R., Klein C., Amar D. et al., Vollstedt E., Bonin M., Usenovic M., Wong Y. C., Maver A., Poths S., Safer H., Corvol J., Lesage S., Lavi O., Deuschl G., Kuhlenbaeumer G., Pawlack H., Ulitsky I., Kasten M., Riess O., Brice A., Peterlin B., Krainc D. (2017), Neurology. 89, 16, p. 1676-1683   |  All authors
  • Scaling single-cell genomics from phenomenology to mechanism

    Tanay A., Regev A. (2017), Nature. 541, 7637, p. 331-338
  • Evidence for a cytoplasmic pool of ribosome-free mRNAs encoding inner membrane proteins in Escherichia coli

    Benhalevy D., Biran I., Bochkareva E. S. et al., Sorek R., Bibi E. (2017), PLoS One. 12, 8, e0183862   |  All authors
  • Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome

    Schwartzman O., Savino A. M., Gombert M. et al., Palmi C., Cario G., Schrappe M., Eckert C., von Stackelberg A., Huang J., Hameiri-Grossman M., Avigad S., te Kronnie G., Geron I., Birger Y., Rein A., Zarfati G., Fischer U., Mukamel Z., Stanulla M., Biondi A., Cazzaniga G., Vetere A., Wagner B. K., Chen Z., Chen S., Tanay A., Borkhardt A., Izraeli S. (2017), Proceedings Of The National Academy Of Sciences Of The United States Of America-Physical Sciences. 114, 20, p. E4030-E4039   |  All authors
  • Sub-cellular mRNA localization modulates the regulation of gene expression by small RNAs in bacteria

    Teimouri H., Korkmazhan E., Stavans J. et al., Levine E. (2017), Physical Biology. 14, 5, 56001   |  All authors
  • Science Forum: The Human Cell Atlas

    Regev A., Teichmann S. A., Lander E. S. et al., Amt I., Benoist C., Birney E., Bodenmiller B., Campbell P., Carninci P., Clatworthy M., Clevers H., Deplancke B., Dunham I., Eberwine J., Elis R., Enard W., Farmer A., Fugger L., Gottgens B., Hacohen N., Haniffa M., Hemberg M., Kim S., Klenerman P., Kriegstein A., Lein E. D., Linnarsson S., Lundberg E., Lundeberg J., Majumder P., Marioni J. C., Merad M., Mhlanga M., Nawijin M., Netea M., Nolan G., Pe'er D., Phillipakis A., Ponting C. P., Quake S., Reik W., Rozenblatt-Rosen O., Sanes J., Satija R., Schumacher T. N., Shalek A., Shapiro E., Sharma P., Shin J. W., Stegle O., (2017), eLife. 6, 27041   |  All authors
  • Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

    Halpern K. B., Shenhav R., Matcovitch-Natan O. et al., Toth B., Lemze D., Golan M., Massasa E. E., Baydatch S., Landen S., Moor A. E., Brandis A., Giladi A., Stokar-Avihail A., David E., Amit I., Itzkovitz S. (2017), Nature. 542, 7641, p. 352-+   |  All authors
  • Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems

    Ushakov K., Koffler-Brill T., Rom A. et al., Perl K., Ulitsky I., Avraham K. B. (2017), Scientific Reports. 7, 8637   |  All authors
  • Dynamic Proteomics of Herpes Simplex Virus Infection

    Drayman N., Karin O., Mayo A. et al., Danon T., Shapira L., Rafael D., Zimmer A., Bren A., Kobiler O., Alon U. (2017), mBio. 8, 6, ARTN e0161   |  All authors
  • Post-dieting weight gain: the role of persistent microbiome changes

    Thaiss C. A., Shapiro H., Elinav E. (2017), Future Microbiology. 12, 7, p. 555-559
  • Dysbiosis and the immune system

    Levy M., Kolodziejczyk A. A., Thaiss C. A. et al., Elinav E. (2017), Nature Reviews Immunology. 17, 4, p. 219-232   |  All authors
  • Maya Schuldiner

    Schuldiner M. (2017), Current Biology. 27, 18, p. R982-R984
  • Lighting Up ERK Activity

    Shilo B., Barkai N. (2017), Developmental Cell. 40, 2, p. 115-116
  • The gut microbiome and hypertension

    Pevsner-Fischer M., Blacher E., Tatirovsky E. et al., Ben-Dov I., Elinav E. (2017), Current Opinion in Nephrology and Hypertension. 26, 1, p. 1-8   |  All authors
  • Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner

    Deczkowska A., Matcovitch-Natan O., Tsitsou-Kampeli A. et al., Ben-Hamo S., Dvir-Szternfeld R., Spinrad A., Singer O., David E., Winter D. R., Smith L. K., Kertser A., Baruch K., Rosenzweig N., Terem A., Prinz M., Villeda S., Citri A., Amit I., Schwartz M. (2017), Nature Communications. 8, 717   |  All authors
  • A reduced-dimensionality approach to uncovering dyadic modes of body motion in conversations

    Gaziv G., Noy L., Liron Y. et al., Alon U. (2017), PLoS One. 12, 1, e0170786   |  All authors
  • The genetic basis for the adaptation of E-coli to sugar synthesis from CO2

    Herz E., Antonovsky N., Bar-On Y. et al., Davidi D., Gleizer S., Prywes N., Noda-Garcia L., Frisch K. L., Zohar Y., Wernick D. G., Savidor A., Barenholz U., Milo R. (2017), Nat Commun. 8, 1705   |  All authors
  • Vesicles Spread Susceptibility to Phages

    Ofir G., Sorek R. (2017), Cell. 168, 1-2, p. 13-15
  • Optimality and sub-optimality in a bacterial growth law

    Towbin B. D., Korem Y., Bren A. et al., Doron S., Sorek R., Alon U. (2017), Nature Communications. 8, 14123   |  All authors
  • Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

    Levo M., Avnit-Sagi T., Lotan-Pompan M. et al., Kalma Y., Weinberger A., Yakhini Z., Segal E. (2017), Molecular Cell. 65, 4, p. 604-+   |  All authors
  • Role of biomechanical forces in hyperfiltration-mediated glomerular injury in congenital anomalies of the kidney and urinary tract

    Srivastava T., Thiagarajan G., Alon U. S. et al., Sharma R., El-Meanawy A., McCarthy E. T., Savin V. J., Sharma M. (2017), Nephrology Dialysis Transplantation. 32, 5, p. 759-765   |  All authors
  • AML1-ETO requires enhanced C/D box snoRNA/RNP formation to induce self-renewal and leukaemia

    Zhou F., Liu Y., Rohde C. et al., Pauli C., Gerloff D., Koehn M., Misiak D., Baeumer N., Cui C., Goellner S., Oellerich T., Serve H., Garcia-Cuellar M., Slany R., Maciejewski J. P., Przychodzen B., Seliger B., Klein H., Bartenhagen C., Berdel W. E., Dugas M., Taketo M. M., Farouq D., Schwartz S., Regev A., Hebert J., Sauvageau G., Pabst C., Huettelmaier S., Mueller-Tidow C. (2017), Nature Cell Biology. 19, 7, p. 844-+   |  All authors
  • Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression

    Fiziev P., Akdemir K. C., Miller J. P. et al., Keung E. Z., Samant N. S., Sharma S., Natale C. A., Terranova C. J., Maitituoheti M., Amin S. B., Martinez-Ledesma E., Dhamdhere M., Axelrad J. B., Shah A., Cheng C. S., Mahadeshwar H., Seth S., Barton M. C., Protopopov A., Tsai K. Y., Davies M. A., Garcia B. A., Amit I., Chin L., Ernst J., Rai K. (2017), Cell Reports. 19, 4, p. 875-889   |  All authors
  • Dicer Deficiency Differentially Impacts Microglia of the Developing and Adult Brain

    Varol D., Mildner A., Blank T. et al., Shemer A., Barashi N., Yona S., David E., Boura-Halfon S., Segal-Hayoun Y., Chappell-Maor L., Keren-Shaul H., Leshkowitz D., Hornstein E., Fuhrmann M., Amit I., Maggio N., Prinz M., Jung S. (2017), Immunity. 46, 6, p. 1030-+   |  All authors
  • Proteins evolve on the edge of supramolecular self-assembly

    Garcia-Seisdedos H., Empereur-Mot C., Elad N. et al., Levy E. D. (2017), eLife. 548, 7666, p. 244-247   |  All authors
  • The remedy within: will the microbiome fulfill its therapeutic promise?

  • The Role of the Immune System in Metabolic Health and Disease

    Zmora N., Bashiardes S., Levy M. et al., Elinav E. (2017), Cell Metabolism. 25, 3, p. 506-521   |  All authors
  • Method for Labeling Transcripts in Individual Escherichia coli Cells for Single-molecule Fluorescence In Situ Hybridization Experiments

    Arbel-Goren R., Shapira Y., Stavans J. (2017), Journal of Visualized Experiments. 130, 56600
  • Gene Architectures that Minimize Cost of Gene Expression

    Frumkin I., Schirman D., Rotman A. et al., Li F., Zahavi L., Mordret E., Asraf O., Wu S., Levy S. F., Pilpel Y. (2017), Molecular Cell. 65, 1, p. 142-153   |  All authors
  • Breaking the population barrier by single cell analysis: one host against one pathogen

  • Microbiome at the Frontier of Personalized Medicine

    Kashyap P. C., Chia N., Nelson H. et al., Segal E., Elinav E. (2017), Mayo Clinic Proceedings. 92, 12, p. 1855-1864   |  All authors
  • Energetic cost of building a virus

  • Computational prediction of regulatory, premature transcription termination in bacteria

    Millman A., Dar D., Shamir M. et al., Sorek R. (2017), Nucleic Acids Research. 45, 2, p. 886-893   |  All authors
  • Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells

    Gispan A., Carmi M., Barkai N. (2017), Genome Research. 27, 2, p. 310-319
  • Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation

    Lim A. I., Li Y., Lopez-Lastra S. et al., Stadhouders R., Paul F., Casrouge A., Serafini N., Puel A., Bustamante J., Surace L., Masse-Ranson G., David E., Strick-Marchand H., Le Bourhis B. L., Cocchi R., Topazio D., Graziano P., Muscarella L. A., Rogge L., Norel X., Sallenave J., Allez M., Graf T., Hendriks R. W., Casanova J., Amit I., Yssel H., Di Santo S. J. P. (2017), Cell. 168, 6, p. 1086-+   |  All authors
  • APOL1-Mediated Cell Injury Involves Disruption of Conserved Trafficking Processes

    Kruzel-Davila E., Shemer R., Ofir A. et al., Bavli-Kertselli I., Darlyuk-Saadon I., Oren-Giladi P., Wasser W. G., Magen D., Zaknoun E., Schuldiner M., Salzberg A., Kornitzer D., Marelja Z., Simons M., Skorecki K. (2017), Journal Of The American Society Of Nephrology. 28, 4, p. 1117-1130   |  All authors
  • Our Gut Microbiome: The Evolving Inner Self

    Kundu P., Blacher E., Elinav E. et al., Pettersson S. (2017), Cell. 171, 7, p. 1481-1493   |  All authors
  • Expression homeostasis during DNA replication

    Voichek Y., Bar-Ziv R., Barkai N. (2017),
  • Comparison of seven single cell Whole Genome Amplification commercial kits using targeted sequencing

    Biezuner T., Raz O., Amir S. et al., Milo L., Adar R., Fried Y., Ainbinder E., Shapiro E. (2017), BioRxiv.   |  All authors
  • Gene architectures that minimize cost of gene expression

    Frumkin I., Schirman D., Rotman A. et al., Pilpel Y. (2017),   |  All authors
  • Cinacalcet as an alternative to phosphate therapy in X-linked hypophosphataemic rickets

    Alon U. S., Jarka D., Monachino P. J. et al., VanSickle J. S., Srivastava T. (2017),   |  All authors
  • Creative foraging: An experimental paradigm for studying exploration and discovery

    Hart Y., Mayo A. E., Mayo R. et al., Rozenkrantz L., Tendler A., Alon U., Noy L. (2017), PLoS One. 12, 8, e0182133   |  All authors
  • Next-generation sequencing technologies for detection of modified nucleotides in RNAs

    Schwartz S., Motorin Y. (2017), RNA Biology. 14, 9, p. 1124-1137
  • Spatial transcriptomics: paving the way for tissue-level systems biology

    Moor A. E., Itzkovitz S. (2017), Current Opinion in Biotechnology. 46, p. 126-133
  • Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs

    Mitsunaga S., Odajima J., Yawata S. et al., Shioda K., Owa C., Isselbacher K. J., Shioda T., Hanna J. (. (2017), Proceedings Of The National Academy Of Sciences Of The United States Of America-Physical Sciences. 114, 46, p. E9913-E9922   |  All authors
  • Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits

    Karin O., Alon U. (2017), Molecular Systems Biology. 13, 6, 933
  • Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses

    Korem T., Zeevi D., Zmora N. et al., Weissbrod O., Bar N., Lotan-Pompan M., Avnit Sagi S. T., Kosower N., Malka G., Rein M., Suez J., Goldberg B. Z., Weinberger A., Levy A., Elinav E., Segal E. (2017), Cell Metabolism. 25, 6, p. 1243-+   |  All authors
  • Corrigendum: TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code

    Safra M., Nir R., Farouq D. et al., Vainberg Slutskin I., Schwartz S. (2017), Genome Research. 27, 8, p. 1460   |  All authors
  • High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency

    Zviran A., Mor N., Rais Y. et al., Gingold H., Peles S., Chomsky E., Viukov S., Buenrostro J. D., Weinberger L., Manor Y. S., Krupalnik V., Zerbib M., Hezroni H., Jaitin D. A., Larastiaso D., Gilad S., Benjamin S., Mousa A., Ayyash M., Sheban D., Bayerl J., Aguilera Castrejon A., Massarwa R., Maza I., Hanna S., Amit I., Stelzer Y., Ulitsky I., Greenleaf W. J., Pilpel Y., Novershtern N., Hanna J. H. (2017), BioRxiv.   |  All authors
  • Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

    Morgenstern M., Stiller S. B., Luebbert P. et al., Peikert C. D., Dannenmaier S., Drepper F., Weill U., Hoess P., Feuerstein R., Gebert M., Bohnert M., van der Laan d. L. M., Schuldiner M., Schuetze C., Oeljeklaus S., Pfanner N., Wiedemann N., Warscheid B. (2017), Cell Reports. 19, 13, p. 2836-2852   |  All authors
  • Microbiome-Modulated Metabolites at the Interface of Host Immunity

    Blacher E., Levy M., Tatirovsky E. et al., Elinav E. (2017), Journal of Immunology. 198, 2, p. 572-580   |  All authors
  • Characterization of proteome dynamics during growth in oleate reveals a new peroxisome-targeting receptor

    Yifrach E., Chuartzman S., Dahan N. et al., Maskit S., Zada L., Weill U., Yofe I., Olender T., Schuldiner M., Zalckvar E. (2016), Journal of Cell Science. 129, 21, p. 4067-4075   |  All authors
  • Microglia development follows a stepwise program to regulate brain homeostasis.

    Matcovitch-Natan O., Winter D. R., Giladi A. et al., Vargas Aguilar A. S., Spinrad A., Sarrazin S., Ben-Yehuda H., David E., Zelada Gonzalez G. F., Perrin P., Keren-Shaul H., Gury M., Lara-Astaiso D., Thaiss C. A., Cohen M., Bahar Halpern H. K., Baruch K., Deczkowska A., Lorenzo Vivas V. E., Itzkovitz S., Elinav E., Sieweke M. H., Schwartz M., Amit I. (2016), Science (New York, N.Y.). 353, 6301, p. aad8670   |  All authors
  • Corrigendum: Failure to replicate the STAP cell phenomenon (vol 525, pg E6, 2015)

    De Los Angeles A., Ferrari F., Fujiwara Y. et al., Mathieu R., Lee S., Lee S., Tu H., Ross S., Chou S., Minh Nguyen, Wu Z., Theunissen T. W., Powell B. E., Imsoonthornruksa S., Chen J., Borkent M., Krupalnik V., Lujan E., Wernig M., Hanna J. H., Hochedlinger K., Pei D., Jaenisch R., Deng H., Orkin S. H., Park P. J., Daley G. Q. (2016),   |  All authors
  • Biological causal links on physiological and evolutionary time scales.

    Karmon A., Pilpel Y. (2016), eLife. 5
  • The Genetic Program of Pancreatic beta-Cell Replication In Vivo

    Klochendler A., Caspi I., Corem N. et al., Moran M., Friedlich O., Elgavish S., Nevo Y., Helman A., Glaser B., Eden A., Itzkovitz S., Dor Y. (2016), Diabetes. 65, 7, p. 2081-2093   |  All authors
  • Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity.

    Spiro A., Shapiro E. (2016), PLoS Computational Biology. 12, 6, 1004983
  • 3 ' UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells

    Hoffman Y., Bublik D. R., Ugalde A. P. et al., Elkon R., Biniashvili T., Agami R., Oren M., Pilpel Y. (2016), PLoS Genetics. p. 260-262   |  All authors
  • Environmentally Optimal, Nutritionally Aware Beef Replacement Plant-Based Diets.

    Eshel G., Shepon A., Noor E. et al., Milo R. (2016), Environmental Science & Technology. 50, 15, p. 8164-8   |  All authors
  • CRISPR-Cas adaptation: insights into the mechanism of action.

    Amitai G., Sorek R. (2016), Nature Reviews Microbiology. 14, 2, p. 67-76
  • Talking about cross-talk: the immune system and the microbiome.

