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检索条件"机构=Program in Computational Biology and Bioinformatics"
524 条 记 录,以下是191-200 订阅
An Open-Source Knowledge Graph Ecosystem for the Life Sciences
arXiv
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arXiv 2023年
作者: Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A
Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significa... 详细信息
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IBEX: An open and extensible method for high content multiplex imaging of diverse tissues
arXiv
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arXiv 2021年
作者: Radtke, Andrea J. Chu, Colin J. Yaniv, Ziv Yao, Li Marr, James Beuschel, Rebecca T. Ichise, Hiroshi Gola, Anita Kabat, Juraj Lowekamp, Bradley Speranza, Emily Croteau, Joshua Thakur, Nishant Jonigk, Danny Davis, Jeremy Hernandez, Jonathan M. Germain, Ronald N. Center for Advanced Tissue Imaging Laboratory of Immune System Biology NIAID NIH BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology NIAID NIH BethesdaMD United States Translational Health Sciences Bristol Medical School University of Bristol United Kingdom Bioinformatics and Computational Bioscience Branch NIAID NIH BethesdaMD United States Howard Hughes Medical Institute Chevy ChaseMD United States Leica Microsystems Inc. Wetzlar Germany Howard Hughes Medical Institute Robin Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Biological Imaging Section Research Technologies Branch NIAID NIH BethesdaMD United States Innate Immunity and Pathogenesis Section Laboratory of Virology NIAID NIH HamiltonMT United States Department of Business Development BioLegend Inc. San DiegoCA United States Institute of Pathology Hannover Medical School Hannover Germany Surgical Oncology Program Metastasis Biology Section Center for Cancer Research National Cancer Institute NIH BethesdaMD United States
High content imaging is needed to catalogue the variety of cellular phenotypes and multi-cellular ecosystems present in metazoan tissues. We recently developed Iterative Bleaching Extends multi-pleXity (IBEX), an iter... 详细信息
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Expanding the computational Toolbox for Single-Particle Cryo-Electron Microscopy
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Microscopy and Microanalysis 2019年 第S2期25卷 2686-2687页
作者: Alberto Bartesaghi Department of Computer Science Trinity College of Arts & Sciences Department of Biochemistry Duke University School of Medicine Department of Electrical and Computer Engineering Pratt School of Engineering Duke Institute for Brain Sciences Computational Biology and Bioinformatics Program Duke University Durham NC USA.
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Distinct adipose progenitor cells emerging with age drive active adipogenesis
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Science (New York, N.Y.) 2025年 第6745期388卷 eadj0430页
作者: Wang, Guan Li, Gaoyan Song, Anying Zhao, Yutian Yu, Jiayu Wang, Yifan Dai, Wenting Salas, Martha Qin, Hanjun Medrano, Leonard Dow, Joan Li, Aimin Armstrong, Brian Fueger, Patrick T. Yu, Hua Zhu, Yi Shao, Mengle Wu, Xiwei Jiang, Lei Campisi, Judith Yang, Xia Wang, Qiong A. Department of Molecular and Cellular Endocrinology Arthur Riggs Diabetes and Metabolism Research Institute City of Hope Medical Center Duarte CA USA Department of Integrative Biology and Physiology University of California Los Angeles CA United States Light Microscopy Core City of Hope Medical Center Duarte CA USA The Integrative Genomics Core City of Hope Medical Center Duarte CA USA Division of Developmental and Translational Diabetes and Endocrinology Research City of Hope Medical Center Duarte CA USA Comprehensive Metabolic Phenotyping Core City of Hope Medical Center Duarte CA USA Pathology Core of Shared Resources City of Hope Medical Center Duarte CA USA Comprehensive Cancer Center Beckman Research Institute City of Hope Medical Center Duarte CA USA Children's Nutrition Research Center Department of Pediatrics Baylor College of Medicine Houston TX United States Key Laboratory of Immune Response and Immunotherapy Shanghai Institute of Immunity and Infection Chinese Academy of Sciences Shanghai China Buck Institute for Research on Aging Novato CA United States Bioinformatics Interdepartmental Program University of California Los Angeles CA United States Institute for Quantitative and Computational Biosciences University of California Los Angeles CA United States Molecular and Medical Pharmacology University of California Los Angeles CA United States
Starting at middle age, adults often suffer from visceral adiposity and associated adverse metabolic disorders. Lineage tracing in mice revealed that adipose progenitor cells (APCs) in visceral fat undergo extensive a...
