Upcoming

All upcoming events

MicroEco 2020

Date:
06
Wednesday
January
2021
-
07
Thursday
January
2021
Conference
Time: 08:00
Location: David Lopatie Conference Centre

EMBO Meeting on Cell Size and Growth Regulation

Date:
20
Sunday
June
2021
-
22
Tuesday
June
2021
Conference
Time: 08:00
Location: David Lopatie Conference Centre
Organizer: The Dimitris N. Chorafas Institute for Scientific Exchange

Cancer ImmunoMetabolism 2021

Date:
12
Sunday
September
2021
-
14
Tuesday
September
2021
Conference
Time: 08:00
Location: David Lopatie Conference Centre

    Past

    All Events

    The power of ONE: Immunology in the age of single cell genomics

    Date:
    02
    Thursday
    July
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Ido Amit
    Organizer: Dwek Institute for Cancer Therapy Research

    Frontiers in Systems Biology

    Date:
    09
    Tuesday
    June
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Lacra Bintu
    Organizer: Azrieli Institute for Systems Biology

    Cancer Research Club - Prof Dan Landau: Novel genomics perspectives on cancer evolution: from basic principles to therapeutic optimization

    Date:
    04
    Thursday
    June
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Dan Landau
    Organizer: Department of Biological Regulation

    Frontiers in Systems Biology

    Date:
    05
    Tuesday
    May
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Nassos Typas
    Organizer: Azrieli Institute for Systems Biology

    Frontiers in Systems Biology

    Date:
    21
    Tuesday
    April
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Azrieli Institute for Systems Biology

    Azrieli Institute for Systems Biology

    Date:
    04
    Wednesday
    March
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Title: “Does host-pathogen coevolution explain extraordinary genetic diversity”
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Dieter Ebert
    Organizer: Azrieli Institute for Systems Biology

    The Biological Age Concept: Predicting Healthspan and Lifespan using Genomics, Epigenomics and Proteomics from Saliva and Plasma

    Date:
    27
    Thursday
    February
    2020
    Lecture / Seminar
    Time: 14:00-15:00
    Title: Guest Talk with Prof Jaap Goudsmit
    Location: Wolfson Building for Biological Research
    Lecturer: Prof. Jaap Goudsmit
    Organizer: Department of Molecular Cell Biology
    Details: The Biological Age Concept: Predicting Healthspan and Lifespan using Genomics, E ... Read more The Biological Age Concept: Predicting Healthspan and Lifespan using Genomics, Epigenomics and Proteomics from Saliva and Plasma Jaap Goudsmit, MD, PhD Departments of Immunology & Infectious Diseases and Epidemiology, Harvard T.H. Chan School of Public Health The moment the first age-related disease manifests itself defines healthspan, like the moment of death does for lifespan. Lifespan and healthspan are impacted by mutations in a set of genetic loci as well as series of events afterwards impacting epigenetic changes downregulating the transcription of DNA to RNA (DNAm) or the translation of RNA to protein (microRNAs). Age, like sex, impacts lifespan most during life as a marker independent from individual age-related diseases. The length of the period after the healthspan ends is characterized by a stochastic accumulation of morbidities that each in combination or on their own can shorten lifespan. Biological age can be viewed as a metric defining the link between healthspan and lifespan. The best algorithm for biological age includes a combination of organ system markers including a marker for deterioration of the brain, which we call “Biosystem Age”, calibrated on the stringency of predicting lifespan independent of chronological age. Biosystem Age predicts healthspan as well as individual age-related diseases better than chronological age and has a very specific age-related microRNA signature. We propose that each change of events or genetic pathway during life that at first hand appears to be associated with disease or death rates is heavily influenced by Biosystem Age. We plan to test whether immune responsiveness to vaccines declining with age is dependent of Biosystem Age.
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    Assurance of Clonality Next-Generation Single-Cell Dispensing in Cell Line Development and Single-Cell Genomics

    Date:
    24
    Monday
    February
    2020
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Presentation & ‘Cytena f.sight’ hands-on
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Adrian Zambrano
    Organizer: Department of Life Sciences Core Facilities

    Language of Evolution and Evolution of Language

    Date:
    23
    Sunday
    February
    2020
    -
    24
    Monday
    February
    2020
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre

    The Genomics of Fasting and Inflammation Reveals Dynamic Cooperativity Between Transcription Factors

    Date:
    09
    Sunday
    February
    2020
    Lecture / Seminar
    Time: 15:00-16:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Ido Goldstein
    Organizer: Life Sciences

    Insights into human evolution from a new high-coverage Neandertal genome and thousands of present-day human ones

    Date:
    04
    Tuesday
    February
    2020
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Fabrizio Mafessoni
    Organizer: Department of Plant and Environmental Sciences
    Details: Hosts: Prof. Avi Levy

    Next Gen Immunology 2020

    Date:
    02
    Sunday
    February
    2020
    -
    05
    Wednesday
    February
    2020
    Conference
    Time: 08:00
    Location: Michael Sela Adutitorium
    Organizer: Azrieli Institute for Systems Biology

    New Approaches for Structure Determination of Protein Complexes by Mass Spectrometry

    Date:
    13
    Monday
    January
    2020
    Colloquium
    Time: 11:00-12:15
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof. Vicki Wysocki
    Organizer: Faculty of Chemistry
    Abstract: Characterization of the overall topology and inter-subunit contacts of protein c ... Read more Characterization of the overall topology and inter-subunit contacts of protein complexes, and their assembly/disassembly and unfolding pathways, is critical because protein complexes regulate key biological processes, including processes important in understanding and controlling disease. Tools to address structural biology problems continue to improve. Native mass spectrometry (nMS) and associated technologies such as ion mobility are becoming an increasingly important component of the structural biology toolbox. When the mass spectrometry approach is used early or mid-course in a structural characterization project, it can provide answers quickly using small sample amounts and samples that are not fully purified. Integration of sample preparation/purification with effective dissociation methods (e.g., surface-induced dissociation), ion mobility, and computational approaches provide a MS workflow that can be enabling in biochemical, synthetic biology, and systems biology approaches. Native MS can determine whether the complex of interest exists in a single or in multiple oligomeric states and can provide characterization of topology/intersubunit connectivity, and other structural features. Beyond its strengths as a stand-alone tool, nMS can also guide and/or be integrated with other structural biology approaches such as NMR, X-ray crystallography, and cryoEM.
    Close abstract