    Zeevi D., Korem T., Segal E. (2016), GENOME BIOLOGY. 17, 1, p. 50, 26987366
  • Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

    Chen J., Shishkin A. A., Zhu X. et al., Kadri S., Maza I., Guttman M., Hanna J. H., Regev A., Garber M. (2016), GENOME BIOLOGY. 17, 19   |  All authors
  • A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans

    Houri-Ze'evi L., Korem Y., Sheftel H. et al., Faigenbloom L., Toker I. A., Dagan Y., Awad L., Degani L., Alon U., Rechavi O. (2016), Cell. 165, 1, p. 88-99   |  All authors
  • Expression homeostasis during DNA replication

    Voichek Y., Bar-Ziv R., Barkai N. (2016), Science. 351, 6277, p. 1087-1090
  • Mice lacking WRB reveal differential biogenesis requirements of tail-anchored proteins in vivo

    Rivera-Monroy J., Musiol L., Unthan-Fechner K. et al., Farkas A., Clancy A., Coy-Vergara J., Weill U., Gockel S., Lin S., Corey D. P., Kohl T., Stroebel P., Schuldiner M., Schwappach B., Vilardi F. (2016), Scientific Reports. 6, 39464   |  All authors
  • Interaction of Metabolome and Microbiome Contributes to Dietary Glycemia-induced Age-related Macular Degeneration in Aged C57BL/6J Mice

    Rowan S., Iang S., Chang M. et al., Szymanski L., Korem T., Segal E., Cassalman C., McGuire C., Balea J. D., Clish C. B., Taylor A. (2016), Investigative Ophthalmology & Visual Science. 57, 12, p. 5002   |  All authors
  • Would you like to play together? Adults' attachment and the mirror game

    Feniger-Schaal R., Noy L., Hart Y. et al., Koren-Karie N., Mayo A. E., Alon U. (2016), Attachment and Human Development. 18, 1, p. 33-45   |  All authors
  • A systematic view on influenza induced host shutoff

    Bercovich-Kinori A., Tai J., Gelbart I. A. et al., Shitrit A., Ben Moshe M. S., Drori Y., Itzkovitz S., Mandelboim M., Stern-Ginossar N. (2016), eLife. 5, e18311   |  All authors
  • Metabolites: messengers between the microbiota and the immune system

    Levy M., Thaiss C. A., Elinav E. (2016), GENES & DEVELOPMENT. 30, 14, p. 1589-1597
  • LIMT is a novel metastasis inhibiting lncRNA suppressed by EGF and downregulated in aggressive breast cancer.

    Sas-Chen A., Aure M. R., Leibovich L. et al., Carvalho S., Enuka Y., Korner C., Polycarpou-Schwarz M., Lavi S., Nevo N., Kuznetsov Y., Yuan J., Azuaje F., Ulitsky I., Diederichs S., Wiemann S., Yakhini Z., Kristensen V. N., Borresen-Dale A., Yarden Y. (2016), EMBO Molecular Medicine. 8, 9, p. 1052-64   |  All authors
  • Rapid evolutionary adaptation to growth on an 'unfamiliar' carbon source.

    Tamari Z., Yona A. H., Pilpel Y. et al., Barkai N. (2016), BMC Genomics. 17, p. 674   |  All authors
  • > functions of long noncoding RNAs in development and stem cells

    Ulitsky I., Perry R. (2016), Development. 143, 21, p. 3882-3894
  • Regulation of membrane trafficking during glucose starvation

    Hong H., Martinez-Marquez J. Y., Gal L. et al., Schuldiner M., Duncan M. C. (2016),   |  All authors
  • A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells.

    Tichon A., Gil N., Lubelsky Y. et al., Havkin Solomon S. T., Lemze D., Itzkovitz S., Stern-Ginossar N., Ulitsky I. (2016), Nature Communications. 7, p. 12209   |  All authors
  • Pyruvate Formate-Lyase Enables Efficient Growth of Escherichia coli on Acetate and Formate

    Zelcbuch L., Lindner S. N., Zegman Y. et al., Slutskin I. V., Antonovsky N., Gleizer S., Milo R., Bar-Even A. (2016), Biochemistry. 55, 17, p. 2423-2426   |  All authors
  • Natural Diversity in Pentose Fermentation Is Explained by Variations in Histone Deacetylases.

    Tamari Z., Barkai N. (2016), Cell Reports. 14, 3, p. 458, 63
  • Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array

    Goren M. G., Doron S., Globus R. et al., Amitai G., Sorek R., Qimron U. (2016), Cell Reports. 16, 11, p. 2811-2818   |  All authors
  • SnapShot: Timescales in Cell Biology

    Shamir M., Milo R., Bar-On Y. (2016), Cell. 164
  • CEACAM1-Mediated Inhibition of Virus Production

    Vitenshtein A., Weisblum Y., Hauka S. et al., Halenius A., Oiknine-Djian E., Tsukerman P., Bauman Y., Bar-On Y., Stern-Ginossar N., Enk J., Ortenberg R., Tai J., Markel G., Blumberg R. S., Hengel H., Jonjic S., Wolf D. G., Adler H., Kammerer R., Mandelboim O. (2016), Cell Reports. 15, 11, p. 2331-2339   |  All authors
  • Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans.

    Sender R., Fuchs S., Milo R. (2016), Cell. 164, 3, p. 337-340, 40
  • Prediction of multidimensional drug dose responses based on measurements of drug pairs

    Zimmer A., Katzir I., Dekel E. et al., Mayo A. E., Alon U., Arcavi I., Challis P., Chambers K. C., Chen T. -., Cowperthwaite P. S., Gal-Yam A., Hosseinzadeh G., Howell D. A., Inserra C., Kankare E., Magnier E. A., Maguire K., Mazzali P. A., McCully C., Milisavljevic D., Smith K. W., Taubenberger S., Valenti S., Wainscoat R. J., Yaron O., Young D. R. (2016), Proceedings of the National Academy of Sciences of the United States of America. 113, 37, p. 10442-10447   |  All authors
  • Microbiota Diumal Rhythmicity Programs Host Transcriptome Oscillations

    Thaiss C., Levy M., Korem T. et al., Dohnalova L., Shapiro H., Jaitin D., David E., Winter D., Gury-BenAri M., Tatirovsky E., Tuganbaev T., Federici S., Zmora N., Zeevi D., Dori-Bachash M., Pevsner-Fischer M., Kartvelishvily E., Brandis A., Harmelin A., Shibolet O., Halpern Z., Honda K., Amit I., Segal E., Elinav E. (2016), Cell. 167, 6, p. 1495-1510.e12   |  All authors
  • Use of Metatranscriptomics in Microbiome Research.

    Bashiardes S., Zilberman-Schapira G., Elinav E. (2016), Bioinformatics and Biology Insights. 10, p. 19-25
  • The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis

    Amit I., Winter D. R., Jung S. (2016), Nature Immunology. 17, 1, p. 18-25
  • Young phosphorylation is functionally silent

    Matalon O., Dubreuil B., Levy E. D. (2016), Science. 354, 6309, p. 176-177
  • A perspective on single cell behavior during infection

    Avraham R., Hung D. T. (2016), Gut Microbes. Pre print
  • Dynamic stem cell states: naive to primed pluripotency in rodents and humans

    Weinberger L., Ayyash M., Novershtern N. et al., Hanna J. (2016), Nature Reviews Molecular Cell Biology. 17, 3, p. 155-169   |  All authors
  • Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model

    Yosef I., Edgar R., Levy A. et al., Amitai G., Sorek R., Munitz A., Qimron U., Mueller B., Tarkowski P., Weiss D. (2016), Nature Microbiology. 1, 6, 16047   |  All authors
  • Cinacalcet as adjunctive therapy in pseudohypoparathyroidism type 1b

    Srivastava T., Krudys J., Mardis N. J. et al., Sebestyen-VanSickle J., Alon U. S. (2016), Pediatric Nephrology. 31, 5, p. 795-800   |  All authors
  • Regioselectivity of third-row maingroup dicarbides, C2X (X = K-Br) for CO interaction: Fukui function and topological analyses

    Parida S. K., Sahu S., Sharma S. et al., Mao R., Pevsner-Fischer M., Ben-horin S., Elinav E., Zeng Z., Chen B., He Y., Xiang A. P., Chen M. (2016), Chemical Physics Letters. 659, p. 216-220   |  All authors
  • eSTGt: a programming and simulation environment for population dynamics

    Spiro A., Shapiro E. (2016), BMC Bioinformatics. 17, 187
  • Non-alcoholic fatty liver and the gut microbiota.

    Bashiardes S., Shapiro H., Rozin S. et al., Shibolet O., Elinav E. (2016), Molecular Metabolism. 5, 9, p. 782-94   |  All authors
  • Persistent microbiome alterations modulate the rate of post-dieting weight regain

    Thaiss C. A., Itav S., Rothschild D. et al., Meijer M. T., Levy M., Moresi C., Dohnalová L., Braverman S., Rozin S., Malitsky S., Dori-Bachash M., Kuperman Y., Biton I., Gertler A., Harmelin A., Shapiro H., Halpern Z., Aharoni A., Segal E., Elinav E. (2016), Nature. 540, 7634, p. 544-551   |  All authors
  • PD-1 immune checkpoint blockade reduces pathology and improves memory in mouse models of Alzheimer's disease

    Baruch K., Deczkowska A., Rosenzweig N. et al., Tsitsou-Kampeli A., Sharif A. M., Matcovitch-Natan O., Kertser A., David E., Amit I., Schwartz M. (2016), Nature Medicine. 22, 2, p. 135-137   |  All authors
  • Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

  • Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates

    Bar Yaacov Y. D., Frumkin I., Yashiro Y. et al., Chujo T., Ishigami Y., Chemla Y., Blumberg A., Schlesinger O., Bieri P., Greber B., Ban N., Zarivach R., Alfonta L., Pilpel Y., Suzuki T., Mishmar D. (2016), PLoS Biology. 14, 9, e1002557   |  All authors
  • Pax6 role in the regulation of retinal pigmented epithelium maturation

    Cohen Y., Blinder P., Idelson M. et al., Reubinoff B., Itzkovitz S., Ashery-Padan R. (2016),   |  All authors
  • Manipulating the Placebo Response in Experimental Pain by Altering Doctor's Performance Style

    Czerniak E., Biegon A., Ziv A. et al., Karnieli-Miller O., Weiser M., Alon U., Citron A. (2016), Frontiers in Psychology. 7, 874   |  All authors
  • The mutation spectrum in genomic late replication domains shapes mammalian GC content

    Kenigsberg E., Yehuda Y., Marjavaara L. et al., Keszthelyi A., Chabes A., Tanay A., Simon I. (2016), Nucleic Acids Research. 44, 9, p. 4222-32, 27085808   |  All authors
  • Exit from Synchrony in Joint Improvised Motion

    Dahan A., Noy L., Hart Y. et al., Mayo A., Alon U. (2016), PLoS One. 11, 10, e0160747   |  All authors
  • Making Sense of the Yeast Sphingolipid Pathway

    Megyeri M., Riezman H., Schuldiner M. et al., Futerman A. H. (2016), Journal of Molecular Biology. 428, 24, p. 4765-4775   |  All authors
  • Water-Transfer Slows Aging in Saccharomyces cerevisiae

    Cohen A., Weindling E., Rabinovich E. et al., Nachman I., Fuchs S., Chuartzman S., Gal L., Schuldiner M., Bar-Nun S. (2016), PLoS One. 11, 2, 0148650   |  All authors
  • Energy and protein feed-to-food conversion efficiencies in the US and potential food security gains from dietary changes

    Shepon A., Eshel G., Noor E. et al., Milo R. (2016),   |  All authors
  • Tumor suppressor crosstalk: Modulation of p53 activity by the Hippo pathway

    Oren M., Furth N., Ben-Moshe N. B. et al., Porat Z., Domany E., Pozniak Y., Geiger T., Aylon Y. (2016), Cancer Research. 76, 2016   |  All authors
  • Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-BindingRegions in BR-C

    Hitrik A., Popliker M., Gancz D. et al., Mukamel Z., Lifshitz A., Schwartzman O., Tanay A., Gilboa L. (2016), PLoS Genetics. 12, 11, e1006330   |  All authors
  • Parkinson disease (PARK) genes are somatically mutated in cutaneous melanoma.

    Inzelberg R., Samuels Y., Azizi E. et al., Qutob N., Inzelberg L., Domany E., Schechtman E., Friedman E. (2016), Neurology. Genetics. 2, 3, e70   |  All authors
  • A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.

    Avraham R., Haseley N., Fan A. et al., Bloom-Ackermann Z., Livny J., Hung D. T. (2016), Nature protocols. 11, 8, p. 1477-91, 27442864   |  All authors
  • The multicellular nature of filamentous heterocyst-forming cyanobacteria

    Stavans J., Flores E., Herrero A. (2016), FEMS Microbiology Reviews. 40, 6, p. 831-854
  • A Tether is a Tether is a Tether: Tethering at Membrane Contact Sites

    Eisenberg-Bord M., Shai N., Schuldiner M. et al., Bohnert M. (2016), Developmental Cell. 39, 4, p. 395-409   |  All authors
  • Distinct biological events generated by ECM proteolysis by two homologous collagenases

    Solomonov I., Zehorai E., Talmi-Frank D. et al., Wolf S. G., Shainskaya A., Zhuravlev A., Kartvelishvily E., Visse R., Levin Y., Kampf N., Jaitin D. A., David E., Amit I., Nagase H., Sagi I. (2016), Proceedings of the National Academy of Sciences of the United States of America. 113, 39, p. 10884-10889   |  All authors
  • Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease.

    Zmora N., Zeevi D., Korem T. et al., Segal E., Elinav E. (2016), Cell Host & Microbe. 19, 1, p. 12-20   |  All authors
  • Transcriptome dynamics of a broad host-range cyanophage and its hosts

    Doron S., Fedida A., Hernandez-Prieto M. A. et al., Sabehi G., Karunker I., Stazic D., Feingersch R., Steglich C., Futschik M., Lindell D., Sorek R. (2016), ISME Journal. 10, 6, p. 1437-1455   |  All authors
  • Post-translational modification profiling - A novel tool for mapping the protein modification landscape in cancer

    Eisenberg-Lerner A., Ciechanover A., Merbl Y. (2016), Experimental Biology and Medicine. 241, 14, p. 1475-1482
  • Extracellular Matrix Proteolysis by MT1-MMP Contributes to InfluenzaInfluenza-Related Tissue Damage and Mortality

    Talmi-Frank D., Altboum Z., Solomonov I. et al., Ziv T., Amit I., Sagi I. (2016), Cell Host & Microbe. 20   |  All authors
  • A role for Rtt109 in buffering gene-dosage imbalance during DNA replication

    Voichek Y., Bar-Ziv R., Barkai N. (2016), Nucleus-Austin. 7, 4, p. 375-381
  • Capturing pairwise and multi-way chromosomal conformations using chromosomal walks

    Olivares-Chauvet P. H., Mukamel Z., Lifshitz A. et al., Schwartzman O., Elkayam N., Lubling Y., Deikus G., Sebra R., Tanay A. (2016), Nature. 540, 7632, p. 296-300   |  All authors
  • Voices Of Biotech

    Amit I., Baker D., Barker R. et al., Berger B., Bertozzi C., Bhatia S., Biffi A., Demichelis F., Doudna J., Dowdy S. F., Endy D., Helmstaedter M., Junca H., June C., Kamb S., Khvorova A., Kim D., Kim J., Krishnan Y., Lakadamyali M., Lappalainen T., Lewin S., Liao J., Loman N., Lundberg E., Lynd L., Martin C., Mellman I., Miyawaki A., Mummery C., Nelson K., Paz J., Peralta-Yahya P., Picotti P., Polyak K., Prather K., Qin J., Quake S., Regev A., Rogers J. A., Shetty R., Sommer M., Stevens M., Stolovitzky G., Takahashi M., Tang F., Teichmann S., Torres-Padilla M., Tripathi L., Vemula P., Verdine G., Vollmer F., Wang J., Ying J. Y., Zhang F., Zhang T. (2016), Nature Biotechnology. 34, 3, p. 270-275   |  All authors
  • A two-step patterning process increases the robustness of periodic patterning in the fly eye

  • The microbiome and innate immunity

    Thaiss C. A., Zmora N., Levy M. et al., Elinav E. (2016), Nature. 535, 7610, p. 65-74   |  All authors
  • A Unique Assemblage of Engraved Plaquettes from Ein Qashish South, Jezreel Valley, Israel: Figurative and Non-Figurative Symbols of Late Pleistocene Hunters-Gatherers in the Levant

    Yaroshevich A., Bar-Yosef O., Boaretto E. et al., Caracuta V., Greenbaum N., Porat N., Roskin J., Alon U. (2016), PLoS One. 11, 8, e0160687   |  All authors
  • The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

    Noor E., Flamholz A., Bar-Even A. et al., Davidi D., Milo R., Liebermeister W. (2016), PLoS Computational Biology. 12, 11   |  All authors
  • M-sec regulates polarized secretion of inflammatory endothelial chemokines and facilitates CCL2-mediated lymphocyte transendothelial migration

    Barzilai S., Blecher-Gonen R., Barnett Itzhaki Z. et al., Zauberman A., Lebel-Haziv Y., Amit I., Alon R. (2016), Journal of Leukocyte Biology. 99, 6, p. 1045-1055   |  All authors
  • One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.

    Yofe I., Weill U., Meurer M. et al., Chuartzman S., Zalckvar E., Goldman O., Ben-Dor S., Schutze C., Wiedemann N., Knop M., Khmelinskii A., Schuldiner M. (2016), Nature Methods. 13, 4, p. 371-8   |  All authors
  • Dynamical compensation in physiological circuits

    Karin O., Swisa A., Glaser B. et al., Dor Y., Alon U. (2016), Molecular Systems Biology. 12, 11, 886   |  All authors
  • Integration of Innate Immune Signaling.

    Thaiss C. A., Levy M., Itav S. et al., Elinav E. (2016), Trends in Immunology. 37, 2, p. 84-101, 101   |  All authors
  • The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome.

    Gury-BenAri M., Thaiss C. A., Serafini N. et al., Winter D. R., Giladi A., Lara Astiaso A. D., Levy M., Salame T. M., Weiner A., David E., Shapiro H., Dori-Bachash M., Pevsner-Fischer M., Lorenzo Vivas V. E., Keren-Shaul H., Paul F., Harmelin A., Eberl G., Itzkovitz S., Tanay A., Di Santo S. J. P., Elinav E., Amit I. (2016), Cell. 166, 5, p. 1231-1246.e13   |  All authors
  • Widespread formation of alternative 3 ' UTR isoforms via transcription termination in archaea

    Dar D., Prasse D., Schmitz R. A. et al., Sorek R. (2016), Nature Microbiology. 1, 10, 16143   |  All authors
  • The Protease Ste24 Clears Clogged Translocons.

    Ast T., Michaelis S., Schuldiner M. (2016), Cell. 164, 1-2, p. 103-114
  • Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

    Jaitin D. A., Weiner A., Yofe I. et al., Lara Astiaso D., Keren-Shaul H., David E., Salame T. M., Tanay A., van Oudenaarden A., Amit I. (2016), Cell. 167, 7, p. 1883-+   |  All authors
  • Nanoscale Engineering of Designer Cellulosomes

    Gunnoo M., Cazade P., Galera-Prat A. et al., Nash M. A., Czjzek M., Cieplak M., Alvarez B., Morzaev D., Kahana-Edwin S., Yosepovich A., Gal-Yam E. N., Berger R., Barshack I., Domany E., Kaufman B. (2016), Advanced Materials. 28, 27, p. 5619-5647   |  All authors
  • A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1

    Hollander D., Donyo M., Atias N. et al., Mekahel K., Melamed Z., Yannai S., Lev-Maor G., Shilo A., Schwartz S., Barshack I., Sharan R., Ast G. (2016), Genome Research. 26, p. 541-553   |  All authors
  • Periodic Patterning Of The Drosophila Eye Is Stabilized By The Diffusible Activator Scabrous

    Gavish A., Shwartz A., Weizman A. et al., Schejter E., Shilo B., Barkai N. (2016), Nature Communications. 7, 10461   |  All authors
  • Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli.

