1. PathBLAST: a tool for alignment of protein interaction networks Kelley, Brian P.; Yuan, Bingbing; Sharan, Roded; Lewitter, Fran; Stockwell, Brent R.; Ideker, Trey 2004 Articles GenomicsProtein-protein interactionsGenetics
2. Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling Bilal, Erhan; Dutkowski, Janusz; Guinney, Justin; Jang, In Sock; Logsdon, Benjamin A.; Mecham, Brigham H.; Pandey, Gaurav; Vollan, Hans Kristian Moen; Sauerwine, Benjamin A.; Shimoni, Yishai; Rueda, Oscar M.; Curtis, Christina; Tost, Jorg; Alvarez, Mariano Javier; Kristensen, Vessela N.; Aparicio, Samuel; Børresen-Dale, Anne-Lise; Califano, Andrea; Caldas, Carlos; Friend, Stephen H.; Ideker, Trey; Stolovitzky, Gustavo A.; Schadt, Eric E.; Margolin, Adam A. 2013 Articles PrognosisMachine learningBreast--CancerMedicine
3. Host Cell Factors in HIV Replication: Meta-Analysis of Genome-Wide Studies Bushman, Frederic D.; Fernandes, Jason; D'Orso, Ivan; Malani, Nirav; Zhou, Honglin; Hazuda, Daria J.; Espeseth, Amy S.; Konig, Renate; Bandyopadhyay, Sourav; Ideker, Trey; Cagney, Gerard; Diamond, Tracy L.; Goff, Stephen P.; Krogan, Nevan J.; Frankel, Alan D.; Young, John A. T.; Chanda, Sumit K. 2009 Articles PathologyGeneticsCytology
4. DNA methylation aging clocks: challenges and recommendations Bell, Christopher G.; Lowe, Robert; Adams, Peter D.; Baccarelli, Andrea A.; Beck, Stephan; Bell, Jordana T.; Christensen, Brock C.; Gladyshev, Vadim N.; Heijmans, Bastiaan T.; Horvath, Steve; Ideker, Trey; Issa, Jean-Pierre J.; Kelsey, Karl T.; Marioni, Riccardo E.; Reik, Wolf; Relton, Caroline L.; Schalkwyk, Leonard C.; Teschendorff, Andrew E.; Wagner, Wolfgang; Zhang, Kang; Rakyan, Vardhman K. 2019 Articles DNA--MethylationEpigeneticsAging--Measurement
5. Conserved pathways within bacteria and yeast as revealed by global protein network alignment Kelly, Brian P.; Sharan, Roded; Karp, Richard; Sittler, Taylor; Root, David; Stockwell, Brent R.; Ideker, Trey 2003 Articles Saccharomyces cerevisiaeHelicobacter pyloriMolecular biologyProtein-protein interactionsBiology