    Adaptation of bacteria with CRISPR and adaptation on a rugged fitness landscape

    Date:
    06
    Monday
    January
    2020
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Marija Vucelja
    Organizer: Department of Physics of Complex Systems
    Abstract: I will tell you two stories of adaptation of populations aided and enriched by s ... Read more I will tell you two stories of adaptation of populations aided and enriched by statistical physics approaches. The first story is about the adaptation of bacteria with CRISPR. CRISPR-Cas is a famous biology buzz word, due to its applications to gene editing. However, CRISPR-Cas is also a prokaryote immune system. It works as a “library” of previous infections. This library contains snippets of exogenous genetic material. With a new infection, the library is consulted, and if a match is found, the attempt will be made to neutralize the intruding genome. Bacteria use CRISPR-Cas as an immune system against phages and plasmids. Such immunity is hereditary and dynamic — it can be gained and lost during the lifetime of the single bacteria. Also, the process of acquiring snippets when exposed to the same phage is stochastic, and the same strain bacteria in a population contain different CRISPR loci content and thus variable immunity to the phage. We use dynamical systems approaches to predict the shape of this diverse distribution of CRISPR loci content within a bacterial population as a function of two crucial parameters — the rate of acquisition and the immunity to the phage. The second story is about adaptation on a rugged fitness landscape. A crude measure of adaption to a new environment called fitness. Often one defines fitness as the expected growth rate. The higher the fitness, the more thriving is a population. What happens over long times for a population with a finite genome — when all beneficial, fitness mutations, are exhausted? Contrary to expectations, the experiments show that fitness does not reach a plateau. Here we introduce a spin-glass microscopic model, where a genome can be represented as a spin configuration, and individual spins are genes. The fitness plays the role of minus the Hamiltonian of the system. We use numerical approaches and estimates to study hopping between metastable states on a rugged fitness landscape. We show that with gene interactions (interacting spins), double beneficial mutations (flipping of pairs of spins) can lead to a slow, logarithmic increase of fitness in a wide class of cases.
    Close abstract

    Adaptation of bacteria with CRISPR and adaptation on a rugged fitness landscape

    Date:
    06
    Monday
    January
    2020
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Marija Vucelja
    Organizer: Department of Physics of Complex Systems
    Abstract: I will tell you two stories of adaptation of populations aided and enriched by s ... Read more I will tell you two stories of adaptation of populations aided and enriched by statistical physics approaches. The first story is about the adaptation of bacteria with CRISPR. CRISPR-Cas is a famous biology buzz word, due to its applications to gene editing. However, CRISPR-Cas is also a prokaryote immune system. It works as a “library” of previous infections. This library contains snippets of exogenous genetic material. With a new infection, the library is consulted, and if a match is found, the attempt will be made to neutralize the intruding genome. Bacteria use CRISPR-Cas as an immune system against phages and plasmids. Such immunity is hereditary and dynamic — it can be gained and lost during the lifetime of the single bacteria. Also, the process of acquiring snippets when exposed to the same phage is stochastic, and the same strain bacteria in a population contain different CRISPR loci content and thus variable immunity to the phage. We use dynamical systems approaches to predict the shape of this diverse distribution of CRISPR loci content within a bacterial population as a function of two crucial parameters — the rate of acquisition and the immunity to the phage. The second story is about adaptation on a rugged fitness landscape. A crude measure of adaption to a new environment called fitness. Often one defines fitness as the expected growth rate. The higher the fitness, the more thriving is a population. What happens over long times for a population with a finite genome — when all beneficial, fitness mutations, are exhausted? Contrary to expectations, the experiments show that fitness does not reach a plateau. Here we introduce a spin-glass microscopic model, where a genome can be represented as a spin configuration, and individual spins are genes. The fitness plays the role of minus the Hamiltonian of the system. We use numerical approaches and estimates to study hopping between metastable states on a rugged fitness landscape. We show that with gene interactions (interacting spins), double beneficial mutations (flipping of pairs of spins) can lead to a slow, logarithmic increase of fitness in a wide class of cases.
    Close abstract

    How ancient genomes aid in tracing human mobility and disease

    Date:
    02
    Thursday
    January
    2020
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Michal Feldman
    Abstract: Recent technological advances such as next-generation sequencing and new capture ... Read more Recent technological advances such as next-generation sequencing and new capture and sampling techniques have enabled the retrieval of genomic information from archaeological human remains, even from regions previously known to have poor conditions for DNA preservation, such as the Near East. I will describe two studies in which these methods helped us in recording the past by tracing human mobility and disease. In the first study, we retrieved a high-coverage Y. pestis genome from the remains of a 6th century victim of the Justinianic Plague, the first of three historic pandemics caused by Y. pestis. The results confirmed a central or south Asian origin of the strain and demonstrated its presence in rural south Germany where no historical source records it. In a second study, genome-wide data was reconstructed from human remains recovered from the ancient seaport of Ashkelon, identified as “Philistine” during the Iron Age. The comparison of Bronze and Iron Age individuals was used to address whether the cultural transition observed in the archaeological record was mirrored by a foreign genetic influx.
    Close abstract

    The LSCF Bioinformatics Unit Achievements & Challenges

    Date:
    02
    Thursday
    January
    2020
    Lecture / Seminar
    Time: 09:00-10:00
    Title: LSCF departmental seminar
    Location: Max and Lillian Candiotty Building
    Lecturer: Dr. Dena Leshkowitz
    Organizer: Department of Life Sciences Core Facilities

    Physical Genomics Harnessing physics and chemistry for single-molecule analysis of the human genome

    Date:
    30
    Monday
    December
    2019
    Lecture / Seminar
    Time: 14:15
    Location: Edna and K.B. Weissman Building of Physical Sciences
    Lecturer: Yuval Ebenstein, TAU
    Organizer: Department of Physics of Complex Systems
    Abstract: DNA is an amazing memory device that holds the operating system of life. However ... Read more DNA is an amazing memory device that holds the operating system of life. However, DNA sequencing fails to extract the full range of information associated with genetic material and is lacking in its ability to resolve variations between genomes. As a consequence, many genomic features remain poorly characterized in the human genome reference. In addition, the information content of the genome extends beyond the base sequence in the form of chemical modifications such as DNA methylation or DNA damage lesions that chemically encode our life experiences in our DNA. By applying experimental principles of single molecule detection we gain access to the structural variation and long range patterns of genetic and epigenetic information. We show how physical extension of long DNA molecules on surfaces and in nanofluidic channels reveals such information in the form of a linear, optical “barcode” showing distinct types of observables. Recent results from our lab demonstrate our ability to detect epigenetic marks and various forms of DNA damage on individual genomic DNA molecules and use this information for medical diagnostics.
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    Hyperactive FOXA1 Signaling in Breast Cancer Endocrine Resistance and Metastasis - When Genomics Meet Epigenomics

    Date:
    26
    Thursday
    December
    2019
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Dr. Rachel Schiff
    Organizer: Department of Biological Regulation

    Transposable elements as drivers of structural and functional variations in wheat genome

    Date:
    10
    Tuesday
    December
    2019
    Lecture / Seminar
    Time: 11:30-12:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Khalil Kashkush
    Organizer: Department of Plant and Environmental Sciences
    Details: Hosts: Dr. Cathy Bessudo and Dr. Hadas Zehavi

    Spatial Transcriptomics: A getting started guide to the 10x genomics Visium Spatial Gene expression Solution

    Date:
    03
    Tuesday
    December
    2019
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Nicola Cahill
    Organizer: Department of Life Sciences Core Facilities
    Abstract: The Visium Spatial Gene Expression Solution from 10x Genomics analyzes complete ... Read more The Visium Spatial Gene Expression Solution from 10x Genomics analyzes complete transcriptomes in intact tissue sections, allowing you to discover genes and markers relevant to your research without having to rely on known targets. Preserving spatial resolution offers critical information for understanding the relationships between cellular function, phenotype, and location in the tissue.
    Close abstract

