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检索条件"机构=Systems Biology and Computer Science Program"
179 条 记 录,以下是61-70 订阅
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c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont (vol 15, pg 554, 2018)
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NATURE 2019年 第7744期566卷 E7-E7页
作者: Xu, Mo Pokrovskii, Maria Ding, Yi Yi, Ren Au, Christy Harrison, Oliver J. Galan, Carolina Belkaid, Yasmine Bonneau, Richard Littman, Dan R. Molecular Pathogenesis Program The Kimmel Center for Biology and Medicine of the Skirball Institute New York University School of Medicine New York USA Department of Pathology and Laboratory Medicine University of Rochester Medical Center Rochester USA Courant Institute of Mathematical Sciences Computer Science Department New York University New York USA The Howard Hughes Medical Institute New York University School of Medicine New York USA Mucosal Immunology Section Laboratory of Parasitic Diseases National Institute of Allergy and Infectious Diseases NIH Bethesda USA NIAID Microbiome Program NIH Bethesda USA Center for Genomics and Systems Biology Department of Biology New York University New York USA Center for Computational Biology Flatiron Institute Simons Foundation New York USA
In this Letter, the 'Competing interests' statement should have stated: 'D.R.L. consults for and has equity in Vedanta Biosciences.' The original Letter has not been corrected.
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A Guide to Tracking Phylogenies in Parallel and Distributed Agent-based Evolution Models
arXiv
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arXiv 2024年
作者: Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States
computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry ... 详细信息
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Distributional bias compromises leave-one-out cross-validation
arXiv
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arXiv 2024年
作者: Austin, George I. Pe’er, Itsik Korem, Tal Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY United States Program for Mathematical Genomics Department of Systems Biology Columbia University Irving Medical Center New YorkNY United States Department of Computer Science Columbia University New YorkNY United States Department of Obstetrics and Gynecology Columbia University Irving Medical Center New YorkNY United States
Cross-validation is a common method for estimating the predictive performance of machine learning models. In a data-scarce regime, where one typically wishes to maximize the number of instances used for training the m... 详细信息
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Colloidal Structure and Proton Conductivity of the Gel within the Electrosensory Organs of Cartilaginous Fishes
SSRN
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SSRN 2021年
作者: Phillips, Molly Wheeler, Alauna Robinson, Matthew J. Leppert, Valerie Jia, Manping Rolandi, Marco Hirst, Linda S. Amemiya, Chris T. Department of Biology University of Washington SeattleWA98195 United States Department of Molecular and Cell Biology University of California Merced MercedCA95343 United States Department of Physics University of California Merced MercedCA95343 United States Department of Materials Science and Engineering University of California Merced MercedCA95343 United States Department of Electrical and Computer Engineering Baskin School of Engineering University of California Santa Cruz Santa CruzCA95064 United States Quantitative and Systems Biology Program University of California Merced MercedCA95343 United States
Cartilaginous fishes possess gel-filled tubular sensory organs called Ampullae of Lorenzini (AoL) that are used to detect electric fields. Although recent studies have identified various components of AoL gel, it has ... 详细信息
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Structured Downsampling for Fast, Memory-efficient Curation of Online Data Streams
arXiv
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arXiv 2024年
作者: Moreno, Matthew Andres Zaman, Luis Dolson, Emily Department of Ecology and Evolutionary Biology Ann Arbor United States Center for the Study of Complex Systems Ann Arbor United States Michigan Institute for Data and AI in Society Ann Arbor United States University of Michigan Ann Arbor United States Department of Computer Science and Engineering East Lansing United States Program in Ecology Evolution and Behavior East Lansing United States Michigan State University East Lansing United States
Operations over data streams typically hinge on efficient mechanisms to aggregate or summarize history on a rolling basis. For high-volume data steams, it is critical to manage state in a manner that is fast and memor... 详细信息
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Ten simple rules for reproducible research in jupyter notebooks
arXiv
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arXiv 2018年
作者: Rule, Adam Birmingham, Amanda Zuniga, Cristal Altintas, Ilkay Huang, Shih-Cheng Knight, Rob Moshiri, Niema Nguyen, Mai H. Rosenthal, Sara Brin Pérez, Fernando Rose, Peter W. Design Lab UC San Diego San DiegoCA United States Center for Computational Biology and Bioinformatics UC San Diego San DiegoCA United States Department of Pediatrics UC San Diego San DiegoCA United States Data Science Hub San Diego Supercomputer Center UC San Diego San DiegoCA United States Departments of Bioengineering and Computer Science and Engineering Center for Microbiome Innovation UC San Diego San DiegoCA United States Bioinformatics and Systems Biology Graduate Program UC San Diego San DiegoCA United States Department of Statistics Berkeley Institute for Data Science UC Berkeley Lawrence Berkeley National Laboratory BerkeleyCA United States Biomedical Informatics Graduate Program Stanford University StanfordCA United States
Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and th... 详细信息
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cytoNet: Spatiotemporal network analysis of cell communities (vol 18, e1009846, 2022)
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PLOS COMPUTATIONAL biology 2022年 第11期18卷 e1009846页
作者: Mahadevan, A. S. Long, B. L. Hu, C. W. Ryan, D. T. Grandel, N. E. Department of Bioengineering University of Pennsylvania Philadelphia Pennsylvania United States of America. Department of Bioengineering Rice University Houston Texas United States of America. Systems Synthetic and Physical Biology Program Rice University Houston Texas United States of America. Department of Biomedical Engineering University of Texas at San Antonio San Antonio Texas United States of America. Biophysics Graduate Program University of California Berkeley California United States of America. Department of Oral & Maxillofacial Surgery University of Texas Health Science Center at San Antonio San Antonio Texas United States of America. Department of Electrical and Computer Engineering Rice University Houston Texas United States of America.
