Weizmann-Harvard Meeting on SYSTEMS BIOLOGY Ebner Auditorium, Weizmann Institute of Science | March, 13-17, 2011

Total Page:16

File Type:pdf, Size:1020Kb

Weizmann-Harvard Meeting on SYSTEMS BIOLOGY Ebner Auditorium, Weizmann Institute of Science | March, 13-17, 2011 Weizmann-Harvard meeting on SYSTEMS BIOLOGY Ebner Auditorium, Weizmann Institute of Science | March, 13-17, 2011 Systems Biology is a new multidisciplinary field that studies the behavior of systems of biological components. The components can be molecules, cells, tissues, organisms or even species; we aim to understand how interactions among the parts lead to complex behaviors. The Weizmann and Harvard University each have world-leading programs in this young field and have already discovered commonalities of interest through individual collaborations and visits. This conference will be the first opportunity for the two groups to work together on a large scale to build new connections and accelerate progress. The meeting will feature oral presentations along with extensive opportunities for informal exchange of ideas, discussion of open questions and challenges as well as social interactions. Our goal is to build on existing connections to develop a new level of collegiality and shared purpose, so that Boston/Cambridge and Rehovot can together address some of the key challenges in biology and medicine. Weizmann Institute of Science Harvard University USA Speakers Speakers Uri Alon Ido Amit Naama Barkai Angela DePace Organizing Committee Eytan Domany Allan Drummond Yitzhak Pilpel (WIS) Nir Friedman Rachel Dutton Rebecca Ward (Harvard) Jacob Hanna John Higgins Doron Lancet Suckjoon Jun Conference Coordinator Ron Milo Marc Kirschner Yitzhak Pilpel Roy Kishony Judith Gan (WIS) Elad Schneidman Galit Lahav [email protected] Maya Schuldiner Debora Marks Sponsors Eran Segal Vamsi Mootha Ehud Shapiro Dan Needleman Weizmann Institute of Science Yoav Soen Johan Paulsson The Kahn Family Research Rotem Sorek Pamela Silver Center for Systems Biology of Joel Stavans Michael Springer the Human Cell Amos Tanay Peter Turnbaugh The Crown Human Genome Center Dan Tawfik Peng Yin Yosef Yarden Arthur and Rochelle Belfer Institute of Mathematics and Computer Science The Y. Leon Benoziyo Institute For more information, please visit: for Molecular Medicine The Clore Center for www.weizmann.ac.il/conferences/SystemsBiology Biological Physics.
Recommended publications
  • A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast
    A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast By Jessica M. Vera B.S. University of Wisconsin-Madison, 2007 A thesis submitted to the Faculty of the Graduate School in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Molecular, Cellular, and Developmental Biology 2015 This thesis entitled: A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast written by Jessica M. Vera has been approved for the Department of Molecular, Cellular, and Developmental Biology Tom Blumenthal Robin Dowell Date The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline iii Vera, Jessica M. (Ph.D., Molecular, Cellular and Developmental Biology) A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast Thesis Directed by Robin Dowell Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. I sought to ascertain the extent of conserved CUT expression across a variety of Saccharomyces yeast strains to further understand and characterize the nature of CUT expression. To this end I designed a Hidden Markov Model (HMM) to analyze strand-specific RNA sequencing data from nuclear exosome rrp6Δ mutants to identify and compare CUTs in four different yeast strains: S288c, Σ1278b, JAY291 (S.cerevisiae) and N17 (S.paradoxus).
