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检索条件"机构=Interdepartmental Graduate Program in Bioinformatics and Computational Biology"
178 条 记 录,以下是121-130 订阅
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Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation
Research Square
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Research Square 2021年
作者: Freedman, Matthew L. Baca, Sylvan C. Singler, Cassandra Zacharia, Soumya Seo, Ji-Heui Morova, Tunc Hach, Faraz Ding, Yi Schwarz, Tommer Huang, Chia-Chi Flora Kalita, Cynthia Groha, Stefan Pomerantz, Mark M. Wang, Victoria Linder, Simon Sweeney, Christopher J. Zwart, Wilbert Lack, Nathan A. Pasaniuc, Bogdan Takeda, David Y. Gusev, Alexander Department of Medical Oncology Dana-Farber Cancer Institute BostonMA United States Center for Functional Cancer Epigenetics Dana-Farber Cancer Institute BostonMA United States The Eli and Edythe L. Broad Institute CambridgeMA United States Laboratory of Genitourinary Cancer Pathogenesis Center for Cancer Research National Cancer Institute BethesdaMD United States Vancouver Prostate Centre University of British Columbia VancouverBC Canada Bioinformatics Interdepartmental Program UCLA Los AngelesCA United States Division of Genetics Brigham & Women’s Hospital BostonMA United States Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute BostonMA United States Department of Biostatistics Harvard School of Public Health BostonMA United States Division of Oncogenomics Oncode Institute The Netherlands Cancer Institute Amsterdam Netherlands Laboratory of Chemical Biology Institute for Complex Molecular Systems Department of Biomedical Engineering Eindhoven University of Technology Eindhoven Netherlands School of Medicine Koç University Istanbul Turkey Department of Computational Medicine David Geffen School of Medicine at UCLA Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine at UCLA Los AngelesCA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine at UCLA Los AngelesCA United States
Methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs), are widely used to functionally annotate trait-associated variants, but they are limited ... 详细信息
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Ten quick tips for deep learning in biology
arXiv
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arXiv 2021年
作者: Lee, Benjamin D. Gitter, Anthony Greene, Casey S. Raschka, Sebastian Maguire, Finlay Titus, Alexander J. Kessler, Michael D. Lee, Alexandra J. Chevrette, Marc G. Stewart, Paul Allen Britto-Borges, Thiago Cofer, Evan M. Yu, Kun-Hsing Carmona, Juan Jose Fertig, Elana J. Kalinin, Alexandr A. Signal, Beth Lengerich, Benjamin J. Triche, Timothy J. Boca, Simina M. In-Q-Tel Labs School of Engineering and Applied Sciences Harvard University Department of Genetics Harvard Medical School United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Statistics University of Wisconsin Madison United States Faculty of Computer Science Dalhousie University Canada University of New Hampshire Bioeconomy.XYZ United States Department of Oncology Johns Hopkins University United States Institute for Genome Sciences University of Maryland School of Medicine United States Genomics and Computational Biology Graduate Program University of Pennsylvania United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania United States Wisconsin Institute for Discovery Department of Plant Pathology University of Wisconsin-Madison United States Department of Biostatistics and Bioinformatics Moffitt Cancer Center TampaFL United States Section of Bioinformatics and Systems Cardiology Klaus Tschira Institute for Integrative Computational Cardiology University Hospital Heidelberg Germany University Hospital Heidelberg Germany Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ United States Graduate Program in Quantitative and Computational Biology Princeton University PrincetonNJ United States Department of Biomedical Informatics Harvard Medical School United States Department of Pathology Brigham and Women's Hospital United States Philips Healthcare CambridgeMA United States Philips Research
Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and us... 详细信息
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Random-effects substitution models for phylogenetics via scalable gradient approximations
arXiv
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arXiv 2023年
作者: Magee, Andrew F. Holbrook, Andrew J. Pekar, Jonathan E. Caviedes-Solis, Itzue W. Matsen, Fredrick A. Baele, Guy Wertheim, Joel O. Ji, Xiang Lemey, Philippe Suchard, Marc A. Department of Biostatistics Jonathan and Karin Fielding School of Public Health University of California Los Angeles Los AngelesCA United States Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA United States Department of Biomedical Informatics University of California San Diega La Jolla CA United States Department of Biology Swarthmore College SwarthmorePA United States Howard Hughes Medical Institute SeattleWA United States Computational Biology Program Fred Hutchinson Cancer Research Center SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Department of Statistics University of Washington SeattleWA United States Department of Microbiology Immunology and Transplantation Rega Institute KU Leuven Leuven Belgium Department of Medicine University of California San Diego La Jolla CA United States Department of Mathematics Tulane University New OrleansLA United States Department of Biomathematics David Geffen School of Medicine at UCLA University of California Los Angeles Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine at UCLA Universtiy of California Los Angeles Los AngelesCA United States
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models t... 详细信息
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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials
arXiv
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arXiv 2023年
作者: Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbi... 详细信息
来源: 评论
Comprehensive Functional Characterization of Germline ETV6 Variants Associated with Inherited Predisposition to Acute Lymphoblastic Leukemia in Children