    Arbel-Goren R., Tal A., Parasar B. et al., Dym A., Costantino N., Munoz-Garcia J., Court D. L., Stavans J. (2016), Nucleic Acids Research. 44, 14, p. 6707-6720   |  All authors
  • Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro kcat measurements

    Davidi D., Barenholz U., Goldenfeld M. et al., Milo R. (2016), PNAS. 113   |  All authors
  • A WntD-Dependent Integral Feedback Loop Attenuates Variability in Drosophila Toll Signaling

    Rahimi N., Averbukh I., Haskel Ittah I. M. et al., Degani N., Schejter E., Barkai N., Shilo B. (2016), Developmental Cell. 36, 4, p. 401-414   |  All authors
  • An unrecognized function for COPII components in recruiting the viral replication protein BMV 1a to the perinuclear ER

    Li J., Fuchs S., Zhang J. et al., Wellford S., Schuldiner M., Wang X. (2016), Journal of Cell Science. 129, 19, p. 3597-3608   |  All authors
  • Bursting Through The Cell Cycle

    Ben Moshe M. S., Itzkovitz S. (2016), eLife. 5, e14953
  • The SND proteins constitute an alternative targeting route to the endoplasmic reticulum

    Aviram N., Ast T., Costa E. A. et al., Arakel E. C., Chuartzman S. G., Jan C. H., Hassenteufel S., Dudek J., Jung M., Schorr S., Zimmermann R., Schwappach B., Weissman J. S., Schuldiner M. (2016), eLife. 540, 7631, p. 134-+   |  All authors
  • Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution.

    Weiner A., Lara Astiaso A. D., Krupalnik V. et al., Gafni O., David E., Winter D. R., Hanna J. H., Amit I. (2016), Nature Biotechnology. 34, 9, p. 953-61   |  All authors
  • Protein-fragment complementation assays for large-scale analysis, functional dissection, and spatiotemporal dynamic studies of protein-protein interactions in living cells

    Michnick S. W., Landry C. R., Levy E. D. et al., Diss G., Ear P. H., Kowarzyk J., Malleshaiah M. K., Messier V., Tchekanda E. (2016), Cold Spring Harbor Protocols. 2016, 11, p. 917-919   |  All authors
  • A Minimalistic Resource Allocation Model to Explain Ubiquitous Increase in Protein Expression with Growth Rate

    Barenholz U., Keren L., Segal E. et al., Milo R. (2016), PLoS One. 11, 4, p. e0153344, e0153344   |  All authors
  • Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness.

    Keren L., Hausser J., Lotan-Pompan M. et al., Vainberg Slutskin S. I., Alisar H., Kaminski S., Weinberger A., Alon U., Milo R., Segal E. (2016), Cell. 166, 5, p. 1282-1294.e18   |  All authors
  • Glucose becomes one of the worst carbon sources for E-coli on poor nitrogen sources due to suboptimal levels of cAMP

    Bren A., Park J. O., Towbin B. D. et al., Dekel E., Rabinowitz J. D., Alon U. (2016), Scientific Reports. 6, 24834   |  All authors
  • Chromatin dynamics during DNA replication.

    Bar-Ziv R., Voichek Y., Barkai N. (2016), Genome Research. 26, 9, p. 1245-56
  • The Cost of Protein Production.

    Kafri M., Metzl-Raz E., Jona G. et al., Barkai N. (2016), Cell Reports. 14, 1, p. 22-31   |  All authors
  • Automated Video Analysis of Non-verbal Communication in a Medical Setting

    Hart Y., Czerniak E., Karnieli-Miller O. et al., Mayo A. E., Ziv A., Biegon A., Citron A., Alon U. (2016), Frontiers in Psychology. 7, 1130   |  All authors
  • Role of the microbiome in non-gastrointestinal cancers.

    Pevsner-Fischer M., Tuganbaev T., Meijer M. et al., Zhang S., Zeng Z., Chen M., Elinav E. (2016), World Journal of Clinical Oncology. 7, 2, p. 200-13, 27081642   |  All authors
  • A generic, cost-effective, and scalable cell lineage analysis platform

    Biezuner T., Spiro A., Raz O. et al., Amir S., Milo L., Adar R., Chapal Ilani I. N., Berman V., Fried Y., Ainbinder E., Cohen G., Barr H. M., Halaban R., Shapiro E. (2016), Genome Research. 26, 11, p. 1588-1599   |  All authors
  • Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor

    Enuka Y., Lauriola M., Sas-Chen A. et al., Ulitsky I., Yarden Y. (2016), Nucleic Acids Research. 44, 3, p. 1370-1383   |  All authors
  • Sumoylation coordinates the repression of inflammatory and anti-viral gene-expression programs during innate sensing

    Decque A., Joffre O., Magalhaes J. G. et al., Cossec J., Blecher-Gonen R., Lapaquette P., Silvin' A., Mane N., Joubert P. -., Seeler J., Albert M. L., Amit I., Amigorena S., Dejean A. (2016), Nature Immunology. 17, 2, p. 140-149   |  All authors
  • Cracking the epitranscriptome.

    Schwartz S. (2016), RNA. 22, 2, p. 169-174
  • No peroxisome is an island - Peroxisome contact sites.

    Shai N., Schuldiner M., Zalckvar E. (2016), Biochimica Et Biophysica Acta. 1863, 5, p. 1061-9, 26384874
  • CRISPR-Cas: Spacer Diversity Determines the Efficiency of Defense

    Lopatina A., Sorek R. (2016), Current Biology. 26, 14, p. R683-R685
  • Evolution of domain-peptide interactions to coadapt specificity and affinity to functional diversity

  • Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues.

    Bahar Halpern H. K., Itzkovitz S. (2016), Methods (San Diego, Calif.). 98, p. 134-42
  • An essential role for UTX in resolution and activation of bivalent promoters

    Dhar S. S., Lee S., Chen K. et al., Zhu G., Oh W., Allton K., Gafni O., Kim Y. Z., Tomoiga A. S., Barton M. C., Hanna J. H., Wang Z., Li W., Lee M. G. (2016), Nucleic Acids Research. 44, 8, p. 3659-3674   |  All authors
  • Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

    Dar D., Shamir M., Mellin J. R. et al., Koutero M., Stern-Ginossar N., Cossart P., Sorek R. (2016), Science. 352, 6282, p. 187-+, aad9822   |  All authors
  • Dealing with Gene-Dosage Imbalance during S Phase

    Bar-Ziv R., Voichek Y., Barkai N. (2016), Trends in Genetics. 32, 11, p. 717-723
  • Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

  • pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism

    Mangan N. M., Flamholz A., Hood R. D. et al., Milo R., Savage D. F. (2016), Proceedings of the National Academy of Sciences of the United States of America. 113, 36, p. E5354-E5362   |  All authors
  • The dihydrofolate reductase protein-fragment complementation assay: A survival-selection assay for large-scale analysis of protein-protein interactions

    Michnick S. W., Levy E. D., Landry C. R. et al., Kowarzyk J., Messier V. (2016), Cold Spring Harbor Protocols. 2016, 11, p. 963-971   |  All authors
  • Sugar Synthesis from CO2 in Escherichia coli

    Antonovsky N., Gleizer S., Noor E. et al., Zohar Y., Herz E., Barenholz U., Zelcbuch L., Amram S., Wides A., Tepper N., Davidi D., Bar-On Y., Bareia T., Wernick D. G., Shani I., Malitsky S., Jona G., Bar-Even A., Milo R. (2016), Cell. 166, 1, p. 115-125   |  All authors
  • Revised Estimates for the Number of Human and Bacteria Cells in the Body.

    Sender R., Fuchs S., Milo R. (2016), PLoS Biology. 14, 8, p. e1002533
  • Systematic discovery of cap-independent translation sequences in human and viral genomes

    Weingarten-Gabbay S., Elias-Kirma S., Nir R. et al., Gritsenko A. A., Stern-Ginossar N., Yakhini Z., Weinberger A., Segal E. (2016), Science. 351, 6270, p. 240-U144   |  All authors
  • Synthesis And Cell-Free Cloning Of Dna Libraries Using Programmable Microfluidics

    Ben-Yehezkel T., Rival A., Raz O. et al., Cohen R., Marx Z., Camara M., Dubern J., Koch B., Heeb S., Krasnogor N., Delattre C., Shapiro E. (2016), Nucleic Acids Research. 44, 4, e35   |  All authors
  • Cell scientist to watch - Maya Schuldiner

    Bobrowska A., Schuldiner M. (2015), Journal of Cell Science. 128, 22, p. 4029-4031
  • A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

    Fields A. P., Rodriguez E. H., Jovanovic M. et al., Stern-Ginossar N., Haas B. J., Mertins P., Raychowdhury R., Hacohen N., Carr S. A., Ingolia N. T., Regev A., Weissman J. S. (2015), Molecular Cell. 60, 5, p. 816-827   |  All authors
  • Nuclear Retention of mRNA in Mammalian Tissues

    Halpern K. B., Caspi I., Lemze D. et al., Levy M., Landen S., Elinav E., Ulitsky I., Itzkovitz S. (2015), Cell Reports. 13, 12, p. 2653-2662   |  All authors
  • Decoding a neural circuit controlling global animal state in C-elegans

    Laurent P., Soltesz Z., Nelson G. et al., Chen C., Arellano-Carbajal F., Levy E., de Bono M. (2015), eLife. 4, 04241   |  All authors
  • Reactivation of epigenetically silenced miR-512 and miR-373 sensitizes lung cancer cells to cisplatin and restricts tumor growth

    Harel S., Ben-Moshe N., Aylon Y. et al., Bublik D., Moskovits N., Toperoff G., Azaiza D., Biagoni F., Fuchs G., Wilder S., Hellman A., Blandino G., Domany E., Oren M. (2015), Cell Death and Differentiation. 22, 8, p. 1328-1340   |  All authors
  • Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

    Paul F., Arkin Y., Giladi A. et al., Jaitin D. A., Kenigsberg E., Keren-Shaul H., Winter D., Lara-Astiaso D., Gury M., Weiner A., David E., Cohen N., Lauridsen F. K. B., Haas S., Schlitzer A., Mildner A., Ginhoux F., Jung S., Trumpp A., Porse B. T., Tanay A., Amit I. (2015), Cell. 163, 7, p. 1663-1677   |  All authors
  • Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

    Korem T., Zeevi D., Suez J. et al., Weinberger A., Avnit Sagi S. T., Pompan-Lotan M., Matot E., Jona G., Harmelin A., Cohen N., Sirota-Madi A., Thaiss C. A., Pevsner-Fischer M., Sorek R., Xavier R. J., Elinav E., Segal E. (2015), Science (New York, N.Y.). 349, 6252, p. 1101-1106   |  All authors
  • DNA Crossover Motifs Associated with Epigenetic Modifications Delineate Open Chromatin Regions in Arabidopsis.

    Shilo S., Melamed-Bessudo C., Dorone Y. et al., Barkai N., Levy A. (2015), The Plant cell. 27, 9, p. 2427-36, 26381163   |  All authors
  • Peroxisystem: Harnessing systems cell biology to study peroxisomes

    Schuldiner M., Zalckvar E. (2015), Biology of the Cell. 107, 4, p. 89-97
  • Diurnal suppression of EGFR signaling by glucocorticoids: implications for tumor progression and treatment

    Lauriola M., Enuka Y., Zeisel A. et al., D'Uva G. M., Roth L., Carvalho S., Solmi R., Domany E., Yarden Y. (2015),   |  All authors
  • Lipid Droplets Are Essential for Efficient Clearance of Cytosolic Inclusion Bodies

    Moldavski O., Amen T., Levin-Zaidman S. et al., Eisenstein M., Rogachev I., Brandis A., Kaganovich D., Schuldiner M. (2015), Developmental Cell. 33, 5, p. 603-610   |  All authors
  • Quantitative visualization of alternative exon expression from RNA-seq data

    Katz Y., Wang E. T., Silterra J. et al., Schwartz S., Wong B., Thorvaldsdottir H., Robinson J. T., Mesirov J. P., Airoldi E. M., Burge C. B. (2015), Bioinformatics. 31, 14, p. 2400-2402   |  All authors
  • Reply to Tichenor: Proposed update to beef greenhouse gas footprint is numerically questionable and well within current uncertainty bounds

    Eshel G., Shepon A., Makov T. et al., Milo R. (2015),   |  All authors
  • One library to make them all: Streamlining yeast library creation by a SWAp-Tag (SWAT) strategy

    Weill U., Yofe I., Chuartzman S. et al., Schuldiner M. (2015), Yeast. 32, p. S77-S77   |  All authors
  • Taming the inflammasome

    Levy M., Thaiss C. A., Elinav E. (2015), Nature Medicine. 21, 3, p. 213-215
  • Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling.

    Levy M., Thaiss C. A., Zeevi D. et al., Dohnalova L., Zilberman-Schapira G., Mahdi J. A., David E., Savidor A., Korem T., Herzig Y., Pevsner-Fischer M., Shapiro H., Christ A., Harmelin A., Halpern Z., Latz E., Flavell R. A., Amit I., Segal E., Elinav E. (2015), Cell. 163, 6, p. 1428-1443   |  All authors
  • SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate

    Irie N., Weinberger L., Tang W. W. C. et al., Kobayashi T., Viukov S., Manor Y. S., Dietmann S., Hanna J. H., Surani M. A. (2015), Cell. 160, 1-2, p. 253-268   |  All authors
  • Third Report on Chicken Genes and Chromosomes 2015

    Schmid M., Smith J., Burt D. W. et al., Aken B. L., Antin P. B., Archibald A. L., Ashwell C., Blackshear P. J., Boschiero C., Brown C. T., Burgess S. C., Cheng H. H., Chow W., Coble D. J., Cooksey A., Crooijmans R. P. M. A., Damas J., Davis R. V. N., de Koning K. D., Delany M. E., Derrien T., Desta T. T., Dunn I. C., Dunn M., Ellegren H., Eoery L., Erb I., Farre M., Fasold M., Fleming D., Flicek P., Fowler K. E., Fresard L., Froman D. P., Garceau V., Gardner P. P., Gheyas A. A., Griffin D. K., Groenen M. A. M., Haaf T., Hanotte O., Hart A., Haesler J., Hedges S. B., Hertel J., Howe K., Hubbard A., Hume D. A., Kaiser P., Kedra D., Kemp S. J., Klopp C., Kniel K. E., Kuo R., Lagarrigue S., Lamont S. J., Larkin D. M., Lawal R. A., Markland S. M., McCarthy F., McCormack H. A., McPherson M. C., Motegi A., Muljo S. A., Muensterberg A., Nag R., Nanda I., Neuberger M., Nitsche A., Notredame C., Noyes H., O'Connor R., O'Hare E. A., Oler A. J., Ommeh S. C., Pais H., Persia M., Pitel F., Preeyanon L., Barja P. P., Pritchett E. M., Rhoads D. D., Robinson C. M., Romanov M. N., Rothschild M., Roux P., Schmidt C. J., Schneider A., Schwartz M. G., Searle S. M., Skinner M. A., Smith C. A., Stadler P. F., Steeves T. E., Steinlein C., Sun L., Takata M., Ulitsky I., Wang Q., Wang Y., Warren W. C., Wood J. M. D., Wragg D., Zhou H. (2015), Cytogenetic and Genome Research. 145, 1424-8581   |  All authors
  • Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape

    Winter D. R., Jung S., Amit I. (2015), Nature Reviews Immunology. 15, 9, p. 585-594
  • Noise in gene expression is coupled to growth rate.

    Keren L., Van Dijk D. D., Weingarten-Gabbay S. et al., Davidi D., Jona G., Weinberger A., Milo R., Segal E. (2015), Genome Research. 25, 12, p. 1893-902   |  All authors
  • Derivation of novel human ground state naive pluripotent stem cells (vol 504, pg 282, 2013)

    Gafni O., Weinberger L., Mansour A. A. et al., Manor Y. S., Chomsky E., Ben-Yosef D., Kalma Y., Viukov S., Maza I., Zviran A., Rais Y., Shipony Z., Mukamel Z., Krupalnik V., Zerbib M., Geula S., Caspi I., Schneir D., Shwartz T., Gilad S., Amann-Zalcenstein D., Benjamin S., Amit I., Tanay A., Massarwa R., Novershtern N., Hanna J. H. (2015), Nature. 520, 7549   |  All authors
  • High-Resolution Chromatin Dynamics during a Yeast Stress Response

    Weiner A., Hsieh T. S., Appleboim A. et al., Chen H. V., Rahat A., Amit I., Rando O. J., Friedman N. (2015), Molecular Cell. 58, 2, p. 371-386   |  All authors
  • DCs are ready to commit

    Winter D., Amit I. (2015), Nature Immunology. 16, 7, p. 683-685
  • Diversion of aspartate in ASS1-deficient tumours fosters de novo pyrimidine synthesis

    Rabinovich S., Adler L., Yizhak K. et al., Sarver A., Silberman A., Agron S., Stettner N., Sun Q., Brandis A., Helbling D., Korman S., Itzkovitz S., Dimmock D., Ulitsky I., Nagamani S. C. S., Ruppin E., Erez A. (2015), Nature. 527, 7578, p. 379-+   |  All authors
  • MicroRNAs silence the noisy genome

    Hoffman Y., Pilpel Y. (2015), Science. 348, 6230, p. 41-42
  • Partitioning United States' feed consumption among livestock categories for improved environmental cost assessments

    Eshel G., Shepon A., Makov T. et al., Milo R. (2015), Journal of Agricultural Science. 153, 3, p. 432-445   |  All authors
  • Integration of gene expression and GWAS results supports involvement of calcium signaling in Schizophrenia

    Hertzberg L., Katsel P., Roussos P. et al., Haroutunian V., Domany E. (2015), Schizophrenia Research. 164, 3-Jan, p. 92-99   |  All authors
  • Tumor evolution inferred by patterns of miRNA expression through the course of disease, therapy and recurrence in breast cancer

    Dadiani M., Bossel N., Paluch-Shimon S. et al., Peri G., Pavlovski A., Kahana-Edwin S., Balint N., Yosepovich A., Zundelevich A., Gal-Yam E., Berger R., Barshack I., Domany E., Kaufman B. (2015),   |  All authors
  • Lymphatic vessels arise from specialized angioblasts within a venous niche

    Nicenboim J., Malkinson G., Lupo T. et al., Asaf L., Sela Y., Mayseless O., Gibbs-Bar L., Senderovich N., Hashimshony T., Shin M. S., Jerafi-Vider A., Avraham-Davidi I., Krupalnik V., Hofi R., Almog G., Astin J. W., Golani O., Ben-Dor S., Crosier P. S., Herzog W., Lawson N. D., Hanna J. H., Yanai I., Yaniv K. (2015), Nature. 522, 7554, p. 56-U100   |  All authors
  • A cellular and regulatory map of the cholinergic nervous system of C. elegans

    Pereira L., Kratsios P. P., Serrano-Saiz E. et al., Sheftel H., Mayo A. E., Hall D. H., White J. G., LeBoeuf B., Garcia L. R., Alon U., Hobert O. (2015), eLife. 4, 12432   |  All authors
  • Epithelial IL-18 Equilibrium Controls Barrier Function in Colitis

    Nowarski R., Jackson R., Gagliani N. et al., de Zoete M. R., Palm N. W., Bailis W., Low J. S., Harman C. C. D., Graham M., Elinav E., Flavell R. A. (2015), Cell. 163, 6, p. 1444-1456   |  All authors
  • Chronobiomics: The Biological Clock as a New Principle in Host-Microbial Interactions.

