Trey Ideker

Research interests

Publications

• Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients

  Nature Cancer · 2021 · https://doi.org/10.1038/s43018-020-00169-2

• DNA methylation aging clocks: challenges and recommendations

  Genome biology · 2019 · https://doi.org/10.1186/s13059-019-1824-y

• Using deep learning to model the hierarchical structure and function of a cell

  Nature Methods · 2018 · https://doi.org/10.1038/nmeth.4627

• Network propagation: a universal amplifier of genetic associations

  Nature Reviews Genetics · 2017 · https://doi.org/10.1038/nrg.2017.38

• Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems

  Cell Systems · 2016 · https://doi.org/10.1016/j.cels.2016.02.003

• Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders

  Science · 2014 · https://doi.org/10.1126/science.1247363

• Integrated Genomic Characterization of Papillary Thyroid Carcinoma

  Cell · 2014 · https://doi.org/10.1016/j.cell.2014.09.050

• Network-based stratification of tumor mutations

  Nature Methods · 2013 · 10.1038/nmeth.2651

• A travel guide to Cytoscape plugins

  Nature Methods · 2012 · https://doi.org/10.1038/nmeth.2212

• Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates

  Molecular Cell · 2012 · https://doi.org/10.1016/j.molcel.2012.10.016

• Differential network biology

  Molecular Systems Biology · 2012 · 10.1038/msb.2011.99

• Cytoscape 2.8: new features for data integration and network

  Journal · 2011

• An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

  Cell · 2010 · 10.1016/j.cell.2010.01.044

• Cytoscape 2.8: new features for data integration and network visualization

  Bioinformatics · 2010 · https://doi.org/10.1093/bioinformatics/btq675

• Human host factors required for influenza virus replication

  Nature · 2009 · 10.1038/nature08699

• Protein networks in disease

  Genome Research · 2008 · 10.1101/gr.071852.107

• Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication

  Cell · 2008 · 10.1016/j.cell.2008.07.032

• NetworkBLAST: comparative analysis of protein networks

  Bioinformatics · 2008 · https://doi.org/10.1093/bioinformatics/btm630

• Integration of biological networks and gene expression data using Cytoscape

  Nature Protocols · 2007 · https://doi.org/10.1038/nprot.2007.324

• SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments

  Bioinformatics · 2007 · https://doi.org/10.1093/bioinformatics/btm170

• Network‐based classification of breast cancer metastasis

  Molecular Systems Biology · 2007 · 10.1038/msb4100180

• Modeling cellular machinery through biological network comparison

  Nature Biotechnology · 2006 · https://doi.org/10.1038/nbt1196

• Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

  Journal of Computational Biology · 2006 · https://doi.org/10.1089/cmb.2006.13.133

• Systematic identification of functional orthologs based on protein network comparison

  Genome Research · 2006 · https://doi.org/10.1101/gr.4526006

• A direct comparison of protein interaction confidence assignment schemes

  BMC Bioinformatics · 2006 · https://doi.org/10.1186/1471-2105-7-360

• Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data

  Journal of Computational Biology · 2005 · https://doi.org/10.1089/cmb.2005.12.835

• Conserved patterns of protein interaction in multiple species

  Proceedings of the National Academy of Sciences · 2005 · 10.1073/pnas.0409522102

• Physical Network Models

  Journal of Computational Biology · 2004 · https://doi.org/10.1089/1066527041410382

• PathBLAST: a tool for alignment of protein interaction networks

  Nucleic Acids Research · 2004 · https://doi.org/10.1093/nar/gkh411

• Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

  Genome Research · 2003 · https://doi.org/10.1101/gr.1239303

• Conserved pathways within bacteria and yeast as revealed by global protein network alignment

  Proceedings of the National Academy of Sciences · 2003 · https://doi.org/10.1073/pnas.1534710100

• Discovering regulatory and signalling circuits in molecular interaction networks

  Bioinformatics · 2002 · 10.1093/bioinformatics/18.suppl_1.s233

• A N EW A PPROACH TO D ECODING L IFE : Systems Biology

  Annual Review of Genomics and Human Genetics · 2001 · 10.1146/annurev.genom.2.1.343

• Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network

  Science · 2001 · 10.1126/science.292.5518.929

Current projects

No projects listed.