Genomics: Publications

Chikina, M D, C P Gerald, X Li, Y Ge, H Pincas, V D Nair, A K Wong, et al. 2015. “Low-Variance RNAs Identify Parkinson’s Disease Molecular Signature in Blood.” Mov Disord 30 (6): 813–21. doi:10.1002/mds.26205.

Dolinski, K, and O G Troyanskaya. 2015. “Implications of Big Data for Cell Biology.” Mol Biol Cell 26 (14): 2575–78. doi:10.1091/mbc.E13-12-0756.

Goya, J, A K Wong, V Yao, A Krishnan, M Homilius, and O G Troyanskaya. 2015. “FNTM: A Server for Predicting Functional Networks of Tissues in Mouse.” Nucleic Acids Res 43 (W1): W182–87. doi:10.1093/nar/gkv443.

Greene, Casey S, Arjun Krishnan, Aaron K Wong, Emanuela Ricciotti, Rene A Zelaya, Daniel S Himmelstein, Ran Zhang, et al. 2015. “Understanding Multicellular Function and Disease with Human Tissue-Specific Networks.” Nat Genet advance on (April). Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

Park, C Y, A Krishnan, Q Zhu, A K Wong, Y S Lee, and O G Troyanskaya. 2015. “Tissue-Aware Data Integration Approach for the Inference of Pathway Interactions in Metazoan Organisms.” Bioinformatics 31 (7): 1093–1101. doi:10.1093/bioinformatics/btu786.

Quigley, D, L Silwal-Pandit, R Dannenfelser, A Langerod, H K Vollan, C Vaske, J U Siegel, et al. 2015. “Lymphocyte Invasion in IC10/Basal-Like Breast Tumors Is Associated with Wild-Type TP53.” Mol Cancer Res 13 (3): 493–501. doi:10.1158/1541-7786.MCR-14-0387.

VanderSluis, B, D C Hess, C Pesyna, E W Krumholz, T Syed, B Szappanos, C Nislow, et al. 2014. “Broad Metabolic Sensitivity Profiling of a Prototrophic Yeast Deletion Collection.” Genome Biol 15 (4): R64. doi:10.1186/gb-2014-15-4-r64.

Wong, A K, A Krishnan, V Yao, A Tadych, and O G Troyanskaya. 2015. “IMP 2.0: A Multi-Species Functional Genomics Portal for Integration, Visualization and Prediction of Protein Functions and Networks.” Nucleic Acids Res 43 (W1): W128–33. doi:10.1093/nar/gkv486.

Zhou, J, and O G Troyanskaya. 2015. “Predicting Effects of Noncoding Variants with Deep Learning-Based Sequence Model.” Nat Methods. doi:10.1038/nmeth.3547.

Zhu, Qian, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, Ran Zhang, David C Corney, et al. 2015. “Targeted Exploration and Analysis of Large Cross-Platform Human Transcriptomic Compendia.” Nat Meth advance on (January). Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

Zhou, J, and O G Troyanskaya. 2014. “Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction.” Proceedings of the International Conference on Machine Learning.

Zhou, J, and O G Troyanskaya. 2014. “Global Quantitative Modeling of Chromatin Factor Interactions.” PLoS Computational Biology 10 (3): e1003525. doi:10.1371/journal.pcbi.1003525.

Aure, M R, S K Leivonen, T Fleischer, Q Zhu, J Overgaard, J Alsner, T Tramm, et al. 2013. “Individual and Combined Effects of DNA Methylation and Copy Number Alterations on miRNA Expression in Breast Tumors.” Genome Biol 14 (11): R126. doi:10.1186/gb-2013-14-11-r126.

Caudy, A A, Y Guan, Y Jia, C Hansen, C DeSevo, A P Hayes, J Agee, et al. 2013. “A New System for Comparative Functional Genomics of Saccharomyces Yeasts.” Genetics 195 (1): 275–87. doi:10.1534/genetics.113.152918.