    [Show full text]
  • EMBO Encounters Issue43.Pdf
    WINTER 2019/2020 ISSUE 43 Nine group leaders selected Meet the first EMBO Global Investigators PAGE 6 Accelerating scientific publishing EMBO publishing costs Review Commons Making our journals’ platform announced finances public PAGE 3 PAGES 10 – 11 Welcome, Young Investigators! Contract replaces stipend Marking ten years 27 group leaders join the programme EMBO Postdoctoral Fellowships EMBO Molecular Medicine receive an update celebrates anniversary PAGES 4 – 5 PAGE 7 PAGE 13 www.embo.org TABLE OF CONTENTS EMBO NEWS EMBO news Review Commons: accelerating publishing Page 3 EMBO Molecular Medicine turns ten © Marietta Schupp, EMBL Photolab Marietta Schupp, © Page 13 Editorial MBO was founded by scientists for Introducing 27 new Young Investigators scientists. This philosophy remains at Pages 4-5 Ethe heart of our organization until today. EMBO Members are vital in the running of our Meet the first EMBO Global programmes and activities: they screen appli- Accelerating scientific publishing 17 journals on board Investigators cations, interview candidates, decide on fund- Review Commons will manage the transfer of ing, and provide strategic direction. On pages EMBO and ASAPbio announced pre-journal portable review platform the manuscript, reviews, and responses to affili- Page 6 8-9 four members describe why they chose to ate journals. A consortium of seventeen journals New members meet in Heidelberg dedicate their time to an EMBO Committee across six publishers (see box) have joined the Fellowships: from stipends to contracts Pages 14 – 15 and what they took away from the experience. n December 2019, EMBO, in partnership with decide to submit their work to a journal, it will project by committing to use the Review Commons Page 7 When EMBO was created, the focus lay ASAPbio, launched Review Commons, a multi- allow editors to make efficient editorial decisions referee reports for their independent editorial deci- specifically on fostering cross-border inter- Ipublisher partnership which aims to stream- based on existing referee comments.
    [Show full text]
  • UCLA UCLA Electronic Theses and Dissertations
    UCLA UCLA Electronic Theses and Dissertations Title Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods Permalink https://escholarship.org/uc/item/0tr9j01r Author Sun, Yidan Publication Date 2021 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Statistics by Yidan Sun 2021 © Copyright by Yidan Sun 2021 ABSTRACT OF THE DISSERTATION Bipartite Network Community Detection: Development and Survey of Algorithmic and Stochastic Block Model Based Methods by Yidan Sun Doctor of Philosophy in Statistics University of California, Los Angeles, 2021 Professor Jingyi Li, Chair In a bipartite network, nodes are divided into two types, and edges are only allowed to connect nodes of different types. Bipartite network clustering problems aim to identify node groups with more edges between themselves and fewer edges to the rest of the network. The approaches for community detection in the bipartite network can roughly be classified into algorithmic and model-based methods. The algorithmic methods solve the problem either by greedy searches in a heuristic way or optimizing based on some criteria over all possible partitions. The model-based methods fit a generative model to the observed data and study the model in a statistically principled way. In this dissertation, we mainly focus on bipartite clustering under two scenarios: incorporation of node covariates and detection of mixed membership communities.
    [Show full text]
  • Bioengineering Professor Trey Ideker Wins 2009 Overton Prize
    Bioengineering Professor Trey Ideker Wins 2009 Overton Prize March 13, 2009 Daniel Kane University of California, San Diego bioengineering professor Trey Ideker-a network and systems biology pioneer-has won the International Society for Computational Biology's Overton Prize. The Overton prize is awarded each year to an early-to-mid-career scientist who has already made a significant contribution to the field of computational biology. Trey Ideker is an Associate Professor of Bioengineering at UC San Diego's Jacobs School of Engineering, Adjunct Professor of Computer Science, and member of the Moores UCSD Cancer Center. He is a pioneer in using genome-scale measurements to construct network models of cellular processes and disease. His recent research activities include development of software and algorithms for protein network analysis, network-level comparison of pathogens, and genome-scale models of the response to DNA-damaging agents. "Receiving this award is a wonderful honor and helps to confirm that the work we have been doing for the past several years has been useful to people," said Ideker. "This award also provides great recognition to UC San Diego which has fantastic bioinformatics programs both at the undergraduate and graduate level. I could never have done it without the help of some really first-rate bioinformatics and bioengineering graduate students," said Ideker. Ideker is on the faculty of the Jacobs School of Engineering's Department of Bioengineering, which ranks 2nd in the nationfor biomedical engineering, according to the latest US News rankings. The bioengineering department has ranked among the top five programs in the nation every year for the past decade.
