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Genetics

D-Index
114
Citations
128042
World Ranking
459
National Ranking
236

Research.com Recognitions

  • 2014 - Fellow of the Indian National Academy of Engineering (INAE)
  • 2014 - Fellow of the American Association for the Advancement of Science (AAAS)

Overview

Trey Ideker is affiliated with the University of California, San Diego in the United States. Their research primarily spans the fields of Biochemistry, Genetics, and Molecular Biology, with a total of 221 publications in these areas. Within these broad fields, their work delves into several subfields including Molecular Biology, Computational Theory and Mathematics, Biophysics, Genetics, and Cancer Research.

The scientist's research topics include Bioinformatics and Genomic Networks, Computational Drug Discovery Methods, Cancer Genomics and Diagnostics, Cell Image Analysis Techniques, CRISPR and Genetic Engineering, Genetics, Bioinformatics, and Biomedical Research, as well as Single-cell and Spatial Transcriptomics.

Notable recent papers by Trey Ideker include:

  • Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells, 2020, Cancer Cell
  • A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing, 2020, bioRxiv (Cold Spring Harbor Laboratory)
  • Multivariate analysis of 1.5 million people identifies genetic associations with traits related to self-regulation and addiction, 2021, Nature Neuroscience
  • Functional landscape of SARS-CoV-2 cellular restriction, 2021, Molecular Cell
  • Understudied proteins: opportunities and challenges for functional proteomics, 2022, Nature Methods

The scientist frequently publishes in venues such as:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Cancer Research
  • Zenodo (CERN European Organization for Nuclear Research)
  • Cell Systems
  • Cell Reports

Frequent coauthors contributing to their work include Dexter Pratt, Jason F. Kreisberg, Christopher Churas, Nevan J. Krogan, and Fan Zheng, reflecting collaborations across diverse research efforts.

Awards received by Trey Ideker include:

  • Fellow of the American Association for the Advancement of Science (AAAS), 2014
  • Fellow of the Indian National Academy of Engineering (INAE), 2014

Best Publications

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

    Paul Shannon;Andrew Markiel;Owen Ozier;Nitin S. Baliga

  • A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

    David E. Gordon;Gwendolyn M. Jang;Mehdi Bouhaddou;Jiewei Xu

  • Cytoscape 2.8

    Michael E. Smoot;Keiichiro Ono;Johannes Ruscheinski;Peng-Liang Wang

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

    Gregory Hannum;Justin Guinney;Ling Zhao;Ling Zhao;Li Zhang

  • Integration of biological networks and gene expression data using Cytoscape

    Melissa S Cline;Michael Smoot;Ethan Cerami;Allan Kuchinsky

  • Integrated Genomic Characterization of Papillary Thyroid Carcinoma

    Nishant Agrawal;Rehan Akbani;B. Arman Aksoy;Adrian Ally

  • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.

    Trey Ideker;Vesteinn Thorsson;Jeffrey A. Ranish;Rowan Christmas

  • A NEW APPROACH TO DECODING LIFE: Systems Biology

    Trey Ideker;Timothy Galitski;Leroy Hood

  • Network-based classification of breast cancer metastasis.

    Han‐Yu Chuang;Eunjung Lee;Eunjung Lee;Yu‐Tsueng Liu;Doheon Lee

  • A travel guide to Cytoscape plugins

    Rintaro Saito;Michael E Smoot;Keiichiro Ono;Johannes Ruscheinski

  • Discovering regulatory and signalling circuits in molecular interaction networks.

    Trey Ideker;Owen Ozier;Benno Schwikowski;Andrew F. Siegel

  • Cytoscape 2.8: new features for data integration and network

    E. Smoot;Keiichiro Ono;Johannes Ruscheinski;Peng-Liang Wang

  • Global analysis of host-pathogen interactions that regulate early stage HIV-1 replication

    Renate König;Yingyao Zhou;Daniel Elleder;Tracy L. Diamond

  • Human host factors required for influenza virus replication

    Renate König;Silke Stertz;Yingyao Zhou;Atsushi Inoue

  • Protein networks in disease.

    Trey Ideker;Roded Sharan

  • Conserved patterns of protein interaction in multiple species

    Roded Sharan;Silpa Suthram;Ryan M. Kelley;Tanja Kuhn

  • Network based stratification of tumor mutations

    Trey Ideker;Matan Hofree;John Paul Shen

  • Differential network biology

    Trey Ideker;Nevan J Krogan;Nevan J Krogan;Nevan J Krogan

  • An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

    Timothy Ravasi;Harukazu Suzuki;Carlo Vittorio Cannistraci;Shintaro Katayama

  • Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae

    Timothy J. Griffin;Steven P. Gygi;Trey Ideker;Beate Rist

Frequent Co-Authors

Nevan J. Krogan
Nevan J. Krogan University of California, San Francisco
Roded Sharan
Roded Sharan Tel Aviv University
Hannah Carter
Hannah Carter University of California, San Diego
Leroy Hood
Leroy Hood University of Washington
Nicholas J. Schork
Nicholas J. Schork Translational Genomics Research Institute
Sumit K. Chanda
Sumit K. Chanda Discovery Institute
Peter D. Adams
Peter D. Adams Sanford Burnham Prebys Medical Discovery Institute
Jeffrey R. Johnson
Jeffrey R. Johnson Icahn School of Medicine at Mount Sinai
Haico van Attikum
Haico van Attikum Leiden University Medical Center
Richard M. Karp
Richard M. Karp University of California, Berkeley

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