We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network scienc... 详细信息
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Predictable and precise template-free CRISPR editing of pathogenic variants (vol 563, pg 646, 2018)
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NATURE 2019年 第7746期567卷 E1-E2页
作者: Shen, Max W. Arbab, Mandana Hsu, Jonathan Y. Worstell, Daniel Culbertson, Sannie J. Krabbe, Olga Cassa, Christopher A. Liu, David R. Gifford, David K. Sherwood, Richard I. Computational and Systems Biology Program Massachusetts Institute of Technology Cambridge USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge USA Merkin Institute of Transformative Technologies in Healthcare Broad Institute of Harvard and MIT Cambridge USA Department of Chemistry and Chemical Biology Harvard University Cambridge USA Howard Hughes Medical Institute Harvard University Cambridge USA Department of Biological Engineering Massachusetts Institute of Technology Cambridge USA Molecular Pathology Unit Center for Cancer Research and Center for Computational and Integrative Biology Massachusetts General Hospital Charlestown USA Division of Genetics Department of Medicine Brigham and Women’s Hospital and Harvard Medical School Boston USA Hubrecht Institute for Developmental Biology and Stem Cell Research Royal Netherlands Academy of Arts and Sciences (KNAW) Utrecht The Netherlands Broad Institute of MIT and Harvard Cambridge USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge USA
In this Article, a data processing error affected Fig. 3e and Extended Data Table 2; these errors have been corrected online.
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Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes (vol 12, pg 631, 2020)
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GENETICS IN MEDICINE 2020年 第8期22卷 1427-1427页
作者: Chang, Willie H. Mashouri, Pouria Lozano, Alexander X. Johnstone, Brittney Husic, Mia Olry, Annie Maiella, Sylvie Balci, Tugce B. Sawyer, Sarah L. Robinson, Peter N. Rath, Ana Brudno, Michael Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada Department of Computer Science Princeton University Princeton NJ USA Faculty of Medicine University of Toronto Toronto ON Canada Department of Materials Science & Engineering Stanford University Stanford CA USA Sunnybrook Health Sciences Centre Toronto ON Canada Orphanet Institut national de la santé et de la recherche médicale Paris France Medical Genetics Program of Southwestern Ontario London Health Sciences Centre London ON Canada Department of Genetics Children’s Hospital of Eastern Ontario and Children’s Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON Canada The Jackson Laboratory for Genomic Medicine Farmington CT USA Institute for Systems Genomics University of Connecticut Farmington CT USA Department of Computer Science University of Toronto Toronto ON Canada Genetics and Genome Biology Program The Hospital for Sick Children Toronto ON Canada University Health Network Toronto ON Canada
PurposeComputational documentation of genetic disorders is highly reliant on structured data for differential diagnosis, pathogenic variant identification, and patient matchmaking. However, most information on rare di... 详细信息
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DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
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Nature 2015年 第7583期528卷 517-522页
作者: Huang, Wendy Thomas, Benjamin Flynn, Ryan A. Gavzy, Samuel J. Wu, Lin Kim, Sangwon V. Hall, Jason A. Miraldi, Emily R. Ng, Charles P. Rigo, Frank W. Meadows, Sarah Montoya, Nina R. Herrera, Natalia G. Domingos, Ana I. Rastinejad, Fraydoon Myers, Richard M. Fuller-Pace, Frances V. Bonneau, Richard Chang, Howard Y. Acuto, Oreste Littman, Dan R. Kimmel Center for Biology and Medicine Skirball Institute New York University School of Medicine New York 10016 NY United States Sir William Dunn School of Pathology University of Oxford Oxford OX1 3RE United Kingdom Center for Personal Dynamic Regulomes Stanford University Stanford 94305 CA United States Center for Genomics and Systems Biology Department of Biology New York University New York 10003 NY United States Courant Institute of Mathematical Sciences Computer Science Department New York University New York 10012 NY United States Simons Center for Data Analysis Simons Foundation New York 10010 NY United States Isis Pharmaceuticals Carlsbad 92010 CA United States HudsonAlpha Institute for Biotechnology Huntsville 35806 AL United States Instituto Gulbenkian de Ciencia Oeiras 2780-156 Portugal Integrative Metabolism Program Sanford Burnham Prebys Medical Discovery Institute Orlando 32827 FL United States Division of Cancer Research University of Dundee Dundee DD1 9SY United Kingdom Howard Hughes Medical Institute New York University School of Medicine New York 10016 NY United States
T helper 17 (TH17) lymphocytes protect mucosal barriers from infections, but also contribute to multiple chronic inflammatory diseases. Their differentiation is controlled by RORγt, a ligand-regulated nuclear recepto...
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