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Trey Ideker
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Cytoscape: a software environment for integrated models of biomolecular interaction networks
P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, ...
Genome research 13 (11), 2498-2504, 2003
418122003
Cytoscape 2.8: new features for data integration and network visualization
ME Smoot, K Ono, J Ruscheinski, PL Wang, T Ideker
Bioinformatics 27 (3), 431-432, 2011
50342011
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
DE Gordon, GM Jang, M Bouhaddou, J Xu, K Obernier, KM White, ...
Nature 583 (7816), 459-468, 2020
44162020
Genome-wide methylation profiles reveal quantitative views of human aging rates
G Hannum, J Guinney, L Zhao, LI Zhang, G Hughes, SV Sadda, B Klotzle, ...
Molecular cell 49 (2), 359-367, 2013
32432013
Integration of biological networks and gene expression data using Cytoscape
MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, ...
Nature protocols 2 (10), 2366-2382, 2007
27422007
Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
T Ideker, V Thorsson, JA Ranish, R Christmas, J Buhler, JK Eng, ...
Science 292 (5518), 929-934, 2001
26342001
Integrated genomic characterization of papillary thyroid carcinoma
N Agrawal, R Akbani, BA Aksoy, A Ally, H Arachchi, SL Asa, JT Auman, ...
Cell 159 (3), 676-690, 2014
25302014
A NEW APPROACH TO DECODING LIFE: Systems Biology
T Ideker, T Galitski, L Hood
Annual review of genomics and human genetics 2 (1), 343-372, 2001
23762001
Network‐based classification of breast cancer metastasis
HY Chuang, E Lee, YT Liu, D Lee, T Ideker
Molecular systems biology 3 (1), 140, 2007
17912007
A travel guide to Cytoscape plugins
R Saito, ME Smoot, K Ono, J Ruscheinski, PL Wang, S Lotia, AR Pico, ...
Nature methods 9 (11), 1069-1076, 2012
14982012
Discovering regulatory and signalling circuits in molecular interaction networks
T Ideker, O Ozier, B Schwikowski, AF Siegel
Bioinformatics 18 (suppl_1), S233-S240, 2002
14602002
Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication
R König, Y Zhou, D Elleder, TL Diamond, GMC Bonamy, JT Irelan, ...
Cell 135 (1), 49-60, 2008
11772008
Protein networks in disease
T Ideker, R Sharan
Genome research 18 (4), 644-652, 2008
9872008
Human host factors required for influenza virus replication
R König, S Stertz, Y Zhou, A Inoue, HH Hoffmann, S Bhattacharyya, ...
Nature 463 (7282), 813-817, 2010
9682010
Conserved patterns of protein interaction in multiple species
R Sharan, S Suthram, RM Kelley, T Kuhn, S McCuine, P Uetz, T Sittler, ...
Proceedings of the National Academy of Sciences 102 (6), 1974-1979, 2005
9622005
Network-based stratification of tumor mutations
M Hofree, JP Shen, H Carter, A Gross, T Ideker
Nature methods 10 (11), 1108-1115, 2013
8832013
Differential network biology
T Ideker, NJ Krogan
Molecular systems biology 8 (1), 565, 2012
8722012
Complementary profiling of gene expression at the transcriptome and proteome levels in saccharomyces cerevisiae* S
TJ Griffin, SP Gygi, T Ideker, B Rist, J Eng, L Hood, R Aebersold
Molecular & Cellular Proteomics 1 (4), 323-333, 2002
8422002
An atlas of combinatorial transcriptional regulation in mouse and man
T Ravasi, H Suzuki, CV Cannistraci, S Katayama, VB Bajic, K Tan, ...
Cell 140 (5), 744-752, 2010
8342010
DNA methylation aging clocks: challenges and recommendations
CG Bell, R Lowe, PD Adams, AA Baccarelli, S Beck, JT Bell, ...
Genome biology 20, 1-24, 2019
7032019
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