De Renzis, Stefano, Olivier Elemento, Saeed Tavazoie, and Eric F Wieschaus. (2007) 2007. “Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo.”. PLoS Biol 5 (5): e117.

Khan, Zia, Joshua S Bloom, Sasan Amini, Mona Singh, David H Perlman, Amy A Caudy, and Leonid Kruglyak. 2012. “Quantitative Measurement of Allele-Specific Protein Expression in a Diploid Yeast Hybrid by LC-MS.”. Mol Syst Biol 8: 602.

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

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.

Chen, Lin S, and John D Storey. (2008) 2008. “Eigen-R2 for Dissecting Variation in High-Dimensional Studies.”. Bioinformatics 24 (19): 2260-2.

Dolinski, Kara, and David Botstein. (2005) 2005. “Changing Perspectives in Yeast Research Nearly a Decade After the Genome Sequence.”. Genome Res 15 (12): 1611-9.

Novoradovskaya, Natalia, Michael L Whitfield, Lee S Basehore, Alexey Novoradovsky, Robert Pesich, Jerry Usary, Mehmet Karaca, et al. (2004) 2004. “Universal Reference RNA As a Standard for Microarray Experiments.”. BMC Genomics 5 (1): 20.

Morrison, Alexander H, Martin Scheeler, Julien Dubuis, and Thomas Gregor. (2012) 2012. “Quantifying the Bicoid Morphogen Gradient in Living Fly Embryos.”. Cold Spring Harb Protoc 2012 (4): 398-406.

Tu, I-Ping, Marci Schaner, Maximilian Diehn, Branimir I Sikic, Patrick O Brown, David Botstein, and Michael J Fero. (2004) 2004. “A Method for Detecting and Correcting Feature Misidentification on Expression Microarrays.”. BMC Genomics 5: 64.

Lakhina, Vanisha, Rachel Arey, Rachel Kaletsky, Amanda Kauffman, Geneva Stein, William Keyes, Daniel Xu, and Coleen T Murphy. (2015) 2015. “Genome-Wide Functional Analysis of CREB Long-Term Memory-Dependent Transcription Reveals Distinct Basal and Memory Gene Expression Programs.”. Neuron 85 (2): 330-45.

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.

Pollack, Jonathan R, Matt van de Rijn, and David Botstein. (2002) 2002. “Challenges in Developing a Molecular Characterization of Cancer.”. Semin Oncol 29 (3): 280-5.

Christiaen, Lionel, Brad Davidson, Takeshi Kawashima, Weston Powell, Hector Nolla, Karen Vranizan, and Michael Levine. (2008) 2008. “The Transcription Migration Interface in Heart Precursors of Ciona Intestinalis.”. Science 320 (5881): 1349-52.

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

Slavov, Nikolai, Joanna Macinskas, Amy A Caudy, and David Botstein. (2011) 2011. “Metabolic Cycling Without Cell Division Cycling in Respiring Yeast.”. Proc Natl Acad Sci U S A 108 (47): 19090-5.

Rees, Christian A, Janos Demeter, John C Matese, David Botstein, and Gavin Sherlock. (2004) 2004. “GeneXplorer: An Interactive Web Application for Microarray Data Visualization and Analysis.”. BMC Bioinformatics 5: 141.

Garber, M E, O G Troyanskaya, K Schluens, S Petersen, Z Thaesler, M Pacyna-Gengelbach, M van de Rijn, et al. (2001) 2001. “Diversity of Gene Expression in Adenocarcinoma of the Lung.”. Proc Natl Acad Sci U S A 98 (24): 13784-9.

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

Edwards, Alexis C, Julien Ayroles, Eric A Stone, Mary Anna Carbone, Richard F Lyman, and Trudy F C Mackay. 2009. “A Transcriptional Network Associated With Natural Variation in Drosophila Aggressive Behavior.”. Genome Biol 10 (7): R76.