Guan, Y, M J Dunham, O G Troyanskaya, and A A Caudy. 2013. “Comparative Gene Expression between Two Yeast Species.” BMC Genomics 14: 33. doi:10.1186/1471-2164-14-33.

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

Lee, Y S, A Krishnan, Q Zhu, and O G Troyanskaya. 2013. “Ontology-Aware Classification of Tissue and Cell-Type Signals in Gene Expression Profiles across Platforms and Technologies.” Bioinformatics 29 (23): 3036–44. doi:10.1093/bioinformatics/btt529.

Park, Christopher Y, Aaron K Wong, Casey S Greene, Jessica Rowland, Yuanfang Guan, Lars A Bongo, Rebecca D Burdine, and Olga G Troyanskaya. 2013. “Functional Knowledge Transfer for High-Accuracy Prediction of under-Studied Biological Processes.” PLoS Computational Biology 9 (3): e1002957. doi:10.1371/journal.pcbi.1002957.

Chikina, M D, and O G Troyanskaya. 2012. “An Effective Statistical Evaluation of ChIPseq Dataset Similarity.” Bioinformatics 28 (5): 607–13. doi:10.1093/bioinformatics/bts009.

Greene, C S, and O G Troyanskaya. 2012. “Accurate Evaluation and Analysis of Functional Genomics Data and Methods.” Ann N Y Acad Sci 1260: 95–100. doi:10.1111/j.1749-6632.2011.06383.x.

Greene, C S, and O G Troyanskaya. 2012. “Chapter 2: Data-Driven View of Disease Biology.” PLoS Computational Biology 8 (12): e1002816. doi:10.1371/journal.pcbi.1002816.

Guan, Yuanfang, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K Wong, John C Schimenti, Mary Ann Handel, Carol J Bult, Matthew A Hibbs, and Olga G Troyanskaya. 2012. “Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes.” Edited by Christos A. Ouzounis. PLoS Computational Biology 8 (9). Public Library of Science: e1002694. doi:10.1371/journal.pcbi.1002694.

Kristensen, V N, C J Vaske, J Ursini-Siegel, P Van Loo, S H Nordgard, R Sachidanandam, T Sorlie, et al. 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. doi:10.1073/pnas.1108781108.

Nair, V D, Y Ge, N Balasubramaniyan, J Kim, Y Okawa, M Chikina, O Troyanskaya, and S C Sealfon. 2012. “Involvement of Histone Demethylase LSD1 in Short-Time-Scale Gene Expression Changes during Cell Cycle Progression in Embryonic Stem Cells.” Mol Cell Biol 32 (23): 4861–76. doi:10.1128/MCB.00816-12.

Wong, Aaron K, Christopher Y Park, Casey S Greene, Lars A Bongo, Yuanfang Guan, and Olga G Troyanskaya. 2012. “IMP: A Multi-Species Functional Genomics Portal for Integration, Visualization and Prediction of Protein Functions and Networks.” Nucleic Acids Research 40 (Web Server issue): W484–90. doi:10.1093/nar/gks458.

Chikina, Maria D, and Olga G Troyanskaya. 2011. “Accurate Quantification of Functional Analogy among Close Homologs.” PLoS Computational Biology 7 (2): e1001074. doi:10.1371/journal.pcbi.1001074.

Greene, Casey S, and Olga G Troyanskaya. 2011. “PILGRM: An Interactive Data-Driven Discovery Platform for Expert Biologists.” Nucleic Acids Research 39 (Web Server issue): W368–74. doi:10.1093/nar/gkr440.

Guan, Y, V Yao, K Tsui, M Gebbia, M J Dunham, C Nislow, and O G Troyanskaya. 2011. “Nucleosome-Coupled Expression Differences in Closely-Related Species.” BMC Genomics 12: 466. doi:10.1186/1471-2164-12-466.