    Special Guest Seminar

    Date:
    02
    Monday
    December
    2019
    Lecture / Seminar
    Time: 12:00
    Title: “Using Systems Approaches to Understand the Mechanism of Disease”
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Nevan Krogan
    Organizer: Azrieli Institute for Systems Biology

    Integrating 3D structure into Systems Biology

    Date:
    19
    Tuesday
    November
    2019
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Prof. Barry Honig
    Organizer: Department of Structural Biology

    Life Science Colloquium- Prof Feng Zhang

    Date:
    06
    Wednesday
    November
    2019
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Exploration of Microbial Diversity for Genome Editing and Beyond
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: TBD
    Organizer: Life Sciences

    Pre-SAAC symposium on Systems Biology

    Date:
    03
    Sunday
    November
    2019
    Conference
    Time: 09:00-14:30
    Location: David Lopatie Conference Centre

    Special Guest Seminar with Anat Zimmer

    Date:
    03
    Thursday
    October
    2019
    Lecture / Seminar
    Time: 14:00-15:00
    Title: "Analyzing PD3 clouds using PAReto Task Inference".
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Anat Zimmer
    Organizer: Azrieli Institute for Systems Biology
    Abstract: It is a challenge to answer questions like: why some people develop a disease, r ... Read more It is a challenge to answer questions like: why some people develop a disease, react to a specific treatment and/or develop severe side-effects while others don’t. In order to explain these occurrences, one has to take a holistic approach and study the body physiology from a systems level perspective. Longitudinal multi-omics measurements together with genetics, on a large population, can serve such a purpose and help in predicting, reasoning, and preventing diseases. In partnership with Arivale Inc., we have developed infrastructure to collect longitudinal Personalized Dense Dynamic Data clouds (PD3 clouds) on thousands of individuals, which include genetics and longitudinal measurements of clinical labs, microbiome, metabolome, proteome, and self-reported data. The value of these extremely high-dimensional data clouds is clear; however, it also comprises a challenge in data analysis and interpretation. One way to reduce data dimensionality is called Pareto Task Inference (PARTI, Hart et al. 2015). We used this method to analyze the clinical labs and found that the data falls on a significant tetrahedron. The 4 vertices are archetypes that specialize in a certain task. Using all other datatypes, we identified enriched traits next to every archetype and revealed the underline tradeoffs that shape the data. This distinctive analysis uncovers unexpected relationships between datasets such as metabolomics, proteomics and clinical labs, and helps in interconnecting the different datatypes to characterize different states of human health.
    Close abstract

    Special Guest Seminar with Dr. Johnathan Cooper-Knock

    Date:
    05
    Thursday
    September
    2019
    Lecture / Seminar
    Time: 11:00-12:00
    Title: Unbiased genome-wide screen identifies new ALS risk variants within gene-regulatory elements.
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Johnathan Cooper-Knock
    Organizer: Department of Molecular Genetics

    Special Guest Seminar with Ophir Shalem

    Date:
    22
    Thursday
    August
    2019
    Lecture / Seminar
    Time: 10:00
    Title: “CRISPR screens, proteostasis and rapid control of proteins at scale”
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Ophir Shalem, Ph.D
    Organizer: Azrieli Institute for Systems Biology

    RNASEQ Predicts Major Breast Cancer Subtype and Potential to Respond to Cancer Immunotherapy.

    Date:
    18
    Tuesday
    June
    2019
    Lecture / Seminar
    Time: 10:00-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Daniel Harari
    Organizer: Department of Biomolecular Sciences
    Abstract: Breast cancer (BC) divides into three major subtypes. 1) Estrogen/Progesterone ... Read more Breast cancer (BC) divides into three major subtypes. 1) Estrogen/Progesterone Receptor positive (ER+ve), 2) ErbB2/Her2 genome amplified (Her2+), and for cancers exhibiting none of these markers, triple negative breast cancer (TNBC). These classifications defined by histo-pathologists have important ramifications as they indicate alternative therapy options best suited to treat a given patient. We have used high throughput transcriptomic data from > 1000 breast cancer biopsies derived from The Cancer Genome Atlas (TCGA) and demonstrate that RNASEQ can with high fidelity subcategorize BC into one of these three major subgroups. Surprisingly, we found that three levels of ErbB2 expression ErbBLOW, ErbB2MED and ErbB2HIGH closely correlate with TNBC, ER+ and HER+ tumor subtypes respectively, a finding not paralleled by genome copy-number alone. Pathway analyses of differentially expressed genes demonstrated that TNBCs are particularly enriched for “Lymphocyte Activation” correlating with “chemotaxis”, “NK-cell activation” and “IFN-gamma signaling”. These immune-related gene signatures may provide an additional layer of clinically-relevant patient information as others have reported that T-cell infiltration into tumors indicate potential good response to cancer immunotherapy (e.g. Anti-PD1, Anti-CTLA4 drugs). We can use these transcriptomic immune signatures to determine their level of expression in individual patients, thus providing context for predicting response to immunotherapy in personalized medicinal manner.
    Close abstract

    Departmental Seminar

    Date:
    26
    Sunday
    May
    2019
    Lecture / Seminar
    Time: 13:00-14:00
    Title: Developing a highly sensitive CRISPR based platform for virus and host functional genomics
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Yaara Finkel
    Organizer: Department of Molecular Genetics

    CRASH COURSE ON GENOMICS and BIOINFORMATICS OF CANCER

    Date:
    18
    Thursday
    April
    2019
    Lecture / Seminar
    Time: 11:45-14:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Prof. Eytan Ruppin, Prof. Itay Tirosh
    Organizer: Department of Biomolecular Sciences

    The genetics of epigenetics

    Date:
    16
    Tuesday
    April
    2019
    Lecture / Seminar
    Time: 11:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Magnus Nordborg
    Organizer: Department of Plant and Environmental Sciences
    Details: Host: Tal Dahan If you wish to meet Prof. Nordborg, please contact tal.dahan@we ... Read more Host: Tal Dahan If you wish to meet Prof. Nordborg, please contact tal.dahan@weizmann.ac.il
    Close details
    Abstract: Epigenetics continues to fascinate, especially the notion that it blurs the line ... Read more Epigenetics continues to fascinate, especially the notion that it blurs the line between “nature and nurture” and could make Lamarckian adaptation via the inheritance of acquired characteristics possible. That this is in principle possible is clear: in the model plant Arabidopsis thaliana (thale cress), experimentally induced DNA methylation variation can be inherited and affect important traits. The question is whether this is important in nature. Recent studies of A. thaliana have revealed a pattern of correlation between levels of methylation and climate variables that strongly suggests that methylation is important in adaptation. However, somewhat paradoxically, the experiments also showed that much of the variation for this epigenetic trait appears to have a genetic rather than an epigenetic basis. This suggest that epigenetics may indeed be important for adaptation, but as part of a genetic mechanism that is currently not understood. Genome-wide association studies revealed a striking genetic architecture of methylation variation, involving major-effect polymorphisms in many genes involved in silencing, and this can be utilized to determine whether the global pattern of methylation variation has a genetic or an epigenetic cause, and to elucidate the ultimate cause of the global pattern of variation: natural selection.
    Close abstract

