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检索条件"机构=Interdepartmental Program of Bioinformatics"
70 条 记 录,以下是1-10 订阅
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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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Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States
Learning Multi-cellular Representations of Single-Cell Tran...
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29th International Conference on Research in Computational Molecular Biology, RECOMB 2025
作者: Liu, Tianyu De Brouwer, Edward Kuo, Tony Diamant, Nathaniel Missarova, Alsu Wang, Hanchen Hao, Minsheng Bravo, Hector Corrada Scalia, Gabriele Regev, Aviv Heimberg, Graham Research and Early Development Genentech South San FranciscoCA94080 United States Interdepartmental Program in Computational Biology and Bioinformatics Yale University New HavenCT06511 United States Roche Informatics F. Hoffmann-La Roche Ltd. Mississauga Canada Department of Computer Science Stanford University Palo AltoCA94035 United States
Single-cell RNA-seq (scRNA-seq) has become a prominent tool for studying human biology and disease. The availability of massive scRNA-seq datasets and advanced machine learning techniques has recently driven the devel... 详细信息
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Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses
Synthetic Control Removes Spurious Discoveries from Double ...
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29th International Conference on Research in Computational Molecular Biology, RECOMB 2025
作者: Song, Dongyuan Chen, Siqi Lee, Christy Li, Kexin Ge, Xinzhou Li, Jingyi Jessica Department of Genetics and Genome Sciences University of Connecticut Health Center FarmingtonCT06032 United States Interdepartmental Program of Bioinformatics University of California Los Angeles Los AngelesCA90095-7246 United States Department of Statistics and Data Science University of California Los Angeles Los AngelesCA90095-1554 United States Department of Statistics Oregon State University CorvallisOR97331-4606 United States
Double dipping is a common analytical pitfall in single-cell and spatial transcriptomics data analysis: after a clustering algorithm finds clusters as putative cell types or spatial domains, statistical tests are appl... 详细信息
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ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types
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Genome biology 2025年 第1期26卷 123页
作者: Tevfik Umut Dincer Jason Ernst Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles CA 90095 USA. Department of Biological Chemistry University of California Los Angeles Los Angeles CA 90095 USA. Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Department of Biological Chemistry University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Computer Science Department University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Jonsson Comprehensive Cancer Center University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Molecular Biology Institute University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu. Department of Computational Medicine University of California Los Angeles Los Angeles CA 90095 USA. jason.ernst@ucla.edu.
We introduce ChromActivity, a computational framework for predicting and annotating regulatory activity across the genome through integration of multiple epigenomic maps and various functional characterization dataset... 详细信息
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Multitissue single-cell analysis reveals differential cellular and molecular sensitivity between fructose and high-fat high-sucrose diets
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Cell Reports 2025年 第5期44卷 115690页
作者: Chen, Yen-Wei Ahn, In Sook Wang, Susanna Sue-Ming Majid, Sana Diamante, Graciel Cely, Ingrid Zhang, Guanglin Cabanayan, Angelus Komzyuk, Sergey Bonnett, Jack Arneson, Douglas Yang, Xia Department of Integrative Biology & Physiology University of California Los Angeles Los Angeles CA United States Interdepartmental Program of Molecular Toxicology University of California Los Angeles Los Angeles CA United States Interdepartmental Program of Bioinformatics University of California Los Angeles Los Angeles CA United States Department of Molecular and Medical Pharmacology University of California Los Angeles Los Angeles CA United States
Metabolic syndrome (MetS), a conglomerate of dysregulated metabolic traits that vary between individuals, is partially driven by modern diets high in fat, sucrose, or fructose and their interactions with host genes in... 详细信息
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Doubly-stochastic normalization of the Gaussian kernel is robust to heteroskedastic noise
arXiv
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arXiv 2020年
作者: Landa, Boris Coifman, Ronald R. Kluger, Yuval Program in Applied Mathematics Yale University Interdepartmental Program in Computational Biology and Bioinformatics Yale University Department of Pathology Yale University School of Medicine
A fundamental step in many data-analysis techniques is the construction of an affinity matrix describing similarities between data points. When the data points reside in Euclidean space, a widespread approach is to fr... 详细信息
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BRAINLM: A FOUNDATION MODEL FOR BRAIN ACTIVITY RECORDINGS  12
BRAINLM: A FOUNDATION MODEL FOR BRAIN ACTIVITY RECORDINGS
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12th International Conference on Learning Representations, ICLR 2024
作者: Caro, Josue Ortega de Fonseca, Antonio H. Rizvi, Syed A. Rosati, Matteo Averill, Christopher Cross, James L. Mittal, Prateek Zappala, Emanuele Dhodapkar, Rahul M. Abdallah, Chadi G. van Dijk, David Wu Tsai Institute United States Interdepartmental Neuroscience Program Yale University United States Baylor College of Medicine United States Department of Computer Science United States Yale School of Medicine United States University of Southern California United States Interdepartmental Program in Computational Biology & Bioinformatics United States Internal Medicine United States Cardiovascular Research Center Yale University United States Department of Mathematics and Statistics Idaho State University United States
We introduce the Brain Language Model (BrainLM), a foundation model for brain activity dynamics trained on 6,700 hours of fMRI recordings. Utilizing self-supervised masked-prediction training, BrainLM demonstrates pro... 详细信息
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Hyperbolic procrustes analysis using riemannian geometry  21
Hyperbolic procrustes analysis using riemannian geometry
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Proceedings of the 35th International Conference on Neural Information Processing Systems
作者: Ya-Wei Eileen Lin Yuval Kluger Ronen Talmon Viterbi Faculty of Electrical and Computer Engineering Technion Program in Applied Mathematics Yale University and Interdepartmental Program in Computational Biology and Bioinformatics Yale University and Department of Pathology Yale University
Label-free alignment between datasets collected at different times, locations, or by different instruments is a fundamental scientific task. Hyperbolic spaces have recently provided a fruitful foundation for the devel...
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Hyperbolic Diffusion Procrustes Analysis for Intrinsic Representation of Hierarchical Data Sets
Hyperbolic Diffusion Procrustes Analysis for Intrinsic Repre...
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International Conference on Acoustics, Speech, and Signal Processing (ICASSP)
作者: Ya-Wei Eileen Lin Yuval Kluger Ronen Talmon Viterbi Faculty of Electrical and Computer Engineering Technion Interdepartmental Program in Computational Biology and Bioinformatics Yale University Applied Math Program Yale University Department of Pathology School of Medicine Yale University
In this paper, we present Hyperbolic Diffusion Procrustes Analysis (HDPA), a new method for informative representation of hierarchical datasets based on hyperbolic geometry, diffusion geometry, and Procrustes analysis...
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Use of Bayesian networks to dissect the complexity of genetic disease: application to the Genetic Analysis Workshop 17 simulated data
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BMC proceedings 2011年 第9-sup期5 Suppl 9卷 S37页
作者: Jia Kang Wei Zheng Lun Li Joon Sang Lee Xiting Yan Hongyu Zhao Interdepartmental Program in Computational Biology and Bioinformatics Yale University PO Box 208009 New Haven CT 06520-8114 USA. hongyu.zhao@yale.edu.
Complex diseases are often the downstream event of a number of risk factors, including both environmental and genetic variables. To better understand the mechanism of disease onset, it is of great interest to systemat... 详细信息
来源: 评论