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检索条件"机构=Systems Biology and Computer Science Program"
179 条 记 录,以下是31-40 订阅
排序:
Mixture-of-experts variational autoencoder for clustering and generating from similarity-based representations
arXiv
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arXiv 2019年
作者: Kopf, Andreas Fortuin, Vincent Somnath, Vignesh Ram Claassen, Manfred Institute of Molecular Systems Biology Department of Biology ETH Zürich Switzerland Biomedical Informatics Group Department of Computer Science ETH Zürich Switzerland Switzerland Life Science Graduate School Zurich PhD Program Systems Biology Switzerland
Clustering high-dimensional data, such as images or biological measurements, is a long-standing problem and has been studied extensively. Recently, Deep Clustering gained popularity due to the non-linearity of neural ... 详细信息
来源: 评论
Computationally designed proteins mimic antibody immune evasion in viral evolution
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Immunity 2025年
作者: Youssef, Noor Gurev, Sarah Ghantous, Fadi Brock, Kelly P. Jaimes, Javier A. Thadani, Nicole N. Dauphin, Ann Sherman, Amy C. Yurkovetskiy, Leonid Soto, Daria Estanboulieh, Ralph Kotzen, Ben Notin, Pascal Kollasch, Aaron W. Cohen, Alexander A. Dross, Sandra E. Erasmus, Jesse Fuller, Deborah H. Bjorkman, Pamela J. Lemieux, Jacob E. Luban, Jeremy Seaman, Michael S. Marks, Debora S. Department of Systems Biology Harvard Medical School Boston 02115 MA United States Broad Institute of Harvard and MIT Cambridge 02139 MA United States Department of Electrical Engineering and Computer Science MIT Cambridge 02139 MA United States Center for Virology and Vaccine Research Beth Israel Deaconess Medical Center Boston 02215 MA United States Program in Molecular Medicine University of Massachusetts Chan Medical School Worcester 01655 MA United States Division of Infectious Diseases Department of Medicine Brigham and Women's Hospital Boston 02115 MA United States Massachusetts General Hospital Boston 02114 MA United States Division of Biology and Biological Engineering California Institute of Technology Pasadena 91125 CA United States Department of Microbiology University of Washington Seattle 98195 WA United States National Primate Research Center Seattle 98109 WA United States HDT Bio Seattle 98109 WA United States Massachusetts Consortium on Pathogen Readiness Boston 02115 MA United States Ragon Institute of MGH MIT and Harvard Cambridge 02139 MA United States
Recurrent waves of viral infection necessitate vaccines and therapeutics that remain effective against emerging viruses. Our ability to evaluate interventions is currently limited to assessments against past or circul... 详细信息
来源: 评论
SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest
SeqScreen: a biocuration platform for robust taxonomic and b...
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IEEE International Conference on Bioinformatics and Biomedicine
作者: Dreycey Albin Dan Nasko R. A. Leo Elworth Jacob Lu Advait Balaji Christian Diaz Nidhi Shah Jeremy Selengut Chris Hulme-Lowe Pravin Muthu Gene Godbold Mikael Lindvall Madeline Diep Adam Porter Mihai Pop Krista Ternus Todd J. Treangen Program in Systems Synthetic and Physical Biology Rice University Center for Bioinformatics and Computational Biology University of Maryland Department of Computer Science Rice University Signature Science LLC Fraunhofer Center for Experimental Software Engineering Department of Computer Science University of Maryland
Rapid advancements in synthetic biology and nucleic acid synthesis, in particular concerns about its intentional or accidental misuse, call for more sophisticated screening tools to identify genes of interest within s... 详细信息
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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
The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2
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Cell 2025年
作者: Pekar, Jonathan E. Lytras, Spyros Ghafari, Mahan Magee, Andrew F. Parker, Edyth Wang, Yu Ji, Xiang Havens, Jennifer L. Katzourakis, Aris Vasylyeva, Tetyana I. Suchard, Marc A. Hughes, Alice C. Hughes, Joseph Rambaut, Andrew Robertson, David L. Dellicour, Simon Worobey, Michael Wertheim, Joel O. Lemey, Philippe Institute of Ecology and Evolution University of Edinburgh Edinburgh United Kingdom Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla 92093 CA United States Department of Biomedical Informatics University of California San Diego La Jolla 92093 CA United States Department of Medicine University of California San Diego La Jolla 92093 CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Medical Research Council University of Glasgow Centre for Virus Research Glasgow United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States Department of Immunology and Microbiology The Scripps Research Institute La Jolla 92037 CA United States Institute of Genomics and Global Health Redeemer's University Osun State Ede Nigeria Department of Computer Science and Engineering University of California San Diego La Jolla 92093 CA United States Department of Mathematics School of Science and Engineering Tulane University New Orleans LA United States Department of Population Health and Disease Prevention University of California Irvine Irvine 92617 CA United States Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles 90095 CA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States School of Biological Sciences University of Hong Kong Hong Kong Hong Kong China Biodiversity Green Development Foundation Beijing China Spatial Epidemiology Lab (SpELL) Université Libre de Bruxelles CP160/12 50 av. FD Roosevelt Bruxelles 1050 Belgium Department of Microbiology Immunology and Transplantation Rega Institute
