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检索条件"机构=Systems Biology and Computer Science Program"
179 条 记 录,以下是41-50 订阅
排序:
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
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PLoS Computational biology 2022年 第6期18卷 e1010238页
作者: Lu, Alex X. Lu, Amy X. Pritišanac, Iva Zarin, Taraneh Forman-Kay, Julie D. Moses, Alan M. Department of Computer Science University of Toronto Toronto Canada Department of Cell and Systems Biology University of Toronto Toronto Canada Program in Molecular Medicine Hospital for Sick Children Toronto Canada Department of Biochemistry University of Toronto Toronto Canada
A major challenge to the characterization of intrinsically disordered regions (IDRs), which are widespread in the proteome, but relatively poorly understood, is the identification of molecular features that mediate fu... 详细信息
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K-Means Clustering Model to Discriminate Copper-Resistant Bacteria as Bioremediation Agents
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Procedia computer science 2021年 179卷 804-812页
作者: Ika Nurlaila Wahyu Irawati Kartika Purwandari Bens Pardamean Information Systems Department BINUS Online Learning Bina Nusantara University Jakarta Indonesia 11480 Department of Biology Education Faculty of Education Pelita Harapan University Tangerang Indonesia 15811 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480
Copper (Cu) has been excessively used for some valuable commodities and this creates environmental problems. The inorganic element becomes toxic when presents beyond the recommended tolerated concentration. Bacterial-... 详细信息
来源: 评论
TERMinator: A Neural Framework for Structure-Based Protein Design using Tertiary Repeating Motifs
arXiv
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arXiv 2022年
作者: Li, Alex J. Sundar, Vikram Grigoryan, Gevorg Keating, Amy E. Department of Chemistry Massachusetts Institute of Technology United States Computational and Systems Biology Program Massachusetts Institute of Technology United States Department of Computer Science Dartmouth College United States Departments of Biology and Biological Engineering Massachusetts Institute of Technology United States
Computational protein design has the potential to deliver novel molecular structures, binders, and catalysts for myriad applications. Recent neural graph-based models that use backbone coordinate-derived features show... 详细信息
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FaNDOM: Fast Nested Distance-Based Seeding of Optical Maps
SSRN
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SSRN 2021年
作者: Dehkordi, Siavash Raeisi Luebeck, Jens Bafna, Vineet Department of Computer Science & Engineering University of California San Diego San diegoCA92093 United States Bioinformatics & Systems Biology Graduate Program University of California San Diego San diegoCA92093 United States
Optical mapping provides single-molecule readouts of the locations of fluorescently labeled sequence motifs on long fragments of DNA, resolved to nucleotide-level coordinates. With the advent of microfluidic technolog... 详细信息
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International Workshop on Applications of Probability and Statistics to biology,July 11-13,2019--In Honor of Professor Minping Qian’s 80th Birthday
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Quantitative biology 2020年 第2期8卷 177-186页
作者: Minghua Deng Jianfeng Feng Hong Qian Lin Wan Fengzhu Sun Center for Quantitative Biology Peking UniversityBeijing 100871China LMAM Center for Statistical ScienceSchool of Mathematical SciencesPeking UniversityBeijing 100871China Institute of Science and Technology for Brain-inspired Intelligence Fudan UniversityShanghai 200433China School of Mathematical Sciences Fudan UniversityShanghai 200433China Centre for Computational Systems Biology Fudan UniversityShanghai 200433China Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence at Fudan University Ministry of EducationShanghai 200433China Department of Computer Science University of WarwickCoventryCV47ALUnited Kingdom Department of Applied Mathematics University of WashingtonSeattleWA 98195USA NCMIS Academy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematical Sciences University of Chinese Academy of SciencesBeijing 100049China Quantitative and Computational Biology Program University of Southern CaliforniaLos AngelesCA 90089USA
The International Workshop on Applications of Probability and Statistics to biology(APSB)was successfully held in Shanghai,China,July 11-13,*** workshop was hosted by the Institute of science and Technology for Brain-... 详细信息
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Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis (vol 56, pg 627, 2024)
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NATURE GENETICS 2024年 第6期56卷 1319-1319页
作者: Mitra, Sneha Malik, Rohan Wong, Wilfred Rahman, Afsana Hartemink, Alexander J. Pritykin, Yuri Dey, Kushal K. Leslie, Christina S. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA Rye Country Day School Rye NY USA Tri-Institutional Training Program in Computational Biology and Medicine New York City NY USA Hunter College City University of New York New York City NY USA Department of Computer Science Duke University Durham NC USA Program in Computational Biology and Bioinformatics Duke University Durham NC USA Center for Genomic and Computational Biology Duke University Durham NC USA Department of Computer Science Princeton University Princeton NJ USA Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton NJ USA
