Feinberg Graduate School 2012 Graduates Feinberg Graduate School
Total Page:16
File Type:pdf, Size:1020Kb
Load more
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). -
Annual Report 2010 © Copyright 2011
Centre for Genomic Regulation Annual Report 2010 © Copyright 2011 Produced by: Department of Communication & Public Relations Centre for Genomic Regulation (CRG) Dr. Aiguader, 88 08003 Barcelona, Spain www.crg.eu Texts and graphics: CRG Researchers, Department of Communication and Public Relations Graphic Design: Genoma ArtStudio SCP (www.genoma-artstudio.com) Photography: Ivan Martí Printing: Novoprint, S.A. Legal deposit: B-24966-2011 CONTENTS CRG Scientific Structure 6 CRG Core Facilities Structure 8 CRG Management Structure 10 CRG Scientific Advisory Board (SAB) 12 CRG Business Board 13 Year Retrospect by the Director of the CRG: Miguel Beato 14 Research Programmes Gene Regulation 16 > Chromatin and gene expression 18 > Regulation of alternative pre-mRNA splicing during cell differentiation, development and disease 22 > Regulation of protein synthesis in eukaryotes 26 > Translational control of gene expression 29 Differentiation and Cancer 34 > Hematopoietic differentiation and stem cell biology 36 > Reprogramming and regeneration 40 > Epigenetics events in cancer 43 > Epithelial homeostasis and cancer 48 > Mechanisms of cancer and aging 51 Genes and Disease 54 > Genetic causes of disease 56 > Gene therapy 65 > Gene Function and murine models of disease 69 > Neurobehavioral phenotyping of mouse models of disease 73 > Genomic and epigenomic variation in disease 77 Bioinformatics and Genomics 82 > Bioinformatics and genomics 84 > Comparative bioinformatics 92 > Comparative genomics 96 > Evolutionary genomics 101 > Gene function and evolution -
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. -
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. -
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. -
Seminar 2021 | א“פשת רנימס
סמינר תשפ“א | Seminar 2021 Adams Seminar 2021 סמינר אדמס תשפ“א Guest Lecturer Prof. Daniel A. Chamovitz Professor of Plant Pathology President, Ben-Gurion University of the Negev Editors Deborah Greniman, Bob Lapidot Photographer Michal Fattal Graphic Design Navi Katzman-Kaduri The Israel Academy of Sciences and Humanities P.O.Box 4040 Jerusalem 9104001 Tel 972-2-5676207 E-mail [email protected] www.adams.academy.ac.il The Adams Fellowships is a joint program of the late Mr. Marcel Adams of Canada and the Israel Academy of Sciences and Humanities. Chartered by law in 1961, the Israel Academy of Sciences and Humanities acts as a national focal point for Israeli scholarship in both the natural sciences and the humanities and social sciences. The Academy consists of approximately 135 of Israel’s most distinguished scientists and scholars, who, with the help of the Academy’s staff and committees, monitor and promote Israeli intellectual excellence, advise the government on scientific planning, fund and publish research of lasting merit, and maintain active contact with the broader international scientific and scholarly community. For more information, please send an e-mail to [email protected] or call 972-2-5676207. Visit our website: adams.academy.ac.il Adams Seminar 2021 | 3 Adams Fellowships Marcel Adams Hebrew-speaking philanthropist Marcel Adams, who escaped from a forced-labor camp in Romania in 1944, fought in Israel’s War of Independence and made his fortune in Montreal, has endowed the Adams Fellowship Program to support Israel’s brightest doctoral students in the natural and exact sciences each year. -
EMBO Facts & Figures
excellence in life sciences young investigators|courses,workshops,conference series & symposia|installation grantees|long-term fellows|short-term fellows|policy, science & society|the EMBO Journal|EMBO reports|molecular systems biology|EMBO molecular medicine|global exchange|gold medal|the EMBO meeting|women in science| EMBO reports|molecular systems biology|EMBO molecular medicine|global exchange|gold medal|the EMBO meeting|women in science|young investigators|courses,workshops,conference series & symposia|installation grantees|long-term fellows|short-term fellows|policy, science & society|the EMBO Journal| global exchange|gold medal|the EMBO meeting|women in science|young investigators|long-term fellows|short-term fellows|policy, science & society|the EMBO