Guan, Yuanfang, Maitreya Dunham, and Olga G Troyanskaya. (2007) 2007. “Functional Analysis of Gene Duplications in Saccharomyces Cerevisiae.”. Genetics 175 (2): 933-43.

Huttenhower, Curtis, Erin M Haley, Matthew A Hibbs, Vanessa Dumeaux, Daniel R Barrett, Hilary A Coller, and Olga G Troyanskaya. (2009) 2009. “Exploring the Human Genome With Functional Maps.”. Genome Res 19 (6): 1093-106.

Deng, Yi, Philip Coen, Mingzhai Sun, and Joshua W Shaevitz. 2013. “Efficient Multiple Object Tracking Using Mutually Repulsive Active Membranes.”. PLoS One 8 (6): e65769.

Ober, Ulrike, Julien Ayroles, Eric A Stone, Stephen Richards, Dianhui Zhu, Richard A Gibbs, Christian Stricker, et al. 2012. “Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila Melanogaster.”. PLoS Genet 8 (5): e1002685.

Myers, Chad L, Drew Robson, Adam Wible, Matthew A Hibbs, Camelia Chiriac, Chandra L Theesfeld, Kara Dolinski, and Olga G Troyanskaya. 2005. “Discovery of Biological Networks from Diverse Functional Genomic Data.”. Genome Biol 6 (13): R114.

Park, Christopher Y, David C Hess, Curtis Huttenhower, and Olga G Troyanskaya. 2010. “Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.”. PLoS Comput Biol 6 (11): e1001009.

Putnam, Andrea S, Mark Scriber, and Peter Andolfatto. (2007) 2007. “Discordant Divergence Times Among Z-Chromosome Regions Between Two Ecologically Distinct Swallowtail Butterfly Species.”. Evolution 61 (4): 912-27.

Huttenhower, Curtis, Matt Hibbs, Chad Myers, and Olga G Troyanskaya. (2006) 2006. “A Scalable Method for Integration and Functional Analysis of Multiple Microarray Datasets.”. Bioinformatics 22 (23): 2890-7.

Huttenhower, Curtis, Tsheko Mutungu, Natasha Indik, Woongcheol Yang, Mark Schroeder, Joshua J Forman, Olga G Troyanskaya, and Hilary A Coller. (2009) 2009. “Detailing Regulatory Networks through Large Scale Data Integration.”. Bioinformatics 25 (24): 3267-74.

Guan, Yuanfang, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy, and Olga G Troyanskaya. 2008. “Predicting Gene Function in a Hierarchical Context With an Ensemble of Classifiers.”. Genome Biol 9 Suppl 1: S3.

Bradley, Patrick H, Matthew J Brauer, Joshua D Rabinowitz, and Olga G Troyanskaya. (2009) 2009. “Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces Cerevisiae.”. PLoS Comput Biol 5 (1): e1000270.

Wilson, Daniel J, Ryan D Hernandez, Peter Andolfatto, and Molly Przeworski. (2011) 2011. “A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences.”. PLoS Genet 7 (12): e1002395.

Greene, Casey S, and Olga G Troyanskaya. 2012. “Chapter 2: Data-Driven View of Disease Biology.”. PLoS Comput Biol 8 (12): e1002816.

Lee, Young-suk, Arjun Krishnan, Qian Zhu, and Olga G Troyanskaya. (2013) 2013. “Ontology-Aware Classification of Tissue and Cell-Type Signals in Gene Expression Profiles across Platforms and Technologies.”. Bioinformatics 29 (23): 3036-44.

Troyanskaya, Olga G, Kara Dolinski, Art B Owen, Russ B Altman, and David Botstein. (2003) 2003. “A Bayesian Framework for Combining Heterogeneous Data Sources for Gene Function Prediction (in Saccharomyces cerevisiae).”. Proc Natl Acad Sci U S A 100 (14): 8348-53.

Greene, Casey S, and Olga G Troyanskaya. (2010) 2010. “Integrative Systems Biology for Data-Driven Knowledge Discovery.”. Semin Nephrol 30 (5): 443-54.

Huttenhower, Curtis, and Olga G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.”. Comput Syst Bioinformatics Conf, 341-51.

Pop, Ana, Curtis Huttenhower, Anjali Iyer-Pascuzzi, Philip N Benfey, and Olga G Troyanskaya. 2010. “Integrated Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis Thaliana.”. BMC Syst Biol 4: 180.

Thornton, Kevin, and Peter Andolfatto. (2006) 2006. “Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila Melanogaster.”. Genetics 172 (3): 1607-19.

Huelsenbeck, John P, and Peter Andolfatto. (2007) 2007. “Inference of Population Structure under a Dirichlet Process Model.”. Genetics 175 (4): 1787-802.

Jensen, Jeffrey D, Kevin R Thornton, and Peter Andolfatto. 2008. “An Approximate Bayesian Estimator Suggests Strong, Recurrent Selective Sweeps in Drosophila.”. PLoS Genet 4 (9): e1000198.

Barutcuoglu, Zafer, Robert E Schapire, and Olga G Troyanskaya. (2006) 2006. “Hierarchical Multi-Label Prediction of Gene Function.”. Bioinformatics 22 (7): 830-6.

Chikina, Maria D, and Olga G Troyanskaya. 2011. “Accurate Quantification of Functional Analogy Among Close Homologs.”. PLoS Comput Biol 7 (2): e1001074.

Guan, Yuanfang, Chad L Myers, Rong Lu, Ihor R Lemischka, Carol J Bult, and Olga G Troyanskaya. 2008. “A Genomewide Functional Network for the Laboratory Mouse.”. PLoS Comput Biol 4 (9): e1000165.

Gorenshteyn, Dmitriy, Elena Zaslavsky, Miguel Fribourg, Christopher Y Park, Aaron K Wong, Alicja Tadych, Boris M Hartmann, et al. (2015) 2015. “Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.”. Immunity 43 (3): 605-14.

Park, Christopher Y, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca Burdine, and Olga G Troyanskaya. 2013. “Functional Knowledge Transfer for High-Accuracy Prediction of under-Studied Biological Processes.”. PLoS Comput Biol 9 (3): e1002957.

Guan, Yuanfang, Cheryl L Ackert-Bicknell, Braden Kell, Olga G Troyanskaya, and Matthew A Hibbs. 2010. “Functional Genomics Complements Quantitative Genetics in Identifying Disease-Gene Associations.”. PLoS Comput Biol 6 (11): e1000991.