Baryshnikova, A, M Costanzo, Y Kim, H Ding, J Koh, K Toufighi, J Y Youn, et al. 2010. “Quantitative Analysis of Fitness and Genetic Interactions in Yeast on a Genome Scale.” Nat Methods 7 (12): 1017–24. doi:10.1038/nmeth.1534.

Costanzo, Michael, Anastasia Baryshnikova, Jeremy Bellay, Yungil Kim, Eric D Spear, Carolyn S Sevier, Huiming Ding, et al. 2010. “The Genetic Landscape of a Cell.” Science (New York, N.Y.) 327 (5964): 425–31. doi:10.1126/science.1180823.

Greene, C S, and O G Troyanskaya. 2010. “Integrative Systems Biology for Data-Driven Knowledge Discovery.” Semin Nephrol 30 (5): 443–54. doi:10.1016/j.semnephrol.2010.07.002.

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 Computational Biology 6 (11): e1000991. doi:10.1371/journal.pcbi.1000991.

Guan, Yuanfang, Maitreya Dunham, Amy Caudy, and Olga Troyanskaya. 2010. “Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.” PLoS Computational Biology 6 (3): e1000698. doi:10.1371/journal.pcbi.1000698.

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 Computational Biology 6 (12): e1001034. doi:10.1371/journal.pcbi.1001034.

Park, C Y, D C Hess, C Huttenhower, and O G Troyanskaya. 2010. “Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components.” PLoS Computational Biology 6 (11): e1001009. doi:10.1371/journal.pcbi.1001009.

Pop, A, C Huttenhower, A Iyer-Pascuzzi, P N Benfey, and O G Troyanskaya. 2010. “Integrated Functional Networks of Process, Tissue, and Developmental Stage Specific Interactions in Arabidopsis Thaliana.” BMC Syst Biol 4: 180. doi:10.1186/1752-0509-4-180.

Airoldi, Edoardo M, Curtis Huttenhower, David Gresham, Charles Lu, Amy A Caudy, Maitreya J Dunham, James R Broach, David Botstein, and Olga G Troyanskaya. 2009. “Predicting Cellular Growth from Gene Expression Signatures.” PLoS Computational Biology 5 (1): e1000257. doi:10.1371/journal.pcbi.1000257.

Barutcuoglu, Z, E M Airoldi, V Dumeaux, R E Schapire, and O G Troyanskaya. 2009. “Aneuploidy Prediction and Tumor Classification with Heterogeneous Hidden Conditional Random Fields.” Bioinformatics 25 (10): 1307–13. doi:10.1093/bioinformatics/btn585.

Bradley, P H, M J Brauer, J D Rabinowitz, and O G Troyanskaya. 2009. “Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces Cerevisiae.” PLoS Computational Biology 5 (1): e1000270. doi:10.1371/journal.pcbi.1000270.

Butte, A J, I N Sarkar, M Ramoni, Y Lussier, and O Troyanskaya. 2009. “Selected Proceedings of the First Summit on Translational Bioinformatics 2008.” BMC Bioinformatics 10 Suppl 2: I1. doi:10.1186/1471-2105-10-S2-I1.

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

Hess, David C, Chad L Myers, Curtis Huttenhower, Matthew A Hibbs, Alicia P Hayes, Jadine Paw, John J Clore, et al. 2009. “Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis.” PLoS Genetics 5 (3): e1000407.

Hibbs, Matthew A, Chad L Myers, Curtis Huttenhower, David C Hess, Kai Li, Amy A Caudy, and Olga G Troyanskaya. 2009. “Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis.” Edited by Andrey Rzhetsky. PLoS Computational Biology 5 (3). Public Library of Science: e1000322. doi:10.1371/journal.pcbi.1000322.

Huttenhower, C, C L Myers, M A Hibbs, and O G Troyanskaya. 2009. “Computational Analysis of the Yeast Proteome: Understanding and Exploiting Functional Specificity in Genomic Data.” Methods Mol Biol 548: 273–93. doi:10.1007/978-1-59745-540-4_15.