    Thaiss C. A., Levy M., Elinav E. (2015), PLoS Pathogens. 11, 10, p. e1005113, 26448621
  • Spatial Fluctuations in Expression of the Heterocyst Differentiation Regulatory Gene hetR in Anabaena Filaments

    Corrales-Guerrero L., Tal A., Arbel-Goren R. et al., Mariscal V., Flores E., Herrero A., Stavans J. (2015), PLoS Genetics. 11, 4, p. e10005031, e1005031   |  All authors
  • The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness

    Bar-Even A., Milo R., Noor E. et al., Tawfik D. (2015), Biochemistry. 54, 32   |  All authors
  • Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells

    Tendler A., Mayo A., Alon U. (2015), BMC Systems Biology. 9, 12
  • Personalized Nutrition by Prediction of Glycemic Responses.

    Zeevi D., Korem T., Zmora N. et al., Israeli D., Rothschild D., Weinberger A., Ben-Yacov O., Lador D., Avnit Sagi S. T., Lotan-Pompan M., Suez J., Mahdi J. A., Matot E., Malka G., Kosower N., Rein M., Zilberman-Schapira G., Dohnalova L., Pevsner-Fischer M., Bikovsky R., Halpern Z., Elinav E., Segal E. (2015), Cell. 163, 5, p. 1079-94   |  All authors
  • m(6)A mRNA methylation facilitates resolution of naive pluripotency toward differentiation

    Geula S., Moshitch-Moshkovitz S., Dominissini D. et al., Mansour A. A., Kol N., Salmon-Divon M., Hershkovitz V., Peer E., Mor N., Manor Y. S., Ben-Haim M., Eyal E., Yunger S., Pinto Y., Jaitin D. A., Viukov S., Rais Y., Krupalnik V., Chomsky E., Zerbib M., Maza I., Rechavi Y., Massarwa R., Hanna S., Amit I., Levanon E. Y., Amariglio N., Stern-Ginossar N., Novershtern N., Rechavi G., Hanna J. H. (2015), Science. 347, 6225, p. 1002-1006   |  All authors
  • Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics

    Jaitin D. A., Keren-Shaul H., Elefant N. et al., Amit I. (2015), Seminars in Immunology. 27, 1, p. 67-71   |  All authors
  • Starvation-Dependent Regulation of Golgi Quality Control Links the TOR Signaling and Vacuolar Protein Sorting Pathways

    Dobzinski N., Chuartzman S. G., Kama R. et al., Schuldiner M., Gerst J. (2015), Cell Reports. 12, 11, p. 1876-1886   |  All authors
  • NF-kappa B Regulation by NLRs: T Cells Join the Club

    Thaiss C. A., Elinav E. (2015), Immunity. 42, 4, p. 595-597
  • Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants

    Ben-Yehezkel T., Atar S., Zur H. et al., Diament A., Goz E., Marx T., Cohen R., Dana A., Feldman A., Shapiro E., Tuller T. (2015), RNA Biology. 12, 9, p. 972-984   |  All authors
  • Aging, clonal hematopoiesis and preleukemia: not just bad luck?

    Shlush L. I., Zandi S., Itzkovitz S. et al., Schuh A. C. (2015), International Journal of Hematology. 102, 5, p. 513-522   |  All authors
  • Lam6 Regulates the Extent of Contacts between Organelles

    Elbaz-Alon Y., Eisenberg-Bord M., Shinder V. et al., Stiller S., Shimoni E., Wiedemann N., Geiger T., Schuldiner M. (2015), Cell Reports. 12, 1, p. 7-14   |  All authors
  • The J protein Djp1 is involved in the targeting of mitochondrial precursor proteins

    Hansen K. G., Aviram N., Schuldiner M. et al., Herrmann J. M. (2015), FEBS Journal. 282, p. 101-101   |  All authors
  • Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens

    Jovanovic M., Rooney M. S., Mertins P. et al., Przybylski D., Chevrier N., Satija R., Rodriguez E. H., Fields A. P., Schwartz S., Raychowdhury R., Mumbach M. R., Eisenhaure T., Rabani M., Gennert D., Lu D., Delorey T., Weissman J. S., Carr S. A., Hacohen N., Regev A. (2015), Science (New York, N.Y.). 347, 6226, p. 1259038   |  All authors
  • Decoding Viral Infection by Ribosome Profiling

    Stern-Ginossar N. (2015), Journal of Virology. 89, 12, p. 6164-6166
  • Systematic Dissection of the Sequence Determinants of Gene 3 ' End Mediated Expression Control

    Shalem O., Sharon E., Lubliner S. et al., Regev I., Lotan-Pompan M., Yakhini Z., Segal E. (2015), PLoS Genetics. 11, 4, e1005147   |  All authors
  • BREX is a novel phage resistance system widespread in microbial genomes

    Goldfarb T., Sberro H., Weinstock E. et al., Cohen O., Doron S., Charpak-Amikam Y., Afik S., Ofir G., Sorek R. (2015), EMBO Journal. 34, 2, p. 169-183   |  All authors
  • From mass cytometry to cancer prognosis

    Winter D. R., Ledergor G., Amit I. (2015), Nature Biotechnology. 33, 9
  • Failure to replicate the STAP cell phenomenon

    De Los Angeles L. A. A., Ferrari F., Fujiwara Y. et al., Mathieu R., Lee S., Lee S., Tu H., Ross S., Chou S., Nguyen M., Wu Z., Theunissen T. W., Powell B. E., Imsoonthornruksa S., Chen J., Borkent M., Krupalnik V., Lujan E., Wernig M., Hanna J. H., Hochedlinger K., Pei D., Jaenisch R., Deng H., Orkin S. H., Park P. J., Daley G. Q. (2015), Nature. 525, 7570, p. E6-E9   |  All authors
  • Down-regulation of LATS kinases alters p53 to promote cell migration.

    Furth N., Bossel Ben-Moshe B. N., Pozniak Y. et al., Porat Z., Geiger T., Domany E., Aylon Y., Oren M. (2015), GENES & DEVELOPMENT. 29, 22, p. 2325-30   |  All authors
  • Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

    Rudan M. V., Barrington C., Henderson S. et al., Ernst C., Odom D. T., Tanay A., Hadjur S. (2015), Cell Reports. 10, 8, p. 1297-1309   |  All authors
  • A Relay Race on the Evolutionary Adaptation Spectrum

    Yona A. H., Frumkin I., Pilpel Y. (2015), Cell. 163, 3, p. 549-559
  • Ribosome Profiling As A Tool To Decipher Viral Complexity

    Stern-Ginossar N., Ingolia N. T. (2015), Annual Review of Virology. p. 335-349
  • Inflammasomes and the microbiota-partners in the preservation of mucosal homeostasis

    Levy M., Thaiss C. A., Katz M. N. et al., Suez J., Elinav E. (2015), Seminars in Immunopathology. 37, 1, p. 39-46   |  All authors
  • Transcription factor binding dynamics during human ES cell differentiation

    Tsankov A. M., Gu H., Akopian V. et al., Ziller M. J., Donaghey J., Amit I., Gnirke A., Meissner A. (2015), Nature. 518, 7539   |  All authors
  • Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors

    Maza I., Caspi I., Zviran A. et al., Chomsky E., Rais Y., Viukov S., Geula S., Buenrostro J., Weinberger L., Krupalnik V., Hanna S., Zerbib M., Dutton J., Greenleaf W., Massarwa R., Novershtern N., Hanna J. (2015), Nature Biotechnology. 33, 7, p. 769-774   |  All authors
  • GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms

    Manor O., Segal E. (2015), Bioinformatics. 31, 11, p. 1848-1850
  • Distinct Murine Mucosal Langerhans Cell Subsets Develop from Pre-dendritic Cells and Monocytes

    Capucha T., Mizraji G., Segev H. et al., Blecher-Gonen R., Winter D., Khalaileh A., Tabib Y., Attal T., Nassar M., Zelentsova K., Kisos H., Zenke M., Sere K., Hieronymus T., Burstyn-Cohen T., Amit I., Wilensky A., Hovav A. (2015), Immunity. 43, 2, p. 369-381   |  All authors
  • Inferring biological tasks using Pareto analysis of high-dimensional data

    Hart Y., Sheftel H., Hausser J. et al., Szekely P., Ben-Moshe N. B., Korem Y., Tendler A., Mayo A. E., Alon U. (2015), Nature Methods. 12, 3, p. 233-+   |  All authors
  • The Transcription and Translation Landscapes during Human Cytomegalovirus Infection Reveal Novel Host-Pathogen Interactions.

    Tirosh O., Cohen Y., Shitrit A. et al., Shani O., Le-Trilling V. T. K., Trilling M., Friedlander G., Tanenbaum M., Stern-Ginossar N. (2015), PLoS Pathogens. 11, 11, p. e1005288-e1005288, e1005288   |  All authors
  • Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

    Avraham R., Haseley N., Brown D. et al., Penaranda C., Jijon H. B., Trombetta J. J., Satija R., Shalek A. K., Xavier R. J., Regev A., Hung D. T. (2015), Cell. 162, 6, p. 1309-1321   |  All authors
  • Deterministic direct reprogramming of somatic cells to pluripotency (vol 502, pg 65, 2013)

    Rais Y., Zviran A., Geula S. et al., Gafni O., Chomsky E., Viukov S., Mansour A. A., Caspi I., Krupalnik V., Zerbib M., Maza I., Mor N., Baran D., Weinberger L., Jaitin D. A., Lara-Astiaso D., Blecher-Gonen R., Shipony Z., Mukamel Z., Hagai T., Gilad S., Amann-Zalcenstein D., Tanay A., Amit I., Novershtern N., Hanna J. H. (2015), Nature. 520, 7549, p. 710-710   |  All authors
  • Editorial overview: Genome architecture and expression

  • Editorial overview: Cell organelles: Organelle communication: new means and new views.

  • Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

    Nagano T., Lubling Y., Yaffe E. et al., Wingett S. W., Dean W., Tanay A., Fraser P. (2015), Nature protocols. 10, 12, p. 1986-2003   |  All authors
  • Corrective jitter motion shows similar individual frequencies for the arm and the finger

    Noy L., Alon U., Friedman J. (2015), Experimental Brain Research. 233, 4, p. 1307-1320
  • Guanine polynucleotides are self-antigens for human natural autoantibodies and are significantly reduced in the human genome

    Fattal I., Shental N., Ben-Dor S. et al., Molad Y., Gabrielli A., Pokroy-Shapira E., Oren S., Livneh A., Langevitz P., Zandman-Goddard G., Sarig O., Margalit R., Gafter U., Domany E., Cohen I. R. (2015), Immunology. 146, 3, p. 401-410   |  All authors
  • Symmetry Breaking in Homo-Oligomers: The Curious Case of Mega-Hemocyanin

    Seisdedos H. G., Steinberg A., Levy E. D. (2015), Structure. 23, 1, p. 3-5
  • The Evolutionary Potential of Phenotypic Mutations

    Yanagida H., Gispan A., Kadouri N. et al., Rozen S., Sharon M., Barkai N., Tawfik D. S. (2015), PLoS Genetics. 11, 8, 1005445   |  All authors
  • Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome.

    Levy M., Thaiss C. A., Elinav E. (2015), Genome Medicine. 7, 1, p. 120-120
  • The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space.

    Szekely P., Korem Y., Moran U. et al., Mayo A., Alon U. (2015), PLoS Computational Biology. 11, 10, p. e1004524, 26465336   |  All authors
  • Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq

    Fuchs G., Voichek Y., Rabani M. et al., Benjamin S., Gilad S., Amit I., Oren M. (2015), Nature Protocols. 10, 4, p. 605-618   |  All authors
  • Chromosome 7 gain and DNA hypermethylation at the HOXA10 locus are associated with expression of a stem cell related HOX-signature in glioblastoma

    Kurscheid S., Bady P., Sciuscio D. et al., Samarzija I., Shay T., Vassallo I., Criekinge W. V., Daniel R. T., van den Bent d. B. M. J., Marosi C., Weller M., Mason W. P., Domany E., Stupp R., Delorenzi M., Hegi M. E. (2015), GENOME BIOLOGY. 16, 16   |  All authors
  • Recurrent inactivating RASA2 mutations in melanoma

    Arafeh R., Qutob N., Emmanuel R. et al., Keren-Paz A., Madore J., Elkahloun A., Wilmott J. S., Gartner J. J., Di Pizio A., Winograd-Katz S., Sindiri S., Rotkopf R., Dutton-Regester K., Johansson P., Pritchard A. L., Waddell N., Hill V. K., Lin J. C., Hevroni Y., Rosenberg S. A., Khan J., Ben-Dor S., Niv M. Y., Ulitsky I., Mann G. J., Scolyer R. A., Hayward N. K., Samuels Y. (2015), Nature Genetics. 47, 12, p. 1408-1410   |  All authors
  • Bursty Gene Expression in the Intact Mammalian Liver

    Halpern K. B., Tanami S., Landen S. et al., Chapal M., Szlak L., Hutzler A., Nizhberg A., Itzkovitz S. (2015), Molecular Cell. 58, 1, p. 147-156   |  All authors
  • A novel regulator determines the extent of contacts between organelles

    Schuldiner M. (2015), FEBS Journal. 282, p. 10-10
  • Genome-Wide Screens in Saccharomyces cerevisiae Highlight a Role for Cardiolipin in Biogenesis of Mitochondrial Outer Membrane Multispan Proteins.

    Sauerwald J., Jores T., Eisenberg-Bord M. et al., Chuartzman S. G., Schuldiner M., Rapaport D. (2015), Molecular and Cellular Biology. 35, 18, p. 3200-3211   |  All authors
  • Artificial Sweeteners Induce Glucose Intolerance by Altering the Gut Microbiota: Editorial comment

    Suez J., Korem T., Zeevi D. et al., Zilberman-Schapira G., Thaiss C. A., Maza O., Israeli D., Zmora N., Gilad S., Weinberger A., Kuperman Y., Harmelin A., Kolodkin-Gal I., Shapiro H., Halpern Z., Segal E., Elinav E. (2015), Obstetrical & Gynecological Survey. 70, 1, p. 31-32   |  All authors
  • An In Vivo Metabolic Approach for Deciphering the Product Specificity of Glycerate Kinase Proves that Both E. coli's Glycerate Kinases Generate 2-Phosphoglycerate

    Zelcbuch L., Razo-Mejia M., Herz E. et al., Yahav S., Antonovsky N., Kroytoro H., Milo R., Bar-Even A. (2015), PLoS One. 10, 3, e0122957   |  All authors
  • The Lamarckian chicken and the Darwinian egg

    Pilpel Y., Rechavi O. (2015), Biology Direct. 10, 34
  • Single-cell epigenomics: techniques and emerging applications

    Schwartzman O., Tanay A. (2015), Nature Reviews Genetics. 16, 12, p. 716-726
  • CRISPR adaptation biases explain preference for acquisition of foreign DNA

    Levy A., Goren M. G., Yosef I. et al., Auster O., Manor M., Amitai G., Edgar R., Qimron U., Sorek R. (2015), Nature. 520, 7548, p. 505-+   |  All authors
  • The interplay between the innate immune system and the microbiota

    Thaiss C. A., Levy M., Suez J. et al., Elinav E. (2014), Current Opinion in Immunology. 26, p. 41-48   |  All authors
  • Pregnancy-Associated Listeriosis: Clinical Characteristics and Geospatial Analysis of a 10-Year Period in Israel

    Elinav H., Hershko-Klement A., Valinsky L. et al., Jaffe J., Wiseman A., Shimon H., Braun E., Paitan Y., Block C., Sorek R., Nir-Paz R. (2014), Clinical Infectious Diseases. 59, 7, p. 953-961   |  All authors
  • Epstein-Barr virus antibodies mark systemic lupus erythematosus and scleroderma patients negative for anti-DNA

    Fattal I., Shental N., Molad Y. et al., Gabrielli A., Pokroy-Shapira E., Oren S., Livneh A., Langevitz P., Pauzner R., Sarig O., Gafter U., Domany E., Cohen I. R. (2014), Immunology. 141, 2, p. 276-285   |  All authors
  • Aging-induced immunological signature of the brain's choroid plexus negatively regulates neurogenesis and cognitive function

    Deczkowska A., Baruch K., David E. et al., Castellano J. M., Miller O., Kertser A., Berkutzki T., Barnett Itzhaki I. Z., Bezalel D., Wyss-coray T., Amit I., Schwartz M. (2014),   |  All authors
  • A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

    Bloom-Ackermann Z., Navon S., Gingold H. et al., Towers R., Pilpel Y., Dahan O. (2014), PLoS Genetics. 10, 1, e1004084   |  All authors
  • Visual account of protein investment in cellular functions

    Liebermeister W., Noor E., Flamholz A. et al., Davidi D., Bernhardt J., Milo R. (2014), Proceedings of the National Academy of Sciences of the United States of America. 111, 23, p. 8488-8493   |  All authors
  • Artificial sweeteners induce glucose intolerance by altering the gut microbiota

    Suez J., Korem T., Zeevi D. et al., Zilberman-Schapira G., Thaiss C. A., Maza O., Israeli D., Zmora N., Gilad S., Weinberger A., Kuperman Y., Harmelin A., Kolodkin-Gal I., Shapiro H., Halpern Z., Segal E., Elinav E. (2014), Nature. 514, 7521, p. 181-186   |  All authors
  • Phenotypic noise: effects of post-transcriptional regulatory processes affecting mRNA

    Arbel-Goren R., Tal A., Stavans J. (2014), Wiley Interdisciplinary Reviews-Rna. 5, 2, p. 197-207
  • A shared architecture for promoters and enhancers

    Weingarten-Gabbay S., Segal E. (2014), Nature Genetics. 46, 12, p. 1253-1254
  • Embracing the void-how much do we really know about targeting and translocation to the endoplasmic reticulum?