    Caltech-Weizmann Symposium on Systems Biology and Neuroscience

    Date:
    18
    Monday
    February
    2019
    -
    19
    Tuesday
    February
    2019
    Lecture / Seminar
    Time: 09:00 - 17:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Nachum Ulanovsky, Rony Paz, Shalev Itzkovitz, Ilan Lampl, Mietal Oren, Ofer Yizhar, Rotem Sorek,Ron Milo, Nir Friedman, Yraon Antebi, Michal Rivlin, Yaniv Ziv, Naama Barkai, Long Cai Katalin Fejes-Toth, Alexei Aravin, Rebecca Vorhees,Victoria Orphan, El
    Organizer: Department of Biomolecular Sciences
    Details: February 18th. *Opening Remarks - Daniel Zajfman *Nachum Ulanovsky - Neural co ... Read more February 18th. *Opening Remarks - Daniel Zajfman *Nachum Ulanovsky - Neural codes for natural navigation in the bat brain. *Rony Paz - A neural tradeoff across brain regions and primate species. *Shalev Itzkovitz - Spatial transcriptomics of mammalian tissues. *Long Cai - Spatial Genomics: analysis of single cell in situ. *Katalin Fejes-Toth - The SUMO ligase Su(var)2-10 links piRNA-guided target recognition to chromatin-mediated transcriptional silencing. *Ilan Lampl - Interhemispheric subthreshold correlations in the somatosensory cortex of awake mice. *Meital Oren - Insights into the mechanism of sexually dimorphic synaptic connectivity. *Ofer Yizhar - Autism-associated disruption of social representations in the mouse prefrontal cortex. *Alexei Aravin - piRNA and a new view on mechanisms that regulate genes expression. *Rotem Sorek - The immune system of bacteria - beyond CRISPR. *Rebecca Vorhees - Selective protein targeting to the endoplasmic reticulum. February.19th *Ron Milo - The biomass distribution on Earth.  *Victoria Orphan - Studying microbial physiology and ecological interactions at the energetic edge of life: methane-fueled syntrophy between archaea and bacteria. *Nir Friedman - Collective induction of immune memory. *Elliot Meyerowitz - Mechanical Signaling in a Plant Stem Cell Population. *Yraon Antebi - Computations From Promiscuous Interactions in the BMP Pathway. *Michal Rivlin - It’s all about timing: the computation of motion direction in the retina. *Mikhail Shapiro - Biomolecular engineering for non-invasive imaging and control of cellular function *Yaniv Ziv - Revealing the neural correlates of behavior without relying on behavioral measurements. *Lior Pachter - Computational and experimental foundations for single-cell RNA-seq. *Naama Barkai - Resolving regulatory interplay by gene duplication.
    Close details

    Sequencing giants - the wild emmer wheat genome assembly

    Date:
    05
    Tuesday
    February
    2019
    Lecture / Seminar
    Time: 11:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Raz Avni
    Organizer: Department of Plant and Environmental Sciences
    Details: Host:Dr. Einat Segev

    Special Guest Seminar with Ariel Schwartz

    Date:
    17
    Thursday
    January
    2019
    Lecture / Seminar
    Time: 10:00
    Title: “Deep Semantic Genome and Protein Representation for Annotation, Discovery, and Engineering”
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Ariel Schwartz
    Organizer: Department of Molecular Genetics
    Abstract: Computational assignment of function to proteins with no known homologs is still ... Read more Computational assignment of function to proteins with no known homologs is still an unsolved problem. We have created a novel, function-based approach to protein annotation and discovery called D-SPACE (Deep Semantic Protein Annotation Classification and Exploration), comprised of a multi-task, multi-label deep neural network trained on over 70 million proteins. Distinct from homology and motif-based methods, D-SPACE encodes proteins in high-dimensional representations (embeddings), allowing the accurate assignment of over 180,000 labels for 13 distinct tasks. The embedding representation enables fast searches for functionally related proteins, including homologs undetectable by traditional approaches. D-SPACE annotates all 109 million proteins in UniProt in under 35 hours on a single computer and searches the entirety of these in seconds. D-SPACE further quantifies the relative functional effect of mutations, facilitating rapid in-silico mutagenesis for protein engineering applications. D-SPACE incorporates protein annotation, search, and other exploratory efforts into a single cohesive model. We have recently extended this work from protein to DNA, enabling assignment of function to whole genomes and metagenomic contigs in seconds. Conserved genomic motifs as well as the functional impact of mutations in coding as well as non-coding genomic regions can be predicted directly from raw DNA sequence without the use of traditional comparative genomics approaches for motif detection, such as multiple sequence alignments, PSSMs, and profile HMMs.
    Close abstract

    Special Guest Seminar with Dr. Shai Carmi

    Date:
    16
    Wednesday
    January
    2019
    Lecture / Seminar
    Time: 11:30
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. Shai Carmi
    Organizer: Department of Molecular Genetics
    Abstract: In this talk, I will review recent work by myself and others on Jewish populatio ... Read more In this talk, I will review recent work by myself and others on Jewish population and medical genetics, focusing on Ashkenazi Jews (AJ). I will describe the mixture events of AJ in Europe, the founder event they have experienced in the late Middle Ages, and their connections to ancient populations of the Levant. I will then describe large-scale genomic databases that we have recently generated for AJ, and the opportunities they open in medical genetics given the unique AJ demographic history. I will describe a few medical genetics projects including carrier screening, genome-wide association studies of microbiome composition and other traits, and preimplantation genetic diagnosis.
    Close abstract

    Exploring the informational properties of genomic sequences

    Date:
    15
    Tuesday
    January
    2019
    Lecture / Seminar
    Time: 10:15-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Yuval Bussi
    Organizer: Department of Biomolecular Sciences
    Abstract: Information theory, originally developed for mathematical analysis of communicat ... Read more Information theory, originally developed for mathematical analysis of communication systems, has been applied to molecular biology for decades. In this context, the concept of entropy is utilized to measure the compositional complexity of genomes, wherein all of the hereditary information necessary to build and maintain an organism is stored. The recent explosion in the availability of genomic data, coupled with the considerable improvements in computational processing power, presents opportunities for investigating genomes far beyond the scope and depth previously achievable. In this work, we propose to characterize the informational properties of ~5000 genomes by assessing the statistical abundance and sequence space coverage of fixed-length substrings (known as ‘kmers’). Additionally, we aim to identify unique kmers that can be used as genome-specific markers for taxonomic profiling purposes.
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    Genetic tricks in a green playground - Genome-wide discovery of essential pathways in the plant superkingdom

    Date:
    26
    Wednesday
    December
    2018
    Lecture / Seminar
    Time: 11:45
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Michal Breker
    Organizer: Department of Plant and Environmental Sciences
    Details: Host: Prof. Yuval Eshed

    Genome wide-data from Prehistoric Anatolians shed light on the origins of the first farmers of Anatolia

