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检索条件"机构=Computational and Systems Biology PhD Program"
21 条 记 录,以下是1-10 订阅
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Machine learning approaches enable the discovery of therapeutics across domains
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Molecular Therapy 2025年 第5期33卷 2269-2278页
作者: Chhibbar, Prabal Das, Jishnu Centre for Systems Immunology Department of Immunology School of Medicine University of Pittsburgh Pittsburgh 15213 PA United States Department of Computational and Systems Biology School of Medicine University of Pittsburgh Pittsburgh 15213 PA United States Integrative Systems Biology PhD Program School of Medicine University of Pittsburgh Pittsburgh 15213 PA United States
Multi-modal datasets have grown exponentially in the last decade. This has created an enormous demand for machine learning models that can predict complex outcomes by leveraging cellular, molecular, and humoral profil... 详细信息
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Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences
Dish-Trend: Intervention Modeling Simulator That Accounts fo...
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2021 Winter Simulation Conference, WSC 2021
作者: Andjelkovic, Stefan Miskov-Zivanov, Natasa Computational and Systems Biology Joint Carnegie Mellon University University of Pittsburgh Computational Biology PhD Program University of Pittsburgh PittsburghPA15213 United States Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh PittsburghPA15213 United States
Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation ... 详细信息
来源: 评论
COEM: Cross-Modal Embedding for MetaCell Identification
arXiv
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arXiv 2022年
作者: Mao, Haiyi Jia, Minxue Dou, Jason Xiaotian Zhang, Haotian Benos, Panayiotis V. Department of Computational and Systems Biology University of Pittsburgh PA United States Joint Carnegie Mellon University University of Pittsburgh PhD Program in Computational Biology United States Department of Electrical and Computer Engineering University of Pittsburgh PA United States
Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though ... 详细信息
来源: 评论
Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences
Dish-Trend: Intervention Modeling Simulator That Accounts fo...
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Simulation Winter Conference
作者: Stefan Andjelkovic Natasa Miskov-Zivanov Computational and Systems Biology Joint Carnegie Mellon University and University of Pittsburgh Computational Biology PhD Program University of Pittsburgh Pittsburgh PA USA Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh Pittsburgh PA USA
Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation ... 详细信息
来源: 评论
Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods
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Current Opinion in Structural biology 2023年 78卷 102517页
作者: Banerjee, Anupam Saha, Satyaki Tvedt, Nathan C. Yang, Lee-Wei Bahar, Ivet Computational and Systems Biology University of Pittsburgh School of Medicine Pittsburgh 15261 PA United States Computational and Applied Mathematics and Statistics The College of William and Mary Williamsburg 23185 VA United States Institute of Bioinformatics and Structural Biology and PhD Program in Biomedical Artificial Intelligence National Tsing Hua University Hsinchu 300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei 106319 Taiwan
Proteins sample an ensemble of conformers under physiological conditions, having access to a spectrum of modes of motions, also called intrinsic dynamics. These motions ensure the adaptation to various interactions in...
