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检索条件"机构=Interdepartmental Program in Computational Biology and Bioinformatics"
46 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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Building a unified model for drug synergy analysis powered by large language models
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Nature Communications 2025年 第1期16卷 1-17页
作者: Liu, Tianyu Chu, Tinyi Luo, Xiao Zhao, Hongyu Interdepartmental Program in Computational Biology & Bioinformatics Yale University New Haven CT United States Department of Biostatistics Yale University New Haven CT United States Department of Computer Science University of California Los Angeles Los Angeles CA United States
Drug synergy prediction is a challenging and important task in the treatment of complex diseases including cancer. In this manuscript, we present a unified Model, known as BAITSAO, for tasks related to drug synergy pr...
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Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States  29th
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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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 1-30页
作者: Dincer, Tevfik Umut Ernst, Jason Bioinformatics Interdepartmental Program University of California Los Angeles Los Angeles 90095 CA United States Department of Biological Chemistry University of California Los Angeles Los Angeles 90095 CA United States Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California Los Angeles Los Angeles 90095 CA United States Computer Science Department University of California Los Angeles Los Angeles 90095 CA United States Jonsson Comprehensive Cancer Center University of California Los Angeles Los Angeles 90095 CA United States Molecular Biology Institute University of California Los Angeles Los Angeles 90095 CA United States Department of Computational Medicine University of California Los Angeles Los Angeles 90095 CA United States
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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MetNetAPI: A flexible method to access and manipulate biological network data from MetNet
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BMC Research Notes 2010年 第1期3卷 1-9页
作者: Sucaet, Yves Wurtele, Eve Syrkin Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 United States Interdepartmental Program in Bioinformatics and Computational Biology Iowa State University Ames IA 50011 United States
Background. Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice... 详细信息
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Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq
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Nature Communications 2025年 第1期16卷 1-21页
作者: Hefei Zhang Xuhang Li Shivani Nanda Albertha J. M. Walhout Dongyuan Song Jingyi Jessica Li Onur Yukselen Alper Kucukural Manuel Garber Department of Systems Biology University of Massachusetts Chan Medical School Worcester MA USA Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles CA USA Department of Statistics and Data Science Department of Biostatistics Department of Computational Medicine and Department of Human Genetics University of California Los Angeles CA USA Via Scientific Inc. Cambridge MA USA Department of Genomics and Computational Biology University of Massachusetts Chan Medical School Worcester MA USA
Transcriptomes provide highly informative molecular phenotypes that, combined with gene perturbation, can connect genotype to phenotype. An ultimate goal is to perturb every gene and measure transcriptome changes, how...
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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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An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping
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BMC Research Notes 2009年 第1期2卷 1-7页
作者: Sasidharan, Rajkumar Agarwal, Ashish Rozowsky, Joel Gerstein, Mark Molecular Biophysics and Biochemistry Department Yale University New Haven CT 06520 United States Department of Plant Biology Carnegie Institution for Science Stanford CA 94305 United States Interdepartmental Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 United States Department of Computer Science Yale University New Haven CT 06520 United States
Background. There are two main technologies for transcriptome profiling, namely, tiling microarrays and high-throughput sequencing. Recently there has been a tremendous amount of excitement about the latter because of... 详细信息
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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
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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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