    Date:
    20
    Thursday
    December
    2018
    Lecture / Seminar
    Time: 13:00
    Location: Helen and Martin Kimmel Center for Archaeological Science
    Lecturer: Dr Michal Feldman

    one2many2018 - A System View of Biology

    Date:
    09
    Sunday
    December
    2018
    -
    10
    Monday
    December
    2018
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre
    Organizer: Azrieli Institute for Systems Biology

    Developmental Club Series 2018-2019, special guest seminar

    Date:
    05
    Wednesday
    December
    2018
    Lecture / Seminar
    Time: 10:00
    Title: “Lineage segregation of three germ layers in post-implantation mouse embryos”
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Naihe Jing
    Organizer: Department of Molecular Genetics
    Abstract: During postimplantation development of the mouse embryo, descendants of the inne ... Read more During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naïve pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpins the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized in situ gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo.
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    A new way cancer cells cope with proteotoxic stress

    Date:
    28
    Wednesday
    November
    2018
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Peter Tsvetkov
    Organizer: Department of Biomolecular Sciences
    Abstract: Maintaining protein homeostasis is crucial for cell survival and coping with env ... Read more Maintaining protein homeostasis is crucial for cell survival and coping with environmental stressors. The mechanisms that cells deploy to cope with increased proteotoxic burden are still poorly understood. In this work, using genetic screens, cancer genomics analysis and biochemical validations we determine a new way cancer cells can cope with increased proteotoxic burden. This mechanism involves two complementary cellular adaptations that are sufficient to promote cell survival when proteasome function is suppressed. These cellular adaptations are naturally occurring in many cancer types and evolutionary conserved and entail a vulnerability that can be targeted with a newly identified mitochondrial pathway inhibitor for which the unique mechanism of action we describe.
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    Spotlight on Science

    Date:
    21
    Wednesday
    November
    2018
    Lecture / Seminar
    Time: 12:00
    Title: Single-Cell Genomics Reveals a Novel Regulatory Role of the Immune System in Obesity
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr. Diego Jaitin

    Nuclear Genome Nanostructure Imaging at Single Molecule Resolution

    Date:
    20
    Tuesday
    November
    2018
    Lecture / Seminar
    Time: 10:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Christoph Cremer
    Organizer: Department of Molecular Genetics
    Abstract: Super-resolution fluorescence microscopy allows quantitative studies of nuclear ... Read more Super-resolution fluorescence microscopy allows quantitative studies of nuclear genome organization on the nanoscale1. Here we report on results obtained by single molecule localization microscopy (SMLM). SMLM has made possible to explore chromatin nanostructure down to the imaging of single histones, of short oligosequences, or single DNA sites; presently, an intranuclear optical resolution down to the 5 nm range has been achieved. Applying a novel SMLM technique (fBALM)2, the DNA distribution across entire nuclei at nanoscale resolution was quantitatively determined, localizing in individual nuclear optical sections up to ~4 million individual DNA bound single fluorophore molecule positions, corresponding to about one position per nucleosome. Intensity profile analyses of the intranuclear DNA distributions indicated sharp transitions between high-density domains and low-density compartments, with differences up to almost two orders of magnitude; compacted regions had a minimum diameter down to ca. 50 nm diameter. In contrast to these results, conventional resolution imaging of the same nuclear sites indicated only small differences in the compaction of different regions, combined with very smooth density transitions. Taken together, the quantitative compaction estimates support models of a nuclear organization based on highly compartmentalized chromatin nanostructures3.
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    Serotonin and Autism Therapeutics: Insights from Human Mutations and Mouse Models

    Date:
    14
    Sunday
    October
    2018
    Lecture / Seminar
    Time: 10:30
    Location: Gerhard M.J. Schmidt Lecture Hall
    Lecturer: Dr. Randy Blakely
    Organizer: Department of Neurobiology
    Details: Host: Prof. Menahem Segal Menahem.segal@weizmann.ac.il tel: 2553 For assistanc ... Read more Host: Prof. Menahem Segal Menahem.segal@weizmann.ac.il tel: 2553 For assistance with accessibility issues, please contact naomi.moses@weizmann.ac.il
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    Abstract: Signs of serotonergic dysfunction appeared more than 50 years ago with findings ... Read more Signs of serotonergic dysfunction appeared more than 50 years ago with findings of hyperserotonemia in a subset of subjects with ASD, work replicated in multiple studies across the years, and accompanied by supportive data in human and animal studies. Owing to the early elaboration of serotonergic neurons in the mammalian CNS, and genetic evidence for male-specific linkage to ASD overlying the SERT gene locus, we screened multiplex ASD families for evidence of penetrant coding variants in the serotonin transporter, SERT, reporting these in 2005 and evidence that the most common of these, SERT Ala56, demonstrates alterations in the three core domains of the disorder when introduced into the mouse genome, in 2012. More recently, we have identified signaling pathways that lead to aberrant hyperactivity of SERT Ala56 in vitro and in vivo, leading to a novel therapeutic approach, involving manipulation of p38 MAPK. The talk will review the history of the work and next steps in understanding the serotonergic contribution to ASD features arising from other mutations and environmental perturbations.
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    5th round of Systems Biology Innovative Student-Awards Series

    Date:
    16
    Sunday
    September
    2018
    Conference
    Time: 09:30-14:00
    Location: Botnar auditorium, Belfer Bldg.
    Organizer: Azrieli Institute for Systems Biology

    Interphase Human Chromosome Exhibits Out of Equilibrium Glassy Dynamics

    Date:
    15
    Sunday
    July
    2018
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Dave Thirumalai
    Organizer: Department of Materials and Interfaces
    Abstract: Fingerprints of the three-dimensional organization of genomes have emerged usi ... Read more Fingerprints of the three-dimensional organization of genomes have emerged using recent advances, but genome dynamics is poorly understood. Here, we create the Chromosome Copolymer Model (CCM) by representing chromosomes as a copolymer with two epigenetic loci types corresponding to euchromatin and heterochromatin. We establish quantitatively that the chromosomes 5 and 10 topology from our model and from experiment are in good agreement. Chromatin exhibits glassy dynamics with coherent motion on micron scale. The broad distribution of the diffusion exponents, which quantitatively agrees with experiments, is suggestive of highly heterogeneous dynamics, reflected in the cell- to-cell variations in the contact maps. Chromosome organization is hierarchical, involving the formation of chromosome droplets, followed by coalescence, reminiscent of Ostwald ripening.
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    Single-molecule Visualization of Long-range Epigenetic Regulation

    Date:
    12
    Thursday
    July
    2018
    Lecture / Seminar
    Time: 14:00-15:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Prof. Yuval Ebenstein
    Organizer: Department of Biological Regulation
    Abstract: Epigenetic regulation by DNA methylation is well established in the context of t ... Read more Epigenetic regulation by DNA methylation is well established in the context of the classical Promoter:Coding box. Recent genome-wide association studies (GWAS) indicate that the methylation state of distant enhancers play a critical role in gene expression. In cancer, such distant epigenetic aberrations can have significant effects on carcinogenesis. In order to uncover these long-range interactions on the single-cell level, I present an epigenome-mapping technology based on fluorescent tagging of epigenetic marks on long individual DNA molecules. Information is read as a fluorescent genetic/epigenetic barcode that provides genome-scale profiles with extremely long reads. I discuss our progress towards simultaneous recording of methylation and transcription information from the same molecules with the aim of discovering and characterizing epigenetic gene-regulation at a distance.
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    PHYSICISTS WORKING ON CANCER