    [Show full text]
  • Rich Probabilistic Models for Genomic Data
    RICH PROBABILISTIC MODELS FOR GENOMIC DATA a dissertation submitted to the department of computer science and the committee on graduate studies of stanford university in partial fulfillment of the requirements for the degree of doctor of philosophy Eran Segal August 2004 c Copyright by Eran Segal 2004 All Rights Reserved ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Daphne Koller Department of Computer Science Stanford University (Principal Adviser) I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Nir Friedman School of Computer Science and Engineering Hebrew University I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Stuart Kim Department of Developmental Biology Stanford University I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. David Haussler Department of Computer Science University of California Santa Cruz Approved for the University Committee on Graduate Studies. iii iv To Gal. v vi Abstract Genomic datasets, spanning many organisms and data types, are rapidly being pro- duced, creating new opportunities for understanding the molecular mechanisms un- derlying human disease, and for studying complex biological processes on a global scale.
    [Show full text]
  • Proceedings of the Eighteenth International Conference on Machine Learning., 282 – 289
    Abstracts of papers, posters and talks presented at the 2008 Joint RECOMB Satellite Conference on REGULATORYREGULATORY GENOMICS GENOMICS - SYSTEMS BIOLOGY - DREAM3 Oct 29-Nov 2, 2008 MIT / Broad Institute / CSAIL BMP follicle cells signaling EGFR signaling floor cells roof cells Organized by Manolis Kellis, MIT Andrea Califano, Columbia Gustavo Stolovitzky, IBM Abstracts of papers, posters and talks presented at the 2008 Joint RECOMB Satellite Conference on REGULATORYREGULATORY GENOMICS GENOMICS - SYSTEMS BIOLOGY - DREAM3 Oct 29-Nov 2, 2008 MIT / Broad Institute / CSAIL Organized by Manolis Kellis, MIT Andrea Califano, Columbia Gustavo Stolovitzky, IBM Conference Chairs: Manolis Kellis .................................................................................. Associate Professor, MIT Andrea Califano ..................................................................... Professor, Columbia University Gustavo Stolovitzky....................................................................Systems Biology Group, IBM In partnership with: Genome Research ..............................................................................editor: Hillary Sussman Nature Molecular Systems Biology ............................................... editor: Thomas Lemberger Journal of Computational Biology ...............................................................editor: Sorin Istrail Organizing committee: Eleazar Eskin Trey Ideker Eran Segal Nir Friedman Douglas Lauffenburger Ron Shamir Leroy Hood Satoru Miyano Program Committee: Regulatory Genomics:
    [Show full text]
  • SUNDAY, August 19 MONDAY, August 20
    13th International Conference on Systems Biology August 19 – 23, 2012 Schedule of Events SUNDAY, August 19 12:00 noon - 5:00 pm Registration Concert Hall Foyer 3:00 pm - 3:15 pm Opening Remarks and Welcome Concert Hall Charlie Boone, University of Toronto 3:15 pm - 4:15 pm Plenary Session 1 Concert Hall Chair: Brenda Andrews, University of Toronto Keynote Lecture Exploring the sequence specificty of eukarytic DNA and RNA binding proteins. Timothy Hughes. Keynote Lecture Unraveling principles of gene regulation using thousands of designed promoter sequences. Eran Segal 4:15 pm - 5:00 pm Special Lectures Concert Hall Chair: Charlie Boone, University of Toronto Visualisations of DNA with Hollywood visual effects. Drew Berry. Systems-Biology Applications of Imaging Flow Cytometry. Timothy Galitski. 5:00 pm - 5:30 pm Champagne Reception Concert Hall Foyer 5:30 pm - 6:00 pm Performance byTanya Tagaq Inuit throat singer Concert Hall 6:15 pm - 8:00 pm Opening Reception at the Donnelly Centre Donnelly Centre MONDAY, August 20 9:00 am - 10:00 am Plenary Session II Concert Hall Chair: Fritz Roth, University of Toronto Keynote Lecture Reading and Writing Omes. George Church. Lecture Towards unification of genetic and hierarchy models of tumor heterogeneity. John Dick. 10:00 am - 10:30 am Special Lecture Chair: Corey Nislow, University of Toronto Carl Zimmer, Science Journalist, Birds and Bioterrorists: The (Un)natural History of Influenza 13th International Conference on Systems Biology August 19 – 23, 2012 Schedule of Events 10:30 am - 11:00 am