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BLOOD 2016年 第22期128卷 1085-1085页
作者: Nishii, Rina Baskin, Rebekah Moriyama, Takaya Hoshitsuki, Keito Metzger, Monika L. Wu, Gang Devidas, Meenakshi Yang, Wenjian Tedrick, Paige Quinn, Emily Gastier-Foster, Julie M. Raetz, Elizabeth Larsen, Eric Martin, Paul L. Bowman, W. Paul Winick, Naomi Takagi, Masatoshi Pui, Ching-Hon Evans, William E. Zhang, Jinghui Relling, Mary V. Hunger, Stephen P. Mullighan, Charles Loh, Mignon L. Nichols, Kim E. Yang, Jun J. Hematological Malignancies Program and Department of Pharmaceutical Sciences St. Jude Children's Research Hospital Memphis TN Department of Pediatrics and Developmental Biology Tokyo Medical and Dental University Graduate School of Medicine Tokyo Japan Department of Oncology St. Jude Children's Research Hospital Memphis TN School of Pharmacy University of Pittsburgh Pittsburgh PA Department of Computational Biology St. Jude Children's Research Hospital Memphis TN Department of Biostatistics College of Medicine Public Health and Health Professions University of Florida Gainesville FL Department of Pathology and Laboratory Medicine Nationwide Children's Hospital Columbus OH Huntsman Cancer Institute University of Utah Salt Lake City UT Maine Children's Cancer Program Scarborough ME Department of Pediatrics Duke University Durham NC Cook Children's Medical Center Fort Worth TX Pediatric Hematology Oncology University of Texas Southwestern Medical Center Dallas TX Oncology St. Jude Children's Research Hospital Memphis TN Department of Computational Biology and Bioinformatics St. Jude Children's Research Hospital Memphis TN Department of Pediatrics and Center for Childhood Cancer Research Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine Philadelphia PA Department of Pathology St. Jude Children's Research Hospital Memphis TN Department of Pediatrics Benioff Children's Hospital and Helen Diller Family Comprehensive Cancer Center University of California San Francisco CA
1085
来源: 评论
Technology dictates algorithms: Recent developments in read alignment
arXiv
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arXiv 2020年
作者: Alser, Mohammed Rotman, Jeremy Taraszka, Kodi Shi, Huwenbo Baykal, Pelin Icer Yang, Harry Taegyun Xue, Victor Knyazev, Sergey Singer, Benjamin D. Balliu, Brunilda Koslicki, David Skums, Pavel Zelikovsky, Alex Alkan, Can Mutlu, Onur Mangul, Serghei Computer Science Department ETH Zürich Zürich8092 Switzerland Computer Engineering Department Bilkent University Bilkent Ankara 06800 Turkey Department of Computer Science University of California Los Angeles Los AngelesCA90095 United States Department of Epidemiology Harvard T.H. Chan School of Public Health MA02115 United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA02142 United States Department of Computer Science Georgia State University AtlantaGA30302 United States Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles Los AngelesCA90095 United States Division of Pulmonary and Critical Care Medicine Northwestern University Feinberg School of Medicine ChicagoIL60611 United States Department of Biochemistry & Molecular Genetics Northwestern University Feinberg School of Medicine United States Simpson Querrey Center for Epigenetics Northwestern University Feinberg School of Medicine ChicagoIL60611 United States Department of Computational Medicine University of California Los Angeles Los AngelesCA90095 United States Computer Science and Engineering Pennsylvania State University University ParkPA16801 United States Biology Department Pennsylvania State University University ParkPA16801 United States The Huck Institutes of the Life Sciences Pennsylvania State University University ParkPA16801 United States The Laboratory of Bioinformatics I.M. Sechenov First Moscow State Medical University Moscow119991 Russia Bilkent-Hacettepe Health Sciences and Technologies Program Ankara Turkey Department of Clinical Pharmacy School of Pharmacy University of Southern California Los AngelesCA90089 United States
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate e... 详细信息
来源: 评论
Cover Image, Volume 86, Issue 5
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Proteins: Structure, Function, and bioinformatics 2018年 第5期86卷
作者: J. C. Gaines S. Acebes A. Virrueta M. Butler L. Regan C. S. O'Hern Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) Yale University New Haven Connecticut 06520 Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 Department of Physics and Astronomy University of Southern California Los Angeles California 90007 Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 Department of Chemistry Yale University New Haven Connecticut 06520 Department of Physics Yale University New Haven Connecticut 06520 Department of Applied Physics Yale University New Haven Connecticut 06520
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Front Cover: Design, Synthesis, and Characterization of Novel Styryl Dyes as Fluorescent Probes for Tau Aggregate Detectionin Vitroand in Cells (Chem. Asian J. 6/2024)
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Chemistry – An Asian Journal 2024年 第6期19卷
作者: Withsakorn Sangsuwan Kriangsak Faikhruea Kotchakorn Supabowornsathit Don Sangsopon Praewphan Ingrungruanglert Hathaichanok Chuntakaruk Napatsaporn Nuntavanotayan Kittiporn Nakprasit Nipan Israsena Thanyada Rungrotmongkol Pitak Chuawong Tirayut Vilaivan Chanat Aonbangkhen Center of Excellence in Natural Products Chemistry (CENP) Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science Special Research Unit for Advanced Magnetic Resonance (AMR) Kasetsart University Bangkok 10900 Thailand These authors are contributed equally. Organic Synthesis Research Unit Department of Chemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Stem Cell and Cell Therapy Research Unit and Department of Pharmacology Faculty of Medicine Chulalongkorn University Bangkok 10330 Thailand Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok 10330 Thailand Center of Excellence in Structural and Computational Biology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand
来源: 评论
Cell2Sentence: teaching large language models the language of biology  24
Cell2Sentence: teaching large language models the language o...