    Date:
    01
    Sunday
    July
    2018
    -
    12
    Thursday
    July
    2018
    Conference
    Time: 08:00
    Location: Nella and Leon Benoziyo Physics Library
    Organizer: Faculty of Physics

    The first protein: short, simple and functional

    Date:
    26
    Tuesday
    June
    2018
    Lecture / Seminar
    Time: 10:00-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Dragana Despotovic
    Organizer: Department of Biomolecular Sciences
    Abstract: Researchers hypothesized that the first protein domains arose by joining and swa ... Read more Researchers hypothesized that the first protein domains arose by joining and swapping short lengths of proteins called peptides that had emerged before there were living cells on earth – a time that is often called the “RNA world”. However, the properties of the first proteins remain poorly understood, in part because of the difficulty in studying events that happened billions of years ago. Combining bioinformatics, structural biology and experimental approaches we developed a model system for the first proteins in order to understand the functional and structural transitions that drive protein emergence and evolution.
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    New era in cryo electron microscopy reflected in studies of a bacteriophage phage at near atomic resolution

    Date:
    21
    Thursday
    June
    2018
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Helen and Milton A. Kimmelman Building
    Lecturer: Prof. Elena Orlova
    Organizer: Department of Structural Biology
    Abstract: During the last decade electron microscopy become a powerful tool in structural ... Read more During the last decade electron microscopy become a powerful tool in structural studies of large biological complexes. Cryo electron microscopy enabled us to reveal molecular dynamics of the complexes by analysis of samples in solution. This was made possible by long-standing efforts in sample preparations (cryo-EM imaging), in development of hardware, automation in data collection, methods in image analysis and, eventually, interpretation of results. Here I would like to share my experience in using these approaches in analysis of structural organisation of bacteriophages exemplified by the SPP1 phage. It is important to highlight critical steps in obtaining near-atomic resolution structures of the biocomplexes. We have obtained high resolution structures of main components of the phage such as a capsid and its nano-motor engaged into packaging of genome and its release.
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    FROM CANCER GENOMICS TO IMMUNOTHERAPY

    Date:
    19
    Tuesday
    June
    2018
    Conference
    Time: 08:00-14:00
    Location: Dolfi and Lola Ebner Auditorium

    CRISPRing the Dark Matter of the Genome

    Date:
    10
    Sunday
    June
    2018
    Lecture / Seminar
    Time: 14:00-15:00
    Title: A Genome Wide Approach to Study Functional Non-Coding Genes
    Location: Max and Lillian Candiotty Building
    Lecturer: Dr. Assaf Bester
    Organizer: Department of Biological Regulation

    The multi-scale structure of chromatin in the nucleus

    Date:
    03
    Sunday
    June
    2018
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Perlman Chemical Sciences Building
    Lecturer: Prof. Yuval Garini
    Organizer: Department of Materials and Interfaces
    Abstract: The DNA in a human cell which is ~3 meters long is packed in a tiny nucleus of ... Read more The DNA in a human cell which is ~3 meters long is packed in a tiny nucleus of ~10 μm radius. The DNA is surrounded by thousands of proteins, and it is highly dynamic while taking part in the process of protein expression and cell division. Nevertheless, it must stay organized to prevent chromosome entanglement. Studying this nanometer – micrometer scale structure is difficult, as it falls short of the optical resolution, while electron microscopy is limited due to the need to fixate the sample. We therefore adopted various methods for studying the organization of the genome in the nucleus, including live-cell imaging, time-resolved spectroscopy and single molecule methods such as AFM. It allowed us to identify that a protein, lamin A, forms chromatin loops thereby restricting the chromatin dynamics in the whole nucleus volume. Based on the results, we conclude that the organization of the DNA in the nucleus is based on a “DNA matrix”, a structure that we describe here for the first time. The experimental methods we use necessitate the use of biophysical modeling based on Smoluchowski equation, modified diffusion equations and polymer physics. I will describe the problem, the methods we use, the results and the conclusions as described above.
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    Live demonstration of Redcap – a new system for working with secure clinical online questionnaires

    Date:
    29
    Tuesday
    May
    2018
    Lecture / Seminar
    Time: 11:00-12:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Dr. Ron Rotkopf
    Organizer: Department of Life Sciences Core Facilities
    Abstract: Redcap – a new system for working with clinical online questionnaires Hello a ... Read more Redcap – a new system for working with clinical online questionnaires Hello all, We would like to bring to your attention that we have recently installed REDCap at the Weizmann Institute. REDCap is a secure web application for building and managing online surveys and databases, used by thousands of academic institutions and hospitals around the world. Using REDCap, you can easily create online questionnaires or surveys, and collect responses from your collaborators anywhere, or even from survey participants who are not logged in. This is particularly useful for clinical projects, but can be used for any project that requires collecting data from multiple collaborators. The REDCap interface is user-friendly, and no coding experience is needed to start a new project and create your own questionnaires. After the data is collected, it can be exported easily to Excel or any common statistical packages (e.g. SPSS, SAS, Stata, R). You can read more about REDCap at https://www.project-redcap.org/ The Weizmann installation of REDCap is at https://redcap.weizmann.ac.il/ If you just want to check it out without registering, a demo version is available (only from within the institute) at http://demohealth.weizmann.ac.il/. Do not enter any important/confidential data in the demo version! If you have any questions, or would like to register to REDCap, please contact Ron Rotkopf (ron.rotkopf@weizmann.ac.il) at the LSCF Bioinformatics unit. The demonstration will be held at Candiotty auditorium on Tuesday, May 29th, at 11:00. Registration is not required, but if you plan to come, please take a minute to answer this anonymous survey: http://j.mp/2rtn7a6 The survey was created in Redcap, and we will use it as an example of creating a questionnaire and collecting data.
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    UCSC Genome Browser: New features and hidden features Q & A session

    Date:
    17
    Thursday
    May
    2018
    Lecture / Seminar
    Time: 10:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Kate Rosenbloom
    Organizer: Department of Life Sciences Core Facilities
    Details: Kate Rosenbloom has been a UCSC browser engineer since 2003, working to integrat ... Read more Kate Rosenbloom has been a UCSC browser engineer since 2003, working to integrate scientific data sets and develop visualizations in the areas of comparative genomics, gene regulation, and gene expression, as well as contributing to efforts to improve user interface and overall usability of the site. She served for 5 years as technical project manager for the ENCODE Data Coordination center. Her recent work has focused on creating genome browser resources for the Genotype-Tissue Expression (GTEx) project. Kate will be available for meetings/consultations after the talk, if you are interested please contact Shifra (shifra.ben-dor@weizmann.ac.il)
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    Abstract: For the past several years, a main focus of the UCSC browser group has been deve ... Read more For the past several years, a main focus of the UCSC browser group has been developing data organization and display features in response to the massive expansion of data quantity and variety in the genomics field. There will be a short talk covering recent features motivated by these issues, highlighting two of the newest - the Track Collection Builder tool, and the new pairwise interaction ('interact') track type. This will be followed by a quick tour through some not-so-obvious browser features such as exon-only display, isoform hiding, highlights, and track reordering. There will be ample time for questions, reflections and suggestions about browser features and data.
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    Atlases of structure-function relationships in small motifs: the limits of modularity