    [Show full text]
  • Editorial Submission to Bioinformatics
    Vol. 23 ISMB/ECCB 2007, pages i1–i4 BIOINFORMATICS doi:10.1093/bioinformatics/btm285 ISMB/ECCB 2007 had to have the quality of a regular Editorial submission to Bioinformatics. In addition, they had to make for interesting talks and, finally, they had to be acceptable without major revision, because the timing of the paper ISMB/ECCB 2007 selection process for the conference did not allow for a This volume contains the papers accepted for presentation at second round of reviewing. the Fifteenth Conference on Intelligent Systems for Molecular Corresponding authors of submitted papers came from 42 Biology, which was held jointly with the Sixth European countries, 194 papers were from North America, 140 from Conference on Computational Biology (ISMB/ECCB 2007; Europe and Israel, 69 from Asia, 5 from South America, 7 from http://www.iscb.org/ismbeccb2007/). The conference was held Australia and 2 from Africa. from 21–25 July 2007 at the Austria Center in Vienna, Austria. The contributed papers presented here comprise only one The conference united the annual meetings of the International aspect of the scientific offerings of the conference, albeit a very Society for Computational Biology (ISCB) and of the important one. Ten invited keynotes were held by outstanding European Computational Biology Community. The papers scientists in the field (Table 2), among them this year’s ISCB presented here are noteworthy for several reasons. First, for the Award Winners Eran Segal (Overton Prize) and Temple Smith second time, papers are open access and freely available to the (ISCB Senior Scientist Accomplishment Award). Furthermore, worldwide community ahead of the conference and subse- the conference offered a Highlight Papers Track organized by quently form an online only part of a regular issue of the Burkhard Rost featuring 65 talks on previously published high- journal Bioinformatics.
    [Show full text]
  • Fostering International Collaborations Announcing Life Science Alliance A
    SPRING 2018 ISSUE 38 EMBO Courses & Workshops A look behind the scenes PAGES 12 – 13 New scientific journal Partnership with Chile Announcing Life Science Fostering international Alliance collaborations PAGE 3 PAGE 4 ERC Scientific Council in Heidelberg Facts & Figures “Every question begins with SUMO” Grants under discussion EMBO activities in 2017 at a glance Frauke Melchior receives FEBS | EMBO Women in Science Award PAGE 7 PAGES 10 – 11 PAGE 14 www.embo.org Table of contents EMBO news Science policy Preprint quality control Page 6 DORA relaunch: towards fair evaluation of researchers Page 7 EMBO PRESS Announcing Life Science Alliance Page 3 EMBL Photolab Marietta Schupp, © Chilean researchers now eligible for EMBO Editorial support Page 4 et another journal?” Exchanging ideas in India Page 4 SCIENCE POLICY I would not be surprised if that “Ywas a question that went through Meet the latest Installation EMBL and EMBO host the ERC Scientific your mind when reading the announce- Grantees Page 5 ment of our newest journal, Life Science Council Page 7 Alliance (p3). It is a question we asked ourselves more than once when we first considered adding another publication to EMBO community the EMBO Press portfolio. We came to the conclusion that – Updates from across despite the already crowded journal market Europe Pages 15 – 16 and the development of alternative means of sharing scientific findings – there are good reasons to launch this particular Awards and publications publication. This is in fact not ‘just anoth- EMBO NEWS er journal’. Its raison d'être is to address Achievements and papers by members of some of the existing challenges in scientific Spotlight on the ASCB | EMBO publishing and the needs of the life science Meeting Pages 08 – 09 the EMBO community Page 17 community.
