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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]. -
CHRISTINA “TINA” WARINNER (Last Updated October 18, 2018)
CHRISTINA “TINA” WARINNER (last updated October 18, 2018) Max Planck Institute University of Oklahoma for the Science of Human History (MPI-SHH) Department of Anthropology Department of Archaeogenetics Laboratories of Molecular Anthropology Kahlaische Strasse 10, 07743 Jena, Germany And Microbiome Research (LMAMR) +49 3641686620 101 David L. Boren Blvd, [email protected] Norman, OK 73019 USA www.christinawarinner.com [email protected] http://www.shh.mpg.de/employees/50506/25522 www.lmamr.org APPOINTMENTS W2 Group Leader, Max Planck Institute for the Science of Human History, Germany 2016-present University Professor, Friedrich Schiller University, Jena, Germany 2018-present Presidential Research Professor, Univ. of Oklahoma, USA 2014-present Assistant Professor, Dept. of Anthropology, Univ. of Oklahoma, USA 2014-present Adjunct Professor, Dept. of Periodontics, College of Dentistry, Univ. of Oklahoma, USA 2014-present Visiting Associate Professor, Dept. of Systems Biology, Technical University of Denmark 2015 Research Associate, Dept. of Anthropology, Univ. of Oklahoma, USA 2012-2014 Acting Head of Group, Centre for Evolutionary Medicine, Univ. of Zürich, Switzerland 2011-2012 Research Assistant, Centre for Evolutionary Medicine, Univ. of Zürich, Switzerland 2010-2011 EDUCATION Ph.D., Anthropology, Dept. of Anthropology, Harvard University 2010 Thesis Title: “Life and Death at Teposcolula Yucundaa: Mortuary, Archaeogenetic, and Isotopic Investigations of the Early Colonial Period in Mexico” A.M., Anthropology, Dept. of Anthropology, Harvard University 2008 B.A., with Honors, Anthropology, University of Kansas 2003 B.A., Germanic Literatures and Languages, University of Kansas 2003 SELECTED HONORS, AWARDS, AND FELLOWSHIPS Invited speaker, British Academy, Albert Reckitt Archaeological Lecture (forthcoming) 2019 Invited speaker, EMBL Science and Society (forthcoming, Nov. -
Ayshwarya Subramanian Updated June 10, 2021
Ayshwarya Subramanian Updated June 10, 2021 Contact Kuchroo Lab and Klarman Cell Observatory Information Broad Institute twitter: @ayshwaryas 5407G, 415 Main Street website: ayshwaryas.github.io Cambridge, MA 02412 USA email:[email protected] Areas of Computational Biology (Kidney disease, Cancer, Inflammatory Bowel Disease, RNA Biology), Ge- expertise nomic Data Analysis (Single-cell and Bulk-RNAseq, Metagenomics, Exome and single-nucleus DNA sequencing), Machine Learning, Probabilistic modeling, Phylogenetics, Applied Statistics Education 2013 Ph.D., Biological Sciences Carnegie Mellon University, Pittsburgh, PA USA Doctoral Advisor: Russell Schwartz, Ph.D. Dissertation: Inferring tumor evolution using computational phylogenetics 2007 M.Sc. (Hons), Biological Sciences (Undergraduate degree) Birla Institute of Technology and Science (BITS{Pilani), Rajasthan, India CGPA 9.21/10, Major GPA 10/10, with Distinction Undergraduate Honors Thesis: A mathematical model for phototactic responses in Halobac- terium salinarium, Max Planck Institute for Complex Technical Systems, Germany. Current Computational Scientist, Cambridge MA 2017{Present Appointment Mentors: Aviv Regev, Ph.D. & Vijay Kuchroo, Ph.D., D.V.M Research Summary: Single-cell portraits of disease and normal states using human data, mouse and organoid models Klarman Cell Observatory Broad Institute, Cambridge, MA 02142 Publications Pre-prints/Under review [1] Subramanian A†, Vernon KA†, Zhou Y† et al. Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution. bioRxiv 2021.05.30.446342; doi: https://doi.org/10.1101/2021.05.30.446342. [2] Subramanian A†,Vernon KA†, Slyper M, Waldman J, et al. RAAS blockade, kidney dis- ease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells. -