We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC–seq co-assay) ... 详细信息
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FINDING CONTINUITY AND DISCONTINUITY IN FISH SCHOOLS VIA INTEGRATED INFORMATION THEORY
arXiv
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arXiv 2018年
作者: Niizato, Takayuki Sakamoto, Kotaro Mototake, Yoh-ichi Murakami, Hisashi Tomaru, Takenori Hoshika, Tomotaro Fukushima, Toshiki Faculty of Engineering Information and Systems University of Tsukuba Japan Human Biology Program University of Tsukuba Japan Graduate School of Frontier Sciences University of Tokyo Japan Research Center for Advanced Science and Technology University of Tokyo Japan Department of Computer Science and Engineering Toyohashi University of Technology Japan
Collective behaviour is known to be the result of diverse dynamics and is sometimes likened to a living system. Although many studies have revealed the dynamics of various collective behaviours, their main focus was o... 详细信息
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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles
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Genome biology 2025年 第1期26卷 31页
作者: Jacob Matthew Schreiber Carles A Boix Jin Wook Lee Hongyang Li Yuanfang Guan Chun-Chieh Chang Jen-Chien Chang Alex Hawkins-Hooker Bernhard Schölkopf Gabriele Schweikert Mateo Rojas Carulla Arif Canakoglu Francesco Guzzo Luca Nanni Marco Masseroli Mark James Carman Pietro Pinoli Chenyang Hong Kevin Y Yip Jefrey P Spence Sanjit Singh Batra Yun S Song Shaun Mahony Zheng Zhang Wuwei Tan Yang Shen Yuanfei Sun Minyi Shi Jessika Adrian Richard S Sandstrom Nina P Farrell Jessica M Halow Kristen Lee Lixia Jiang Xinqiong Yang Charles B Epstein J Seth Strattan Bradley E Bernstein Michael P Snyder Manolis Kellis William S Noble Anshul Bharat Kundaje Department of Genetics Stanford University Stanford CA USA. jmschreiber91@***. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA. Department of Genetics Stanford University Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. Department of Research and Development DeepSeq.AI San Francisco CA USA. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department of Empirical Inference Max Planck Institute for Intelligent Systems Stuttgart Germany. School of Life Sciences University of Dundee Dundee UK. Department of Electronics Information and Bioengineering Politecnico Di Milano Milan Italy. Department of Computational Biology University of Lausanne Lausanne Switzerland. Department of Computer Science and Engineering The Chinese University of Hong Kong Sha Tin Hong Kong. Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Department of Statistics University of California Berkeley Berkeley CA USA. Department of Biochemistry & Molecular Biology Center for Eukaryotic Gene Regulation Pennsylvania State University University Park PA USA. Department of Statistics Pennsylvania State University University Park PA USA. Department of Electrical and Computer Engineering Texas A&M University College Station TX USA. Altius Institute Seattle WA USA. Epigenomics Program The Broad Institute of MIT and Harvard Cambridge MA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Computer Science Stanford University Stanford CA USA.
来源: 评论
Disentangling Interpretable Factors with Supervised Independent Subspace Principal Component Analysis
arXiv
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arXiv 2024年
作者: Su, Jiayu Knowles, David A. Rabadan, Raul Program for Mathematical Genomics United States Department of Systems Biology Columbia University United States Department of Biomedical Informatics Columbia University United States Department of Computer Science Columbia University United States New York Genome Center United States
The success of machine learning models relies heavily on effectively representing high-dimensional data. However, ensuring data representations capture human-understandable concepts remains difficult, often requiring ... 详细信息
来源: 评论
Periodicity Scoring of Time Series Encodes Dynamical Behavior of the Tumor Suppressor p53 ⁎ ⁎
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IFAC-PapersOnLine 2021年 第9期54卷 488-495页
作者: Caroline Moosmüller Christopher J. Tralie Mahdi Kooshkbaghi Zehor Belkhatir Maryam Pouryahya José Reyes Joseph O. Deasy Allen R. Tannenbaum Ioannis G. Kevrekidis C. Moosmüller and C. Tralie contributed equally to this work Department of Mathematics University of California San Diego La Jolla CA 92093 USA Department of Medical Physics Memorial Sloan-Kettering Cancer Center NY USA Department of Chemical and Biomolecular Engineering Johns Hopkins University Baltimore MD 21218 USA Department of Mathematics and Computer Science Ursinus College Collegeville PA USA Program in Applied and Computational Mathematics Princeton University NJ USA School of Engineering and Sustainable Development De Montfort University Leicester UK Cancer Biology and Genetics Program and Computational and Systems Biology Program Memorial Sloan-Kettering Cancer Center New York NY 10065 USA and Department of Systems Biology Harvard Medical School Boston MA 02115 USA Departments of Computer Science and Applied Mathematics & Statistics Stony Brook University NY USA
In this paper we analyze the dynamical behavior of the tumor suppressor protein p53, an essential player in the cellular stress response, which prevents a cell from dividing if severe DNA damage is present. When this ... 详细信息
来源: 评论