Huttenhower, Curtis, Erin M Haley, Matthew A Hibbs, Vanessa Dumeaux, Daniel R Barrett, Hilary A Coller, and Olga G Troyanskaya. 2009. “Exploring the Human Genome with Functional Maps.” Genome Research 19 (6): 1093–1106. doi:10.1101/gr.082214.108.

Huttenhower, Curtis, Matthew A Hibbs, Chad L Myers, Amy A Caudy, David C Hess, and Olga G Troyanskaya. 2009. “The Impact of Incomplete Knowledge on Evaluation: An Experimental Benchmark for Protein Function Prediction.” Bioinformatics (Oxford, England) 25 (18): 2404–10. doi:10.1093/bioinformatics/btp397.

Huttenhower, Curtis, Sajid O Mehmood, and Olga G Troyanskaya. 2009. “Graphle: Interactive Exploration of Large, Dense Graphs.” BMC Bioinformatics 10: 417. doi:10.1186/1471-2105-10-417.

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

Lu, R, F Markowetz, R D Unwin, J T Leek, E M Airoldi, B D MacArthur, A Lachmann, et al. 2009. “Systems-Level Dynamic Analyses of Fate Change in Murine Embryonic Stem Cells.” Nature 462 (7271): 358–62. doi:10.1038/nature08575.

Myers, C L, C Chiriac, and O G Troyanskaya. 2009. “Discovering Biological Networks from Diverse Functional Genomic Data.” Methods Mol Biol 563: 157–75. doi:10.1007/978-1-60761-175-2_9.

Brauer, M J, C Huttenhower, E M Airoldi, R Rosenstein, J C Matese, D Gresham, V M Boer, O G Troyanskaya, and D Botstein. 2008. “Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast.” Mol Biol Cell 19 (1): 352–67. doi:10.1091/mbc.E07-08-0779.

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 Biology 9 Suppl 1: S3. doi:10.1186/gb-2008-9-s1-s3.

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 Computational Biology 4 (9): e1000165. doi:10.1371/journal.pcbi.1000165.

Huttenhower, C, and O G Troyanskaya. 2008. “Assessing the Functional Structure of Genomic Data.” Bioinformatics (Oxford, England) 24 (13): i330–38.

Huttenhower, Curtis, Mark Schroeder, Maria D Chikina, and Olga G Troyanskaya. 2008. “The Sleipnir Library for Computational Functional Genomics.” Bioinformatics (Oxford, England) 24 (13): 1559–61. doi:10.1093/bioinformatics/btn237.

Pena-Castillo, Lourdes, Murat Tasan, Chad 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 Biology 9 (Suppl 1): S2.

Chi, A, C Huttenhower, L Y Geer, J J Coon, J E Syka, D L Bai, J Shabanowitz, D J Burke, O G Troyanskaya, and D F Hunt. 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): 2193–98. doi:10.1073/pnas.0607084104.

Guan, Yuanfang, Maitreya J Dunham, and Olga G Troyanskaya. 2007. “Functional Analysis of Gene Duplications in Saccharomyces Cerevisiae.” Genetics 175 (2): 933–43. doi:10.1534/genetics.106.064329.

Haarer, B, S Viggiano, M A Hibbs, O G Troyanskaya, and D C Amberg. 2007. “Modeling Complex Genetic Interactions in a Simple Eukaryotic Genome: Actin Displays a Rich Spectrum of Complex Haploinsufficiencies.” Genes Dev 21 (2): 148–59. doi:10.1101/gad.1477507.

Hibbs, Matthew A., David C. Hess, Chad L. Myers, Curtis Huttenhower, Kai Li, and Olga G. Troyanskaya. 2007. “Exploring the Functional Landscape of Gene Expression: Directed Search of Large Microarray Compendia.” Bioinformatics 23: 2692–99. doi:10.1093/bioinformatics/btm403.

