Huttenhower, Curtis, Mark Schroeder, Maria D Chikina, and Olga G Troyanskaya. (2008) 2008. “The Sleipnir Library for Computational Functional Genomics.”. Bioinformatics 24 (13): 1559-61.

Markowetz, Florian, Dennis Kostka, Olga G Troyanskaya, and Rainer Spang. (2007) 2007. “Nested Effects Models for High-Dimensional Phenotyping Screens.”. Bioinformatics 23 (13).

Sealfon, Rachel S G, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers, and Olga G Troyanskaya. 2006. “GOLEM: An Interactive Graph-Based Gene-Ontology Navigation and Analysis Tool.”. BMC Bioinformatics 7: 443.

Myers, Chad L, Camelia Chiriac, and Olga G Troyanskaya. 2009. “Discovering Biological Networks from Diverse Functional Genomic Data.”. Methods Mol Biol 563: 157-75.

Barutcuoglu, Zafer, Edoardo M Airoldi, Vanessa Dumeaux, Robert E Schapire, and Olga G Troyanskaya. (2009) 2009. “Aneuploidy Prediction and Tumor Classification With Heterogeneous Hidden Conditional Random Fields.”. Bioinformatics 25 (10): 1307-13.

Yao, Victoria, Aaron K Wong, and Olga G Troyanskaya. (2018) 2018. “Enabling Precision Medicine through Integrative Network Models.”. J Mol Biol 430 (18 Pt A): 2913-23. doi:10.1016/j.jmb.2018.07.004.

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.

Huttenhower, Curtis, Avi I Flamholz, Jessica N Landis, Sauhard Sahi, Chad L Myers, Kellen L Olszewski, Matthew A Hibbs, Nathan O Siemers, Olga G Troyanskaya, and Hilary A Coller. 2007. “Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods.”. BMC Bioinformatics 8: 250.

Zhou, Jian, and Olga G Troyanskaya. (2014) 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.”. PLoS Comput Biol 10 (3): e1003525.

Hibbs, Matthew A, Chad L Myers, Curtis Huttenhower, David C Hess, Kai Li, Amy A Caudy, and Olga G Troyanskaya. (2009) 2009. “Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis.”. PLoS Comput Biol 5 (3): e1000322.

Chi, An, Curtis Huttenhower, Lewis Y Geer, Joshua J Coon, John E P Syka, Dina L Bai, Jeffrey Shabanowitz, Daniel J Burke, Olga G Troyanskaya, and Donald F Hunt. (2007) 2007. “Analysis of Phosphorylation Sites on Proteins from Saccharomyces Cerevisiae by Electron Transfer Dissociation (ETD) Mass Spectrometry.”. Proc Natl Acad Sci U S A 104 (7): 2193-8.

Yao, Victoria, Rachel Kaletsky, William Keyes, Danielle E Mor, Aaron K Wong, Salman Sohrabi, Coleen T Murphy, and Olga G Troyanskaya. (2018) 2018. “An Integrative Tissue-Network Approach to Identify and Test Human Disease Genes.”. Nat Biotechnol. doi:10.1038/nbt.4246.

Troyanskaya, Olga G, Ora Arbell, Yair Koren, Gad M Landau, and Alexander Bolshoy. (2002) 2002. “Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity.”. Bioinformatics 18 (5): 679-88.

Haarer, Brian, Susan Viggiano, Mathew A Hibbs, Olga G Troyanskaya, and David C Amberg. (2007) 2007. “Modeling Complex Genetic Interactions in a Simple Eukaryotic Genome: Actin Displays a Rich Spectrum of Complex Haploinsufficiencies.”. Genes Dev 21 (2): 148-59.

Chikina, Maria D, Curtis Huttenhower, Coleen T Murphy, and Olga G Troyanskaya. (2009) 2009. “Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis Elegans.”. PLoS Comput Biol 5 (6): e1000417.

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.

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

Lee, Young-suk, Aaron K Wong, Alicja Tadych, Boris M Hartmann, Christopher Y Park, Veronica A DeJesus, Irene Ramos, Elena Zaslavsky, Stuart C Sealfon, and Olga G Troyanskaya. (2018) 2018. “Interpretation of an Individual Functional Genomics Experiment Guided by Massive Public Data.”. Nat Methods 15 (12): 1049-52. doi:10.1038/s41592-018-0218-5.

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.

Markowetz, Florian, Klaas W Mulder, Edoardo M Airoldi, Ihor R Lemischka, and Olga G Troyanskaya. 2010. “Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells.”. PLoS Comput Biol 6 (12): e1001034.

Brown, James A, Gavin Sherlock, Chad L Myers, Nicola M Burrows, Changchun Deng, Irene Wu, Kelly E McCann, Olga G Troyanskaya, and Martin Brown. 2006. “Global Analysis of Gene Function in Yeast by Quantitative Phenotypic Profiling.”. Mol Syst Biol 2: 2006.0001.

Ju, Wenjun, Casey S Greene, Felix Eichinger, Viji Nair, Jeffrey B Hodgin, Markus Bitzer, Young-suk Lee, et al. (2013) 2013. “Defining Cell-Type Specificity at the Transcriptional Level in Human Disease.”. Genome Res 23 (11): 1862-73.

Greene, Casey S, and Olga G Troyanskaya. (2012) 2012. “Accurate Evaluation and Analysis of Functional Genomics Data and Methods.”. Ann N Y Acad Sci 1260: 95-100.