Journal|courses,workshops,conference series & symposia|EMBO reports|molecular systems biology|EMBO molecular medicine|installation grantees| EMBO molecular medicine|installation grantees|long-term fellows|gold medal|molecular systems biology|short-term fellows|the EMBO meeting|womenReykjavik in science|young investigators|courses,workshops,conference series & symposia|global exchange|EMBO reports|policy, science & society|the EMBO Journal| gold medal|the EMBO meeting|women in science|young investigators|courses,workshops,conference series & symposia|global exchange|policy, science & society|the EMBO Journal|EMBO reports|molecular systems biology|EMBO molecular medicine|installation grantees|long-term fellows|short-term fellows| courses,workshops,conference series & symposia|global -
Conference Program Pierre Monsan Toulouse White Biotechnology, France
Engineering Conferences International ECI Digital Archives Enzyme Engineering XXIV Proceedings 9-24-2017 Conference Program Pierre Monsan Toulouse White Biotechnology, France Magali Remaud-Simeon LISBP-INSA, University of Toulouse, France Follow this and additional works at: http://dc.engconfintl.org/enzyme_xxiv Part of the Engineering Commons Recommended Citation Pierre Monsan and Magali Remaud-Simeon, "Conference Program" in "Enzyme Engineering XXIV", Pierre Monsan, Toulouse White Biotechnology, France Magali Remaud-Simeon, LISBP-INSA, University of Toulouse, France Eds, ECI Symposium Series, (2017). http://dc.engconfintl.org/enzyme_xxiv/179 This Article is brought to you for free and open access by the Proceedings at ECI Digital Archives. It has been accepted for inclusion in Enzyme Engineering XXIV by an authorized administrator of ECI Digital Archives. For more information, please contact [email protected]. Program Enzyme Engineering XXIV September 24 - 28, 2017 Pierre Baudis Congress Center Toulouse, France Conference Co-Chairs Pierre Monsan Toulouse White Biotechnology, France Magali Remaud-Simeon LISBP-INSA, University of Toulouse, France Engineering Conferences International 32 Broadway, Suite 314 New York, NY 10004, USA Phone: 1-212-514-6760 www.engconfintl.org – [email protected] Centre de Congrès Pierre Baudis 11, esplanade Compans Caffarelli BP 88517 31685 Toulouse Cedex 6 France www.centre-congres-toulouse.fr Tel: +33 5 62 25 45 45 Engineering Conferences International (ECI) is a not-for-profit global engineering conferences program, originally established in 1962, that provides opportunities for the exploration of problems and issues of concern to engineers and scientists from many disciplines. ECI BOARD MEMBERS Barry C. Buckland, President Mike Betenbaugh Nick Clesceri Peter Gray Michael King Raymond McCabe David Robinson Eugene Schaefer P. -
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. -
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: -
CURRICULUM VITAE October 201 7 A
MICHAL SHARON CURRICULUM VITAE October 201 7 A. PERSONAL DETAILS Date of Birth: March 25th 1972 Country of Birth: Israel Citizenship: Israeli, German Marital Status: Married, +3 (Ori 1998, Naama 2001, Ronni 2007) Phone: +972-8-9343947 Fax: +972-8-9346010 E-mail: [email protected] Webpage: http://www.weizmann.ac.il/Biomolecular_Sciences/MichalSharon/home B. EDUCATION 2003-2006 Post-doctoral research under Prof. Carol V. Robinson, Department of Chemistry, University of Cambridge, Cambridge, UK. Field of study: Mass spectrometry of large non-covalent complexes. 1996-2003 M.Sc./Ph.D. combined program (direct PhD) under Prof. Jacob Anglister, Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. Field of study: Three-dimensional structure determination of protein complexes using multidimensional NMR Thesis title: Suggested mechanism for HIV-1 coreceptor selectivity unveiled by the NMR structure of a V3MN peptide in complex with a human neutralizing antibody. 1993-1996 B.Sc. Chemistry, The Hebrew University, Jerusalem, Israel, Cum laude. C. EMPLOYMENT 2015-present Associate Professor at the Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel. 2007-2015 Senior Scientist (equivalent to Assistant Professor) at the Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel. 2006-2007 Royal Society Research Fellow, Department of Chemistry, University of Cambridge, Cambridge, UK. D. ACADEMIC ADMINISTRATION 2017-2021 Vice-President, ILANIT/FISEB -
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