1. Influence of metabolic network structure and function on enzyme evolution Vitkup, Dennis; Kharchenko, Peter; Wagner, Andreas 2006 Articles Molecular evolutionSystems biologyGene amplificationBiology
2. Pattern-based mining strategy to detect multi-locus association and gene × environment interaction Li, Zhong; Zheng, Tian; Califano, Andrea; Floratos, Aristidis 2007 Articles GeneticsBiometry
3. Correlating measurements across samples improves accuracy of large-scale expression profile experiments Alvarez, Mariano; Sumazin, Pavel; Rajbhandari, Presha; Califano, Andrea 2009 Articles GeneticsBioinformatics
4. Genome Wide Analysis of Drug-Induced Torsades de Pointes: Lack of Common Variants with Large Effect Sizes Behr, Elijah R.; Ritchie, Marylyn D.; Tanaka, Toshihiro; Kääb, Stefan; Crawford, Dana C.; Nicoletti, Paola; Floratos, Aristidis; Kannankeril, Prince J.; Sinner, Moritz F.; M. Wilde, Arthur A.; Bezzina, Connie R.; Schulze-Bahr, Eric; Zumhagen, Sven; Guicheney, Pascale; Bishopric, Nanette H.; Marshall, Vanessa; Shakir, Saad; Dalageorgou, Chrysoula; Jamshidi, Yalda; Bevan, Steve; Bastiaenen, Rachel; Myerburg, Robert J.; Schott, Jean-Jacques; Camm, A. John; Steinbeck, Gerhard; Norris, Kris; Altman, Russ B.; Tatonetti, Nicholas P.; Jeffery, Steve; Kubo, Michiaki; Nakamura, Yusuke; Shen, Yufeng; George Jr, Alfred L.; Roden, Dan M. 2013 Articles Medical geneticsVentricular tachycardiaDrug interactionsGenomics
5. 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
6. Estimating heritability of drug-induced liver injury from common variants and implications for future study designs Overby, Casey Lynnette; Hripcsak, George M.; Shen, Yufeng 2014 Articles Human genome--ResearchLiver--Wounds and injuriesDrugs--Side effectsHereditySystems biologyBioinformatics
7. Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information Giorgi, Federico M.; Lopez, Gonzalo; Woo, Jung H.; Bisikirska, Brygida; Califano, Andrea; Bansal, Mukesh 2014 Articles Gene expressionGenetic algorithmsTranscription factorsBioinformaticsGeneticsMolecular biology
8. Assembly and Interrogation of Alzheimer’s Disease Genetic Networks Reveal Novel Regulators of Progression Aubry, Soline; Shin, William Kihoon; Crary, John F.; Lefort, Roger; Qureshi, Yasir H.; Lefebvre, Celine; Califano, Andrea; Shelanski, Michael L. 2015 Articles Systems biologyGene regulatory networksAlzheimer's disease--ResearchNeurosciencesChemical engineeringBiochemistry
9. Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks Repunte-Canonigo, Vez; Shin, William Kihoon; Vendruscolo, Leandro F.; Lefebvre, Celine; van der Stap, Lena; Kawamura, Tomoya; Schlosburg, Joel E.; Alvarez, Mariano Javier; Koob, George F.; Califano, Andrea; Sanno, Pietro Paolo 2015 Articles Gene regulatory networksAlcoholismBiology--Classification
10. A novel, rapid method to compare the therapeutic windows of oral anticoagulants using the Hill coefficient Chang, Jeremy B.; Quinnies, Kayla M.; Realubit, Ronald B.; Karan Jr., Charles; Rand, Jacob H.; Tatonetti, Nicholas P. 2016 Articles Anticoagulants (Medicine)Oral medicinePharmacokineticsMedicinePharmacology