Modeling and Analysis of RNA-Seq Data: a Review from a Statistical Perspective
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RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY
RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press ISSN: 1790-5125 www.wseas.org ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press www.wseas.org Copyright © 2009, by WSEAS Press All the copyright of the present book belongs to the World Scientific and Engineering Academy and Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy and Society Press. All papers of the present volume were peer reviewed -
Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
BIOGRAPHICAL SKETCH NAME: Berger
BIOGRAPHICAL SKETCH NAME: Berger, Bonnie eRA COMMONS USER NAME (credential, e.g., agency login): BABERGER POSITION TITLE: Simons Professor of Mathematics and Professor of Electrical Engineering and Computer Science EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, include postdoctoral training and residency training if applicable. Add/delete rows as necessary.) EDUCATION/TRAINING DEGREE Completion (if Date FIELD OF STUDY INSTITUTION AND LOCATION applicable) MM/YYYY Brandeis University, Waltham, MA AB 06/1983 Computer Science Massachusetts Institute of Technology SM 01/1986 Computer Science Massachusetts Institute of Technology Ph.D. 06/1990 Computer Science Massachusetts Institute of Technology Postdoc 06/1992 Applied Mathematics A. Personal Statement Advances in modern biology revolve around automated data collection and sharing of the large resulting datasets. I am considered a pioneer in the area of bringing computer algorithms to the study of biological data, and a founder in this community that I have witnessed grow so profoundly over the last 26 years. I have made major contributions to many areas of computational biology and biomedicine, largely, though not exclusively through algorithmic innovations, as demonstrated by nearly twenty thousand citations to my scientific papers and widely-used software. In recognition of my success, I have just been elected to the National Academy of Sciences and in 2019 received the ISCB Senior Scientist Award, the pinnacle award in computational biology. My research group works on diverse challenges, including Computational Genomics, High-throughput Technology Analysis and Design, Biological Networks, Structural Bioinformatics, Population Genetics and Biomedical Privacy. I spearheaded research on analyzing large and complex biological data sets through topological and machine learning approaches; e.g. -
Program Book
Pacific Symposium on Biocomputing 2016 January 4-8, 2016 Big Island of Hawaii Program Book PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016 Big Island of Hawaii, January 4-8, 2016 Welcome to PSB 2016! We have prepared this program book to give you quick access to information you need for PSB 2016. Enclosed you will find • Logistics information • Menus for PSB hosted meals • Full conference schedule • Call for Session and Workshop Proposals for PSB 2017 • Poster/abstract titles and authors • Participant List Conference materials are also available online at http://psb.stanford.edu/conference-materials/. PSB 2016 gratefully acknowledges the support the Institute for Computational Biology, a collaborative effort of Case Western Reserve University, the Cleveland Clinic Foundation, and University Hospitals; the National Institutes of Health (NIH), the National Science Foundation (NSF); and the International Society for Computational Biology (ISCB). If you or your institution are interested in sponsoring, PSB, please contact Tiffany Murray at [email protected] If you have any questions, the PSB registration staff (Tiffany Murray, Georgia Hansen, Brant Hansen, Kasey Miller, and BJ Morrison-McKay) are happy to help you. Aloha! Russ Altman Keith Dunker Larry Hunter Teri Klein Maryln Ritchie The PSB 2016 Organizers PACIFIC SYMPOSIUM ON BIOCOMPUTING 2016 Big Island of Hawaii, January 4-8, 2016 SPEAKER INFORMATION Oral presentations of accepted proceedings papers will take place in Salon 2 & 3. Speakers are allotted 10 minutes for presentation and 5 minutes for questions for a total of 15 minutes. Instructions for uploading talks were sent to authors with oral presentations. If you need assistance with this, please see Tiffany Murray or another PSB staff member. -
Microblogging the ISMB: a New Approach to Conference Reporting