Huttenhower, C, A I Flamholz, J N Landis, S Sahi, C L Myers, K L Olszewski, M A Hibbs, N O Siemers, O G Troyanskaya, and H A Coller. 2007. “Nearest Neighbor Networks: Clustering Expression Data Based on Gene Neighborhoods.” BMC Bioinformatics 8: 250. doi:10.1186/1471-2105-8-250.

Markowetz, F, D Kostka, O G Troyanskaya, and R Spang. 2007. “Nested Effects Models for High-Dimensional Phenotyping Screens.” Bioinformatics 23 (13): i305–12. doi:10.1093/bioinformatics/btm178.

Markowetz, F, and O G Troyanskaya. 2007. “Computational Identification of Cellular Networks and Pathways.” Mol Biosyst 3 (7): 478–82. doi:10.1039/b617014p.

Myers, Chad L, and Olga G Troyanskaya. 2007. “Context-Sensitive Data Integration and Prediction of Biological Networks.” Bioinformatics 23 (17): 2322–30. doi:10.1093/bioinformatics/btm332.

Troyanskaya, O. 2007. “‘Getting Started In…’: A Series Not to Miss.” PLoS Computational Biology 3 (10): 1841. doi:10.1371/journal.pcbi.0030224.

Troyanskaya, O G. 2007. “Integrated Analysis of Microarray Results.” Methods Mol Biol 382: 429–37. doi:10.1007/978-1-59745-304-2_27.

Barutcuoglu, Zafer, Robert E. Schapire, and Olga G. Troyanskaya. 2006. “Hierarchical Multi-Label Prediction of Gene Function.” Bioinformatics 22: 830–36. doi:10.1093/bioinformatics/btk048.

Brown, J A, G Sherlock, C L Myers, N M Burrows, C Deng, H I Wu, K E McCann, O G Troyanskaya, and J M Brown. 2006. “Global Analysis of Gene Function in Yeast by Quantitative Phenotypic Profiling.” Mol Syst Biol 2: 2006 0001. doi:10.1038/msb4100043.

Huttenhower, C, and O G Troyanskaya. 2006. “Bayesian Data Integration: A Functional Perspective.” Comput Syst Bioinformatics Conf, 341–51.

Huttenhower, Curtis, Matt Hibbs, Chad Myers, and Olga G Troyanskaya. 2006. “A Scalable Method for Integration and Functional Analysis of Multiple Microarray Datasets.” Bioinformatics (Oxford, England) 22 (23): 2890–97. doi:10.1093/bioinformatics/btl492.

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. doi:10.1186/1471-2164-7-187.

Sealfon, R S, M A Hibbs, C Huttenhower, C L Myers, and O G Troyanskaya. 2006. “GOLEM: An Interactive Graph-Based Gene-Ontology Navigation and Analysis Tool.” BMC Bioinformatics 7: 443. doi:10.1186/1471-2105-7-443.

Hibbs, M A, N C Dirksen, K Li, and O G Troyanskaya. 2005. “Visualization Methods for Statistical Analysis of Microarray Clusters.” BMC Bioinformatics 6: 115. doi:10.1186/1471-2105-6-115.

Myers, C L, X Chen, and O G Troyanskaya. 2005. “Visualization-Based Discovery and Analysis of Genomic Aberrations in Microarray Data.” BMC Bioinformatics 6: 146. doi:10.1186/1471-2105-6-146.

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 Biology 6 (13): R114. doi:10.1186/gb-2005-6-13-r114.

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

———. 2005b. “Putting the ‘Bio’ into Bioinformatics.” Genome Biol 6 (10): 351. doi:10.1186/gb-2005-6-10-351.

Wallace, G, O J Anshus, P Bi, H Chen, Y Chen, D Clark, P Cook, et al. 2005. “Tools and Applications for Large-Scale Display Walls.” IEEE Comput Graph Appl 25 (4): 24–33.