Lossos, Izidore S, Debra K Czerwinski, Ash A Alizadeh, Mark A Wechser, Rob Tibshirani, David Botstein, and Ronald Levy. (2004) 2004. “Prediction of Survival in Diffuse Large-B-Cell Lymphoma Based on the Expression of Six Genes.”. N Engl J Med 350 (18): 1828-37.

Silverman, Sanford J, Allegra A Petti, Nikolai Slavov, Lance Parsons, Ryan Briehof, Stephan Y Thiberge, Daniel Zenklusen, et al. (2010) 2010. “Metabolic Cycling in Single Yeast Cells from Unsynchronized Steady-State Populations Limited on Glucose or Phosphate.”. Proc Natl Acad Sci U S A 107 (15): 6946-51.

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.

Shapira, Michael, Eran Segal, and David Botstein. (2004) 2004. “Disruption of Yeast Forkhead-Associated Cell Cycle Transcription by Oxidative Stress.”. Mol Biol Cell 15 (12): 5659-69.

Dubuis, Julien, Reba Samanta, and Thomas Gregor. 2013. “Accurate Measurements of Dynamics and Reproducibility in Small Genetic Networks.”. Mol Syst Biol 9: 639.

Lu, Rong, Florian Markowetz, Richard D Unwin, Jeffrey T Leek, Edoardo M Airoldi, Ben D MacArthur, Alexander Lachmann, et al. (2009) 2009. “Systems-Level Dynamic Analyses of Fate Change in Murine Embryonic Stem Cells.”. Nature 462 (7271): 358-62.

Airoldi, Edoardo M, Curtis Huttenhower, David Gresham, Charles Lu, Amy A Caudy, Maitreya Dunham, James R Broach, David Botstein, and Olga G Troyanskaya. (2009) 2009. “Predicting Cellular Growth from Gene Expression Signatures.”. PLoS Comput Biol 5 (1): e1000257.

Bloom, Joshua S, Zia Khan, Leonid Kruglyak, Mona Singh, and Amy A Caudy. 2009. “Measuring Differential Gene Expression by Short Read Sequencing: Quantitative Comparison to 2-Channel Gene Expression Microarrays.”. BMC Genomics 10: 221.

Liang, Yu, Maximilian Diehn, Nathan Watson, Andrew W Bollen, Ken D Aldape, Kelly Nicholas, Kathleen R Lamborn, et al. (2005) 2005. “Gene Expression Profiling Reveals Molecularly and Clinically Distinct Subtypes of Glioblastoma Multiforme.”. Proc Natl Acad Sci U S A 102 (16): 5814-9.

Gregor, Thomas, William Bialek, Rob R de Ruyter van Steveninck, David W Tank, and Eric F Wieschaus. (2005) 2005. “Diffusion and Scaling During Early Embryonic Pattern Formation.”. Proc Natl Acad Sci U S A 102 (51): 18403-7.

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.

Whitfield, Michael L, Deborah R Finlay, John Isaac Murray, Olga G Troyanskaya, Jen-Tsan Chi, Alexander Pergamenschikov, Timothy H McCalmont, Patrick O Brown, David Botstein, and Kari Connolly. (2003) 2003. “Systemic and Cell Type-Specific Gene Expression Patterns in Scleroderma Skin.”. Proc Natl Acad Sci U S A 100 (21): 12319-24.

Goodliffe, Julie M, Eric Wieschaus, and Michael D Cole. (2005) 2005. “Polycomb Mediates Myc Autorepression and Its Transcriptional Control of Many Loci in Drosophila.”. Genes Dev 19 (24): 2941-6.

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.

Lapointe, Jacques, Chunde Li, John P Higgins, Matt van de Rijn, Eric Bair, Kelli Montgomery, Michelle Ferrari, et al. (2004) 2004. “Gene Expression Profiling Identifies Clinically Relevant Subtypes of Prostate Cancer.”. Proc Natl Acad Sci U S A 101 (3): 811-6.

