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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

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    Computational protein design: basic research and applications

    Date:
    22
    Monday
    March
    2021
    Colloquium
    Time: 11:00-12:00
    Location: https://weizmann.zoom.us/j/98063488104?pwd=N3VqTC9sU1A4RHVDZ1dhOGVxbU1iUT09
    Lecturer: Prof. Sarel Fleishman
    Organizer: Faculty of Chemistry
    Abstract: Until very recently, the accuracy of protein-design calculations was considered ... Read more Until very recently, the accuracy of protein-design calculations was considered too low to enable the design of large proteins of complex fold. As a result, enzyme and binder optimization has relied on random or semi-rational mutagenesis and high-throughput screening. Our lab is developing a unique approach that combines structural bioinformatics analyses with atomistic design calculations to dramatically increase the accuracy of design calculations. Using this strategy, we have developed several general and completely automated methods for optimizing protein stability and activity. I will briefly discuss the fundamentals of this strategy and show case studies of large and complex proteins that we and our collaborators have optimized. Our lab’s long-term and still-unmet research goal is to enable the completely automated design of any biomolecular activity, and I will focus on our current research directions including the design of new enzymes and binders.
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    MicroEco 2020

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

    Understanding the distinctive neuronal epigenome

    Date:
    01
    Tuesday
    December
    2020
    Lecture / Seminar
    Time: 14:00
    Lecturer: Prof. Harrison Gabel
    Organizer: Department of Neurobiology
    Details: Zoom link to join: https://weizmann.zoom.us/j/96608033618?pwd=SEdJUkR2ZzRBZ3laUU ... Read more Zoom link to join: https://weizmann.zoom.us/j/96608033618?pwd=SEdJUkR2ZzRBZ3laUUdGbWR1VFJTdz09 Meeting ID: 966 0803 3618 Password: 564068 Host: Dr. Rita Schmidt rita.schmidt@weizmann.ac.il tel: 9070
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    Abstract: Recent discoveries indicate that the genomes of mammalian neurons are enriched f ... Read more Recent discoveries indicate that the genomes of mammalian neurons are enriched for unique epigenetic modifications, including exceptionally high levels of non-CG DNA methylation. In my seminar, I will present our studies defining how a distinctive DNA methylation landscape is established in neurons and exploring how this methylation is read out to control critical gene expression programs. I will discuss the role of gene expression and genome architecture in shaping genomic profiles of non-CG methylation and highlight emerging mechanistic insights into how non-CG methylation and the Rett syndrome protein, MeCP2, work together to control transcription. Finally, I will outline growing evidence that disruption of this regulatory pathway contributes to neurodevelopmental disorders. Zoom link to join: https://weizmann.zoom.us/j/96608033618?pwd=SEdJUkR2ZzRBZ3laUUdGbWR1VFJTdz09 Meeting ID: 966 0803 3618 Password: 564068 Host: Dr. Rita Schmidt rita.schmidt@weizmann.ac.il tel: 9070
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    Reversing personalized medicine

    Date:
    10
    Thursday
    September
    2020
    Lecture / Seminar
    Time: 13:30-14:30
    Location: Nella and Leon Benoziyo Building for Biological Sciences
    Lecturer: Prof. Gal Markel
    Organizer: Department of Biological Regulation
    Details: the link for the lecture's zoom room https://weizmann.zoom.us/j/5065402023?pwd= ... Read more the link for the lecture's zoom room https://weizmann.zoom.us/j/5065402023?pwd=a3Z6KzRCU0xJaUFoM2Y5emZwZm1oZz09
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    Abstract: Personalized medicine in oncology is focused on fitting drugs to the appropriat ... Read more Personalized medicine in oncology is focused on fitting drugs to the appropriate patients, mainly by identifying unique mutations in tumor genomics and development of highly selective drugs. The main challenge is that the relevant populations grow smaller, while development costs are constant, leading to significant reduction in effective drug development. The immune system provides personalized anti cancer response, and immune checkpoint inhibitors enable decent responses over a wide array of tumors. The outstanding challenge is that efficacy is observed in less than a third of the patients. Here we explore strategies to alter the patient in a way that will enable standard of care immunotherapy to exert its full potential, i.e. fitting the patients to the existing immunotherapeutic medications.
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    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
    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.
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    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.
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    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.
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    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.
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    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 Chemical and 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.
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    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.
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    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.
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    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.
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    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.
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    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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    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

    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