Message from ISCB Microblogging the ISMB: A New Approach to Conference Reporting Neil Saunders1*, Pedro Beltra˜o2, Lars Jensen3, Daniel Jurczak4, Roland Krause5, Michael Kuhn6, Shirley Wu7 1 School of Molecular and Microbial Sciences, University of Queensland, St. Lucia, Brisbane, Queensland, Australia, 2 Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America, 3 Novo Nordisk Foundation Center for Protein Research, Panum Institute, Copenhagen, Denmark, 4 Department of Bioinformatics, University of Applied Sciences, Hagenberg, Freistadt, Austria, 5 Max-Planck-Institute for Molecular Genetics, Berlin, Germany, 6 European Molecular Biology Laboratory, Heidelberg, Germany, 7 Stanford Medical Informatics, Stanford University, Stanford, California, United States of America Cameron Neylon entitled FriendFeed for Claire Fraser-Liggett opened the meeting Scientists: What, Why, and How? (http:// with a review of metagenomics and an blog.openwetware.org/scienceintheopen/ introduction to the human microbiome 2008/06/12/friendfeed-for-scientists-what- project (http://friendfeed.com/search?q = why-and-how/) for an introduction. room%3Aismb-2008+microbiome+OR+ We—a group of science bloggers, most fraser). The subsequent Q&A session of whom met in person for the first time at covered many of the exciting challenges The International Conference on Intel- ISMB 2008—found FriendFeed a remark- for those working in this field. Clearly, ligent Systems for Molecular Biology -
The Basic Units of Life How Cell Atlases Can Shed Light on Disease Mechanisms with Remarkable Accuracy
Press Information, July 28, 2021 Cells: The Basic Units of Life How cell atlases can shed light on disease mechanisms with remarkable accuracy The Schering Stiftung awards the Ernst Schering Prize 2021 to Aviv Regev. A pioneer in the field of single-cell analysis, she successfully combines approaches from biology and computer science and thus revolutionizes the field of precision medicine. Aviv Regev is considered a pioneer in the field of single-cell biology and has broken new ground by combining the disciplines of biology, computation, and genetic engineering. She has uniquely succeeded in combining and refining some of the most important experimental and analytical tools in such a way that she can analyze the genome of hundreds of thousands of single cells simultaneously. This single-cell genome analysis makes it possible to map and characterize a large number of individual tissue cells. Aviv Regev was the first to apply these single-cell technologies to solid tumors and to successfully identify those cells and genes that influence tumor growth and resistance to treatment. In addition, she discovered rare cell types that are involved in cystic fibrosis and ulcerative colitis. Last but not least, together with international research groups, and her colleague Sarah Teichmann she built the Human Cell Atlas and inspired Prof. Aviv Regev, PhD scientists all over the world to use these tools to create a Photo: Casey Atkins comprehensive atlas of all cell types in the human body. These cell atlases of parts of the human body illuminate disease mechanisms with remarkable accuracy and have recently also been used successfully to study disease progression in COVID-19. -
CV Aviv Regev
AVIV REGEV Curriculum Vitae Education and training Ph.D., Computational Biology, Tel Aviv University, Tel Aviv, Israel, 1998-2002 Advisor: Prof. Eva Jablonka (Tel Aviv University) Advisor: Prof. Ehud Shapiro (Computer Science, Weizmann Institute) M.Sc. (direct, Summa cum laude) Tel Aviv University, Tel Aviv, Israel, 1992-1997 Advisor: Prof. Sara Lavi A student in the Adi Lautman Interdisciplinary Program for the Fostering of Excellence (studies mostly in Biology, Computer Science and Mathematics) Post Training Positions Executive Vice President and Global Head, Genentech Research and Early Development, Genentech/Roche, 2020 - Current HHMI Investigator, 2014-2020 Chair of the Faculty (Executive Leadership Team), Broad Institute, 2015 – 2020 Professor, Department of Biology, MIT, 2015-Current (on leave) Founding Director, Klarman Cell Observatory, Broad Institute, 2012-2020 Director, Cell Circuits Program, Broad Institute, 2013 - 2020 Associate Professor with Tenure, Department of Biology, MIT, 2011-2015 Early Career Scientist, Howard Hughes Medical Institute, 2009-2014 Core Member, Broad Institute of MIT and Harvard, 2006-Current (on leave) Assistant Professor, Department of Biology, MIT, 2006-2011 Bauer Fellow, Center for Genomics Research, Harvard University, 2003-2006 International Service Founding Co-Chair, Human Cell Atlas, 2016-Current Honors Vanderbilt Prize, 2021 AACR Academy, Elected Fellow, 2021 AACR-Irving Weinstein Foundation Distinguished Lecturer, 2021 James Prize in Science and Technology Integration, National Academy of -