Zhao, Hongjuan, Anita Langerød, Youngran Ji, Kent W Nowels, Jahn M Nesland, Rob Tibshirani, Ida K Bukholm, et al. (2004) 2004. “Different Gene Expression Patterns in Invasive Lobular and Ductal Carcinomas of the Breast.”. Mol Biol Cell 15 (6): 2523-36.

Wang, Juan, Rachel Kaletsky, Malan Silva, April Williams, Leonard A Haas, Rebecca J Androwski, Jessica N Landis, et al. (2015) 2015. “Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis.”. Curr Biol 25 (24): 3232-8. doi:10.1016/j.cub.2015.10.057.

Guan, Yuanfang, Maitreya Dunham, Amy A Caudy, and Olga Troyanskaya. (2010) 2010. “Systematic Planning of Genome-Scale Experiments in Poorly Studied Species.”. PLoS Comput Biol 6 (3): e1000698.

Greene, Casey S, and Olga G Troyanskaya. (2011) 2011. “PILGRM: An Interactive Data-Driven Discovery Platform for Expert Biologists.”. Nucleic Acids Res 39 (Web Server issue).

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.

Sørlie, Therese, Charles M Perou, Cheng Fan, Stephanie Geisler, Turid Aas, Andrew Nobel, Gun Anker, et al. (2006) 2006. “Gene Expression Profiles Do Not Consistently Predict the Clinical Treatment Response in Locally Advanced Breast Cancer.”. Mol Cancer Ther 5 (11): 2914-8.

Goltsev, Yury, Gustavo L Rezende, Karen Vranizan, Greg Lanzaro, Denise Valle, and Michael Levine. (2009) 2009. “Developmental and Evolutionary Basis for Drought Tolerance of the Anopheles Gambiae Embryo.”. Dev Biol 330 (2): 462-70.

Rangan, Aaditya, V, Caroline C McGrouther, John Kelsoe, Nicholas Schork, Eli Stahl, Qian Zhu, Arjun Krishnan, et al. (2018) 2018. “A Loop-Counting Method for Covariate-Corrected Low-Rank Biclustering of Gene-Expression and Genome-Wide Association Study Data.”. PLoS Comput Biol 14 (5): e1006105. doi:10.1371/journal.pcbi.1006105.

Wang, Wei, Michael Cherry, David Botstein, and Hao Li. (2002) 2002. “A Systematic Approach to Reconstructing Transcription Networks in Saccharomycescerevisiae.”. Proc Natl Acad Sci U S A 99 (26): 16893-8.

Leung, Suet Y, Xin Chen, Kent M Chu, Siu T Yuen, Jonathan Mathy, Jiafu Ji, Annie S Y Chan, et al. (2002) 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.

Troyanskaya, Olga G. 2007. “Integrated Analysis of Microarray Results.”. Methods Mol Biol 382: 429-37.

Linn, Sabine C, Rob B West, Jonathan R Pollack, Shirley Zhu, Tina Hernandez-Boussard, Torsten O Nielsen, Brian P Rubin, et al. (2003) 2003. “Gene Expression Patterns and Gene Copy Number Changes in Dermatofibrosarcoma Protuberans.”. Am J Pathol 163 (6): 2383-95.

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.

Menon, Rajasree, Edgar A Otto, Austin Kokoruda, Jian Zhou, Zidong Zhang, Euisik Yoon, Yu-Chih Chen, et al. (2018) 2018. “Single-Cell Analysis of Progenitor Cell Dynamics and Lineage Specification in the Human Fetal Kidney.”. Development 145 (16). doi:10.1242/dev.164038.

Boldrick, Jennifer C, Ash A Alizadeh, Maximilian Diehn, Sandrine Dudoit, Chih Long Liu, Christopher E Belcher, David Botstein, Louis M Staudt, Patrick O Brown, and David A Relman. (2002) 2002. “Stereotyped and Specific Gene Expression Programs in Human Innate Immune Responses to Bacteria.”. Proc Natl Acad Sci U S A 99 (2): 972-7.

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.