Myers, C L, M J Dunham, S Y Kung, and O G Troyanskaya. 2004. “Accurate Detection of Aneuploidies in Array CGH and Gene Expression Microarray Data.” Bioinformatics 20 (18): 3533–43. doi:10.1093/bioinformatics/bth440.

Bohen, S P, O G Troyanskaya, O Alter, R Warnke, D Botstein, P O Brown, and R Levy. 2003. “Variation in Gene Expression Patterns in Follicular Lymphoma and the Response to Rituximab.” Proc Natl Acad Sci U S A 100 (4): 1926–30. doi:10.1073/pnas.0437875100.

Chen, X, S Y Leung, S T Yuen, K M Chu, J Ji, R Li, A S Chan, et al. 2003. “Variation in Gene Expression Patterns in Human Gastric Cancers.” Mol Biol Cell 14 (8): 3208–15. doi:10.1091/mbc.E02-12-0833.

Chi, J T, H Y Chang, G Haraldsen, F L Jahnsen, O G Troyanskaya, D S Chang, Z Wang, et al. 2003. “Endothelial Cell Diversity Revealed by Global Expression Profiling.” Proc Natl Acad Sci U S A 100 (19): 10623–28. doi:10.1073/pnas.1434429100.

Schaner, M E, D T Ross, G Ciaravino, T Sorlie, O Troyanskaya, M Diehn, Y C Wang, et al. 2003. “Gene Expression Patterns in Ovarian Carcinomas.” Mol Biol Cell 14 (11): 4376–86. doi:10.1091/mbc.E03-05-0279.

Troyanskaya, Olga G, Kara Dolinski, Art B Owen, Russ B Altman, and David Botstein. 2003. “A Bayesian Framework for Combining Heterogeneous Data Sources for Gene Function Prediction (in Saccharomyces Cerevisiae).” Proceedings of the National Academy of Sciences of the United States of America 100 (14): 8348–53. doi:10.1073/pnas.0832373100.

Whitfield, M L, D R Finlay, J I Murray, O G Troyanskaya, J T Chi, A Pergamenschikov, T H McCalmont, P O Brown, D Botstein, and M K Connolly. 2003. “Systemic and Cell Type-Specific Gene Expression Patterns in Scleroderma Skin.” Proc Natl Acad Sci U S A 100 (21): 12319–24. doi:10.1073/pnas.1635114100.

Leung, S Y, X Chen, K M Chu, S T Yuen, J Mathy, J Ji, A S Chan, et al. 2002. “Phospholipase A2 Group IIA Expression in Gastric Adenocarcinoma Is Associated with Prolonged Survival and Less Frequent Metastasis.” Proc Natl Acad Sci U S A 99 (25): 16203–8. doi:10.1073/pnas.212646299.

Troyanskaya, O G, O Arbell, Y Koren, G M Landau, and A Bolshoy. 2002. “Sequence Complexity Profiles of Prokaryotic Genomic Sequences: A Fast Algorithm for Calculating Linguistic Complexity.” Bioinformatics 18 (5): 679–88.

Troyanskaya, O G, M E Garber, P O Brown, D Botstein, and R B Altman. 2002. “Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data.” Bioinformatics 18 (11): 1454–61.

Garber, M E, O G Troyanskaya, K Schluens, S Petersen, Z Thaesler, M Pacyna-Gengelbach, M van de Rijn, et al. 2001. “Diversity of Gene Expression in Adenocarcinoma of the Lung.” Proc Natl Acad Sci U S A 98 (24): 13784–89. doi:10.1073/pnas.241500798.

Troyanskaya, O, M Cantor, G Sherlock, P Brown, T Hastie, R Tibshirani, D Botstein, and R B Altman. 2001. “Missing Value Estimation Methods for DNA Microarrays.” Bioinformatics (Oxford, England) 17: 520–25. doi:10.1093/bioinformatics/17.6.520.