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检索条件"机构=Systems Biology and Computer Science Program"
178 条 记 录,以下是11-20 订阅
排序:
ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data  29th
ALPINE: An Interpretable Approach for Decoding Phenotypes ...
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29th International Conference on Research in Computational Molecular biology, RECOMB 2025
作者: Lee, Wei-Hao Li, Lechuan Dannenfelser, Ruth Yao, Vicky Systems Synthetic and Physical Biology Graduate Program Rice University Houston United States Department of Computer Science Rice University Houston United States Ken Kennedy Institute Rice University Houston United States Rice Synthetic Biology Institute Rice University Houston United States
Advancements in sequencing technology have expanded data availability, capturing diverse phenotypic traits and biological perturbations. However, increased resolution also raises complexity, as studies now examine mul... 详细信息
来源: 评论
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
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
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
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
来源: 评论
Trackable Agent-based Evolution Models at Wafer Scale
arXiv
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arXiv 2024年
作者: Moreno, Matthew Andres Yang, Connor Dolson, Emily Zaman, Luis Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data Science University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States
Continuing improvements in computing hardware are poised to transform capabilities for in silico modeling of cross-scale phenomena underlying major open questions in evolutionary biology and artificial life, such as t... 详细信息
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Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure
arXiv
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arXiv 2024年
作者: Moreno, Matthew Andres Rodriguez-Papa, Santiago Dolson, Emily Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data Science University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States
Evolutionary dynamics are shaped by a variety of fundamental, generic drivers, including spatial structure, ecology, and selection pressure. These drivers impact the trajectory of evolution, and have been hypothesized... 详细信息
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A Multi-phase Deep Learning Approach for Predicting HCC Response to TACE using Complete Computed Tomography
A Multi-phase Deep Learning Approach for Predicting HCC Resp...
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Data science and Engineering in Healthcare, Medicine and biology, IEEE EMBS Special Topic Conference on
作者: Shun Cheng Chang Chien Fu Liu Marta Misztal Yi Hsien Hsieh Che Lin Graduate Institute of Communication Engineering National Taiwan University (NTU) Taiwan School of Electronic Engineering and Computer Science Queen Mary University of London UK Department of Electrical Engineering NTU Taiwan Center for Computational and Systems Biology and Center for Biotechnology NTU Taiwan Smart Medicine and Health Informatics Program NTU Taiwan
In this research study, we compare the predictive performance of two advanced deep learning-based models in order to provide a solution to TACE (Transarterial Chemoembolization) response prediction in HCC (Hepatocellu...
来源: 评论
Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking
Testing the Inference Accuracy of Accelerator-Friendly Appro...
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Computational Intelligence in Artificial Life and Cooperative Intelligent systems (ALIFE-CIS), IEEE Symposium on
作者: Matthew Andres Moreno Anika Ranjan Emily Dolson Luis Zaman Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and AI in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Department of Computer Science and Engineering Michigan State University East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States
computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Su... 详细信息
来源: 评论
Testing the Inference Accuracy of Accelerator-Friendly Approximate Phylogeny Tracking
Testing the Inference Accuracy of Accelerator-Friendly Appro...
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2025 IEEE Symposium on Computational Intelligence in Artificial Life and Cooperative Intelligent systems, ALIFE-CIS 2025
作者: Moreno, Matthew Andres Ranjan, Anika Dolson, Emily Zaman, Luis University of Michigan Department of Ecology and Evolutionary Biology Ann Arbor United States Center for the Study of Complex Systems University of Michigan Ann Arbor United States Michigan Institute for Data and Ai in Society University of Michigan Ann Arbor United States Undergraduate Research Opportunities Program University of Michigan Ann Arbor United States Michigan State University Department of Computer Science and Engineering East Lansing United States Program in Ecology Evolution and Behavior Michigan State University East Lansing United States
computer simulations are an important tool for studying the mechanics of biological evolution. In particular, agent-based approaches provide an opportunity to collect high-quality records of ancestry relationships. Su... 详细信息
来源: 评论