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Tegavivint triggers TECR-dependent nonapoptotic cancer cell death
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Nature chemical biology 2025年 2025 May 26页
作者: Logan Leak Ziwei Wang Alby J Joseph Brianna Johnson Alyssa A Chan Cassandra M Decosto Leslie Magtanong Pin-Joe Ko Weaverly Colleen Lee Joan Ritho Sophia Manukian Alec Millner Shweta Chitkara Jennifer J Salinas Rachid Skouta Matthew G Rees Melissa M Ronan Jennifer A Roth Chad L Myers Jason Moffat Charles Boone Steven J Bensinger David A Nathanson G Ekin Atilla-Gokcumen Everett J Moding Scott J Dixon Department of Biology Stanford University Stanford CA USA. Department of Radiation Oncology Stanford University School of Medicine Stanford CA USA. Department of Chemistry University at Buffalo The State University of New York Buffalo NY USA. Department of Molecular and Medical Pharmacology University of California Los Angeles Los Angeles CA USA. Department of Chemistry University of Massachusetts Amherst Amherst MA USA. Department of Biology University of Massachusetts Amherst Amherst MA USA. Broad Institute of MIT and Harvard Cambridge MA USA. Department of Computer Science and Engineering Bioinformatics and Computational Biology Graduate Program University of Minnesota-Twin Cities Minneapolis MN USA. Program in Genetics & Genome Biology The Hospital for Sick Children Toronto Ontario Canada. Department of Molecular Genetics University of Toronto Toronto Ontario Canada. Donnelly Centre University of Toronto Toronto Ontario Canada. RIKEN Center for Sustainable Resource Science Saitama Japan. Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles Los Angeles CA USA. UCLA Lipidomics Laboratory University of California Los Angeles Los Angeles CA USA. Jonsson Comprehensive Cancer Center David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA. Department of Biology Stanford University Stanford CA USA. sjdixon@stanford.edu.
Small molecules that induce nonapoptotic cell death are of fundamental mechanistic interest and may be useful to treat certain cancers. Here we report that tegavivint, a drug candidate undergoing human clinical trials...
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Author Correction: Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition
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Nature neuroscience 2023年 第11期26卷 2035页
作者: Jessica L Zhou Giordano de Guglielmo Aaron J Ho Marsida Kallupi Narayan Pokhrel Hai-Ri Li Apurva S Chitre Daniel Munro Pejman Mohammadi Lieselot L G Carrette Olivier George Abraham A Palmer Graham McVicker Francesca Telese Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. Integrative Biology Laboratory Salk Institute for Biological Studies La Jolla CA USA. Department of Psychiatry University of California San Diego La Jolla CA USA. Department of Medicine University of California San Diego La Jolla CA USA. Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla CA USA. Center for Immunity and Immunotherapies Seattle Children's Research Institute Seattle WA USA. Department of Pediatrics University of Washington School of Medicine Seattle WA USA. Department of Genome Sciences University of Washington Seattle WA USA. Institute for Genomic Medicine University of California San Diego La Jolla CA USA. Bioinformatics and Systems Biology Program University of California San Diego La Jolla CA USA. gmcvicker@salk.edu. Integrative Biology Laboratory Salk Institute for Biological Studies La Jolla CA USA. gmcvicker@salk.edu. Department of Psychiatry University of California San Diego La Jolla CA USA. ftelese@health.ucsd.edu. Department of Medicine University of California San Diego La Jolla CA USA. ftelese@health.ucsd.edu.
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A Statistical Framework to Identify Cell Types Whose Genetically Regulated Proportions are Associated with Complex Diseases
Research Square
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Research Square 2021年
作者: Zhao, Hongyu Liu, Wei Deng, Wenxuan Chen, Ming Dong, Zihan Zhu, Biqing Yu, Zhaolong Tang, Daiwei Sauler, Maor Wain, Louise V. Cho, Michael H. Kaminski, Naftali Program of Computational Biology and Bioinformatics Yale University New HavenCT06510 United States Department of Biostatistics Yale School of Public Health 60 College Street New HavenCT06510 United States Pulmonary Critical Care and Sleep Medicine Yale School of Medicine New HavenCT06510 United States Department of Health Sciences University of Leicester Leicester United Kingdom National Institute for Health Research Leicester Respiratory Biomedical Research Centre Glenfield Hospital Leicester United Kingdom Channing Division of Network Medicine Brigham and Women's Hospital Harvard Medical School BostonMA United States Pulmonary and Critical Care Medicine Brigham and Women's Hospital Harvard Medical School BostonMA United States
Finding disease-relevant tissues and cell types can facilitate the identification and investigation of functional genes and variants. In particular, cell type proportions can serve as potential disease predictive biom... 详细信息
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Bridging the collaboration gap: Real-time identification of clinical specimens for biomedical research
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Journal of Pathology Informatics 2020年 第1期11卷 1-7页
作者: Durant, Thomas J.S. Gong, Guannan Price, Nathan Schulz, Wade Department of Laboratory Medicine Yale University School of Medicine New Haven CT United States Center for Outcomes Research and Evaluation Yale New Haven Hospital New Haven CT United States Interdepartmental Program in Computational Biology and Bioinformatics Yale University School of Medicine New Haven CT United States Department of Information Technology Yale New Haven Health New Haven CT United States
Introduction: Biomedical and translational research often relies on the evaluation of patients or specimens that meet specific clinical or laboratory criteria. The typical approach used to identify biospecimens is a m... 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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Geometry based data generation  32
Geometry based data generation
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32nd Conference on Neural Information Processing Systems, NeurIPS 2018
作者: Lindenbaum, Ofir Wolf, Guy Stanley, Jay S. Krishnaswamy, Smita Applied Mathematics Program Yale University New HavenCT06511 United States Computational Biology and Bioinformatics Program Yale University New HavenCT06510 United States Departments of Genetics and Computer Science Yale University New HavenCT06510 United States
We propose a new type of generative model for high-dimensional data that learns a manifold geometry of the data, rather than density, and can generate points evenly along this manifold. This is in contrast to existing... 详细信息
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