Case Studies in Bayesian Statistics Workshop 9 Poster Session
Case Studies in Bayesian Statistics Workshop 9 Poster Session Following is a tentative list of posters being presented during the workshop: 1. Edoardo Airoldi, Curtis Huttenhower, Olga Troyanskaya and David Botstein 2. Dipankar Bandyopadhyay, Elizabeth Slate, Debajyoti Sinha, Dikpak Dey and Jyotika Fernandes 3. Brenda Betancourt and Maria-Eglee Perez 4. Sham Bhat, Murali Haran, Julio Molineros and Erick Dewolf 5. Jen-hwa Chu, Merlise A. Clyde and Feng Liang 6. Jason Connor, Scott Berry and Don Berry 7. J. Mark Donovan, Michael R. Elliott and Daniel F. Heitjan 8. Elena A. Erosheva, Donatello Telesca, Ross L. Matsueda and Derek Kreager 9. Xiaodan Fan and Jun S. Liu 10. Jairo A. Fuquene and Luis Raul Pericchi 11. Marti Font, Josep Ginebra, Xavier Puig 12. Isobel Claire Gormley and Thomas Brendan Murphy 13. Cari G. Kaufman and Stephan R. Sain 14. Alex Lenkoski 15. Herbie Lee 16. Fei Liu 17. Jingchen Liu, Xiao-Li Meng, Chih-nan Chen, Margarita Alegria 18. Christian Macaro 19. Il-Chul Moon, Eunice J. Kim and Kathleen M. Carley 20. Christopher Paciorek 21. Susan M. Paddock and Patricia Ebener 22. Nicholas M. Pajewski, L. Thomas Johnson, Thomas Radmer, and Purushottam W. Laud 23. Mark W. Perlin, Joseph B. Kadane, Robin W. Cotton and Alexander Sinelnikov 24. Alicia Quiros, Raquel Montes Diez and Dani Gamerman 25. Eiki Satake and Philip Amato 26. James Scott 27. Russell Steele, Robert Platt and Michelle Ross 28. Alejandro Villagran, Gabriel Huerta, Charles S. Jackson and Mrinal K. Sen 29. Dawn Woodard 30. David C. Wheeler, Lance A. Waller and John O. -
Algorithms for Computational Biology 8Th International Conference, Alcob 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings
Lecture Notes in Bioinformatics 12715 Subseries of Lecture Notes in Computer Science Series Editors Sorin Istrail Brown University, Providence, RI, USA Pavel Pevzner University of California, San Diego, CA, USA Michael Waterman University of Southern California, Los Angeles, CA, USA Editorial Board Members Søren Brunak Technical University of Denmark, Kongens Lyngby, Denmark Mikhail S. Gelfand IITP, Research and Training Center on Bioinformatics, Moscow, Russia Thomas Lengauer Max Planck Institute for Informatics, Saarbrücken, Germany Satoru Miyano University of Tokyo, Tokyo, Japan Eugene Myers Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany Marie-France Sagot Université Lyon 1, Villeurbanne, France David Sankoff University of Ottawa, Ottawa, Canada Ron Shamir Tel Aviv University, Ramat Aviv, Tel Aviv, Israel Terry Speed Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Martin Vingron Max Planck Institute for Molecular Genetics, Berlin, Germany W. Eric Wong University of Texas at Dallas, Richardson, TX, USA More information about this subseries at http://www.springer.com/series/5381 Carlos Martín-Vide • Miguel A. Vega-Rodríguez • Travis Wheeler (Eds.) Algorithms for Computational Biology 8th International