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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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, -
NEWSLETTER Issue: 491 - November 2020
i “NLMS_491” — 2020/10/28 — 11:56 — page 1 — #1 i i i NEWSLETTER Issue: 491 - November 2020 COXETER THE ROYAL INSTITUTION FRIEZES AND PROBABILIST’S CHRISTMAS GEOMETRY URN LECTURER i i i i i “NLMS_491” — 2020/10/28 — 11:56 — page 2 — #2 i i i EDITOR-IN-CHIEF COPYRIGHT NOTICE Eleanor Lingham (Sheeld Hallam University) News items and notices in the Newsletter may [email protected] be freely used elsewhere unless otherwise stated, although attribution is requested when reproducing whole articles. Contributions to EDITORIAL BOARD the Newsletter are made under a non-exclusive June Barrow-Green (Open University) licence; please contact the author or David Chillingworth (University of Southampton) photographer for the rights to reproduce. Jessica Enright (University of Glasgow) The LMS cannot accept responsibility for the Jonathan Fraser (University of St Andrews) accuracy of information in the Newsletter. Views Jelena Grbic´ (University of Southampton) expressed do not necessarily represent the Cathy Hobbs (UWE) views or policy of the Editorial Team or London Christopher Hollings (Oxford) Mathematical Society. Stephen Huggett Adam Johansen (University of Warwick) ISSN: 2516-3841 (Print) Susan Oakes (London Mathematical Society) ISSN: 2516-385X (Online) Andrew Wade (Durham University) DOI: 10.1112/NLMS Mike Whittaker (University of Glasgow) Early Career Content Editor: Jelena Grbic´ NEWSLETTER WEBSITE News Editor: Susan Oakes Reviews Editor: Christopher Hollings The Newsletter is freely available electronically at lms.ac.uk/publications/lms-newsletter. CORRESPONDENTS AND STAFF MEMBERSHIP LMS/EMS Correspondent: David Chillingworth Joining the LMS is a straightforward process. For Policy Digest: John Johnston membership details see lms.ac.uk/membership. -
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. -
Computational Methods Addressing Genetic Variation In
COMPUTATIONAL METHODS ADDRESSING GENETIC VARIATION IN NEXT-GENERATION SEQUENCING DATA by Charlotte A. Darby A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland June 2020 © 2020 Charlotte A. Darby All rights reserved Abstract Computational genomics involves the development and application of computational meth- ods for whole-genome-scale datasets to gain biological insight into the composition and func- tion of genomes, including how genetic variation mediates molecular phenotypes and disease. New biotechnologies such as next-generation sequencing generate genomic data on a massive scale and have transformed the field thanks to simultaneous advances in the analysis toolkit. In this thesis, I present three computational methods that use next-generation sequencing data, each of which addresses the genetic variations within and between human individuals in a different way. First, Samovar is a software tool for performing single-sample mosaic single-nucleotide variant calling on whole genome sequencing linked read data. Using haplotype assembly of heterozygous germline variants, uniquely made possible by linked reads, Samovar identifies variations in different cells that make up a bulk sequencing sample. We apply it to 13cancer samples in collaboration with researchers at Nationwide Childrens Hospital. Second, scHLAcount is a software pipeline that computes allele-specific molecule counts for the HLA genes from single-cell gene expression data. We use a personalized reference genome based on the individual’s genotypes to reveal allele-specific and cell type-specific gene expression patterns. Even given technology-specific biases of single-cell gene expression data, we can resolve allele-specific expression for these genes since the alleles are often quite different between the two haplotypes of an individual. -
Harvard University Department of Mathematics 2020 - 2021 Fall Directory
Harvard University Department of Mathematics 2020 - 2021 Fall Directory Tel: (617) 495-2171 Fax: (617) 495-5132 www.math.harvard.edu DEPARTMENT OF MATHEMATICS DIRECTORY - FALL 2020 ASL: Associate Senior Lecturer PD: Postdoctoral Fellow BP: Benjamin Peirce Fellow S: Staff E: Emeritus SL: Senior Lecturer F: Faculty SP: Senior Preceptor G: Graduate Student V: Visitor L: Lecturer VP: Visiting Professor P: Preceptor GROUP EMAIL ADDRESSES Affiliates Lecturers Emeriti Mainoffice Everyone (Everyone at CMSA) Preceptors Everyone (Everyone at Math Dept) Snr_Fac (Senior Faculty) Grad (Grad students) Staff Jnr_Fac (Junior Faculty) Visitors (PostDocs, Research Associates and Fellows) Department email addresses followed by: @math.harvard.edu; CMSA email addresses followed by: @cmsa.fas.harvard.edu NAME EMAIL OFFICE PHONE # ADHIKARI, Arka (G) adhikari 321b ALAEE, Aghil (V - CMSA) aghil.alaee ARMSTRONG, Maureen (S) maureen 332 5-1980 AUROUX, Denis (F) auroux 539 5-5487 BALIBANU, Ana (BP) anab 236 6-4492 BALL, Andrew (S) ball 242h 6-1986 BAMBERG, Paul (SL) bamberg 322 5-9560 BARKLEY, Grant (G) gbarkley 333e BEJLERI, Dori (BP) bejleri 525 5-2334 BEN-ELIEZER, Omri (PD - CMSA) omribene BETTS, Alex (PD) 226h 5-2124 BOGAEVSKY, Tatyana (S - CMSA) bogaevsky 20 Garden 105 6-1778 BONGERS, Tyler (L) bongers 209.3 5-1365 BORETSKY, Jonathan (G) jboretsky 321c DEPARTMENT OF MATHEMATICS DIRECTORY - FALL 2020 BRALEY, Emily (P) braley 225 6-9122 BRENNECKE, Christian (BP) brennecke 239 5-8797 BRENTANA, Pam (S) pbrentan 325 5-5334 CAIN, Wes (SL) jcain2 515 5-1790 CASS, -
