Related Publications

Following are selected papers that use GenePattern. For an up-to-date listing of Broad Cancer Genomics publications, click here.

• Automated High-dimensional Flow Cytometric Data Analysis
  Saumyadipta Pyne, Xinli Hu, Kui Wang, Elizabeth Rossin, Tsung-I Lin, Lisa M. Maier, Clare Baecher-Allan, Geoffrey J. McLachlan, Pablo Tamayo, David A. Hafler, Philip L. De Jager, and Jill P. Mesirov.
  PNAS (2009) 106:8519-8524.
  GenePattern module: FLAME
• Prediction of high-responding peptides for targeted protein assays by mass spectrometry
  Vincent A. Fusaro, D. R. Mani, Jill P. Mesirov & Steven A. Carr
  Nature Biotechnology (2009) 27:190-198.
  GenePattern module: ESPPredictor
• Perturbational profiling of nanomaterial biologic activity
  Stanley Y. Shaw, Elizabeth C. Westly, Mikael J. Pittet, Aravind Subramanian, Stuart L. Schreiber, and Ralph Weissleder
  Proceedings of the National Academy of Sciences (2008) 105(21): 7387-7392.
• Differential Methylation Hybridization: Profiling DNA Methylation with a High-Density CpG Island Microarray
  Pearlly S. Yan, Dustin Potter, Daniel E. Deatherage, Shili Lin, and Tim H.-M. Huang
  DNA Methylation: Methods and Protocols, Second Edition, vol. 507 (2009), Jörg Tost (ed.)
• NuGO contributions to GenePattern
  P.J. De Groot, C. Reiff, C. Mayer and M. Müller
  Genes Nutr (2008) 3:143-146
• Implementation of GenePattern within the Stanford Microarray Database
  Jeremy Hubble, Janos Demeter, Heng Jin, Maria Mao, Michael Nitzberg, T. B. K. Reddy, Farrell Wymore, Zachariah K. Zachariah, Gavin Sherlock and Catherine A. Ball
  Nucleic Acids Res., 2008 Oct 25
• Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma
  Hoshida Y, Villanueva A, Kobayashi M, Peix J, Chiang D, Camargo A, Gupta S, Moore J, Wrobel MJ, Lerner J, Reich M, Chan JA, Ikeda K, Hashimoto M, Watanabe G, Roayaie S, Schwartz M, Thung S, Gabriel S, Mazzaferro V, Bruix J, Friedman S, Kumada H, Llovet JM, Golub TR
  N Engl J Med, 2008;359
• Using GenePattern for gene expression analysis
  Heidi Kuehn, Arthur Liberzon, Michael Reich, and Jill P. Mesirov
  Curr. Protoc. Bioinform., 22:7.12.1 - 7.12.39.
• Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma
  Rameen Beroukhim, Gad Getz, Leia Nghiemphu, Jordi Barretina, Teli Hsueh, David Linhart, Igor Vivanco, Jeffrey C. Lee, Julie H. Huang, Sethu Alexander, Jinyan Du, Tweeny Kau, Roman K. Thomas, Kinjal Shah, Horacio Soto, Sven Perner, John Prensner, Ralph M. Debiasi, Francesca Demichelis, Charlie Hatton, Mark A. Rubin, Levi A. Garraway, Stan F. Nelson, Linda Liau, Paul Mischel, Tim F. Cloughesy, Matthew Meyerson, Todd R. Golub, Eric S. Lander, Ingo K. Mellinghoff, William R. Sellers
  Proc Natl Acad Sci U S A., 2007 Dec 11;104(50):20007-12
• Gene expression dynamics during germline specification in mice identified by quantitative single-cell gene expression profiling
  Y. Yabuta, K. Kurimoto, Y. Ohinata, Y. Seki, and M. Saitou
  Biology of Reproduction, doi:10.1095/biolreprod.106.053686 (July 26, 2006)
• Comparative Gene Marker Selection Suite
  Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P. Mesirov
  Bioinformatics, doi:10.1093/bioinformatics/btl196
• Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay
  Laurent Perreard, Cheng Fan, John F Quackenbush, Michael Mullins, Nicholas P Gauthier, Edward Nelson, Mary Mone, Heidi Hansen, Saundra S Buys, Karen Rasmussen, Alejandra Ruiz Orrico, Donna Dreher, Rhonda Walters, Joel Parker, Zhiyuan Hu, Xiaping He, Juan P Palazzo, Olufunmilayo I Olopade, Aniko Szabo, Charles M Perou, and Philip S Bernard
  Breast Cancer Research 2006; 8(2): R23, doi: 10.1186/bcr1399. (April 20, 2006)
• An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis
  Kazuki Kurimoto, Yukihiro Yabuta, Yasuhide Ohinata, Yukiko Ono, Kenichiro D. Uno, Rikuhiro G. Yamada, Hiroki R. Ueda, and Mitinori Saitou
  Nucleic Acids Research; 34(5): e42; doi: 10.1093/nar/gkl050 (March 17 2006)
• Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling
  Jean-Pierre Bourquina, Aravind Subramanian, Claudia Langebraked, Dirk Reinhardt, Olivier Bernard, Paola Ballerini, André Baruchel, Hélène Cavé, Nicole Dastugue, Henrik Hasle, Gertjan L. Kaspers, Michel Lessard, Lucienne Michaux, Paresh Vyas, Elisabeth van Wering, Christian M. Zwaan, Todd R. Golub, and Stuart H. Orkin
  PNAS, vol. 103, no. 9, 3339-3344 (February 21, 2006)
• Neighborhood-Based Clustering of Gene-Gene Interactions
  Norberto Díaz–Díaz, Domingo S. Rodríguez–Baena, Isabel Nepomuceno, and Jesús S. Aguilar–Ruiz
  Lecture Notes in Computer Science 4224, pp 1111-1120 (2006)
• A method for high-throughput gene expression signature analysis
  David Peck , Emily D Crawford , Kenneth N Ross , Kimberly Stegmaier , Todd R Golub, and Justin Lamb
  Genome Biology, 7:R61, doi:10.1186/gb-2006-7-7-r61 (2006)
• GenePattern 2.0
  Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo & Jill P Mesirov
  Nat. Genet. 38 no. 5: pp500-501 doi:10.1038/ng0506-500 (2006)
• Epithelial versus Mesenchymal Phenotype Determines In vitro Sensitivity and Predicts Clinical Activity of Erlotinib in Lung Cancer Patients
  Robert L. Yauch, Thomas Januario, David A. Eberhard, Guy Cavet, Wenjing Zhu, Ling Fu, Thinh Q. Pham, Robert Soriano, Jeremy Stinson, Somasekar Seshagiri, Zora Modrusan, Chin-Yu Lin, Vincent O'Neill and Lukas C. Amler
  Clinical Cancer Research Vol. 11, 8686-8698 (December 15, 2005)
• Novel Molecular Signaling and Classification of Human Clinically Nonfunctional Pituitary Adenomas Identified by Gene Expression Profiling and Proteomic Analyses
  Carlos S. Moreno, Chheng-Orn Evans, Xianquan Zhan, Mammerhi Okor, Dominic M. Desiderio, and Nelson M. Oyesiku
  Cancer Research 65, 10214-10222 (November 15, 2005)
• GeneCruiser: a web service for the annotation of microarray data
  Ted Liefeld, Michael Reich, Josh Gould, Peili Zhang, Pablo Tamayo, and Jill P. Mesirov
  Bioinformatics, doi:10.1093/bioinformatics/bti587
• MicroRNA Expression Profiles Classify Human Cancers
  Jun Lu, Gad Getz, Eric A. Miska, Ezequiel A. Alvarez-Saavedra, Justin Lamb, David Peck, Alejandro Sweet-Cordero, Benjamin L. Ebert, Raymond H. Mak, Adolfo A. Ferrando, James R. Downing, Tyler Jacks, H. Robert Horvitz and Todd R. Golub
  Nature 435, 834-838 (9 June 2005)
• Robust Diagnosis of Non-Hodgkin Lymphoma Phenotypes Validated on Gene Expression Data from Different Laboratories
  Gyan Banot, Gabriela Alexe, Arnold J. Levine, and Gustavo Stolovitzky
  Genome Informatics 16(1): 233-244 (2005)
• