Stone, Eric A, and Julien Ayroles. (2009) 2009. “Modulated Modularity Clustering As an Exploratory Tool for Functional Genomic Inference.”. PLoS Genet 5 (5): e1000479.

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.

Tucci, Serena, and Joshua Akey. (2019) 2019. “The Long Walk to African Genomics.”. Genome Biol 20 (1): 130. doi:10.1186/s13059-019-1740-1.

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.

Botstein, David, and Neil Risch. (2003) 2003. “Discovering Genotypes Underlying Human Phenotypes: Past Successes for Mendelian Disease, Future Approaches for Complex Disease.”. Nat Genet 33 Suppl: 228-37.

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.

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

Botstein, David. (2006) 2006. “Willing to Do the Math: An Interview With David Botstein. Interview by Jane Gitschier.”. PLoS Genet 2 (5): e79.

Wong, Aaron K, Christopher Y Park, Casey S Greene, Lars A Bongo, Yuanfang Guan, and Olga G Troyanskaya. (2012) 2012. “IMP: A Multi-Species Functional Genomics Portal for Integration, Visualization and Prediction of Protein Functions and Networks.”. Nucleic Acids Res 40 (Web Server issue).

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.

Nabieva, Elena, Kam Jim, Amit Agarwal, Bernard Chazelle, and Mona Singh. (2005) 2005. “Whole-Proteome Prediction of Protein Function via Graph-Theoretic Analysis of Interaction Maps.”. Bioinformatics 21 Suppl 1.

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.

Broedersz, Chase P, Xindan Wang, Yigal Meir, Joseph J Loparo, David Z Rudner, and Ned S Wingreen. (2014) 2014. “Condensation and Localization of the Partitioning Protein ParB on the Bacterial Chromosome.”. Proc Natl Acad Sci U S A 111 (24): 8809-14.

Ochoa, Alejandro, Manuel Llinás, and Mona Singh. 2011. “Using Context to Improve Protein Domain Identification.”. BMC Bioinformatics 12: 90.

Gresham, David, Douglas M Ruderfer, Stephen C Pratt, Joseph Schacherer, Maitreya Dunham, David Botstein, and Leonid Kruglyak. (2006) 2006. “Genome-Wide Detection of Polymorphisms at Nucleotide Resolution With a Single DNA Microarray.”. Science 311 (5769): 1932-6.

Markowetz, Florian, and Olga G Troyanskaya. (2007) 2007. “Computational Identification of Cellular Networks and Pathways.”. Mol Biosyst 3 (7): 478-82.

Shi, Weiyang, Michael Levine, and Brad Davidson. (2005) 2005. “Unraveling Genomic Regulatory Networks in the Simple Chordate, Ciona Intestinalis.”. Genome Res 15 (12): 1668-74.

Hirschman, Jodi E, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Selina S Dwight, Stacia R Engel, Dianna G Fisk, et al. (2006) 2006. “Genome Snapshot: A New Resource at the Saccharomyces Genome Database (SGD) Presenting an Overview of the Saccharomyces Cerevisiae Genome.”. Nucleic Acids Res 34 (Database issue).

Huttenhower, Curtis, Chad L Myers, Matthew A Hibbs, and Olga G Troyanskaya. 2009. “Computational Analysis of the Yeast Proteome: Understanding and Exploiting Functional Specificity in Genomic Data.”. Methods Mol Biol 548: 273-93.

Diehn, Maximilian, Gavin Sherlock, Gail Binkley, Heng Jin, John C Matese, Tina Hernandez-Boussard, Christian A Rees, et al. (2003) 2003. “SOURCE: A Unified Genomic Resource of Functional Annotations, Ontologies, and Gene Expression Data.”. Nucleic Acids Res 31 (1): 219-23.

Alter, Orly, Patrick O Brown, and David Botstein. (2003) 2003. “Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Data Sets of Two Different Organisms.”. Proc Natl Acad Sci U S A 100 (6): 3351-6.

Gresham, David, Maitreya Dunham, and David Botstein. (2008) 2008. “Comparing Whole Genomes Using DNA Microarrays.”. Nat Rev Genet 9 (4): 291-302.

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.

Consortium, Gene Ontology. (2010) 2010. “The Gene Ontology in 2010: Extensions and Refinements.”. Nucleic Acids Res 38 (Database issue).

Jiang, Peng, and Mona Singh. (2014) 2014. “CCAT: Combinatorial Code Analysis Tool for Transcriptional Regulation.”. Nucleic Acids Res 42 (5): 2833-47.