来源: 评论
EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment
arXiv
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arXiv 2023年
作者: Wang, Yuanqing Pulido, Iván Takaba, Kenichiro Kaminow, Benjamin Scheen, Jenke Wang, Lily Chodera, John D. Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Physiology Biophysics and System Biology Ph.D. Program Weill Cornell Medical College Cornell University New YorkNY10065 United States Pharmaceutical Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Tri-Institutional PhD Program in Computational Biology and Medicine Weill Cornell Medical College Cornell University New YorkNY10065 United States Open Molecular Sciences Foundation DavisCA95618 United States
Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and thereby the potential energy landscape. Traditionally, the... 详细信息
来源: 评论
Dish-trend: Intervention modeling simulator that accounts for trend influences
arXiv
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arXiv 2021年
作者: Andjelkovic, Stefan Miskov-Zivanov, Natasa Computational and Systems Biology Joint Carnegie Mellon University University of Pittsburgh Computational Biology PhD Program University of Pittsburgh 4420 Bayard St PittsburghPA15213 United States Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh 4420 Bayard St PittsburghPA15213 United States
Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation ... 详细信息
来源: 评论
Enhancing Protein-Ligand Binding Affinity Predictions using Neural Network Potentials
arXiv
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arXiv 2024年
作者: Zariquiey, Francesc Sabanés Galvelis, Raimondas Gallicchio, Emilio Chodera, John D. Markland, Thomas E. De Fabritiis, Gianni C Dr. Aiguader 88 Barcelona08003 Spain Acellera Labs C Dr Trueta 183 Barcelona08005 Spain Department of Chemistry Brooklyn College of the City University of New York PhD Program in Chemistry Graduate Center of the City University of New York PhD Program in Biochemistry Graduate Center of the City University of New York NY11210 United States Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Department of Chemistry Stanford University 337 Campus Drive StanfordCA94305 United States Passeig Lluis Companys 23 Barcelona08010 Spain
This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechani... 详细信息
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Spatial atlas of the mouse central nervous system at molecular resolution (vol 622, pg 552, 2023)
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NATURE 2024年 第7993期625卷 E6-E6页
作者: Shi, Hailing He, Yichun Zhou, Yiming Huang, Jiahao Maher, Kamal Wang, Brandon Tang, Zefang Luo, Shuchen Tan, Peng Wu, Morgan Lin, Zuwan Ren, Jingyi Thapa, Yaman Tang, Xin Chan, Ken Y. Deverman, Benjamin E. Shen, Hao Liu, Albert Liu, Jia Wang, Xiao Broad Institute of MIT and Harvard Cambridge MA USA Department of Chemistry Massachusetts Institute of Technology Cambridge MA USA John A. Paulson School of Engineering and Applied Sciences Harvard University Boston MA USA Computational and Systems Biology PhD Program Massachusetts Institute of Technology Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Biology Massachusetts Institute of Technology Cambridge MA USA Klarman Cell Observatory Broad Institute of MIT and Harvard Cambridge MA USA Department of Chemistry and Chemical Biology Harvard University Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA USA
来源: 评论
Author Correction: Progressive plasticity during colorectal cancer metastasis
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Nature 2025年 第8047期637卷 E28页
作者: Andrew Moorman Elizabeth K Benitez Francesco Cambuli Qingwen Jiang Ahmed Mahmoud Melissa Lumish Saskia Hartner Sasha Balkaran Jonathan Bermeo Simran Asawa Canan Firat Asha Saxena Fan Wu Anisha Luthra Cassandra Burdziak Yubin Xie Valeria Sgambati Kathleen Luckett Yanyun Li Zhifan Yi Ignas Masilionis Kevin Soares Emmanouil Pappou Rona Yaeger T Peter Kingham William Jarnagin Philip B Paty Martin R Weiser Linas Mazutis Michael D'Angelica Jinru Shia Julio Garcia-Aguilar Tal Nawy Travis J Hollmann Ronan Chaligné Francisco Sanchez-Vega Roshan Sharma Dana Pe'er Karuna Ganesh Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA. Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York NY USA. Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program New York NY USA. New York Genome Center New York NY USA. Pharmacology Program Weill Cornell Graduate School New York NY USA. Department of Medicine Memorial Sloan Kettering Cancer Center New York NY USA. Case Western Reserve University Cleveland OH USA. Department of Pathology and Laboratory Medicine Memorial Sloan Kettering Cancer Center New York NY USA. Department of Surgery Memorial Sloan Kettering Cancer Center New York NY USA. Tri-Institutional PhD Program in Computational Biology and Medicine New York NY USA. Bristol Myers Squibb Princeton NJ USA. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA. peerd@***. Howard Hughes Medical Institute Chevy Chase MD USA. peerd@***. Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center New York NY USA. ganeshk@***. Department of Medicine Memorial Sloan Kettering Cancer Center New York NY USA. ganeshk@***.
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