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Proceedings of the 41st International Conference on Machine Learning
作者: Daniel Levine Syed Asad Rizvi Sacha Lévy Nazreen Pallikkavaliyaveetil David Zhang Xingyu Chen Sina Ghadermarzi Ruiming Wu Zihe Zheng Ivan Vrkic Anna Zhong Daphne Raskin Insu Han Antonio Henrique De Oliveira Fonseca Josue Ortega Caro Amin Karbasi Rahul M. Dhodapkar David Van Dijk Department of Computer Science Yale University New Haven CT School of Engineering Applied Science University of Pennsylvania Philadelphia PA School of Computer and Communication Sciences Swiss Federal Institute of Technology Lausanne Lausanne Switzerland Department of Computer Science Yale University New Haven CT and Department of Neuroscience Yale School of Medicine New Haven CT Department of Computer Science Yale University New Haven CT and Department of Neuroscience Yale School of Medicine New Haven CT and Wu Tsai Institute Yale University New Haven CT Google and Yale Institute for Foundations of Data Science New Haven CT and Department of Computer Science Yale University New Haven CT and Yale School of Engineering and Applied Science New Haven CT Roski Eye Institute University of Southern California Los Angeles CA and Department of Internal Medicine (Cardiology) Yale School of Medicine New Haven CT Department of Computer Science Yale University New Haven CT and Yale Institute for Foundations of Data Science New Haven CT and Wu Tsai Institute Yale University New Haven CT and Cardiovascular Research Center Yale School of Medicine New Haven CT and Interdepartmental Program in Computational Biology & Bioinformatics Yale University New Haven CT and Department of Internal Medicine (Cardiology) Yale School of Medicine New Haven CT
We introduce Cell2Sentence (C2S), a novel method to directly adapt large language models to a biological context, specifically single-cell transcriptomics. By transforming gene expression data into "cell sentence...
来源: 评论
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data
Research Square
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Research Square 2021年
作者: Zhang, Martin Jinye Hou, Kangcheng Pasaniuc, Bogdan Price, Alkes L. Dey, Kushal K. Jagadeesh, Karthik A. Weinand, Kathryn Sakaue, Saori Taychameekiatchai, Aris Rao, Poorvi Pisco, Angela Oliveira Zou, James Wang, Bruce Gandal, Michael Raychaudhuri, Soumya Harvard University United States Osaka University Japan Department of Epidemiology Harvard T.H. Chan School of Public Health BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Bioinformatics Interdepartmental Program University of California Los Angeles Los AngelesCA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Center for Data Sciences Brigham and Women’s Hospital BostonMA United States Division of Genetics Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Division of Rheumatology Inflammation and Immunity Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States Department of Medicine and Liver Center University of California San Francisco San FranciscoCA United States Developmental and Stem Cell Biology Graduate Program University of California San Francisco San FranciscoCA United States Chan Zuckerberg Biohub San FranciscoCA United States Department of Electrical Engineering Stanford University Palo AltoCA United States Department of Biomedical Data Science Stanford University Palo AltoCA United States Department of Psychiatry David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Program in Neurobehavioral Genetics Semel Institute David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Versus Arthritis Centre for Genetics and Genomic
Gene expression at the individual cell-level resolution, as quantified by single-cell RNA-sequencing (scRNA-seq), can provide unique insights into the pathology and cellular origin of diseases and complex traits. Here... 详细信息
来源: 评论