Conference, AlCoB 2021 Missoula, MT, USA, June 7–11, 2021 Proceedings 123 Editors Carlos Martín-Vide Miguel A. Vega-Rodríguez Rovira i Virgili University University of Extremadura Tarragona, Spain Cáceres, Spain Travis Wheeler University of Montana Missoula, MT, USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Bioinformatics ISBN 978-3-030-74431-1 ISBN 978-3-030-74432-8 (eBook) https://doi.org/10.1007/978-3-030-74432-8 LNCS Sublibrary: SL8 – Bioinformatics © Springer Nature Switzerland AG 2021 This work is subject to copyright. -
Computational Pan-Genomics: Status, Promises and Challenges
bioRxiv preprint doi: https://doi.org/10.1101/043430; this version posted March 12, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Computational Pan-Genomics: Status, Promises and Challenges Tobias Marschall1,2, Manja Marz3,60,61,62, Thomas Abeel49, Louis Dijkstra6,7, Bas E. Dutilh8,9,10, Ali Ghaffaari1,2, Paul Kersey11, Wigard P. Kloosterman12, Veli M¨akinen13, Adam Novak15, Benedict Paten15, David Porubsky16, Eric Rivals17,63, Can Alkan18, Jasmijn Baaijens5, Paul I. W. De Bakker12, Valentina Boeva19,64,65,66, Francesca Chiaromonte20, Rayan Chikhi21, Francesca D. Ciccarelli22, Robin Cijvat23, Erwin Datema24,25,26, Cornelia M. Van Duijn27, Evan E. Eichler28, Corinna Ernst29, Eleazar Eskin30,31, Erik Garrison32, Mohammed El-Kebir5,33,34, Gunnar W. Klau5, Jan O. Korbel11,35, Eric-Wubbo Lameijer36, Benjamin Langmead37, Marcel Martin59, Paul Medvedev38,39,40, John C. Mu41, Pieter Neerincx36, Klaasjan Ouwens42,67, Pierre Peterlongo43, Nadia Pisanti44,45, Sven Rahmann29, Ben Raphael46,47, Knut Reinert48, Dick de Ridder50, Jeroen de Ridder49, Matthias Schlesner51, Ole Schulz-Trieglaff52, Ashley Sanders53, Siavash Sheikhizadeh50, Carl Shneider54, Sandra Smit50, Daniel Valenzuela13, Jiayin Wang70,71,72, Lodewyk Wessels56, Ying Zhang23,5, Victor Guryev16,12, Fabio Vandin57,34, Kai Ye68,69,72 and Alexander Sch¨onhuth5 1Center for Bioinformatics, Saarland University, Saarbr¨ucken, Germany; 2Max Planck Institute for Informatics, Saarbr¨ucken, -
UNIVERSITY of CALIFORNIA SAN DIEGO Making Sense of Microbial
UNIVERSITY OF CALIFORNIA SAN DIEGO Making sense of microbial populations from representative samples A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by James T. Morton Committee in charge: Professor Rob Knight, Chair Professor Pieter Dorrestein Professor Rachel Dutton Professor Yoav Freund Professor Siavash Mirarab 2018 Copyright James T. Morton, 2018 All rights reserved. The dissertation of James T. Morton is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California San Diego 2018 iii DEDICATION To my friends and family who paved the road and lit the journey. iv EPIGRAPH The ‘paradox’ is only a conflict between reality and your feeling of what reality ‘ought to be’ —Richard Feynman v TABLE OF CONTENTS Signature Page . iii Dedication . iv Epigraph . .v Table of Contents . vi List of Abbreviations . ix List of Figures . .x List of Tables . xi Acknowledgements . xii Vita ............................................. xiv Abstract of the Dissertation . xvii Chapter 1 Methods for phylogenetic analysis of microbiome data . .1 1.1 Introduction . .2 1.2 Phylogenetic Inference . .4 1.3 Phylogenetic Comparative Methods . .6 1.4 Ancestral State Reconstruction . .9 1.5 Analysis of phylogenetic variables . 11 1.6 Using Phylogeny-Aware Distances . 15 1.7 Challenges of phylogenetic analysis . 18 1.8 Discussion . 19 1.9 Acknowledgements . 21 Chapter 2 Uncovering the horseshoe effect in microbial analyses . 23 2.1 Introduction . 24 2.2 Materials and Methods . 34 2.3 Acknowledgements . 35 Chapter 3 Balance trees reveal microbial niche differentiation . 36 3.1 Introduction . -