    Aviram N., Schuldiner M. (2014), Current Opinion in Cell Biology. 29, p. 8-17
  • In pursuit of design principles of regulatory sequences

    Levo M., Segal E. (2014), Nature Reviews Genetics. 15, 7, p. 453-468
  • The emergence of proteome-wide technologies: systematic analysis of proteins comes of age

  • Fur Is the Master Regulator of the Extraintestinal Pathogenic Escherichia coli Response to Serum

    Huja S., Oren Y., Biran D. et al., Meyer S., Dobrindt U., Bernhard J., Becher D., Hecker M., Sorek R., Ron E. Z. (2014), mBio. 5, 4, e01460-14   |  All authors
  • Peroxisomes are juxtaposed to strategic sites on mitochondria

    Cohen Y., Klug Y., Dimitrov L. et al., Erez Z., Chuartzman S., Elinger D., Yofe I., Soliman K., Gartner J., Thoms S., Schekman R., Elbaz-Alon Y., Zalckvar E., Schuldiner M. (2014), Molecular BioSystems. 10, 7, p. 1742-1748   |  All authors
  • Host-parasite network structure is associated with community-level immunogenetic diversity

    Pilosof S., Fortuna M. A., Cosson J. et al., Galan M., Kittipong C., Ribas A., Segal E., Krasnov B. R., Morand S., Bascompte J. (2014), Nature Communications. 5   |  All authors
  • Molecular Rules Governing De Novo Methylation in Cancer

    Nejman D., Straussman R., Steinfeld I. et al., Ruvolo M., Roberts D., Yakhini Z., Cedar H. (2014), Cancer Research. 74, 5, p. 1475-1483   |  All authors
  • Single cell analysis exposes intratumor heterogeneity and suggests that FLT3-ITD is a late event in leukemogenesis

    Shouval R., Shlush L. I., Yehudai-Resheff S. et al., Ali S., Pery N., Shapiro E., Tzukerman M., Rowe J. M., Zuckerman T. (2014), Experimental Hematology. 42, 6, p. 457-463   |  All authors
  • Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function

  • Identification of novel DNA-damage tolerance genes reveals regulation of translesion DNA synthesis by nucleophosmin

    Ziv O., Zeisel A., Mirlas-Neisberg N. et al., Swain U., Nevo R., Ben Chetrit C. N., Martelli M. P., Rossi R., Schiesser S., Canman C. E., Carell T., Geacintov N. E., Falini B., Domany E., Livneh Z. (2014), Nature Communications. 5   |  All authors
  • Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

    Jaitin D. A., Kenigsberg E., Keren-Shaul H. et al., Elefant N., Paul F., Zaretsky I., Mildner A., Cohen N., Jung S., Tanay A., Amit I. (2014), Science. 343, 6172, p. 776-779   |  All authors
  • Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5 ' Sites

    Schwartz S., Mumbach M. R., Jovanovic M. et al., Wang T., Maciag K., Bushkin G. G., Mertins P., Ter-Ovanesyan D., Habib N., Cacchiarelli D., Sanjana N. E., Freinkman E., Pacold M. E., Satija R., Mikkelsen T. S., Hacohen N., Zhang F., Carr S. A., Lander E. S., Regev A. (2014), Cell Reports. 8, 1, p. 284-296   |  All authors
  • A simple cage-autonomous method for the maintenance of the barrier status of germ-free mice during experimentation

    Hecht G., Bar-Nathan C., Milite G. et al., Alon I., Moshe Y., Greenfeld L., Dotsenko N., Suez J., Levy M., Thaiss C. A., Dafni H., Elinav E., Harmelin A. (2014), Laboratory Animals. 48, 4, p. 292-297   |  All authors
  • Genetic and Phenotypic Diversity in Breast Tumor Metastases

    Almendro V., Kim H. J., Cheng Y. et al., Goenen M., Itzkovitz S., Argani P., van Oudenaarden O. A., Sukumar S., Michor F., Polyak K. (2014), Cancer Research. 74, 5, p. 1338-1348   |  All authors
  • The role of chromatin dynamics in immune cell development

    Winter D. R., Amit I. (2014), Immunological Reviews. 261, 1, p. 9-22
  • Inflammasomes and Metabolic Disease

    Henao-Mejia J., Elinav E., Thaiss C. A. et al., Flavell R. (2014), Annual Review of Physiology. p. 57-78   |  All authors
  • Reply to Metson et al.: The importance of phosphorus perturbations

    Eshel G., Shepon A., Makov T. et al., Milo R. (2014),   |  All authors
  • A Fundamental Trade-off in Covalent Switching and Its Circumvention by Enzyme Bifunctionality in Glucose Homeostasis

    Dasgupta T., Croll D. H., Owen J. A. et al., Vander Heiden H. M. G., Locasale J. W., Alon U., Cantley L. C., Gunawardena J. (2014), Journal of Biological Chemistry. 289, 19, p. 13010-13025   |  All authors
  • 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

    Fuchs G., Voichek Y., Benjamin S. et al., Gilad S., Amit I., Oren M. (2014), GENOME BIOLOGY. 15, 5, R69   |  All authors
  • The yeast oligopeptide transporter Opt2 is localized to peroxisomes and affects glutathione redox homeostasis

    Elbaz-Alon Y., Morgan B., Clancy A. et al., Amoako T. N. E., Zalckvar E., Dick T. P., Schwappach B., Schuldiner M. (2014), FEMS Yeast Research. 14, 7, p. 1055-1067   |  All authors
  • KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using NextGeneration Sequencing Reveals Novel Genomic and Functional Features

    Arias C., Weisburd B., Stern-Ginossar N. et al., Mercier A., Madrid A. S., Bellare P., Holdorf M., Weissman J. S., Ganem D. (2014), PLoS Pathogens. 10, 1, 1003847   |  All authors
  • Scaling of dorsal-ventral patterning in the Xenopus laevis embryo

    Ben-Zvi D., Fainsod A., Shilo B. et al., Barkai N. (2014), BioEssays. 36, 2, p. 151-156   |  All authors
  • Probing the effect of promoters on noise in gene expression using thousands of designed sequences

    Sharon E., Van Dijk D. D., Kalma Y. et al., Keren L., Manor O., Yakhini Z., Segal E. (2014), Genome Research. 24, 10, p. 1698-1706   |  All authors
  • COMBINATION OF GENE COPY GAIN AND EPIGENETIC DEREGULATION ARE ASSOCIATED WITH THE ABERRANT EXPRESSION OF A STEM CELL RELATED HOX-SIGNATURE IN GLIOBLASTOMA

    Kurscheid S., Bady P., Sciuscio D. et al., Samarzija I., Shay T., Vassallo I., Van Criekinge C. W., Domany E., Stupp R., Delorenzi M., Hegi M. (2014),   |  All authors
  • Primers-4-Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae

    Yofe I., Schuldiner M. (2014), Yeast. 31, 2, p. 77-80
  • Divergence and Selectivity of Expression-Coupled Histone Modifications in Budding Yeasts

    Mosesson Y., Voichek Y., Barkai N. (2014), PLoS One. 9, 7, e101538
  • A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

    Gingold H., Tehler D., Christoffersen N. et al., Nielsen M., Asmar F., Kooistra S., Christophersen N., Christensen L., Borre M., Sorensen K., Andersen L., Andersen C., Hulleman E., Wurdinger T., Ralfkiaer E., Helin K., Gronbaek K., Omtoft T., Waszak S., Dahan O., Pedersen J., Lund A., Pilpel Y. (2014), Cell. 158, 6, p. 1281-1292   |  All authors
  • Diurnal suppression of EGFR signalling by glucocorticoids and implications for tumour progression and treatment

    Lauriola M., Enuka Y., Zeisel A. et al., D'Uva G., Roth L., Sharon-Sevilla M., Lindzen M., Sharma K., Nevo N., Carvalho S., Cohen-Dvashi H., Kedmi M., Ben Chetrit C. N., Chen A., Solmi R., Wiemann S., Schmitt F., Domany E., Yarden Y. (2014), Nature Communications. 5   |  All authors
  • Point of View: Correcting the bias against interdisciplinary research

    Shapiro E. (2014), eLife. 3, 02576
  • Digital cell quantification identifies global immune cell dynamics during influenza infection

    Altboum Z., Steuerman Y., David E. et al., Barnett Itzhaki I. Z., Valadarsky L., Keren-Shaul H., Meningher T., Mendelson E., Mandelboim M., Gat-Viks I., Amit I. (2014), Molecular Systems Biology. 10, 2   |  All authors
  • Loss of growth homeostasis by genetic decoupling of cell division from biomass growth: implication for size control mechanisms

    Schmidt-Glenewinkel H., Barkai N. (2014), Molecular Systems Biology. 10, 12
  • Lucky iPSCs

    Zviran A., Hanna J. (2014), GENOME BIOLOGY. 15, 3, 109
  • Land, irrigation water, greenhouse gas, and reactive nitrogen burdens of meat, eggs, and dairy production in the United States

    Eshel G., Shepon A., Makov T. et al., Milo R. (2014), Proceedings of the National Academy of Sciences of the United States of America. 111, 33, p. 11996-12001   |  All authors
  • Pemphigus vulgaris is characterized by low IgG reactivities to specific self-antigens along with high IgG reactivity to desmoglein 3

    Fattal I., Rimer J., Shental N. et al., Molad Y., Gabrielli A., Livneh A., Sarig O., Goldberg I., Gafter U., Domany E., Cohen I. R. (2014), Immunology. 143, 3, p. 374-380   |  All authors
  • A Dynamic Interface between Vacuoles and Mitochondria in Yeast

    Elbaz-Alon Y., Rosenfeld-Gur E., Shinder V. et al., Futerman A. H., Geiger T., Schuldiner M. (2014), Developmental Cell. 30, 1, p. 95-102   |  All authors
  • Scaling morphogen gradients during tissue growth by a cell division rule

    Averbukh I., Ben-Zvi D., Mishra S. et al., Barkai N. (2014), Development. 141, 10, p. 2150-2156   |  All authors
  • A defect in the RNA-processing protein HNRPDL causes limb-girdle muscular dystrophy 1G (LGMD1G)

    Vieira N. M., Naslavsky M. S., Licinio L. et al., Kok F., Schlesinger D., Vainzof M., Sanchez N., Kitajima J. P., Gal L., Cavacana N., Serafini P. R., Chuartzman S., Vasquez C., Mimbacas A., Nigro V., Pavanello R. C., Schuldiner M., Kunkel L. M., Zatz M. (2014), Human Molecular Genetics. 23, 15, p. 4103-4110   |  All authors
  • Heuristic for Maximizing DNA Reuse in Synthetic DNA Library Assembly

    Blakes J., Raz O., Feige U. et al., Bacardit J., Widera P., Ben-Yehezkel T., Shapiro E., Krasnogor N. (2014), ACS Synthetic Biology. 3, 8, p. 529-542   |  All authors
  • Intratumor DNA Methylation Heterogeneity Reflects Clonal Evolution in Aggressive Prostate Cancer

    Brocks D., Assenov Y., Minner S. et al., Bogatyrova O., Simon R., Koop C., Oakes C., Zucknick M., Lipka D. B., Weischenfeldt J., Feuerbach L., Lari R. C., Lupien M., Brors B., Korbel J., Schlomm T., Tanay A., Sauter G., Gerhaeuser C., Plass C. (2014), Cell Reports. 8, 3, p. 798-806   |  All authors
  • Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA

    Mellin J. R., Koutero M., Dar D. et al., Nahori M., Sorek R., Cossart P. (2014), Science. 345, 6199, p. 940-943   |  All authors
  • miR-661 downregulates both Mdm2 and Mdm4 to activate p53

    Hoffman Y., Bublik D. R., Pilpel Y. et al., Oren M. (2014), Cell Death and Differentiation. 21, 2, p. 302-309   |  All authors
  • Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo

    Tal A., Arbel-Goren R., Costantino N. et al., Court D. L., Stavans J. (2014), Proceedings of the National Academy of Sciences of the United States of America. 111, 20, p. 7308-7312   |  All authors
  • The quantified cell

    Flamholz A., Phillips R., Milo R. (2014), Molecular Biology of the Cell. 25, 22, p. 3497-3500
  • Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions

    Rothschild D., Dekel E., Hausser J. et al., Bren A., Aidelberg G., Szekely P., Alon U. (2014), PLoS Computational Biology. 10, 5, e1003602   |  All authors
  • All roads lead to Rome-SRP independent translocation into the endoplasmic reticulum

    Ast T., Schuldiner M. (2014),
  • The grammar of transcriptional regulation

    Weingarten-Gabbay S., Segal E. (2014), Human Genetics. 133, 6, p. 701-711
  • Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

    Noor E., Bar-Even A., Flamholz A. et al., Reznik E., Liebermeister W., Milo R. (2014), PLoS Computational Biology. 10, 2   |  All authors
  • Paradoxical Signaling by a Secreted Molecule Leads to Homeostasis of Cell Levels

    Hart Y., Reich-Zeliger S., Antebi Y. E. et al., Zaretsky I., Mayo A. E., Alon U., Friedman N. (2014), Cell. 158, 5, p. 1022-1032   |  All authors
  • Expansion of CD16 positive and negative human NK cells in response to tumor stimulation

    Tsukerman P., Stern-Ginossar N., Yamin R. et al., Ophir Y., Miller A., Stanietsky N., Mandelboim O. (2014), European Journal of Immunology. 44, 5, p. 1517-1525   |  All authors
  • The Fire Within: Microbes Inflame Tumors

    Gagliani N., Hu B., Huber S. et al., Elinav E., Flavell R. A. (2014), Cell. 157, 4, p. 776-783   |  All authors
  • Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

    Thaiss C. A., Zeevi D., Levy M. et al., Zilberman-Schapira G., Suez J., Tengeler A. C., Abramson L., Katz M. N., Korem T., Zmora N., Kuperman Y., Biton I., Gilad S., Harmelin A., Shapiro H., Halpern Z., Segal E., Elinav E. (2014), Cell. 159, 3, p. 514-529   |  All authors
  • The Back and Forth of Cargo Exit from the Endoplasmic Reticulum

    Geva Y., Schuldiner M. (2014), Current Biology. 24, 3, p. R130-R136
  • Yeast phospholipid biosynthesis is linked to mRNA localization

    Hermesh O., Genz C., Yofe I. et al., Sinzel M., Rapaport D., Schuldiner M., Jansen R. (2014), Journal of Cell Science. 127, 15, p. 3373-3381   |  All authors
  • Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity

    Almendro V., Cheng Y., Randles A. et al., Itzkovitz S., Marusyk A., Ametller E., Gonzalez-Farre X., Munoz M., Russnes H. G., Helland A., Rye I. H., Borresen-Dale A., Maruyama R., van Oudenaarden O. A., Dowsett M., Jones R. L., Reis-Filho J., Gascon P., Goenen M. (2014), Cell Reports. 6, 3, p. 514-527   |  All authors
  • A cytosolic degradation pathway, prERAD, monitors pre-inserted secretory pathway proteins

    Ast T., Aviram N., Chuartzman S. G. et al., Schuldiner M. (2014), Journal of Cell Science. 127, 14, p. 3017-3023   |  All authors
  • Different subunits belonging to the same protein complex often exhibit discordant expression levels and evolutionary properties

    Matalon O., Horovitz A., Levy E. D. (2014), Current Opinion in Structural Biology. 26, p. 113-120
  • Passage Number is a Major Contributor to Genomic Structural Variations in Mouse iPSCs

    Liu P., Kaplan A., Yuan B. et al., Hanna J. H., Lupski J. R., Reiner O. (2014), Stem Cells. 32, 10, p. 2657-2667   |  All authors
  • Sequential Feedback Induction Stabilizes the Phosphate Starvation Response in Budding Yeast

    Vardi N., Levy S., Gurvich Y. et al., Polacheck T., Carmi M., Jaitin D., Amit I., Barkai N. (2014), Cell Reports. 9, 3, p. 1122-1134   |  All authors
  • Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters

    Zeevi D., Lubliner S., Lotan-Pompan M. et al., Hodis E., Vesterman R., Weinberger A., Segal E. (2014), Genome Research. 24, 12, p. 1991-1999   |  All authors
  • Hierarchy of non-glucose sugars in Escherichia coli

    Aidelberg G., Towbin B. D., Rothschild D. et al., Dekel E., Bren A., Alon U. (2014), BMC Systems Biology. 8, 133   |  All authors
  • High-resolution metagenomics

    Mick E., Sorek R. (2014), Nature Biotechnology. 32, 8, p. 750-751
  • The cross talk between microbiota and the immune system: metabolites take center stage

    Shapiro H., Thaiss C. A., Levy M. et al., Elinav E. (2014), Current Opinion in Immunology. 30, p. 54-62   |  All authors
  • Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae

    Yofe I., Zafrir Z., Blau R. et al., Schuldiner M., Tuller T., Shapiro E., Ben-Yehezkel T. (2014), PLoS Genetics. 10, 6, e1004407   |  All authors
  • Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

    Schwartz S., Bernstein D. A., Mumbach M. R. et al., Jovanovic M., Herbst R. H., Leon-Ricardo B. X., Engreitz J. M., Guttman M., Satija R., Lander E. S., Fink G., Regev A. (2014), Cell. 159, 1, p. 148-162   |  All authors
  • Checkpoint-independent scaling of the Saccharomyces cerevisiae DNA replication program

    Gispan A., Carmi M., Barkai N. (2014), BMC Biology. 12
  • Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

    Shalek A. K., Satija R., Shuga J. et al., Trombetta J. J., Gennert D., Lu D., Chen P., Gertner R. S., Gaublomme J. T., Yosef N., Schwartz S., Fowler B., Weaver S., Wang J., Wang X., Ding R., Raychowdhury R., Friedman N., Hacohen N., Park H., May A. P., Regev A. (2014), eLife. 510, 7505, p. 363-+   |  All authors
  • OM14 is a mitochondrial receptor for cytosolic ribosomes that supports co-translational import into mitochondria

    Lesnik C., Cohen Y., Atir-Lande A. et al., Schuldiner M., Arava Y. (2014), Nature Communications. 5   |  All authors
  • The central nervous system microenvironment imprints microglial inability to switch from pro- to anti-inflammatory phenotype

    Matcovitch O., Cohen M., David E. et al., Barnettitzhaki Z., Keren-Shaul H., Blecher-gonen R., Jaitin D. A., Sica A., Amit I., Schwartz M. (2014),   |  All authors
  • Systematic identification of cell size regulators in budding yeast

    Soifer I., Barkai N. (2014), Molecular Systems Biology. 10, 11
  • The PH gene determines fruit acidity and contributes to the evolution of sweet melons

    Cohen S., Itkin M., Yeselson Y. et al., Tzuri G., Portnoy V., Harel-Baja R., Lev S., Sa'ar U., Davidovitz-Rikanati R., Baranes N., Bar E., Wolf D., Petreikov M., Shen S., Ben-Dor S., Rogachev I., Aharoni A., Ast T., Schuldiner M., Belausov E., Eshed R., Ophir R., Sherman A., Frei B., Neuhaus H. E., Xu Y., Fei Z., Giovannoni J., Lewinsohn E., Tadmor Y., Paris H. S., Katzir N., Burger Y., Schaffer A. A. (2014), Nature Communications. 5, 4026   |  All authors
  • mRNA-programmed translation pauses in the targeting of E. coli membrane proteins.

