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检索条件"机构=Department of Computer Science Bioinformatics and Computational Biology Graduate Program"
296 条 记 录,以下是11-20 订阅
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ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
arXiv
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arXiv 2024年
作者: Viswanath, Siddharth Bhaskar, Dhananjay Johnson, David R. Rocha, João Felipe Castro, Egbert Grady, Jackson D. Grigas, Alex T. Perlmutter, Michael A. O’Hern, Corey S. Krishnaswamy, Smita Department of Computer Science Yale University United States Department of Genetics Yale University United States Program in Computing Boise State University United States Computational Biology and Bioinformatics Program Yale University United States Department of Mathematics Boise State University United States
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motio... 详细信息
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Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships  26th
Uncertainty Quantification Using Subsampling for Assembly-F...
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26th International Conference on Research in computational Molecular biology, RECOMB 2022
作者: Rachtman, Eleonora Sarmashghi, Shahab Bafna, Vineet Mirarab, Siavash Bioinformatics and Systems Biology Graduate Program UC San Diego La JollaCA United States Department of Electrical and Computer Engineering UC San Diego La JollaCA United States Department of Computer Science and Engineering UC San Diego La JollaCA United States
Computing the distance between two genomes, often without using alignments or even access to assembled sequences, is fundamental to many downstream analyses. © 2022, The Author(s), under exclusive license to Spri... 详细信息
来源: 评论
Distribution-based Sketching of Single-Cell Samples
arXiv
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arXiv 2022年
作者: Baskaran, Vishal Athreya Ranek, Jolene Shan, Siyuan Stanley, Natalie Oliva, Junier B. Department of Computer Science UNC-Chapel Hill United States Computational Medicine Program Curriculum in Bioinformatics and Computational Biology UNC-Chapel Hill United States Computational Medicine Program Department of Computer Science UNC-Chapel Hill United States
Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across ... 详细信息
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Transparent Single-Cell Set Classification with Kernel Mean Embeddings
arXiv
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arXiv 2022年
作者: Shan, Siyuan Baskaran, Vishal Athreya Yi, Haidong Ranek, Jolene Stanley, Natalie Oliva, Junier B. Department of Computer Science UNC Chapel Hill United States Computational Medicine Program Curriculum in Bioinformatics and Computational Biology UNC Chapel Hill United States Computational Medicine Program Department of Computer Science UNC Chapel Hill United States
Modern single-cell flow and mass cytometry technologies measure the expression of several proteins of the individual cells within a blood or tissue sample. Each profiled biological sample is thus represented by a set ... 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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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers
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Chinese Chemical Letters 2021年 第4期32卷 1515-1518页
作者: Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China
Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymer... 详细信息
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Pre-Training Genomic Language Model with Variants for Better Modeling Functional Genomics
SSRN
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SSRN 2025年
作者: Liu, Tianyu Zhang, Xiangyu Ying, Rex Zhao, Hongyu Interdepartmental Program in Computational Biology & Bioinformatics Yale University New HavenCT06511 United States Department of Biostatistics Yale University New HavenCT06511 United States Department of Computer Science Yale University New HavenCT06511 United States
Sequence-to-function models can predict gene expression from sequence data and be used to link genetic information with transcriptomics data to understand regulatory processes and their effects on complex phenotypes. ... 详细信息
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Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice
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Plant Communications 2022年 第3期3卷 59-71页
作者: Haidong Yan David C.Haak Song Li Linkai Huang Aureliano Bombarely School of Plant and Environmental Sciences Virginia TechBlacksburgVA 24061USA Graduate Program in Genetics Bioinformatics and Computational Biology(GBCB)Virginia TechBlacksburgVA 24061USA Department of Grassland Science Animal Science and Technology CollegeSichuan Agricultural UniversityChengdu 611130China Department of Bioscience Universita degli Studi di Milano(UNIMI)20133 MilanoItaly Instituto de Biologıa Molecular y Celular de Plantas(IBMCP) UPV-CSIC46022 ValenciaSpain
Transposable elements(TEs)are a major force in the production of new alleles during domestication;nevertheless,their use in association studies has been limited because of their *** have developed a TE genotyping pipe... 详细信息
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Connecting polymer collapse and the onset of jamming
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Physical Review E 2024年 第3期109卷 034406-034406页
作者: Alex T. Grigas Aliza Fisher Mark D. Shattuck Corey S. O'Hern Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut 06520 USA Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of New York New York New York 10031 USA Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA
Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the int... 详细信息
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Bayesian multinomial logistic normal models through marginally latent matrix-T processes
The Journal of Machine Learning Research
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The Journal of Machine Learning Research 2022年 第1期23卷 255-296页
作者: Justin D. Silverman Kimberly Roche Zachary C. Holmes Lawrence A. David Sayan Mukherjee College of Information Science and Technology Department of Statistics and Institute for Computational and Data Science Penn State University University Park PA Program in Computational Biology and Bioinformatics Duke University Durham NC Department of Molecular Genetics and Microbiology Duke University Durham NC Department of Molecular Genetics and Microbiology and Center for Genomic and Computational Biology Duke University Durham NC Departments of Statistical Science Mathematics Computer Science Biostatistics & Bioinformatics Duke University Durham NC
Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covar... 详细信息
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