Lior Pachter Genome Informatics 2013 Keynote
Stories from the Supplement Lior Pachter! Department of Mathematics and Molecular & Cell Biology! UC Berkeley! ! November 1, 2013! Genome Informatics, CSHL The Cufflinks supplements • C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold and L. Pachter, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology 28, (2010), p 511–515. Supplementary Material: 42 pages. • C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, 31 (2012), p 46–53. Supplementary Material: 70 pages. A supplementary arithmetic progression? • C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold and L. Pachter, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nature Biotechnology 28, (2010), p 511–515. Supplementary Material: 42 pages. • C. Trapnell, D.G. Hendrickson, M. Sauvageau, L. Goff, J.L. Rinn and L. Pachter, Differential analysis of gene regulation at transcript resolution with RNA- seq, Nature Biotechnology, 31 (2012), p 46–53. Supplementary Material: 70 pages. • A. Roberts and L. Pachter, Streaming algorithms for fragment assignment, Nature Methods 10 (2013), p 71—73. Supplementary Material: 98 pages? The nature methods manuscript checklist The nature methods manuscript checklist Emperor Joseph II: My dear young man, don't take it too hard. Your work is ingenious. It's quality work. And there are simply too many notes, that's all. -
24019 - Probabilistic Graphical Models
Year : 2019/20 24019 - Probabilistic Graphical Models Syllabus Information Academic Course: 2019/20 Academic Center: 337 - Polytechnic School Study: 3379 - Bachelor's (degree) programme in Telecommunications Network Engineering Subject: 24019 - Probabilistic Graphical Models Credits: 5.0 Course: 3 Teaching languages: Theory: Grup 1: English Practice: Grup 101: English Grup 102: English Seminar: Grup 101: English Grup 102: English Teachers: Vicente Gomez Cerda Teaching Period: Second Quarter Schedule: --- Presentation Probabilistic graphical models (PGMs) are powerful modeling tools for reasoning and decision making under uncertainty. PGMs have many application domains, including computer vision, natural language processing, efficient coding, and computational biology. PGMs connects graph theory and probability theory, and provide a flexible framework for modeling large collections of random variables with complex interactions. This is an introductory course which focuses on two main principles: (1) emphasizing the role of PGMs as a unifying language in machine learning that allows a natural specification of many problem domains with inherent uncertainty, and (2) providing a set of computational tools for probabilistic inference (making predictions that can be used to aid decision making), and learning (estimating the graph structure and their parameters from data). Associated skills Basic Competences That the students can apply their knowledge to their work or vocation of a professional form in a professional way and possess the competences which are usually proved by means of the elaboration and defense of arguments and solving the solution of problems within their study area. That the students have the ability of collecting and interpreting relevant data (normally within their study area) to issue judgements which include a reflection about relevant topics of social, scientific or ethical nature. -
Curriculum Vitae—Nir Friedman