    Fluman N., Navon S., Bibi E. et al., Pilpel Y. (2014), eLife. 3   |  All authors
  • Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

    Ingolia N. T., Brar G. A., Stern-Ginossar N. et al., Harris M. S., Talhouarne G. J. S., Jackson S. E., Wills M. R., Weissman J. S. (2014), Cell Reports. 8, 5, p. 1365-1379   |  All authors
  • Novel Superactive Leptin Antagonists and their Potential Therapeutic Applications

    Gertler A., Elinav E. (2014), Current Pharmaceutical Design. 20, 4, p. 659-665
  • High-Resolution Mapping of Protein Concentration Reveals Principles of Proteome Architecture and Adaptation

    Levy E. D., Kowarzyk J., Michnick S. W. (2014), Cell Reports. 7, 4, p. 1333-1340
  • Chronic exposure to TGF beta 1 regulates myeloid cell inflammatory response in an IRF7-dependent manner

    Cohen M., Matcovitch O., David E. et al., Barnett Itzhaki I. Z., Keren-Shaul H., Blecher-Gonen R., Jaitin D. A., Sica A., Amit I., Schwartz M. (2014), EMBO Journal. 33, 24, p. 2906-2921   |  All authors
  • Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

    Shipony Z., Mukamel Z., Cohen N. M. et al., Landan G., Chomsky E., Zeliger S. R., Fried Y. C., Ainbinder E., Friedman N., Tanay A. (2014), Nature. 513, 7516, p. 115-+   |  All authors
  • Coordination of Gene Expression and Growth-Rate in Natural Populations of Budding Yeast

    Tamari Z., Rosin D., Voichek Y. et al., Barkai N. (2014), PLoS One. 9, 2, e88801   |  All authors
  • Individuality and Togetherness in Joint Improvised Motion

    Hart Y., Noy L., Feniger-Schaal R. et al., Mayo A., Alon U. (2014), PLoS One. 9, 2, e87213   |  All authors
  • Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators

    Raza S., Barnett M. W., Barnett Itzhaki I. Z. et al., Amit I., Hume D. A., Freeman T. C. (2014), Journal of Leukocyte Biology. 96, 2, p. 167-183   |  All authors
  • Lineage grammars: describing, simulating and analyzing population dynamics

    Spiro A., Cardelli L., Shapiro E. (2014), BMC Bioinformatics. 15, 249
  • NLRP6 Inflammasome Orchestrates the Colonic Host-Microbial Interface by Regulating Goblet Cell Mucus Secretion

    Wlodarska M., Thaiss C. A., Nowarski R. et al., Henao-Mejia J., Zhang J., Brown E. M., Frankel G., Levy M., Katz M. N., Philbrick W. M., Elinav E., Finlay B. B., Flavell R. A. (2014), Cell. 156, 5, p. 1045-1059   |  All authors
  • microRNAs and Alu elements in the p53-Mdm2-Mdm4 regulatory network

    Hoffman Y., Pilpel Y., Oren M. (2014), Journal of Molecular Cell Biology. 6, 3, p. 192-197
  • Aging-induced type I interferon response at the choroid plexus negatively affects brain function

    Baruch K., Deczkowska A., David E. et al., Castellano J. M., Miller O., Kertser A., Berkutzki T., Barnett Itzhaki I. Z., Bezalel D., Wyss-Coray T., Amit I., Schwartz M. (2014), Science. 346, 6205, p. 89-93   |  All authors
  • The Biggest Challenges Facing Young Scientists

    Keays D., Barreiro L., Stuart-Fox D. et al., Brar G., Schuldiner M., Tahiliani M. (2014), Cell. 157, 4, p. 763-764   |  All authors
  • Cooperativity, Specificity, and Evolutionary Stability of Polycomb Targeting in Drosophila

    Schuettengruber B., Elkayam N. O., Sexton T. et al., Entrevan M., Stern S., Thomas A., Yaffe E., Parrinello H., Tanay A., Cavalli G. (2014), Cell Reports. 9, 1, p. 219-233   |  All authors
  • Noise Genetics: Inferring Protein Function by Correlating Phenotype with Protein Levels and Localization in Individual Human Cells

    Farkash-Amar S., Zimmer A., Eden E. et al., Cohen A., Geva Zatorsky Z. N., Cohen L., Milo R., Sigal A., Danon T., Alon U. (2014), PLoS Genetics. 10, 3, e1004176   |  All authors
  • A Negative Feedback Loop of Transcription Factors Specifies Alternative Dendritic Cell Chromatin States

    Bornstein C., Winter D., Barnett Itzhaki I. Z. et al., David E., Kadri S., Garber M., Amit I. (2014), Molecular Cell. 56, 6, p. 749-762   |  All authors
  • Using High-Throughput Transcriptomic Data for Prognosis: A Critical Overview and Perspectives

  • The Yeast ER-Intramembrane Protease Ypf1 Refines Nutrient Sensing by Regulating Transporter Abundance

    Avci D., Fuchs S., Schrul B. et al., Fukumori A., Breker M., Frumkin I., Chen C., Biniossek M. L., Kremmer E., Schilling O., Steiner H., Schuldiner M., Lemberg M. K. (2014), Molecular Cell. 56, 5, p. 630-640   |  All authors
  • Fast and Accurate Discovery of Degenerate Linear Motifs in Protein Sequences

    Kelil A., Dubreuil B., Levy E. D. et al., Michnick S. W. (2014), PLoS One. 9, 9, e106081   |  All authors
  • Exploring New Horizons in Microbiome Research

    Thaiss C. A., Elinav E. (2014), Cell Host & Microbe. 15, 6, p. 662-667
  • Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection

    Adler M., Mayo A., Alon U. (2014), PLoS Computational Biology. 10, 8, e1003781
  • High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

    Rabani M., Raychowdhury R., Jovanovic M. et al., Rooney M., Stumpo D. J., Pauli A., Hacohen N., Schier A. F., Blackshear P. J., Friedman N., Amit I., Regev A. (2014), Cell. 159, 7, p. 1698-1710   |  All authors
  • Manipulation of host pathways by human cytomegalovirus: insights from genome-wide studies

    Cohen Y., Stern-Ginossar N. (2014), Seminars in Immunopathology. 36, 6, p. 651-658
  • Blastocyst implantation failure relates to impaired translational machinery gene expression

    Plaks V., Gershon E., Zeisel A. et al., Jacob-Hirsch J., Neeman M., Winterhager E., Rechavi G., Domany E., Dekel N. (2014), Reproduction. 148, 1, p. 87-98   |  All authors
  • STEM CELLS The quest for the perfect reprogrammed cell

    Krupalnik V., Hanna J. H. (2014), Nature. 511, 7508, p. 160-162
  • LoQAtE-Localization and Quantitation ATlas of the yeast proteomE: A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast

    Breker M., Gymrek M., Moldavski O. et al., Schuldiner M. (2014), Nucleic Acids Research. 42, D1, p. D726-D730   |  All authors
  • Landscape and variation of RNA secondary structure across the human transcriptome

    Wan Y., Qu K., Zhang Q. C. et al., Flynn R. A., Manor O., Ouyang Z., Zhang J., Spitale R. C., Snyder M. P., Segal E., Chang H. Y. (2014), Nature. 505, 7485, p. 706-+   |  All authors
  • Subcellular Transcriptomics-Dissection of the mRNA Composition in the Axonal Compartment of Sensory Neurons

    Minis A., Dahary D., Manor O. et al., Leshkowitz D., Pilpel Y., Yaron A. (2014), Developmental Neurobiology. 74, 3, p. 365-381   |  All authors
  • Chromatin state dynamics during blood formation

    Lara Astiaso A. D., Weiner A., Lorenzo Vivas V. E. et al., Zaretsky I., Jaitin D. A., David E., Keren-Shaul H., Mildner A., Winter D., Jung S., Friedman N., Amit I. (2014), Science. 345, 6199, p. 943-949   |  All authors
  • Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

    Lavin Y., Winter D., Blecher-Gonen R. et al., David E., Keren-Shaul H., Merad M., Jung S., Amit I. (2014), Cell. 159, 6, p. 1312-1326   |  All authors
  • Inflammation-induced cancer: crosstalk between tumours, immune cells and microorganisms

    Elinav E., Nowarski R., Thaiss C. A. et al., Hu B., Jin C., Flavell R. A. (2013), Nature Reviews Cancer. 13, 11, p. 759-771   |  All authors
  • Formation and dissociation of proteasome storage granules are regulated by cytosolic pH

    Peters L. Z., Hazan R., Breker M. et al., Schuldiner M., Ben-Aroya S. (2013), Journal of Cell Biology. 201, 5, p. 663-671   |  All authors
  • Determinants of nucleosome positioning

  • Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

    Shalek A. K., Satija R., Adiconis X. et al., Gertner R. S., Gaublomme J. T., Raychowdhury R., Schwartz S., Yosef N., Malboeuf C., Lu D., Trombetta J. J., Gennert D., Gnirke A., Goren A., Hacohen N., Levin J. Z., Park H., Regev A. (2013), Nature. 498, 7453, p. 236-240   |  All authors
  • What is the total number of protein molecules per cell volume? A call to rethink some published values

  • CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea

    Sorek R., Lawrence C. M., Wiedenheft B. (2013), Annual Review of Biochemistry. p. 237-266
  • Microbiota-induced activation of epithelial IL-6 signaling links inflammasome-driven inflammation with transmissible cancer

    Hu B., Elinav E., Huber S. et al., Strowig T., Hao L., Hafemann A., Jin C., Eisenbarth S. C., Flavell R. A. (2013), Proceedings of the National Academy of Sciences of the United States of America. 110, 24, p. 9862-9867   |  All authors
  • High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

    Blecher-Gonen R., Barnett Itzhaki I. Z., Jaitin D. et al., Amann Zalcenstein Z. D., Lara Astiaso A. D., Amit I. (2013), Nature Protocols. 8, 3, p. 539-554   |  All authors
  • Extracting Insight from Noisy Cellular Networks

    Landry C. R., Levy E. D., Abd Rabbo D. et al., Tarassov K., Michnick S. W. (2013), Cell. 155, 5, p. 983-989   |  All authors
  • From rags to riches - The history of the endoplasmic reticulum Preface

  • Mapping the translation initiation landscape of an S-cerevisiae gene using fluorescent proteins

    Ben-Yehezkel T., Zur H., Marx T. et al., Shapiro E., Tuller T. (2013), Genomics. 102, 4, p. 419-429   |  All authors
  • A Network of Cytosolic Factors Targets SRP-Independent Proteins to the Endoplasmic Reticulum

    Ast T., Cohen G., Schuldiner M. (2013), Cell. 152, 5, p. 1134-1145
  • Single-molecule mRNA detection and counting in mammalian tissue

    Lyubimova A., Itzkovitz S., Junker J. P. et al., Fan Z. P., Wu X., van Oudenaarden O. A. (2013), Nature Protocols. 8, 9, p. 1743-1758   |  All authors
  • Promoter Sequence Determines the Relationship between Expression Level and Noise

    Carey L. B., Van Dijk D. D., Sloot P. M. A. et al., Kaandorp J. A., Segal E. (2013), PLoS Biology. 11, 4   |  All authors
  • Role of the intestinal microbiome in liver disease

    Henao-Mejia J., Elinav E., Thaiss C. A. et al., Licona-Limon P., Flavell R. A. (2013), Journal of Autoimmunity. 46, p. 66-73   |  All authors
  • Get3 is a holdase chaperone and moves to deposition sites for aggregated proteins when membrane targeting is blocked

    Powis K., Schrul B., Tienson H. et al., Gostimskaya I., Breker M., High S., Schuldiner M., Jakob U., Schwappach B. (2013), Journal of Cell Science. 126, 2, p. 473-483   |  All authors
  • All roads lead to Rome (but some may be harder to travel): SRP-independent translocation into the endoplasmic reticulum

  • c-Kit is suppressed in human colon cancer tissue and contributes to L1-mediated metastasis

    Gavert N., Shvab A., Sheffer M. et al., Ben Shmuel S. A., Haase G., Bakos E., Domany E., Ben-Ze'ev A. (2013), Cancer Research. 73, 18, p. 5754-5763   |  All authors
  • qCMA: A Desktop Application for Quantitative Collective Cell Migration Analysis

    Zeisel A., Yitzhaky A., Koerner C. et al., Lauriola M., Cohen-Dvashi H., Koestler W. J., Yarden Y., Wiemann S., Domany E. (2013), Journal of Biomolecular Screening. 18, 3, p. 356-360   |  All authors
  • Creating gradients by morphogen shuttling

    Shilo B., Haskel Ittah I. M., Ben-Zvi D. et al., Schejter E. D., Barkai N. (2013), Trends in Genetics. 29, 6, p. 339-347   |  All authors
  • Response to Comment on "Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space"

    Shoval O., Sheftel H., Shinar G. et al., Hart Y., Ramote O., Mayo A., Dekel E., Kavanagh K., Alon U. (2013), Science. 339, 6121   |  All authors
  • Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization

  • Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise

    Dadiani M., Van Dijk D. D., Segal B. et al., Field Y., Ben Artzi A. G., Raveh - Sadka -. S. T., Levo M., Kaplow I., Weinberger A., Segal E. (2013), Genome Research. 23, 6, p. 966-976   |  All authors
  • Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences

    Kenigsberg E., Tanay A. (2013), PLoS Genetics. 9, 5
  • Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations

    Chapal Ilani I. N., Maruvka Y. E., Spiro A. et al., Reizel Y., Adar R., Shlush L. I., Shapiro E. (2013), PLoS Computational Biology. 9, 11, 1003297   |  All authors
  • Hypomethylation marks enhancers within transposable elements

    Mukamel Z., Tanay A. (2013), Nature Genetics. 45, 7, p. 717-718
  • Epidermal Growth-Factor - Induced Transcript Isoform Variation Drives Mammary Cell Migration

    Koestler W. J., Zeisel A., Koerner C. et al., Tsai J. M., Jacob-Hirsch J., Ben Chetrit C. N., Sharma K., Cohen-Dvashi H., Yitzhaky A., Lader E., Tschulena U., Rechavi G., Domany E., Wiemann S., Yarden Y. (2013), PLoS One. 8, 12   |  All authors
  • Temperature Integration: An efficient procedure for calculation of free energy differences

    Farhi A., Hed G., Bon M. et al., Caticha N., Mak C. H., Domany E. (2013), Physica A-Statistical Mechanics And Its Applications. 392, 23, p. 5836-5844   |  All authors
  • Characterization of an M28 metalloprotease family member residing in the yeast vacuole

    Hecht K. A., Wytiaz V. A., Ast T. et al., Schuldiner M., Brodsky J. L. (2013), FEMS Yeast Research. 13, 5, p. 471-484   |  All authors
  • DEVELOPMENTAL BIOLOGY Segmentation within scale

    Barkai N., Shilo B. (2013), Nature. 493, 7430, p. 32-34
  • Measurements of the Impact of 3 ' End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects

    Shalem O., Carey L., Zeevi D. et al., Sharon E., Keren L., Weinberger A., Dahan O., Pilpel Y., Segal E. (2013), PLoS Computational Biology. 9, 3   |  All authors
  • A library of programmable DNAzymes that operate in a cellular environment

    Kahan-Hanum M., Douek Y., Adar R. et al., Shapiro E. (2013), Scientific Reports. 3   |  All authors
  • Derivation of novel human ground state naive pluripotent stem cells

    Gafni O., Weinberger L., Mansour A. A. et al., Manor Y. S., Chomsky E., Ben-Yosef D., Kalma Y., Viukov S., Maza I., Zviran A., Rais Y., Shipony Z., Mukamel Z., Krupalnik V., Zerbib M., Geula S., Caspi I., Schneir D., Shwartz T., Gilad S., Amann Zalcenstein D., Benjamin S., Amit I., Tanay A., Massarwa R., Novershtern N., Hanna J. (. (2013), Nature. 504, 7479, p. 282-286   |  All authors
  • Mononuclear phagocyte miRNome analysis identifies miR-142 as critical regulator of murine dendritic cell homeostasis

    Mildner A., Chapnik E., Manor O. et al., Yona S., Kim K., Aychek T., Varol D., Beck G., Itzhaki Z. B., Feldmesser E., Amit I., Hornstein E., Jung S. (2013), Blood. 121, 6, p. 1016-1027   |  All authors
  • Promoters maintain their relative activity levels under different growth conditions

    Keren L., Zackay O., Lotan-Pompan M. et al., Barenholz U., Dekel E., Sasson V., Aidelberg G., Bren A., Zeevi D., Weinberger A., Alon U., Milo R., Segal E. (2013), Molecular Systems Biology. 9   |  All authors
  • Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein

    Zalckvar E., Paulus C., Tillo D. et al., Asbach-Nitzsche A., Lubling Y., Winterling C., Strieder N., Muecke K., Goodrum F., Segal E., Nevels M. (2013), Proceedings of the National Academy of Sciences of the United States of America. 110, 32, p. 13126-13131   |  All authors
  • Discovery of Functional Toxin/Antitoxin Systems in Bacteria by Shotgun Cloning

    Sberro H., Leavitt A., Kiro R. et al., Koh E., Peleg Y., Qimron U., Sorek R. (2013), Molecular Cell. 50, 1, p. 136-148   |  All authors
  • Quantifying Translational Coupling in E. coli Synthetic Operons Using RBS Modulation and Fluorescent Reporters

    Levin Karp K. A., Barenholz U., Bareia T. et al., Dayagi M., Zelcbuch L., Antonovsky N., Noor E., Milo R. (2013), ACS Synthetic Biology. 2, 6, p. 327-336   |  All authors
  • Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes

    Bar-Even A., Noor E., Flamholz A. et al., Milo R. (2013), Biochimica Et Biophysica Acta-Bioenergetics. 1827, 9-Aug, p. 1039-1047   |  All authors
  • Steady-State Metabolite Concentrations Reflect a Balance between Maximizing Enzyme Efficiency and Minimizing Total Metabolite Load

    Tepper N., Noor E., Amador-Noguez D. et al., Haraldsdottir H. S., Milo R., Rabinowitz J., Liebermeister W., Shlomi T. (2013), PLoS One. 8, 9   |  All authors
  • Single-cell sequencing-based technologies will revolutionize whole-organism science