    [Show full text]
  • Systematic Dissection of Genomic Features Determining Transcription
    Systematic dissection of genomic features determining PNAS PLUS transcription factor binding and enhancer function Sharon R. Grossmana,b,c, Xiaolan Zhanga, Li Wanga, Jesse Engreitza,d, Alexandre Melnikova, Peter Rogova, Ryan Tewheya,e,f, Alina Isakovag,h, Bart Deplanckeg,h, Bradley E. Bernsteina,i,j, Tarjei S. Mikkelsena,k,l, and Eric S. Landera,b,m,1 aBroad Institute, Cambridge, MA 02142; bDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; cHealth Sciences and Technology, Harvard Medical School, Boston, MA 02215; dDivision of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139; eFaculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138; fDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; gInstitute of Bioengineering, CH-1015 Lausanne, Switzerland; hSwiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland; iDepartment of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; jCenter for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; kHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138; lDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138; and mDepartment of Systems Biology, Harvard Medical School, Boston, MA 02215 Contributed by Eric S. Lander, December 25, 2016 (sent for review December 7, 2016; reviewed by Eran Segal and Itai Yanai) Enhancers regulate
    [Show full text]
  • Plos Computational Biology Publishes Research of Exceptional
    A peer-reviewed open-access journal published by the Public Library of Science www.ploscompbiol.org PLoS Computational Biology publishes research of exceptional significance that furthers our understanding of living systems at all scales — from molecules and cells, to patient populations and ecosystems — through the application of computational methods. • Run by an international Editorial Board led by Philip E. Bourne (University of California San Diego, USA). • Featuring high-quality Research Articles, invited Reviews, Tutorials, an outstanding Education section, Image credit: Toma Pigli and our popular Editorial “Ten Simple Rules” series. PLoS Computational Biology (2007) • Funder-compliant — Published articles are Topics include (but are not limited to): immediately deposited in PubMed Central and Molecular Biology subsequently cited in PubMed. Protein-Protein Interactions • Provides constructive peer review and rapid Computational Neuroscience publication. Regulatory Networks • Article-level metrics and web tools to facilitate Computational Immunology community discourse through notes, comments, Sequence Analysis and ratings. Protein Structure & Function Prediction • Highlighted in news outlets and blogs from around Population Biology the world. Cancer Genetics Microarray Data Analysis Gene Expression Synthetic Biology PLoS Computational Biology is published by the Public Machine Learning Library of Science (PLoS), a nonprofit organization committed to making the world’s scientific and medical literature a public resource. Everything we publish is freely available online through- out the world, for anyone to read, download, copy, distribute and use (with attribution). Barrier-free, open access, no permissions required. Image credit: Ryan Davey PLoS Computational Biology (2007) PUBLIC LIBRARY of SCIENCE www.plos.org A peer-reviewed open-access journal published by the Public Library of Science www.ploscompbiol.org Editorial Board Philip E.
    [Show full text]
  • Algorithms for Biological Network Alignment A
    ALGORITHMS FOR BIOLOGICAL NETWORK ALIGNMENT A DISSERTATION SUBMITTED TO THE DEPARTMENT OF COMPUTER SCIENCE AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Jason Flannick August 2009 c Copyright by Jason Flannick 2009 All Rights Reserved ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. (Serafim Batzoglou) Principal Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. (Harley McAdams) I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. (David Dill) Approved for the University Committee on Graduate Studies. iii iv Abstract A major goal in the post-genomic era is to understand how genes and proteins organize to ulti- mately cause complex traits. There are multiple levels of biological organization, such as low-level interactions between pairs of molecules, higher-level metabolic pathways and molecular complexes, and ultimately high-level function of an organism. Interaction networks summarize interactions between pairs of molecules, which are the building blocks for higher levels of molecular organization. As databases of interaction networks continue to grow in size and complexity, new computational tools are needed to search them for these higher levels of organization.
    [Show full text]