Christiaen, Lionel, Eileen Wagner, Weiyang Shi, and Michael Levine. (2009) 2009. “The Sea Squirt Ciona Intestinalis.”. Cold Spring Harb Protoc 2009 (12): pdb.emo138.

Hong, Eurie L, Rama Balakrishnan, Qing Dong, Karen R Christie, Julie Park, Gail Binkley, Maria C Costanzo, et al. (2008) 2008. “Gene Ontology Annotations at SGD: New Data Sources and Annotation Methods.”. Nucleic Acids Res 36 (Database issue).

Di Gregorio, Anna, and Michael Levine. (2002) 2002. “Analyzing Gene Regulation in Ascidian Embryos: New Tools for New Perspectives.”. Differentiation 70 (4-5): 132-9.

Dwight, Selina S, Rama Balakrishnan, Karen R Christie, Maria C Costanzo, Kara Dolinski, Stacia R Engel, Becket Feierbach, et al. (2004) 2004. “Saccharomyces Genome Database: Underlying Principles and Organisation.”. Brief Bioinform 5 (1): 9-22.

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.

Andolfatto, Peter. (2005) 2005. “Adaptive Evolution of Non-Coding DNA in Drosophila.”. Nature 437 (7062): 1149-52.

Heinicke, Sven, Michael S Livstone, Charles Lu, Rose Oughtred, Fan Kang, Samuel Angiuoli V, Owen White, David Botstein, and Kara Dolinski. 2007. “The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists.”. PLoS One 2 (8): e766.

Katz, David J, Michael A Beer, John M Levorse, and Shirley M Tilghman. (2005) 2005. “Functional Characterization of a Novel Ku70 80 Pause Site at the H19 Igf2 Imprinting Control Region.”. Mol Cell Biol 25 (10): 3855-63.

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.

Khan, Zia, Joshua S Bloom, Leonid Kruglyak, and Mona Singh. (2009) 2009. “A Practical Algorithm for Finding Maximal Exact Matches in Large Sequence Datasets Using Sparse Suffix Arrays.”. Bioinformatics 25 (13): 1609-16.

Myers, Chad L, Daniel R Barrett, Matthew A Hibbs, Curtis Huttenhower, and Olga G Troyanskaya. 2006. “Finding Function: Evaluation Methods for Functional Genomic Data.”. BMC Genomics 7: 187.

Przytycki, Pawel F, and Mona Singh. (2017) 2017. “Differential Analysis Between Somatic Mutation and Germline Variation Profiles Reveals Cancer-Related Genes.”. Genome Med 9 (1): 79. doi:10.1186/s13073-017-0465-6.

Uhlmann, Wendy R, Robin Bennett, Jeffrey R Botkin, David Botstein, Joann A Boughman, Aravinda Chakravarti, Ellen Wright Clayton, et al. (2003) 2003. “Planning the Genome institute’s Future.”. Science 299 (5612): 1515; author reply 1515.

Chikina, Maria D, and Olga G Troyanskaya. (2012) 2012. “An Effective Statistical Evaluation of ChIPseq Dataset Similarity.”. Bioinformatics 28 (5): 607-13.

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.

Cui, Rongfeng, Molly Schumer, Karla Kruesi, Ronald Walter, Peter Andolfatto, and Gil G Rosenthal. (2013) 2013. “Phylogenomics Reveals Extensive Reticulate Evolution in Xiphophorus Fishes.”. Evolution 67 (8): 2166-79.

Mackay, Trudy F C, Stephen Richards, Eric A Stone, Antonio Barbadilla, Julien Ayroles, Dianhui Zhu, Sònia Casillas, et al. (2012) 2012. “The Drosophila Melanogaster Genetic Reference Panel.”. Nature 482 (7384): 173-8.

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.

Saldanha, Alok J, Matthew J Brauer, and David Botstein. (2004) 2004. “Nutritional Homeostasis in Batch and Steady-State Culture of Yeast.”. Mol Biol Cell 15 (9): 4089-104.

Shyamsundar, Radha, Young H Kim, John P Higgins, Kelli Montgomery, Michelle Jorden, Anand Sethuraman, Matt van de Rijn, David Botstein, Patrick O Brown, and Jonathan R Pollack. 2005. “A DNA Microarray Survey of Gene Expression in Normal Human Tissues.”. Genome Biol 6 (3): R22.

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.