Sayama, Koichi, Maximilian Diehn, Kentaro Matsuda, Carolina Lunderius, Mindy Tsai, See-Ying Tam, David Botstein, Patrick O Brown, and Stephen J Galli. (2002) 2002. “Transcriptional Response of Human Mast Cells Stimulated via the Fc(epsilon)RI and Identification of Mast Cells As a Source of IL-11.”. BMC Immunol 3: 5.

Yoshimoto, Hiroyuki, Kirstie Saltsman, Audrey P Gasch, Hong Xia Li, Nobuo Ogawa, David Botstein, Patrick O Brown, and Martha S Cyert. (2002) 2002. “Genome-Wide Analysis of Gene Expression Regulated by the Calcineurin Crz1p Signaling Pathway in Saccharomyces Cerevisiae.”. J Biol Chem 277 (34): 31079-88.

Shakoury-Elizeh, Minoo, John Tiedeman, Jared Rashford, Tracey Ferea, Janos Demeter, Emily Garcia, Ronda Rolfes, Patrick O Brown, David Botstein, and Caroline C Philpott. (2004) 2004. “Transcriptional Remodeling in Response to Iron Deprivation in Saccharomyces Cerevisiae.”. Mol Biol Cell 15 (3): 1233-43.

Diehn, Maximilian, Ramona Bhattacharya, David Botstein, and Patrick O Brown. (2006) 2006. “Genome-Scale Identification of Membrane-Associated Human MRNAs.”. PLoS Genet 2 (1): e11.

Nielsen, Torsten O, Forrest D Hsu, John X O’Connell, Blake Gilks, Poul H B Sorensen, Sabine Linn, Robert B West, et al. (2003) 2003. “Tissue Microarray Validation of Epidermal Growth Factor Receptor and SALL2 in Synovial Sarcoma With Comparison to Tumors of Similar Histology.”. Am J Pathol 163 (4): 1449-56.

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.

Roose, Jeroen P, Maximilian Diehn, Michael G Tomlinson, Joseph Lin, Ash A Alizadeh, David Botstein, Patrick O Brown, and Arthur Weiss. (2003) 2003. “T Cell Receptor-Independent Basal Signaling via Erk and Abl Kinases Suppresses RAG Gene Expression.”. PLoS Biol 1 (2): E53.

Chang, Howard Y, Julie B Sneddon, Ash A Alizadeh, Ruchira Sood, Rob B West, Kelli Montgomery, Jen-Tsan Chi, Matt van de Rijn, David Botstein, and Patrick O Brown. (2004) 2004. “Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities Between Tumors and Wounds.”. PLoS Biol 2 (2): E7.

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.

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.

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.

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.

Gollub, Jeremy, Catherine A Ball, Gail Binkley, Janos Demeter, David B Finkelstein, Joan M Hebert, Tina Hernandez-Boussard, et al. (2003) 2003. “The Stanford Microarray Database: Data Access and Quality Assessment Tools.”. Nucleic Acids Res 31 (1): 94-6.

Schaner, Marci E, Douglas T Ross, Giuseppe Ciaravino, Therese Sorlie, Olga Troyanskaya, Maximilian Diehn, Yan C Wang, et al. (2003) 2003. “Gene Expression Patterns in Ovarian Carcinomas.”. Mol Biol Cell 14 (11): 4376-86.

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.

Chen, Xin, Siu Tim Cheung, Samuel So, Sheung Tat Fan, Christopher Barry, John Higgins, Kin-Man Lai, et al. (2002) 2002. “Gene Expression Patterns in Human Liver Cancers.”. Mol Biol Cell 13 (6): 1929-39.

Sorlie, Therese, Robert Tibshirani, Joel Parker, Trevor Hastie, J S Marron, Andrew Nobel, Shibing Deng, et al. (2003) 2003. “Repeated Observation of Breast Tumor Subtypes in Independent Gene Expression Data Sets.”. Proc Natl Acad Sci U S A 100 (14): 8418-23.

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.

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.