    Date:
    08
    Tuesday
    May
    2018
    Lecture / Seminar
    Time: 14:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Dr. James Sharpe
    Organizer: Azrieli Institute for Systems Biology
    Abstract: Abstract: I will discuss our work on visualizing “topology atlases” which a ... Read more Abstract: I will discuss our work on visualizing “topology atlases” which act as a map of possible circuit designs for small 3-node regulatory motifs. These can help in understanding the relationship between a circuit's structure and its function, but how is this relationship affected if the circuit must perform multiple distinct functions within the same organism? In particular, to what extent do multi‐functional circuits contain modules which reflect the different functions? We computationally surveyed a range of bi‐functional circuits which show no simple structural modularity: They can switch between two qualitatively distinct functions, while both functions depend on all genes of the circuit. Our analysis revealed two distinct classes: hybrid circuits which overlay two simpler mono‐functional sub‐circuits within their circuitry, and emergent circuits, which do not. In this second class, the bi‐functionality emerges from more complex designs which are not fully decomposable into distinct modules and are consequently less intuitive to predict or understand. These non‐intuitive emergent circuits are just as robust as their hybrid counterparts, and we therefore suggest that the common bias toward studying modular systems may hinder our understanding of real biological circuits. Relevant papers: 1. A spectrum of modularity in multi-functional gene circuits. Jiménez A, Cotterell J, Munteanu A, Sharpe J. (2017) Mol Syst Biol 13(4):925. doi: 10.15252/msb.20167347 http://msb.embopress.org/content/13/4/925 2. An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients. Cotterell J, Sharpe J. (2010) Mol Syst Biol 6:425. doi: 10.1038/msb.2010.74 http://msb.embopress.org/content/6/1/425 Bio: James Sharpe was originally captivated by computer programming, but upon learning about the digital nature of the genetic code, chose to study Biology for his undergraduate degree at Oxford University (1988-1991). He then did his PhD on the genetic control of embryo development at NIMR, London (1992-1997) and in parallel started writing computer simulations of multicellular development. During his post-doc in Edinburgh, he began modelling the dynamics of limb development, and also invented a new optical imaging technology called Optical Projection Tomography (OPT), which is dedicated to imaging specimens too large for microscopy - tissues and organs. In 2006 he moved to Barcelona, becoming a senior group leader at the Centre for Genomic Regulation, and focusing on a systems biology approach to modelling limb development – combining experimentation with computer modelling. In this way the group demonstrated that the signalling proteins which pattern the fingers during embryogenesis, act as a Turing reaction-diffusion system. In 2011 he became the coordinator of the Systems Biology Program, and in 2017 was recruited to EMBL as Head of the new Barcelona outstation on Tissue Biology and Disease Modelling.
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    G-INCPM Special Seminar - Dr. Daniel Liber, Business Development Manager, Automation, Takara Bio Europe - "SMARTer ICELL8: The Open Platform for Single-Cell Genomics"

    Date:
    01
    Tuesday
    May
    2018
    Lecture / Seminar
    Time: 14:30-15:30
    Location: Gerhard M.J. Schmidt Lecture Hall
    Organizer: Department of Biomolecular Sciences
    Abstract: Single-cell genomics allows to understand cellular heterogeneity at an unprecede ... Read more Single-cell genomics allows to understand cellular heterogeneity at an unprecedented resolution. The SMARTer ICELL8 Single-Cell System gives more control in the experimental design, more confidence in the data and unique workflow flexibilities while reducing the experimental costs. The ICELL8 multi-nanowell chip can isolate hundreds of cells from multiple samples at once, from the very small, like nuclei from frozen tissues, to the very large, like primary cardiomyocytes and spheroids. The SMARTer ICELL8 has been validated for multiple applications, including gene expression analysis, full-length transcriptomics, T-Cell Receptor sequencing and ATAC-seq, which have been developed by Takara Bio’s R&D or ICELL8 users.
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    Computational design of new and improved enzymes

    Date:
    24
    Tuesday
    April
    2018
    Lecture / Seminar
    Time: 10:00-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Dr. Olga Khersonsky
    Organizer: Department of Biomolecular Sciences
    Abstract: Enzymes are potent biocatalysts that are widely used in biotechnology, but their ... Read more Enzymes are potent biocatalysts that are widely used in biotechnology, but their function often has to be altered or optimized. Enzyme evolution and engineering are constrained by epistatic relationships among the positions that make up an active site. A further constraint is due to stability-function tradeoffs, whereby accumulated mutations reduce protein stability and functional expression. To address these problems, we have developed several new methods that use bioinformatics and Rosetta atomistic simulations to stabilize enzymes, improve their activity and make new enzymes by modular backbone assembly.
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    Genome Evolution 2018

    Date:
    16
    Monday
    April
    2018
    Conference
    Time: 08:00-16:15
    Location: David Lopatie Conference Centre

    EMBO workshop on Noncoding RNAs in Development and Cell Differentiation

    Date:
    08
    Sunday
    April
    2018
    -
    11
    Wednesday
    April
    2018
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre

    Guest Seminar

    Date:
    22
    Thursday
    March
    2018
    Lecture / Seminar
    Time: 12:30-14:00
    Title: Genome Decoding: Learning and Following Sequence Patterns
    Location: Elaine and Bram Goldsmith Building for Mathematics and Computer Sciences
    Lecturer: Mark Borodovsky
    Organizer: Faculty of Mathematics and Computer Science,Department of Computer Science and Applied Mathematics,Department of Mathematics
    Abstract: Genome-wide forces of mutation and selection create local and global sequence pa ... Read more Genome-wide forces of mutation and selection create local and global sequence patterns that carry information on functional role of genomic DNA. I will describe algorithmic approaches to genome analysis that decode sequence patterns and identify features of structural gene organization and gene expression (e.g. leaderless transcription). The algorithms make unsupervised inference of the structure of underlying graphical model and its parameters. The subsequently developed software tools were, among other applications, used at NCBI (Bethesda, MD) to annotate and re-annotate 2,500 fungal genomes and 130,000 prokaryotic genomes. Yet another algorithm was employed by DOE JGI (Walnut Creek, CA) to annotate the largest collection of metagenomes. Speaker’s short Bio Mark Borodovsky, PhD, a Regents' Professor at the Joint Georgia Tech and Emory University Department of Biomedical Engineering and the School of Computational Science and Engineering. Since 1990 when he arrived to Atlanta from Moscow, Dr Borodovsky had also joint faculty appointments at the School of Biology and the School of Mathematics. Dr. Borodovsky is a Founder of the Georgia Tech Bioinformatics graduate program.
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    Synthetic Biology Applications for a Livable Future

