Standout Papers

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Net... 2001 2026 2009 2017 33.4k
  1. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks (2003)
    Paul Shannon, Owen Ozier et al. Genome Research
  2. Cytoscape 2.8: new features for data integration and network visualization (2010)
    Michael Smoot, Keiichiro Ono et al. Bioinformatics
  3. Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates (2012)
    Gregory Hannum, Justin Guinney et al. Molecular Cell
  4. Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network (2001)
    Trey Ideker, Vésteinn Thórsson et al. Science
  5. A travel guide to Cytoscape plugins (2012)
    Rintaro Saito, Michael Smoot et al. Nature Methods
  6. A NEWAPPROACH TODECODINGLIFE: Systems Biology (2001)
    Trey Ideker, Timothy Galitski et al. Annual Review of Genomics and Human Genetics
  7. Network‐based classification of breast cancer metastasis (2007)
    Han‐Yu Chuang, Eunjung Lee et al. Molecular Systems Biology
  8. Discovering regulatory and signalling circuits in molecular interaction networks (2002)
    Trey Ideker, Owen Ozier et al. Bioinformatics
  9. Protein networks in disease (2008)
    Trey Ideker, Roded Sharan Genome Research
  10. Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae (2002)
    Timothy J. Griffin, Steven P. Gygi et al. Molecular & Cellular Proteomics
  11. Network-based stratification of tumor mutations (2013)
    Matan Hofree, John Paul Shen et al. Nature Methods
  12. Differential network biology (2012)
    Trey Ideker, Nevan J. Krogan Molecular Systems Biology
  13. Network propagation: a universal amplifier of genetic associations (2017)
    Lenore Cowen, Trey Ideker et al. Nature Reviews Genetics
  14. DNA Methylation Clocks in Aging: Categories, Causes, and Consequences (2018)
    Neil Robertson, Tina Wang et al. Molecular Cell
  15. Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells (2020)
    Brent M. Kuenzi, Jisoo Park et al. Cancer Cell

Immediate Impact

6 by Nobel laureates 45 from Science/Nature 78 standout
Sub-graph 1 of 21

Citing Papers

Mass-spectrometry-based proteomics: from single cells to clinical applications
2025 StandoutNature
Spatially organized cellular communities form the developing human heart
2024 StandoutNature
16 intermediate papers

Works of Trey Ideker being referenced

Unveiling Complexity and Multipotentiality of Early Heart Fields
2021
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
2003 Standout
and 5 more

Author Peers

Author Last Decade Papers Cites
Trey Ideker 44414 7931 4609 6165 236 63.2k
Christian von Mering 43997 7284 4570 6063 132 66.8k
Lars Juhl Jensen 47759 7950 7086 6291 232 71.9k
Susumu Goto 30569 4841 3423 4227 139 45.6k
Nitin S. Baliga 25778 5741 1934 3763 140 40.2k
Gavin Sherlock 33340 4556 1766 6070 123 46.6k
Minoru Kanehisa 73697 11792 7025 9876 253 109.5k
Richard A. Lempicki 36036 10828 1467 7420 125 59.5k
Damian Szklarczyk 30724 6487 3315 4389 40 48.7k
David S. Wishart 47041 2954 6411 4843 537 73.1k
Mark Gerstein 46809 7660 2104 8430 543 59.7k

All Works

Loading papers...

Rankless by CCL
2026