    Shapiro E., Biezuner T., Linnarsson S. (2013), Nature Reviews Genetics. 14, 9, p. 618-630
  • Spanning high-dimensional expression space using ribosome-binding site combinatorics

    Zelcbuch L., Antonovsky N., Bar-Even A. et al., Levin Karp A., Barenholz U., Dayagi M., Liebermeister W., Flamholz A., Noor E., Amram S., Brandis A., Bareia T., Yofe I., Jubran H., Milo R. (2013), Nucleic Acids Research. 41, 9   |  All authors
  • High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

    Schwartz S., Agarwala S. D., Mumbach M. R. et al., Jovanovic M., Mertins P., Shishkin A., Tabach Y., Mikkelsen T. S., Satija R., Ruvkun G., Carr S. A., Lander E. S., Fink G. R., Regev A. (2013), Cell. 155, 6, p. 1409-1421   |  All authors
  • A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

    Breker M., Gymrek M., Schuldiner M. (2013), Journal of Cell Biology. 200, 6, p. 839-850
  • tRNA genes rapidly change in evolution to meet novel translational demands

    Yona A. H., Bloom-Ackermann Z., Frumkin I. et al., Hanson-Smith V., Charpak-Amikam Y., Feng Q., Boeke J. D., Dahan O., Pilpel Y. (2013), eLife. 2   |  All authors
  • A Global Transcriptional Switch between the Attack and Growth Forms of Bdellovibrio bacteriovorus

    Karunker I., Rotem O., Dori-Bachash M. et al., Jurkevitch E., Sorek R. (2013), PLoS One. 8, 4   |  All authors
  • The Yeast P5 Type ATPase, Spf1, Regulates Manganese Transport into the Endoplasmic Reticulum

    Cohen Y., Megyeri M., Chen O. C. W. et al., Condomitti G., Riezman I., Loizides-Mangold U., Abdul-Sada A., Rimon N., Riezman H., Platt F. M., Futerman A. H., Schuldiner M. (2013), PLoS One. 8, 12   |  All authors
  • A versatile genome-scale PCR-based pipeline for high-definition DNA FISH

    Klemm S., Itzkovitz S., van Oudenaarden O. A. (2013), Nature Methods. 10, 2, p. 122-124
  • EcoTime-An intuitive quantitative sustainability indicator utilizing a time metric

    Shepon A., Israeli T., Eshel G. et al., Milo R. (2013), Ecological Indicators. 24, p. 240-245   |  All authors
  • Computational evaluation of cellular metabolic costs successfully predicts genes whose expression is deleterious

    Wagner A., Zarecki R., Reshef L. et al., Gochev C., Sorek R., Gophna U., Ruppin E. (2013), Proceedings of the National Academy of Sciences of the United States of America. 110, 47, p. 19166-19171   |  All authors
  • Robust Prediction of Expression Differences among Human Individuals Using Only Genotype Information

    Manor O., Segal E. (2013), PLoS Genetics. 9, 3
  • Oct4 shuffles Sox partners to direct cell fate

    Mansour A. A., Hanna J. H. (2013), EMBO Journal. 32, 7, p. 917-919
  • Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms

    Manor O., Segal E. (2013), PLoS Computational Biology. 9, 8
  • The Expression of the Beta Cell-Derived Autoimmune Ligand for the Killer Receptor Nkp46 Is Attenuated in Type 2 Diabetes

    Gur C., Enk J., Weitman E. et al., Bachar E., Suissa Y., Cohen G., Schyr R. B., Sabanay H., Horwitz E., Glaser B., Dor Y., Pribluda A., Hanna J. H., Leibowitz G., Mandelboim O. (2013), PLoS One. 8, 8   |  All authors
  • Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

    Nagano T., Lubling Y., Stevens T. J. et al., Schoenfelder S., Yaffe E., Dean W., Laue E. D., Tanay A., Fraser P. (2013), Nature. 502, 7469, p. 59-+   |  All authors
  • The Contribution of Systematic Approaches to Characterizing the Proteins and Functions of the Endoplasmic Reticulum

    Schuldiner M., Weissman J. S. (2013), Cold Spring Harbor perspectives in biology. 5, 3
  • Comparing Apples and Oranges: Fold-Change Detection of Multiple Simultaneous Inputs

    Hart Y., Mayo A. E., Shoval O. et al., Alon U. (2013), PLoS One. 8, 3   |  All authors
  • Expression of TP53 mutation-associated microRNAs predicts clinical outcome in head and neck squamous cell carcinoma patients

    Ganci F., Sacconi A., Ben-Moshe N. B. et al., Manciocco V., Sperduti I., Strigari L., Covello R., Benevolo M., Pescarmona E., Domany E., Muti P., Strano S., Spriano G., Fontemaggi G., Blandino G. (2013), Annals of Oncology. 24, 12, p. 3082-3088   |  All authors
  • DNA computing Molecules reach consensus

    Shapiro E., Ran T. (2013),
  • Deciphering the rules by which 5 '-UTR sequences affect protein expression in yeast

    Dvir S., Velten L., Sharon E. et al., Zeevi D., Carey L. B., Weinberger A., Segal E. (2013), Proceedings of the National Academy of Sciences of the United States of America. 110, 30, p. E2792-E2801   |  All authors
  • The Role of Djp1 in Import of the Mitochondrial Protein Mim1 Demonstrates Specificity between a Cochaperone and Its Substrate Protein

    Papic D., Elbaz-Alon Y., Koerdt S. N. et al., Leopold K., Worm D., Jung M., Schuldiner M., Rapaport D. (2013), Molecular and Cellular Biology. 33, 20, p. 4083-4094   |  All authors
  • Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

    Gat-Viks I., Chevrier N., Wilentzik R. et al., Eisenhaure T., Raychowdhury R., Steuerman Y., Shalek A. K., Hacohen N., Amit I., Regev A. (2013), Nature Biotechnology. 31, 4, p. 342-+   |  All authors
  • A new algorithm for combinatorial dna library assembly

    Blakes J., Raz O., Krasnogor N. et al., Shapiro E. (2013), 5th International Workshop on Bio-Design Automation (IWBDA 2013).   |  All authors
  • Harnessing Nanomedicine for Mucosal Theranostics-A Silver Bullet at Last?

    Elinav E., Peer D. (2013), ACS Nano. 7, 4, p. 2883-2890
  • An accessible database for mouse and human whole transcriptome qPCR primers

    Zeisel A., Yitzhaky A., Ben-Moshe N. B. et al., Domany E. (2013), Bioinformatics. 29, 10, p. 1355-1356   |  All authors
  • lincRNAs: Genomics, Evolution, and Mechanisms

    Ulitsky I., Bartel D. P. (2013), Cell. 154, 1, p. 26-46
  • Differential Translation Tunes Uneven Production of Operon-Encoded Proteins

    Quax T. E. F., Wolf Y. I., Koehorst J. J. et al., Wurtzel O., van der Oost d. O. R., Ran W., Blombach F., Makarova K. S., Brouns S. J. J., Forster A. C., Wagner E. G. H., Sorek R., Koonin E. V., van der Oost d. O. J. (2013), Cell Reports. 4, 5, p. 938-944   |  All authors
  • Pathway-based personalized analysis of cancer

  • Increasing population growth by asymmetric segregation of a limiting resource during cell division

    Avraham N., Soifer I., Carmi M. et al., Barkai N. (2013), Molecular Systems Biology. 9   |  All authors
  • The last generation of bacterial growth in limiting nutrient

    Bren A., Hart Y., Dekel E. et al., Koster D., Alon U. (2013), BMC Systems Biology. 7   |  All authors
  • Holding a grudge: Persisting anti-phage CRISPR immunity in multiple human gut microbiomes

    Mick E., Stern A., Sorek R. (2013), RNA Biology. 10, 5, p. 900-906
  • A synthetic biology approach for evaluating the functional contribution of designer cellulosome components to deconstruction of cellulosic substrates

    Vazana Y., Barak Y., Unger T. et al., Peleg Y., Shamshoum M., Ben-Yehezkel T., Mazor Y., Shapiro E., Lamed R., Bayer E. (2013), Biotechnology for Biofuels. 6, 182   |  All authors
  • Cohesin-mediated interactions organize chromosomal domain architecture

    Sofueva S., Yaffe E., Chan W. et al., Georgopoulou D., Rudan M. V., Mira-Bontenbal H., Pollard S. M., Schroth G. P., Tanay A., Hadjur S. (2013), EMBO Journal. 32, 24, p. 3119-3129   |  All authors
  • Glycolytic strategy as a tradeoff between energy yield and protein cost

    Flamholz A., Noor E., Bar-Even A. et al., Liebermeister W., Milo R. (2013), Proceedings of the National Academy of Sciences of the United States of America. 110, 24, p. 10039-10044   |  All authors
  • Entrainment of noise-induced and limit cycle oscillators under weak noise

    Mitarai N., Alon U., Jensen M. H. (2013), Chaos. 23, 2
  • CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

    Gilbert L. A., Larson M. H., Morsut L. et al., Liu Z., Brar G. A., Torres S. E., Stern-Ginossar N., Brandman O., Whitehead E. H., Doudna J. A., Lim W. A., Weissman J. S., Qi L. S. (2013), Cell. 154, 2, p. 442-451   |  All authors
  • Fixated on fixation: using ChIP to interrogate the dynamics of chromatin interactions

    Keren L., Segal E. (2013), GENOME BIOLOGY. 14, 11
  • Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins

    Rockah-Shmuel L., Toth-Petroczy A., Sela A. et al., Wurtzel O., Sorek R., Tawfik D. (2013), PLoS Genetics. 9, 10   |  All authors
  • Individual and meta-immune networks

    Bransburg-Zabary S., Kenett D. Y., Dar G. et al., Madi A., Merbl Y., Quintana F. J., Tauber A. I., Cohen I. R., Ben-Jacob E. (2013), Physical Biology. 10, 2   |  All authors
  • The locus of microRNA-10b A critical target for breast cancer insurgence and dissemination

    Biagioni F., Ben-Moshe N. B., Fontemaggi G. et al., Yarden Y., Domany E., Blandino G. (2013), Cell Cycle. 12, 15, p. 2371-2375   |  All authors
  • The excludon: a new concept in bacterial antisense RNA-mediated gene regulation

    Sesto N., Wurtzel O., Archambaud C. et al., Sorek R., Cossart P. (2013), Nature Reviews Microbiology. 11, 2, p. 75-82   |  All authors
  • Sequence features of yeast and human core promoters that are predictive of maximal promoter activity

    Lubliner S., Keren L., Segal E. (2013), Nucleic Acids Research. 41, 11, p. 5569-5581
  • Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems

    Szekely P., Sheftel H., Mayo A. et al., Alon U. (2013), PLoS Computational Biology. 9, 8   |  All authors
  • The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery

    Hoffman Y., Dahary D., Bublik D. R. et al., Oren M., Pilpel Y. (2013), Bioinformatics. 29, 7, p. 894-902   |  All authors
  • Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli

    Arbel-Goren R., Tal A., Friedlander T. et al., Meshner S., Costantino N., Court D. L., Stavans J. (2013), Nucleic Acids Research. 41, 9, p. 4825-4834   |  All authors
  • Deterministic direct reprogramming of somatic cells to pluripotency

    Rais Y., Zviran A., Geula S. et al., Gafni O., Chomsky E., Viukov S., Mansour A. A., Caspi I., Krupalnik V., Zerbib M., Maza I., Mor N., Baran D., Weinberger L., Jaitin D. A., Lara Astiaso A. D., Blecher-Gonen R., Shipony Z., Mukamel Z., Hagai T., Gilad S., Amann Zalcenstein D., Tanay A., Amit I., Novershtern N., Hanna J. (. (2013), Nature. 502, 7469, p. 65-+   |  All authors
  • The Intestinal Microbiota in Chronic Liver Disease

    Henao-Mejia J., Elinav E., Thaiss C. A. et al., Flavell R. A. (2013),   |  All authors
  • Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

    Auyeung V. C., Ulitsky I., McGeary S. E. et al., Bartel D. P. (2013), Cell. 152, 4, p. 844-858   |  All authors
  • Addiction of t(8;21) and inv(16) Acute Myeloid Leukemia to Native RUNX1

    Ben Ami A. O., Friedman D., Leshkowitz D. et al., Goldenberg D., Orlovsky K., Pencovich N., Lotem J., Tanay A., Groner Y. (2013), Cell Reports. 4, 6, p. 1131-1143   |  All authors
  • The geometry of the Pareto front in biological phenotype space

    Sheftel H., Shoval O., Mayo A. et al., Alon U. (2013), Ecology and Evolution. 3, 6, p. 1471-1483   |  All authors
  • Consistent Estimation of Gibbs Energy Using Component Contributions

    Noor E., Haraldsdottir H. S., Milo R. et al., Fleming R. M. T. (2013), PLoS Computational Biology. 9, 7   |  All authors
  • Linking the signaling cascades and dynamic regulatory networks controlling stress responses

    Gitter A., Carmi M., Barkai N. et al., Bar-Joseph Z. (2013), Genome Research. 23, 2, p. 365-376   |  All authors
  • Budding Yeast Escape Commitment to the Phosphate Starvation Program Using Gene Expression Noise

    Vardi N., Levy S., Assaf M. et al., Carmi M., Barkai N. (2013), Current Biology. 23, 20, p. 2051-2057   |  All authors
  • Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m(5)C within Archaeal mRNAs

    Edelheit S., Schwartz S., Mumbach M. R. et al., Wurtzel O., Sorek R. (2013), PLoS Genetics. 9, 6   |  All authors
  • Cell-Autonomous Function of Runx1 Transcriptionally Regulates Mouse Megakaryocytic Maturation

    Pencovich N., Jaschek R., Dicken J. et al., Amit A., Lotem J., Tanay A., Groner Y. (2013), PLoS One. 8, 5   |  All authors
  • Developmental bias in the evolution of phalanges

    Kavanagh K. D., Shoval O., Winslow B. B. et al., Alon U., Leary B. P., Kan A., Tabin C. J. (2013), Proceedings of the National Academy of Sciences of the United States of America. 110, 45, p. 18190-18195   |  All authors
  • Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems

    Friedlander T., Mayo A. E., Tlusty T. et al., Alon U. (2013), PLoS One. 8, 8   |  All authors
  • Structural, Evolutionary, and Assembly Principles of Protein Oligomerization

    Levy E. D., Teichmann S. (2013),
  • The Utility of Paradoxical Components in Biological Circuits

    Hart Y., Alon U. (2013), Molecular Cell. 49, 2, p. 213-221
  • Semiconductor-based DNA sequencing of histone modification states

    Cheng C. S., Rai K., Garber M. et al., Hollinger A., Robbins D., Anderson S., Macbeth A., Tzou A., Carneiro M. O., Raychowdhury R., Russ C., Hacohen N., Gershenwald J. E., Lennon N., Nusbaum C., Chin L., Regev A., Amit I. (2013), Nature Communications. 4   |  All authors
  • A note on the kinetics of enzyme action: A decomposition that highlights thermodynamic effects

    Noor E., Flamholz A., Liebermeister W. et al., Bar-Even A., Milo R. (2013), FEBS Letters. 587, 17, p. 2772-2777   |  All authors
  • Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

    Meyer P., Siwo G., Zeevi D. et al., Sharon E., Norel R., Segal E., Stolovitzky G. (2013), Genome Research. 23, 11, p. 1928-1937   |  All authors
  • RNF20 and USP44 Regulate Stem Cell Differentiation by Modulating H2B Monoubiquitylation

    Fuchs G., Shema E., Vesterman R. et al., Kotler E., Wolchinsky Z., Wilder S., Golomb L., Pribluda A., Zhang F., Haj-Yahya M., Feldmesser E., Brik A., Yu X., Hanna J., Aberdam D., Domany E., Oren M. (2012), Molecular Cell. 46, 5, p. 662-673   |  All authors
  • Improved readout precision of the Bicoid morphogen gradient by early decoding

  • Cellular crowding imposes global constraints on the chemistry and evolution of proteomes

  • Tracing the genesis of human embryonic stem cells

    Pribluda A., Hanna J. H. (2012), Nature Biotechnology. 30, 3, p. 247-249
  • Extensive alternative polyadenylation during zebrafish development

    Ulitsky I., Shkumatava A., Jan C. H. et al., Subtelny A. O., Koppstein D., Bell G. W., Sive H., Bartel D. P. (2012), Genome Research. 22, 10, p. 2054-2066   |  All authors
  • Modeling ductal carcinoma in situ: a HER2-Notch3 collaboration enables luminal filling

    Pradeep C., Koestler W. J., Lauriola M. et al., Granit R. Z., Zhang F., Jacob-Hirsch J., Rechavi G., Nair H. B., Hennessy B. T., Gonzalez-Angulo A. M., Tekmal R. R., Ben-Porath I., Mills G. B., Domany E., Yarden Y. (2012), Oncogene. 31, 7, p. 907-917   |  All authors
  • Pharyngeal mesoderm regulatory network controls cardiac and head muscle morphogenesis

    Harel I., Maezawa Y., Avraham R. et al., Rinon A., Ma H., Cross J. W., Leviatan N., Hegesh J., Roy A., Jacob-Hirsch J., Rechavi G., Carvajal J., Tole S., Kioussi C., Quaggin S., Tzahor E. (2012), Proceedings of the National Academy of Sciences of the United States of America. 109, 46, p. 18839-18844   |  All authors
  • Comparative transcriptomics of pathogenic and non-pathogenic Listeria species

    Wurtzel O., Sesto N., Mellin J. R. et al., Karunker I., Edelheit S., Becavin C., Archambaud C., Cossart P., Sorek R. (2012), Molecular Systems Biology. 8   |  All authors
  • Expression Noise and Acetylation Profiles Distinguish HDAC Functions

    Weinberger L., Voichek Y., Tirosh I. et al., Hornung G., Amit I., Barkai N. (2012), Molecular Cell. 47, 2, p. 193-202   |  All authors
  • Regulation of signalling by microRNAs

    Avraham R., Yarden Y. (2012), Biochemical Society Transactions. 40, p. 26-30
  • A mechanical Turing machine: blueprint for a biomolecular computer

  • Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons

    Gelfman S., Burstein D., Penn O. et al., Savchenko A., Amit M., Schwartz S., Pupko T., Ast G. (2012), Genome Research. 22, 1, p. 35-50   |  All authors
  • Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information

  • Surface Growth of a Motile Bacterial Population Resembles Growth in a Chemostat

    Koster D. A., Mayo A., Bren A. et al., Alon U. (2012), Journal of Molecular Biology. 424, 4-Mar, p. 180-191   |  All authors
  • Chromosomal duplication is a transient evolutionary solution to stress