    Date:
    18
    Sunday
    March
    2018
    Conference
    Time: 08:30-18:30

    Special Seminar: "Single molecule, real-time (SMRT) sequencing - advanced genomics with long read sequencing"

    Date:
    15
    Thursday
    March
    2018
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Max and Lillian Candiotty Building
    Lecturer: Dr. Swati Ranade
    Organizer: Department of Life Sciences Core Facilities

    G-INCPM-Special Seminar - Dr. Shalev Itzkovitz, Dept. of Molecular Cell Biology, Weizmann - "Spatial Transcriptomics of Mammalian Tissues"

    Date:
    14
    Wednesday
    March
    2018
    Lecture / Seminar
    Time: 11:00-12:30
    Location: Nancy and Stephen Grand Israel National Center for Personalized Medicine
    Lecturer: Dr. Shalev Itzkovitz
    Organizer: Department of Biomolecular Sciences
    Abstract: Mammalian tissues are often composed of repeating anatomical units that are pola ... Read more Mammalian tissues are often composed of repeating anatomical units that are polarised by morphogens or directional blood flow. Thus single cells at different tissue coordinates operate in distinct microenvironment. This spatial diversity enables optimisation of tissue function by allocating different tasks to cells that reside in distinct tissue locations. To explore this spatial division of labor on a genome-wide scale we are combining single cell transcriptomics with in-situ measurements in intact tissues to enable inference of the sequenced cells’ original tissue locations. This approach enables reconstructing global spatial gene expression atlases. I will demonstrate these approaches on two stereotypical and highly structured organs - the liver and the intestinal epithelium.
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    Mini-Symposium on Genome, Transcriptome and Proteome

    Date:
    11
    Sunday
    March
    2018
    Lecture / Seminar
    Time: 14:30-16:30
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Organizer: Department of Molecular Genetics
    Details: 14:30 Dr. Grzegorz Kudla, U. Edinburgh RNA Genotype-Phenotype Mapping 15:20 ... Read more 14:30 Dr. Grzegorz Kudla, U. Edinburgh RNA Genotype-Phenotype Mapping 15:20 Prof. Yoni Savir, Technion Understanding combinatorial signal processing and its failure due to age 15:50 Prof. Yitzhak Pilpel, Weizmann Institute of Science Errors and Edits in the Central Dogma Organizer: Prof. Yitzhak Pilpel, Tel: 6058
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    Optimizations and trade-offs in cellular growth and survial

    Date:
    25
    Sunday
    February
    2018
    -
    27
    Tuesday
    February
    2018
    Conference
    Time: 08:00
    Location: David Lopatie Conference Centre
    Organizer: Azrieli Institute for Systems Biology

    Cell-Weizmann Institute of Science Symposium: Next Gen Immunology

    Date:
    11
    Sunday
    February
    2018
    -
    14
    Wednesday
    February
    2018
    Conference
    Time: 08:00
    Location: Michael and Anna Wix Auditorium

    Noncoding RNA in Health and Disease

    Date:
    30
    Tuesday
    January
    2018
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Nikolaus Rajewsky
    Organizer: Azrieli Institute for Systems Biology

    Functions and regulation of 3D genome organisation in development and disease

    Date:
    23
    Tuesday
    January
    2018
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Francois Spitz
    Organizer: Azrieli Institute for Systems Biology
    Abstract: The complex hierarchy of three-dimensional patterns that characterize the 3D fol ... Read more The complex hierarchy of three-dimensional patterns that characterize the 3D folding of mammalian chromosomes appears as an important element in controlling gene expression. At the megabase scale, chromosomes are partitioned into domains that define two main compartments, corresponding to transcriptionally active and inactive regions, respectively. Each compartment domain is itself composed of distinct domains characterized by increased self-interactions called topological domains (TADs). Recent high-resolution Hi-C approaches revealed a finer-scale organisation of the genome in smaller “contact domains”, often associated with loops linking specific points. At these different scales, the spatial organisation of the genome shows tight correlation with its chromatin structure and its transcriptional activity. However, while steady progress is being made in describing the 3D folding of the genome at increased resolution, the mechanisms that determine this folding, its dynamic properties and the functional implications of these emerging features are still poorly understood. We use advanced genome tagging and engineering strategies, as well as targeted inactivation of factors involved in chromosomal folding to unravel the elements and mechanisms that drive the folding of large loci in specific yet dynamic conformations and their influence on gene expression. Our recent results show that the complex patterns of vertebrate HiC maps result from the superimposition of two distinct mechanisms: 1) a cohesin-independent mechanism which brings together regions of similar chromatin states 2) a cohesin-dependent folding that associate different small compartments into TADs. Within TADS, we show as well that enhancers are not acting in a homogeneous manner, but that their influence is distributed in complex patterns, partially guided by the underlying structure. I will discuss the different implications of these findings for our views of genome organisation.
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    Frontiers in Systems Biology: Prof. Anshule Kundaje

    Date:
    16
    Tuesday
    January
    2018
    Lecture / Seminar
    Time: 10:00-11:00
    Title: Machine learning approaches to denoise, integrate, impute and decode functional genomic data
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Anshule Kundaje
    Organizer: Department of Molecular Genetics

    Unique cellulosome system of (Pseudo)Bacteroides cellulosolvens unravels inimitable ways of biomass degradation.

    Date:
    16
    Tuesday
    January
    2018
    Lecture / Seminar
    Time: 10:00-10:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Olga Zhivin-Nissan
    Organizer: Department of Biomolecular Sciences
    Abstract: Current global prosperity is based on fossil fuels that provides energy required ... Read more Current global prosperity is based on fossil fuels that provides energy required for our luxuriant way of life but are unsustainable. Biofuels, produced mainly from cellulosic plant-derived biomass, are the current practical alternative. The cellulolytic bacterium (Pseudo)Bacteroides cellulosolvens is a good candidate for biomass degradation towards improved biofuels production. Recently, we sequenced the B. cellulosolvens genome, and discovered that this bacterium produces the most intricate multi-enzyme cellulosome system known. Subsequent comprehensive bioinformatic analysis revealed an unprecedented number of cellulosome-related components, thus providing novel insight into the architecture, composition and function of the most intricate and extensive cellulosomal system known today.
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    Single cell analysis of rare events in cancer

    Date:
    09
    Tuesday
    January
    2018
    Lecture / Seminar
    Time: 10:00-11:00
    Location: Arthur and Rochelle Belfer Building for Biomedical Research
    Lecturer: Prof. Arjun Raj
    Organizer: Azrieli Institute for Systems Biology

    From Statistical Mechanics to Cancer Genomics

    Date:
    16
    Tuesday
    May
    2017
    -
    17
    Wednesday
    May
    2017
    Retreat
    Time: 09:00 - 18:00
    Location: Weissman Auditorium, Physics Building
    Organizer: Department of Physics of Complex Systems

    System Biology Symposium

    Date:
    15
    Sunday
    January
    2017
    Retreat
    Time: 00:00
    Location: Ein-Gedi
    Organizer: Department of Computer Science and Applied Mathematics