The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecovir... 详细信息
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Rewriting regulatory DNA to dissect and reprogram gene expression
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Cell 2025年
作者: Martyn, Gabriella E. Montgomery, Michael T. Jones, Hank Guo, Katherine Doughty, Benjamin R. Linder, Johannes Bisht, Deepa Xia, Fan Cai, Xiangmeng S. Chen, Ziwei Cochran, Kelly Lawrence, Kathryn A. Munson, Glen Pampari, Anusri Fulco, Charles P. Sahni, Nidhi Kelley, David R. Lander, Eric S. Kundaje, Anshul Engreitz, Jesse M. Department of Genetics Stanford University School of Medicine Stanford 94305 CA United States Basic Science and Engineering Initiative Stanford Children's Health Betty Irene Moore Children's Heart Center Stanford 94305 CA United States Calico Life Sciences LLC South San Francisco 94080 CA United States Department of Genitourinary Medical Oncology Division of Cancer Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Genomic Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Computer Science Stanford University Stanford 94305 CA United States Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard Cambridge 02142 MA United States Gene Regulation Observatory Broad Institute of MIT and Harvard Cambridge 02142 MA United States Broad Institute of MIT and Harvard Cambridge 02142 MA United States Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Quantitative and Computational Biosciences Program Baylor College of Medicine Houston 77030 TX United States Department of Biology MIT Cambridge 02139 MA United States Department of Systems Biology Harvard Medical School Boston 02115 MA United States Stanford Cardiovascular Institute Stanford University Stanford 94305 CA United States
Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to ma... 详细信息
来源: 评论
Orchard: building large cancer phylogenies using stochastic combinatorial search
arXiv
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arXiv 2023年
作者: Kulman, Ethan Kuang, Rui Morris, Quaid Computational and Systems Biology Program Sloan Kettering Institute New YorkNY United States Department of Computer Science and Engineering University of Minnesota MinneapolisMN United States
Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment ... 详细信息
来源: 评论
Dental Disease Detection based on CNN for Panoramic Dental Radiographs  11
Dental Disease Detection based on CNN for Panoramic Dental R...
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11th IEEE International Conference on Intelligent Computing and Information systems, ICICIS 2023
作者: El Bagoury, Manar Al-Shetairy, Mirna Ahmed, Omar Mehanny, Samah S Hamdy, Tassneem Omar, Gihan Akram, Marwan Mohamed, Rana Amr, Hebatullah Gad, Walaa Ain Shams University Faculty of Computer and Information Sciences Bioinformatics Program Cairo Egypt Ain Shams University Faculty of Computer and Information Sciences Computer Science Department Cairo Egypt Faculty of Dentistry Cairo and Galala Universities Oral Biology Department Cairo Egypt Cairo University Faculty of Dentistry Oral and Maxillofacial Radiology Department Cairo Egypt Future University in Egypt Faculty of Oral and Dental Medicine Oral Radiology Department Cairo Egypt Ain Shams University Faculty of Computer and Information Sciences Information Systems Department Cairo Egypt
Panoramic dental radiography is one of the examination tools frequently performed in dental clinics and hospitals as it captures a wide range of the dental region and its surroundings, but due to the complex structure... 详细信息
来源: 评论
COULD DROPPING A FEW CELLS CHANGE THE TAKEAWAYS FROM DIFFERENTIAL EXPRESSION?
arXiv
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arXiv 2023年
作者: Shiffman, Miriam Giordano, Ryan Broderick, Tamara MIT Computational & Systems Biology Program United States MIT Dept. of Electrical Engineering & Computer Science United States UC Berkeley Dept. of Statistics United States
Analysis of differential gene expression plays a fundamental role in biology toward illuminating the molecular mechanisms driving a difference between groups (e.g., due to treatment or disease). While any analysis is ... 详细信息
来源: 评论
Latent space temporal model of microbial abundance to predict domination and bacteremia
arXiv
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arXiv 2018年
作者: Zhong, Ruiqi Joseph, Tyler Xavier, Joao B. Pe'Er, Itsik Department of Computer Science Columbia University New YorkNY United States Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New YorkNY United States
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dyn... 详细信息
来源: 评论