Nir Friedman Last update: February 14, 2019 Curriculum Vitae|Nir Friedman School of Computer Science and Engineering email: [email protected] Alexander Silberman Institute of Life Sciences Office: +972-73-388-4720 Hebrew University of Jerusalem Cellular: +972-54-882-0432 Jerusalem 91904, ISRAEL Professional History Professor 2009{present Alexander Silberman Institute of Life Sciences The Hebrew University of Jerusalem Professor 2007{present School of Computer Science & Engineering The Hebrew University of Jerusalem Associate Professor 2002{2007 School of Computer Science & Engineering The Hebrew University of Jerusalem Senior Lecturer 1998{2002 School of Computer Science & Engineering The Hebrew University of Jerusalem Postdoctoral Scholar 1996{1998 Division of Computer Science University of California, Berkeley Education Ph.D. Computer Science, Stanford University 1992{1997 M.Sc. Math. & Computer Science, Weizmann Institute of Science 1990{1992 B.Sc. Math. & Computer Science, Tel-Aviv University 1983{1987 Awards Alexander von Humboldt Foundation Research Award 2015 Fellow of the International Society of Computational Biology 2014 European Research Council \Advanced Grant" research award 2014-2018 \Test of Time" Award Research in Computational Molecular Biology (RECOMB) 2012 Most cited paper in 12-year window in RECOMB Michael Bruno Memorial Award 2010 \Israeli scholars and scientists of truly exceptional promise, whose achievements to date sug- gest future breakthroughs in their respective fields” [age < 50] European Research Council \Advanced -
Steven L. Salzberg
Steven L. Salzberg McKusick-Nathans Institute of Genetic Medicine Johns Hopkins School of Medicine, MRB 459, 733 North Broadway, Baltimore, MD 20742 Phone: 410-614-6112 Email: [email protected] Education Ph.D. Computer Science 1989, Harvard University, Cambridge, MA M.Phil. 1984, M.S. 1982, Computer Science, Yale University, New Haven, CT B.A. cum laude English 1980, Yale University Research Areas: Genomics, bioinformatics, gene finding, genome assembly, sequence analysis. Academic and Professional Experience 2011-present Professor, Department of Medicine and the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University. Joint appointments as Professor in the Department of Biostatistics, Bloomberg School of Public Health, and in the Department of Computer Science, Whiting School of Engineering. 2012-present Director, Center for Computational Biology, Johns Hopkins University. 2005-2011 Director, Center for Bioinformatics and Computational Biology, University of Maryland Institute for Advanced Computer Studies 2005-2011 Horvitz Professor, Department of Computer Science, University of Maryland. (On leave of absence 2011-2012.) 1997-2005 Senior Director of Bioinformatics (2000-2005), Director of Bioinformatics (1998-2000), and Investigator (1997-2005), The Institute for Genomic Research (TIGR). 1999-2006 Research Professor, Departments of Computer Science and Biology, Johns Hopkins University 1989-1999 Associate Professor (1996-1999), Assistant Professor (1989-1996), Department of Computer Science, Johns Hopkins University. On leave 1997-99. 1988-1989 Associate in Research, Graduate School of Business Administration, Harvard University. Consultant to Ford Motor Co. of Europe and to N.V. Bekaert (Kortrijk, Belgium). 1985-1987 Research Scientist and Senior Knowledge Engineer, Applied Expert Systems, Inc., Cambridge, MA. Designed expert systems for financial services companies. -
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction Serafim Batzoglou,1,4,7 Lior Pachter,2,7 Jill P. Mesirov,3 Bonnie Berger,1,4,6 and Eric S. Lander3,5,6 1Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA; 2Department of Mathematics, University of California Berkeley, Berkeley, California 94720 USA; 3Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 USA; 4Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA; 5Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 USA We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of similarity in the number, size and sequence of exons and introns. We then developed an approach for recognizing genes within such orthologous regions by first aligning the regions using an iterative global alignment system and then identifying genes based on conservation of exonic features at aligned positions in both species. The alignment and gene recognition are performed by new programs called GLASS and ROSETTA, respectively. ROSETTA performed well at exact identification of coding exons in 117 orthologous pairs tested. A fundamental task in analyzing genomes is to identify by comparison of syntenic human and mouse genomic the genes. This is relatively straightforward for organ- sequences. isms with compact genomes (such as bacteria, yeast, It is well known that cross-species sequence com- flies and worms) because exons tend to be large and the parison can help highlight important functional ele- introns are either non-existent or tend to be short.