Harder, Jennifer L, Rajasree Menon, Edgar A Otto, Jian Zhou, Sean Eddy, Noel L Wys, Christopher O’Connor, et al. (2019) 2019. “Organoid Single Cell Profiling Identifies a Transcriptional Signature of Glomerular Disease.”. JCI Insight 4 (1). doi:10.1172/jci.insight.122697.

Baryshnikova, Anastasia, Michael Costanzo, Yungil Kim, Huiming Ding, Judice Koh, Kiana Toufighi, Ji-Young Youn, et al. (2010) 2010. “Quantitative Analysis of Fitness and Genetic Interactions in Yeast on a Genome Scale.”. Nat Methods 7 (12): 1017-24.

Chikina, Maria D, Christophe P Gerald, Xianting Li, Yongchao Ge, Hanna Pincas, Venugopalan D Nair, Aaron K Wong, et al. (2015) 2015. “Low-Variance RNAs Identify Parkinson’s Disease Molecular Signature in Blood.”. Mov Disord 30 (6): 813-21.

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.

Peña-Castillo, Lourdes, Murat Tasan, Chad L Myers, Hyunju Lee, Trupti Joshi, Chao Zhang, Yuanfang Guan, et al. 2008. “A Critical Assessment of Mus Musculus Gene Function Prediction Using Integrated Genomic Evidence.”. Genome Biol 9 Suppl 1: S2.

Myers, Chad L, Maitreya Dunham, S Y Kung, and Olga G Troyanskaya. (2004) 2004. “Accurate Detection of Aneuploidies in Array CGH and Gene Expression Microarray Data.”. Bioinformatics 20 (18): 3533-43.

Zhou, Jian, Christopher Y Park, Chandra L Theesfeld, Aaron K Wong, Yuan Yuan, Claudia Scheckel, John J Fak, et al. (2019) 2019. “Whole-Genome Deep-Learning Analysis Identifies Contribution of Noncoding Mutations to Autism Risk.”. Nat Genet 51 (6): 973-80. doi:10.1038/s41588-019-0420-0.

Troyanskaya, Olga G. 2005. “Putting the ’bio’ into Bioinformatics.”. Genome Biol 6 (10): 351.

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

Costanzo, Michael, Anastasia Baryshnikova, Jeremy Bellay, Yungil Kim, Eric D Spear, Carolyn S Sevier, Huiming Ding, et al. (2010) 2010. “The Genetic Landscape of a Cell.”. Science 327 (5964): 425-31.

Brauer, Matthew J, Curtis Huttenhower, Edoardo M Airoldi, Rachel Rosenstein, John C Matese, David Gresham, Viktor M Boer, Olga G Troyanskaya, and David Botstein. (2008) 2008. “Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast.”. Mol Biol Cell 19 (1): 352-67.

Zhou, Jian, and Olga G Troyanskaya. 2016. “Probabilistic Modelling of Chromatin Code Landscape Reveals Functional Diversity of Enhancer-Like Chromatin States.”. Nat Commun 7: 10528.

Chen, Kathleen M, Evan M Cofer, Jian Zhou, and Olga G Troyanskaya. (2019) 2019. “Selene: A PyTorch-Based Deep Learning Library for Sequence Data.”. Nat Methods 16 (4): 315-18. doi:10.1038/s41592-019-0360-8.

Myers, Chad L, Xing Chen, and Olga G Troyanskaya. 2005. “Visualization-Based Discovery and Analysis of Genomic Aberrations in Microarray Data.”. BMC Bioinformatics 6: 146.

Troyanskaya, Olga G. (2005) 2005. “Putting Microarrays in a Context: Integrated Analysis of Diverse Biological Data.”. Brief Bioinform 6 (1): 34-43.

Kristensen, Vessela N, Charles J Vaske, Josie Ursini-Siegel, Peter Van Loo, Silje H Nordgard, Ravi Sachidanandam, Therese Sørlie, et al. (2012) 2012. “Integrated Molecular Profiles of Invasive Breast Tumors and Ductal Carcinoma in Situ (DCIS) Reveal Differential Vascular and Interleukin Signaling.”. Proc Natl Acad Sci U S A 109 (8): 2802-7.

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.

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.

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.

Lee, Young-suk, Arjun Krishnan, Rose Oughtred, Jennifer Rust, Christie S Chang, Joseph Ryu, Vessela N Kristensen, Kara Dolinski, Chandra L Theesfeld, and Olga G Troyanskaya. (2019) 2019. “A Computational Framework for Genome-Wide Characterization of the Human Disease Landscape.”. Cell Syst 8 (2): 152-162.e6. doi:10.1016/j.cels.2018.12.010.

Hibbs, Matthew A, Nathaniel C Dirksen, Kai Li, and Olga G Troyanskaya. 2005. “Visualization Methods for Statistical Analysis of Microarray Clusters.”. BMC Bioinformatics 6: 115.

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.

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.

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.

Myers, Chad L, and Olga G Troyanskaya. (2007) 2007. “Context-Sensitive Data Integration and Prediction of Biological Networks.”. Bioinformatics 23 (17): 2322-30.

Roberts, Andrew M, Aaron K Wong, Ian Fisk, and Olga G Troyanskaya. (2016) 2016. “GIANT API: An Application Programming Interface for Functional Genomics.”. Nucleic Acids Res.

Sargin, Derya, Revathy U Chottekalapanda, Kristina E Perit, Victoria Yao, Duong Chu, Daniel W Sparks, Salina Kalik, et al. (2019) 2019. “Mapping the Physiological and Molecular Markers of Stress and SSRI Antidepressant Treatment in S100a10 Corticostriatal Neurons.”. Mol Psychiatry. doi:10.1038/s41380-019-0473-6.