    Yona A. H., Manor Y. S., Herbst R. H. et al., Romano G. H., Mitchell A., Kupiec M., Pilpel Y., Dahan O. (2012), Proceedings of the National Academy of Sciences of the United States of America. 109, 51, p. 21010-21015   |  All authors
  • Axonal transcription factors signal retrogradely in lesioned peripheral nerve

    Ben Yaakov Y. K., Dagan S. Y., Segal-Ruder Y. et al., Shalem O., Vuppalanchi D., Willis D. E., Yudin D., Rishal I., Rother F., Bader M., Blesch A., Pilpel Y., Twiss J. L., Fainzilber M. (2012), EMBO Journal. 31, 6, p. 1350-1363   |  All authors
  • Efficiency in Evolutionary Trade-Offs

    Noor E., Milo R. (2012), Science. 336, 6085, p. 1114-1115
  • Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

    Landan G., Cohen N. M., Mukamel Z. et al., Bar A., Molchadsky A., Brosh R., Horn-Saban S., Zalcenstein D. A., Goldfinger N., Zundelevich A., Gal-Yam E. N., Rotter V., Tanay A. (2012), Nature Genetics. 44, 11, p. 1207-1214   |  All authors
  • Silencing of a large microRNA cluster on human chromosome 14q32 in melanoma: biological effects of mir-376a and mir-376c on insulin growth factor 1 receptor

    Zehavi L., Avraham R., Barzilai A. et al., Bar-Ilan D., Navon R., Sidi Y., Avni D., Leibowitz-Amit R. (2012), Molecular Cancer. 11   |  All authors
  • Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes

    Krumpe K., Frumkin I., Herzig Y. et al., Rimon N., Oezbalci C., Bruegger B., Rapaport D., Schuldiner M. (2012), Molecular Biology of the Cell. 23, 20, p. 3927-3935   |  All authors
  • Design principles of cell circuits with paradoxical components

    Hart Y., Antebi Y. E., Mayo A. E. et al., Friedman N., Alon U. (2012), Proceedings of the National Academy of Sciences of the United States of America. 109, 21, p. 8346-8351   |  All authors
  • Dynamic Proteomics of Human Protein Level and Localization across the Cell Cycle

    Farkash-Amar S., Eden E., Cohen A. et al., Geva Zatorsky Z. N., Cohen L., Milo R., Sigal A., Danon T., Alon U. (2012), PLoS One. 7, 11   |  All authors
  • Thermodynamic constraints shape the structure of carbon fixation pathways

    Bar-Even A., Flamholz A., Noor E. et al., Milo R. (2012), Biochimica Et Biophysica Acta-Bioenergetics. 1817, 9, p. 1646-1659   |  All authors
  • A Systematic Approach to Pair Secretory Cargo Receptors with Their Cargo Suggests a Mechanism for Cargo Selection by Erv14

    Herzig Y., Sharpe H. J., Elbaz Y. et al., Munro S., Schuldiner M. (2012), PLoS Biology. 10, 5   |  All authors
  • Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions

    Pradeep C., Zeisel A., Koestler W. J. et al., Lauriola M., Jacob-Hirsch J., Haibe-Kains B., Amariglio N., Ben Chetrit C. N., Emde A. M., Solomonov I., Neufeld G., Piccart M., Sagi I., Sotiriou C., Rechavi G., Domany E., Desmedt C., Yarden Y. (2012), Oncogene. 31, 31, p. 3569-3583   |  All authors
  • Clonal allelic predetermination of immunoglobulin-kappa rearrangement

    Farago M., Rosenbluh C., Tevlin M. et al., Fraenkel S., Schlesinger S., Masika H., Gouzman M., Teng G., Schatz D., Rais Y., Hanna J. H., Mildner A., Jung S., Mostoslavsky G., Cedar H., Bergman Y. (2012), Nature. 490, 7421, p. 561-+   |  All authors
  • The Single-Nucleotide Resolution Transcriptome of Pseudomonas aeruginosa Grown in Body Temperature

    Wurtzel O., Yoder-Himes D. R., Han K. et al., Dandekar A. A., Edelheit S., Greenberg E. P., Sorek R., Lory S. (2012), PLoS Pathogens. 8, 9   |  All authors
  • New insights into replication origin characteristics in metazoans

    Cayrou C., Coulombe P., Puy A. et al., Rialle S., Kaplan N., Segal E., Mechali M. (2012), Cell Cycle. 11, 4, p. 658-667   |  All authors
  • A vast collection of microbial genes that are toxic to bacteria

    Kimelman A., Levy A., Sberro H. et al., Kidron S., Leavitt A., Amitai G., Yoder-Himes D. R., Wurtzel O., Zhu Y., Rubin E. M., Sorek R. (2012), Genome Research. 22, 4, p. 802-809   |  All authors
  • Widespread promoter-mediated coordination of transcription and mRNA degradation

    Dori-Bachash M., Shalem O., Manor Y. S. et al., Pilpel Y., Tirosh I. (2012), Genome Biology. 13, 12   |  All authors
  • The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

    Mansour A. A., Gafni O., Weinberger L. et al., Zviran A., Ayyash M., Rais Y., Krupalnik V., Zerbib M., Amann Zalcenstein Z. D., Maza I., Geula S., Viukov S., Holtzman L., Pribluda A., Canaani E., Horn-Saban S., Amit I., Novershtern N., Hanna J. H. (2012), Nature. 488, 7411, p. 409-+   |  All authors
  • Transcriptome-wide discovery of circular RNAs in Archaea

    Danan M., Schwartz S., Edelheit S. et al., Sorek R. (2012), Nucleic Acids Research. 40, 7, p. 3131-3142   |  All authors
  • Topology of the human and mouse m(6)A RNA methylomes revealed by m(6)A-seq

    Dominissini D., Moshitch-Moshkovitz S., Schwartz S. et al., Salmon-Divon M., Ungar L., Osenberg S., Cesarkas K., Jacob-Hirsch J., Amariglio N., Kupiec M., Sorek R., Rechavi G. (2012), Nature. 485, 7397, p. 201-U84   |  All authors
  • From catalogue to function

    Segal E. (2012), Nature. 489, 7414, p. 55-55
  • Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

    Gingold H., Dahan O., Pilpel Y. (2012), Nucleic Acids Research. 40, 20, p. 10053-10063
  • Decoding Human Cytomegalovirus

    Stern-Ginossar N., Weisburd B., Michalski A. et al., Vu Thuy Khanh Le, Hein M. Y., Huang S., Ma M., Shen B., Qian S., Hengel H., Mann M., Ingolia N. T., Weissman J. S. (2012), Science. 338, 6110, p. 1088-1093   |  All authors
  • Functional Consequences of Necdin Nucleocytoplasmic Localization

    Lavi-Itzkovitz A., Tcherpakov M., Levy Z. et al., Itzkovitz S., Muscatelli F., Fainzilber M. (2012), PLoS One. 7, 3   |  All authors
  • Recursive construction of perfect DNA molecules and libraries from imperfect oligonucleotides

  • Interactions of subunit CCT3 in the yeast chaperonin CCT/TRiC with Q/N-rich proteins revealed by high-throughput microscopy analysis

    Nadler Holly H. M., Breker M., Gruber R. et al., Azia A., Gymrek M., Eisenstein M., Willison K. R., Schuldiner M., Horovitz A. (2012), Proceedings of the National Academy of Sciences of the United States of America. 109, 46, p. 18833-18838   |  All authors
  • Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

    Sharon E., Kalma Y., Sharp A. et al., Raveh - Sadka -. S. T., Levo M., Zeevi D., Keren L., Yakhini Z., Weinberger A., Segal E. (2012), Nature Biotechnology. 30, 6, p. 521-+   |  All authors
  • Promoter Nucleosome Organization Shapes the Evolution of Gene Expression

    Rosin D., Hornung G., Tirosh I. et al., Gispan A., Barkai N. (2012), PLoS Genetics. 8, 3   |  All authors
  • Robust 4C-seq data analysis to screen for regulatory DNA interactions

    van de Werken d. W. H. J. G., Landan G., Holwerda S. J. B. et al., Hoichman M., Klous P., Chachik R., Splinter E., Valdes-Quezada C., Oz Y., Bouwman B. A. M., Verstegen M. J. A. M., de Wit W. E., Tanay A., de Laat L. W. (2012), Nature Methods. 9, 10, p. 969-+   |  All authors
  • A proof for loop-law constraints in stoichiometric metabolic networks

    Noor E., Lewis N. E., Milo R. (2012), BMC Systems Biology. 6
  • RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs

    Michaeli S., Doniger T., Gupta S. K. et al., Wurtzel O., Romano M., Visnovezky D., Sorek R., Unger R., Ullu E. (2012), Nucleic Acids Research. 40, 3, p. 1282-1298   |  All authors
  • A Crossroad of microRNAs and Immediate Early Genes (IEGs) Encoding Oncogenic Transcription Factors in Breast Cancer

    Sas-Chen A., Avraham R., Yarden Y. (2012), Journal of Mammary Gland Biology and Neoplasia. 17, 1, p. 3-14
  • Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability

    Shlush L. I., Chapal Ilani I. N., Adar R. et al., Pery N., Maruvka Y., Spiro A., Shouval R., Rowe J. M., Tzukerman M., Bercovich D., Izraeli S., Marcucci G., Bloomfield C. D., Zuckerman T., Skorecki K., Shapiro E. (2012), Blood. 120, 3, p. 603-612   |  All authors
  • miR-10b*, a master inhibitor of the cell cycle, is down-regulated in human breast tumours

    Biagioni F., Ben-Moshe N. B., Fontemaggi G. et al., Canu V., Mori F., Antoniani B., Di Benedetto B. A., Santoro R., Germoni S., De Angelis A. F., Cambria A., Avraham R., Grasso G., Strano S., Muti P., Mottolese M., Yarden Y., Domany E., Blandino G. (2012), EMBO Molecular Medicine. 4, 11, p. 1214-1229   |  All authors
  • Cell Lineage Analysis of the Mammalian Female Germline

    Reizel Y., Itzkovitz S., Adar R. et al., Elbaz J., Jinich A., Chapal Ilani I. N., Maruvka Y. E., Nevo N., Marx Z., Horovitz I., Wasserstrom A., Mayo A., Shur I., Benayahu D., Skorecki K., Segal E., Dekel N., Shapiro E. (2012), PLoS Genetics. 8, 2, e1002477   |  All authors
  • Using bleach-chase to measure protein half-lives in living cells

    Geva Zatorsky Z. N., Issaeva I., Mayo A. et al., Cohen A., Dekel E., Danon T., Cohen L., Liron Y., Alon U., Eden E. (2012), Nature Protocols. 7, 4, p. 801-811   |  All authors
  • Achieving Diversity in the Face of Constraints: Lessons from Metabolism

    Milo R., Last R. L. (2012), Science. 336, 6089, p. 1663-1667
  • Disentangling signaling gradients generated by equivalent sources

    Rappaport N., Barkai N. (2012), Journal of Biological Physics. 38, 2, p. 267-278
  • eQuilibrator: the biochemical thermodynamics calculator

    Flamholz A., Noor E., Bar-Even A. et al., Milo R. (2012), Nucleic Acids Research. 40, D1, p. D770-D775   |  All authors
  • Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression

    Salari R., Wojtowicz D., Zheng J. et al., Levens D., Pilpel Y., Przytycka T. M. (2012), PLoS Computational Biology. 8, 8   |  All authors
  • A survey of carbon fixation pathways through a quantitative lens

    Bar-Even A., Noor E., Milo R. (2012), Journal of Experimental Botany. 63, 6, p. 2325-2342
  • Mode of Regulation and the Insulation of Bacterial Gene Expression

    Sasson V., Shachrai I., Bren A. et al., Dekel E., Alon U. (2012), Molecular Cell. 46, 4, p. 399-407   |  All authors
  • Slug and Sox9 Cooperatively Determine the Mammary Stem Cell State

    Shibue T., Tischler V., Reinhardt F. et al., Itzkovitz S., Noske A., Zuerrer-Haerdi U., Bell G., Tam W. L., Mani S. A., van Oudenaarden O. A., Weinberg R. A. (2012), Cell. 148, 5, p. 1015-1028   |  All authors
  • EGR1 and the ERK-ERF axis drive mammary cell migration in response to EGF

    Tarcic G., Avraham R., Pines G. et al., Amit I., Shay T., Lu Y., Zwang Y., Katz M., Ben Chetrit C. N., Jacob-Hirsch J., Virgilio L., Rechavi G., Mavrothalassitis G., Mills G. B., Domany E., Yarden Y. (2012), FASEB Journal. 26, 4, p. 1582-1592   |  All authors
  • A Critical Role for the Wnt Effector Tcf4 in Adult Intestinal Homeostatic Self-Renewal

    Itzkovitz S., Koo B., Boj S. F. et al., Korving J., van den Born d. B. M., van Oudenaarden O. A., Robine S., Clevers H. (2012), Molecular and Cellular Biology. 32, 10, p. 1918-1927   |  All authors
  • Noise-mean relationship in mutated promoters

    Hornung G., Bar-Ziv R., Rosin D. et al., Tokuriki N., Tawfik D., Oren M., Barkai N. (2012), Genome Research. 22, 12, p. 2409-2417   |  All authors
  • Identification of CTCF as a master regulator of the clustered protocadherin genes

    Golan Mashiach M. M., Grunspan M., Emmanuel R. et al., Gibbs-Bar L., Dikstein R., Shapiro E. (2012), Nucleic Acids Research. 40, 8, p. 3378-3391   |  All authors
  • An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

    Noor E., Bar-Even A., Flamholz A. et al., Lubling Y., Davidi D., Milo R. (2012), Bioinformatics. 28, 15, p. 2037-2044   |  All authors
  • Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

    Amit M., Donyo M., Hollander D. et al., Goren A., Kim E., Gelfman S., Lev-Maor G., Burstein D., Schwartz S., Postolsky B., Pupko T., Ast G. (2012), Cell Reports. 1, 5, p. 543-556   |  All authors
  • Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets

    Ben-Moshe N. B., Avraham R., Kedmi M. et al., Zeisel A., Yitzhaky A., Yarden Y., Domany E. (2012), Nucleic Acids Research. 40, 21, p. 10614-10627   |  All authors
  • Confinement to Organelle-Associated Inclusion Structures Mediates Asymmetric Inheritance of Aggregated Protein in Budding Yeast

    Spokoini R., Moldavski O., Nahmias Y. et al., England J. L., Schuldiner M., Kaganovich D. (2012), Cell Reports. 2, 4, p. 738-747   |  All authors
  • Programmable In Vivo Selection of Arbitrary DNA Sequences

    Ben-Yehezkel T., Biezuner T., Linshiz G. et al., Mazor Y., Shapiro E. (2012), PLoS One. 7, 11, e47795   |  All authors
  • Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

    Shoval O., Sheftel H., Shinar G. et al., Hart Y., Ramote O., Mayo A., Dekel E., Kavanagh K., Alon U. (2012), Science. 336, 6085, p. 1157-1160   |  All authors
  • Genome-wide Measurement of RNA Folding Energies

    Wan Y., Qu K., Ouyang Z. et al., Kertesz M., Li J., Tibshirani R., Makino D. L., Nutter R. C., Segal E., Chang H. Y. (2012), Molecular Cell. 48, 2, p. 169-181   |  All authors
  • CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

    Stern A., Mick E., Tirosh I. et al., Sagy O., Sorek R. (2012), Genome Research. 22, 10, p. 1985-1994   |  All authors
  • Inferring Divergence of Context-Dependent Substitution Rates in Drosophila Genomes with Applications to Comparative Genomics

  • Rethinking glycolysis: on the biochemical logic of metabolic pathways

    Bar-Even A., Flamholz A., Noor E. et al., Milo R. (2012), Nature Chemical Biology. 8, 6, p. 509-517   |  All authors
  • The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers

    van de Wetering d. W. M., Koo B., Itzkovitz S. et al., Volckmann R., Kung K. S., Koster J., Radulescu S., Myant K., Versteeg R., Sansom O. J., van Es E. J. H., Barker N., van Oudenaarden O. A., Mohammed S., Heck A. J. R., Clevers H. (2012), EMBO Journal. 31, 14, p. 3079-3091   |  All authors
  • Self-Organized Shuttling: Generating Sharp Dorsoventral Polarity in the Early Drosophila Embryo

    Haskel Ittah I. M., Ben-Zvi D., Branski Arieli A. M. et al., Schejter E. D., Shilo B., Barkai N. (2012), Cell. 150, 5, p. 1016-1028   |  All authors
  • Nucleosome Organization Affects the Sensitivity of Gene Expression to Promoter Mutations

    Hornung G., Oren M., Barkai N. (2012), Molecular Cell. 46, 3, p. 362-368
  • MiR-10b Downregulates the Stress-Induced Cell Surface Molecule MICB, a Critical Ligand for Cancer Cell Recognition by Natural Killer Cells

    Tsukerman P., Stern-Ginossar N., Gur C. et al., Glasner A., Nachmani D., Bauman Y., Yamin R., Vitenshtein A., Stanietsky N., Bar-Mag T., Lankry D., Mandelboim O. (2012), Cancer Research. 72, 21, p. 5463-5472   |  All authors
  • Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

    Raveh - Sadka -. S. T., Levo M., Shabi U. et al., Shany B., Keren L., Lotan-Pompan M., Zeevi D., Sharon E., Weinberger A., Segal E. (2012), Nature Genetics. 44, 7, p. 743-U163   |  All authors
  • Correction:: Programmable In Vivo Selection of Arbitrary DNA Sequences

    Ben Yehezkel T., Biezuner T., Linshiz G. et al., Mazor Y., Shapiro E. (2012), PLoS One. 7, 11   |  All authors
  • A programmable NOR-based device for transcription profile analysis

    Ran T., Douek Y., Milo L. et al., Shapiro E. (2012), Scientific Reports. 2, 641   |  All authors
  • M(odu)LLating the Innate Response

    Blecher-Gonen R., Amit I. (2012), Immunity. 36, 4, p. 551-552
  • Efficiency and specificity in microRNA biogenesis

    Barad O., Mann M., Chapnik E. et al., Shenoy A., Blelloch R., Barkai N., Hornstein E. (2012), Nature Structural & Molecular Biology. 19, 6, p. 650-+   |  All authors
  • Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

    Sexton T., Yaffe E., Kenigsberg E. et al., Bantignies F., Leblanc B., Hoichman M., Parrinello H., Tanay A., Cavalli G. (2012), Cell. 148, 3, p. 458-472   |  All authors
  • Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

    Adadi R., Volkmer B., Milo R. et al., Heinemann M., Shlomi T. (2012), PLoS Computational Biology. 8, 7   |  All authors
  • A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

    Silander O. K., Nikolic N., Zaslaver A. et al., Bren A., Kikoin I., Alon U., Ackermann M. (2012), PLoS Genetics. 8, 1   |  All authors