Chi, Jen-Tsan, Howard Y Chang, Guttorm Haraldsen, Frode L Jahnsen, Olga G Troyanskaya, Dustin S Chang, Zhen Wang, et al. (2003) 2003. “Endothelial Cell Diversity Revealed by Global Expression Profiling.”. Proc Natl Acad Sci U S A 100 (19): 10623-8.

Troyanskaya, Olga G, Mitchell E Garber, Patrick O Brown, David Botstein, and Russ B Altman. (2002) 2002. “Nonparametric Methods for Identifying Differentially Expressed Genes in Microarray Data.”. Bioinformatics 18 (11): 1454-61.

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.

Nielsen, Torsten O, Rob B West, Sabine C Linn, Orly Alter, Margaret A Knowling, John X O’Connell, Shirley Zhu, et al. (2002) 2002. “Molecular Characterisation of Soft Tissue Tumours: A Gene Expression Study.”. Lancet 359 (9314): 1301-7.

Chang, Howard Y, Jen-Tsan Chi, Sandrine Dudoit, Chanda Bondre, Matt van de Rijn, David Botstein, and Patrick O Brown. (2002) 2002. “Diversity, Topographic Differentiation, and Positional Memory in Human Fibroblasts.”. Proc Natl Acad Sci U S A 99 (20): 12877-82.

Pollack, Jonathan R, Therese Sørlie, Charles M Perou, Christian A Rees, Stefanie S Jeffrey, Per E Lonning, Robert Tibshirani, David Botstein, Anne-Lise Børresen-Dale, and Patrick O Brown. (2002) 2002. “Microarray Analysis Reveals a Major Direct Role of DNA Copy Number Alteration in the Transcriptional Program of Human Breast Tumors.”. Proc Natl Acad Sci U S A 99 (20): 12963-8.

Murray, John Isaac, Michael L Whitfield, Nathan D Trinklein, Richard M Myers, Patrick O Brown, and David Botstein. (2004) 2004. “Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells.”. Mol Biol Cell 15 (5): 2361-74.

Chen, Xin, Suet Y Leung, Siu T Yuen, Kent-Man Chu, Jiafu Ji, Rui Li, Annie S Y Chan, et al. (2003) 2003. “Variation in Gene Expression Patterns in Human Gastric Cancers.”. Mol Biol Cell 14 (8): 3208-15.

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.

Dunham, Maitreya, Hassan Badrane, Tracy Ferea, Julian Adams, Patrick O Brown, Frank Rosenzweig, and David Botstein. (2002) 2002. “Characteristic Genome Rearrangements in Experimental Evolution of Saccharomyces Cerevisiae.”. Proc Natl Acad Sci U S A 99 (25): 16144-9.

Bohen, Sean P, Olga G Troyanskaya, Orly Alter, Roger Warnke, David Botstein, Patrick O Brown, and Ronald Levy. (2003) 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.

Whitfield, Michael L, Gavin Sherlock, Alok J Saldanha, John I Murray, Catherine A Ball, Karen E Alexander, John C Matese, et al. (2002) 2002. “Identification of Genes Periodically Expressed in the Human Cell Cycle and Their Expression in Tumors.”. Mol Biol Cell 13 (6): 1977-2000.

Lossos, Izidore S, Ash A Alizadeh, Maximilian Diehn, Roger Warnke, Yvonne Thorstenson, Peter J Oefner, Patrick O Brown, David Botstein, and Ronald Levy. (2002) 2002. “Transformation of Follicular Lymphoma to Diffuse Large-Cell Lymphoma: Alternative Patterns With Increased or Decreased Expression of C-Myc and Its Regulated Genes.”. Proc Natl Acad Sci U S A 99 (13): 8886-91.

Diehn, Maximilian, Ash A Alizadeh, Oliver J Rando, Chih Long Liu, Kryn Stankunas, David Botstein, Gerald R Crabtree, and Patrick O Brown. (2002) 2002. “Genomic Expression Programs and the Integration of the CD28 Costimulatory Signal in T Cell Activation.”. Proc Natl Acad Sci U S A 99 (18): 11796-801.