Big Data, Moocs, and ... (PDF)
HHMI Constellation Studios for Science Education November 13-15, 2015 | HHMI Headquarters | Chevy Chase, MD Big Data, MOOCs, and Quantitative Education for Biologists Co-Chairs Pavel Pevzner, University of California- San Diego Sarah Elgin, Washington University Studio Objectives Discuss existing challenges in bioinformatics education with experts in computational biology and quantitative biology education, Evaluate best practices in teaching quantitative and computational biology, and Collaborate with scientist educators to develop instructional modules to support a biology curriculum that includes quantitative approaches. Friday | November 13 4:00 pm Arrival Registration Desk 5:30 – 6:00 pm Reception Great Hall 6:00 – 7:00 pm Dinner Dining Room 7:00 – 7:15 pm Welcome K202 David Asai, HHMI Cynthia Bauerle, HHMI Pavel Pevzner, University of California-San Diego Sarah Elgin, Washington University Alex Hartemink, Duke University 7:15 – 8:00 pm How to Maximize Interaction and Feedback During the Studio K202 Cynthia Bauerle and Sarah Simmons, HHMI 8:00 – 9:00 pm Keynote Presentation K202 "Computing + Biology = Discovery" Speakers: Ran Libeskind-Hadas, Harvey Mudd College Eliot Bush, Harvey Mudd College 9:00 – 11:00 pm Social The Pilot Saturday | November 14 7:30 – 8:15 am Breakfast Dining Room 8:30 – 10:00 am Lecture session 1 K202 Moderator: Pavel Pevzner 834a-854a “How is body fat regulated?” Laurie Heyer, Davidson College 856a-916a “How can we find mutations that cause cancer?” Ben Raphael, Brown University “How does a tumor evolve over time?” 918a-938a Russell Schwartz, Carnegie Mellon University “How fast do ribosomes move?” 940a-1000a Carl Kingsford, Carnegie Mellon University 10:05 – 10:55 am Breakout working groups Rooms: S221, (coffee available in each room) N238, N241, N140 1. -
Newsletter · Thursday 18Th
KEEP UPDATED NEWSLETTER · THURSDAY 18TH ICIAM'S JOURNEY Like its predecessors, a congress such as ICIAM 2019 would have never been countries like South Africa. ICIAM possible without the organization and supervision of the International Council has the ability to promote for Industrial and Applied Mathematics (ICIAM), a formal entity created in 1990 mathematics all over the world". to supervise these quadrennial meetings. From Paris 1987 to Valencia 2019 many things have changed, and not just in the field of Industrial and Applied The current and future presidents Mathematics. of the Council agree in that ICIAM 2019 in Valencia has been an The original societies that founded ICIAM (GAMM, IMA, SIAM, and SMAI) are absolute success. "In my opinion now surrounded by many other members from around the world and the everything has worked very well Council has expanded its activities significantly since 2004. despite the huge number of participants", says Esteban. "The The Council is responsible for choosing the venue and the 27 invited speakers, conferences are of high quality and which are chosen with a diverse criteria, not only mathematically and in general, especially in the main geographicall, but also with respect to academic vs. industrial work, gender or conferences —invited and prizes— type of academic institution. Furthermore, it is also responsible for overseeing the lecturers have made a real the selection of the five ICIAM prizes —Collatz, Lagrange, Maxwell, Su Buchin, Ya-Xiang Yuan recalls attending ICIAM in effort to present their results in a and Pioneer— awarded every congress. its 1995 edition in Hamburg. "We were comprehensible and pleasant way only 20 Chinese and now we're like 300, for a great variety of participants as well as create a database with all so the same thing can happen to working in very diverse areas ". -
Marshall Hall's Conjecture and Gaps Between Integer Points on Mordell
On Marshall Hall's Conjecture and Gaps Between Integer Points on Mordell Elliptic Curves Ryan D'Mello Benet Academy, Lisle, IL Mailing address: Benet Academy, 2200 Maple Avenue, Lisle, IL 60532, USA e-mail: [email protected] October 2, 2014 Abstract 3 For a non-square integer x 2 N, let kx denote the distance between x and the perfect 3 p square closest to x . A conjecture of Marshall Hall states that the ratios rx = x=kx, are bounded above. (Elkies has shown that any such bound must exceed 46.6.) Let fxng be the sequence of "Hall numbers": positive non-square integers for which rxn exceeds 1. Extensive computer searches have identified approximately 50 Hall numbers. (It can be proved that infinitely many exist.) In this paper we study the minimum gap between consecutive Hall 1 1 6 numbers. We prove that for all n, xn+1 − xn > 5 xn , with stronger gaps applying when 1 1 3 4 xn is close to perfect even or odd squares (≈ xn or ≈ xn , respectively). This result has obvious implications for the minimum "horizontal gap" (and hence straight line and arc distance) between integer points (whose x-coordinates exceed k2) on the Mordell elliptic curves x3 − y2 = k , a question that does not appear to have been addressed. 1 Introduction [Appendix A includes a detailed expository coverage of interesting and relevant history and background on Hall's conjecture, its relationship to other math questions/conjectures, topics, and techniques; and some key applications of these techniques.] 3 For a non-square integer x 2 N, let kx denote the distance between x and the perfect square 3 p closest to x . -
Computational Biology and Bioinformatics
Vol. 30 ISMB 2014, pages i1–i2 BIOINFORMATICS EDITORIAL doi:10.1093/bioinformatics/btu304 Editorial This special issue of Bioinformatics serves as the proceedings of The conference used a two-tier review system, a continuation the 22nd annual meeting of Intelligent Systems for Molecular and refinement of a process begun with ISMB 2013 in an effort Biology (ISMB), which took place in Boston, MA, July 11–15, to better ensure thorough and fair reviewing. Under the revised 2014 (http://www.iscb.org/ismbeccb2014). The official confer- process, each of the 191 submissions was first reviewed by at least ence of the International Society for Computational Biology three expert referees, with a subset receiving between four and (http://www.iscb.org/), ISMB, was accompanied by 12 Special eight reviews, as needed. These formal reviews were frequently Interest Group meetings of one or two days each, two satellite supplemented by online discussion among reviewers and Area meetings, a High School Teachers Workshop and two half-day Chairs to resolve points of dispute and reach a consensus on tutorials. Since its inception, ISMB has grown to be the largest each paper. Among the 191 submissions, 29 were conditionally international conference in computational biology and bioinfor- accepted for publication directly from the first round review Downloaded from matics. It is expected to be the premiere forum in the field for based on an assessment of the reviewers that the paper was presenting new research results, disseminating methods and tech- clearly above par for the conference. A subset of 16 papers niques and facilitating discussions among leading researchers, were viewed as potentially in the top tier but raised significant practitioners and students in the field. -
Notices of the AMS 595 Mathematics People NEWS
NEWS Mathematics People contrast electrical impedance Takeda Awarded 2017–2018 tomography, as well as model Centennial Fellowship reduction techniques for para- bolic and hyperbolic partial The AMS has awarded its Cen- differential equations.” tennial Fellowship for 2017– Borcea received her PhD 2018 to Shuichiro Takeda. from Stanford University and Takeda’s research focuses on has since spent time at the Cal- automorphic forms and rep- ifornia Institute of Technology, resentations of p-adic groups, Rice University, the Mathemati- especially from the point of Liliana Borcea cal Sciences Research Institute, view of the Langlands program. Stanford University, and the He will use the Centennial Fel- École Normale Supérieure, Paris. Currently Peter Field lowship to visit the National Collegiate Professor of Mathematics at Michigan, she is Shuichiro Takeda University of Singapore and deeply involved in service to the applied and computa- work with Wee Teck Gan dur- tional mathematics community, in particular on editorial ing the academic year 2017–2018. boards and as an elected member of the SIAM Council. Takeda obtained a bachelor's degree in mechanical The Sonia Kovalevsky Lectureship honors significant engineering from Tokyo University of Science, master's de- contributions by women to applied or computational grees in philosophy and mathematics from San Francisco mathematics. State University, and a PhD in 2006 from the University —From an AWM announcement of Pennsylvania. After postdoctoral positions at the Uni- versity of California at San Diego, Ben-Gurion University in Israel, and Purdue University, since 2011 he has been Pardon Receives Waterman assistant and now associate professor at the University of Missouri at Columbia.