120421-24Recombschedule FINAL.Xlsx
Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3. -
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. -
Standardised Benchmarking in the Quest for Orthologs
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Harvard University - DASH Standardised Benchmarking in the Quest for Orthologs The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Altenhoff, A. M., B. Boeckmann, S. Capella-Gutierrez, D. A. Dalquen, T. DeLuca, K. Forslund, J. Huerta-Cepas, et al. 2016. “Standardised Benchmarking in the Quest for Orthologs.” Nature methods 13 (5): 425-430. doi:10.1038/nmeth.3830. http://dx.doi.org/10.1038/ nmeth.3830. Published Version doi:10.1038/nmeth.3830 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:29408292 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Methods Manuscript Author . Author manuscript; Manuscript Author available in PMC 2016 October 04. Published in final edited form as: Nat Methods. 2016 May ; 13(5): 425–430. doi:10.1038/nmeth.3830. Standardised Benchmarking in the Quest for Orthologs Adrian M. Altenhoff1,2, Brigitte Boeckmann3, Salvador Capella-Gutierrez4,5,6, Daniel A. Dalquen7, Todd DeLuca8, Kristoffer Forslund9, Jaime Huerta-Cepas9, Benjamin Linard10, Cécile Pereira11,12, Leszek P. Pryszcz4, Fabian Schreiber13, Alan Sousa da Silva13, Damian Szklarczyk14,15, Clément-Marie Train1, Peer Bork9,16,17, Odile Lecompte18, Christian von Mering14,15, Ioannis Xenarios3,19,20, Kimmen Sjölander21, Lars Juhl Jensen22, Maria J. -
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. -
Conference Proceedingssmall
1 COMMITTEES Steering Committee Phil Bourne - University of California, San Diego Eric Davidson - California Institute of Technology Steven Salzberg - The Institute for Genomic Research John Wooley - University of California San Diego, San Diego Supercomputer Center Organizing Committee Pat Blauvelt – LSS Membership Director Karen Hauge – Palo Alto Medical Foundation, Local Arangements Kass Goldfein - Finance Consultant AlishaHolloway – The J. David Gladstone Institutes, Tutorial Chair Sami Khuri – San Jose State University, Poster Chair Ann Loraine – University of North Carolina at Charlotte, CSB Publication Chair Fenglou Mao – University of Georgia, On-Line Registration and Refereeing Website Peter Markstein – in silico Labs, Program Co-Chair Vicky Markstein - Life Sciences Society, Conference Chair, LSS President Jean Tsukamoto - Graphics Design Bill Wang - Sun Microsystems Inc, LSS Information Technology Director Ying Xu – University of Georgia, Program Co-Chair Program Committee Tatsuya Akutsu – Kyoto University Chris Bailey-Kellogg – Dartmouth College Pierre Baldi – University of California Irvine Liming Cai – University of Georgia Bill Cannon – Pacific Northwest National Laboratory Jake Chen – Indiana University Bhaskar DasGupta – University of Illinois Chicago Andrey Gorin – Oak Ridge National Laboratory Matt Hibbs – Princeton University Wen-Lian Hsu – Academia Sinica Tamer Kahveci – University of Florida Carl Kingsford – University of Maryland Christina Leslie – Memorial Sloan-Kettering Cancer Center Jing Li – Case Western Reserve