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检索条件"机构=Computational Science and Engineering Program"
866 条 记 录,以下是451-460 订阅
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DP-GEN: A concurrent learning platform for the generation of reliable deep learning based potential energy models
arXiv
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arXiv 2019年
作者: Wang, Haidi Chen, Weijie Zeng, Jinzhe Zhang, Linfeng Wang, Han Zhang, Yuzhi Weinan, E. Yuanpei College of Peking University Beijing100871 China School of Electronic Science and Applied Physics Hefei University of Technology Hefei230601 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Huayuan Road 6 Beijing100088 China Beijing Institute of Big Data Research Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Beijing Institute of Big Data Research Beijing100871 China
In recent years, promising deep learning based interatomic potential energy surface (PES) models have been proposed that can potentially allow us to perform molecular dynamics simulations for large scale systems with ... 详细信息
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Void distributions reveal structural link between jammed packings and protein cores
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Physical Review E 2019年 第2期99卷 022416-022416页
作者: John D. Treado Zhe Mei Lynne Regan Corey S. O'Hern Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical & Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Chemistry Yale University New Haven Connecticut 06520 USA Department of Molecular Biophysics & Biochemistry Yale University New Haven Connecticut 06520 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA
Dense packing of hydrophobic residues in the cores of globular proteins determines their stability. Recently, we have shown that protein cores possess packing fraction ϕ≈0.56, which is the same as dense, random packi... 详细信息
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Integrating yeast chemical genomics and mammalian cell pathway analysis
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中国药理学报(英文版) 2019年 第9期40卷 1245-1255页
作者: Fu-lai Zhou Sheena C Li Yue Zhu Wan-jing Guo Li-jun Shao Justin Nelson Scott Simpkins De-hua Yang Qing Liu Yoko Yashiroda Jin-biao Xu Yao-yue Fan Jian-min Yue Minoru Yoshida Tian Xia Chad L Myers Charles Boone Ming-wei Wang The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research Shanghai Institute of Materia MedicaChinese Academy of Sciences(CAS)Shanghai 201203China University of Chinese Academy of Sciences Beijing 100049China RIKEN Center for Sustainable Resource Science WakoSaitama 3510198Japan Bioinformatics and Computational Biology Program University of Minnesota-Twin CitiesMinneapolisMinnesota 55455USA The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research Shanghai Institute of Materia MedicaChinese Academy of Sciences(CAS)Shanghai 201203China The State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China RIKEN Center for Sustainable Resource Science WakoSaitama 3510198Japan Department of Biology The University of TokyoBunkyo-kuTokyo 1138657Japan Collaborative Research for Innovative Microbiology The University of TokyoBunkyo-kuTokyo 1138657Japan Department of Electronics and Information Engineering Huazhong University of Science and TechnologyWuhan 430074China RIKEN Center for Sustainable Resource Science WakoSaitama 3510198Japan Donnelly Centre and Department of Molecular Genetics University of TorontoOntario M5S 3E1Canada
Chemical genomics has been applied extensively to evaluate small molecules that modulate biological processes in Saccharomyces ***,we use yeast as a surrogate system for studying compounds that are active against meta... 详细信息
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SUBCELLULAR TO TISSUE SCALE MODELING OF ISCHEMIA AND SPREADING DEPOLARIZATION
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IBRO Neuroscience Reports 2023年 15卷 S792-S792页
作者: Adam Newton Craig Kelley Amy Guo Joy Wang Sydney Zink Marcello Distasio Robert A Mcdougal William Lytton SUNY Downstate Health Sciences University Physiology And Pharamcology New York United States of America SUNY Downstate Health Sciences University Program In Biomedical Engineering New York United States of America Yale School of Public Health Health Informatics Program NEW HAVEN United States of America Yale School of Medicine Department Of Pathology NEW HAVEN United States of America Yale University Department Of Biostatistics NEW HAVEN United States of America Yale University Center For Medical Informatics NEW HAVEN United States of America Yale University Program In Computational Biology And Bioinformatic NEW HAVEN United States of America Yale University Wu Tsai Institute NEW HAVEN United States of America SUNY Downstate Health Sciences University Department Of Neurology New York United States of America Kings County Hospital Center Department Of Neurology New York United States of America SUNY Downstate Health Sciences University The Robert F. Furchgott Center Neural And Behavioral Science New York United States of America
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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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Current md forcefields fail to capture key features of protein structure and fluctuations: a case study of cyclophilin a and t4 lysozyme
arXiv
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arXiv 2020年
作者: Mei, Zhe Grigas, Alex T. Treado, John D. Corres, Gabriel Melendez Vuorte, Maisa Sammalkorpi, Maria Regan, Lynne Levine, Zachary A. O’Hern, Corey S. Department of Chemistry Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Biology UPR Humacao Puerto RicoHumacao00792 Puerto Rico Department of Chemistry and Materials Science School of Chemical Engineering Aalto University Aalto Finland Department of Bioproducts and Biosystems School of Chemical Engineering Aalto University Aalto Finland Institute of Quantitative Biology Biochemistry and Biotechnology Center for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Edinburgh United Kingdom Department of Pathology Yale School of Medicine New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, ... 详细信息
来源: 评论
Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis
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Cancer Cell 2025年 第6期43卷 1159-1174.e8页
作者: Dang, Derek Deogharkar, Akash McKolay, John Smith, Kyle S. Panwalkar, Pooja Hoffman, Simon Tian, Wentao Ji, Sunjong Azambuja, Ana P. Natarajan, Siva Kumar Lum, Joanna Bayliss, Jill Manzeck, Katie Sweha, Stefan R. Hamanishi, Erin Pun, Matthew Patel, Diya Rau, Sagar Animasahun, Olamide Achreja, Abhinav Ogrodzinski, Martin P. Diessl, Jutta Cotter, Jennifer Hawes, Debra Yang, Fusheng Doherty, Robert Franson, Andrea T. Hanaford, Allison R. Eberhart, Charles G. Raabe, Eric H. Orr, Brent A. Wechsler-Reya, Robert J. Chen, Brandon Lyssiotis, Costas A. Shah, Yatrik M. Lunt, Sophia Y. Banerjee, Ruma Judkins, Alexander R. Prensner, John R. Koschmann, Carl Waszak, Sebastian M. Nagrath, Deepak Simoes-Costa, Marcos Northcott, Paul A. Venneti, Sriram Laboratory of Brain Tumor Metabolism and Epigenetics Department of Pathology University of Michigan Ann Arbor MI United States Department of Developmental Neurobiology Neurobiology and Brain Tumor Program St. Jude Children's Research Hospital Memphis TN United States Center of Excellence in Neuro-Oncology Sciences St. Jude Children's Research Hospital Memphis TN United States Department of Pediatrics Michigan Medicine Ann Arbor MI United States Department of Pathology Boston Children's Hospital Boston MA United States Department of Systems Biology Harvard Medical School Boston MA United States Cancer Biology and Genetics Program Memorial Sloan Kettering Cancer Center New York NY United States Department of Chemical Engineering University of Michigan Ann Arbor MI United States Laboratory for Systems Biology of Human Diseases University of Michigan Ann Arbor MI United States Biointerfaces Institute University of Michigan Ann Arbor MI United States Department of Biomedical Engineering University of Michigan Ann Arbor MI United States Rogel Cancer Center University of Michigan Ann Arbor MI United States Department of Biochemistry and Molecular Biology Michigan State University East Lansing MI United States Department of Biological Chemistry University of Michigan Medical School Ann Arbor 48109 MI United States Department of Pathology and Laboratory Medicine Children's Hospital Los Angeles Los Angeles CA United States Keck School of Medicine University of Southern California Los Angeles CA United States Department of Pathology Johns Hopkins School of Medicine Baltimore MD United States Division of Neuropathology Department of Pathology School of Medicine Johns Hopkins University Baltimore MD United States Sidney Kimmel Comprehensive Cancer Center School of Medicine Johns Hopkins University Baltimore MD United States Division of Pediatric Oncology Department of Oncology School of Medicine Johns Hopkins University Baltimore MD United
MYC-driven group-3 medulloblastomas (MBs) are malignant pediatric brain cancers without cures. To define actionable metabolic dependencies, we identify upregulation of dihydrolipoyl transacetylase (DLAT), the E2-subun... 详细信息
来源: 评论
An integrative systems-biology approach defines mechanisms of Alzheimer’s disease neurodegeneration
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Nature Communications 2025年 第1期16卷 1-21页
作者: Leventhal, Matthew J. Zanella, Camila A. Kang, Byunguk Peng, Jiajie Gritsch, David Liao, Zhixiang Bukhari, Hassan Wang, Tao Pao, Ping-Chieh Danquah, Serwah Benetatos, Joseph Nehme, Ralda Farhi, Samouil Tsai, Li-Huei Dong, Xianjun Scherzer, Clemens R. Feany, Mel B. Fraenkel, Ernest MIT Ph.D. Program in Computational and Systems Biology Cambridge MA United States Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA United States Broad Institute of Harvard and MIT Cambridge MA United States Department of Pathology Brigham and Women’s Hospital and Harvard Medical School Boston MA United States Spatial Technology Platform Broad Institute of Harvard and MIT Cambridge MA United States Precision Neurology Program Brigham and Women’s Hospital and Harvard Medical school Boston MA United States APDA Center for Advanced Parkinson’s Disease Research Brigham and Women’s Hospital and Harvard Medical School Boston MA United States Picower Institute for Learning and Memory Massachusetts Institute of Technology Cambridge MA United States Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA United States Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA United States School of Computer Science Northwestern Polytechnical University Xi’an China Stephen and Denise Adams Center of Yale School of Medicine New Haven CT United States
Despite years of intense investigation, the mechanisms underlying neuronal death in Alzheimer’s disease, remain incompletely understood. To define relevant pathways, we conducted an unbiased, genome-scale forward gen...
来源: 评论
Modeling state-transition dynamics in resting-state brain signals by the hidden Markov and Gaussian mixture models
arXiv
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arXiv 2020年
作者: Ezaki, Takahiro Himeno, Yu Watanabe, Takamitsu Masuda, Naoki Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba Meguro-ku Tokyo153-8904 Japan PRESTO JST 4-1-8 Honcho Kawaguchi Saitama332-0012 Japan Department of Aeronautics and Astronautics The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-8656 Japan Laboratory for Cognition Circuit Dynamics RIKEN Centre for Brain Science Saitama351-0198 Japan International Research Center for Neurointelligence The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo113-0033 Japan Department of Mathematics State University of New York at Buffalo BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States
Recent studies have proposed that one can summarize brain activity into dynamics among a relatively small number of hidden states and that such an approach is a promising tool for revealing brain function. Hidden Mark... 详细信息
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Using physical features of protein core packing to distinguish real proteins from decoys
arXiv
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arXiv 2020年
作者: Grigas, Alex T. Mei, Zhe Treado, John D. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the... 详细信息
来源: 评论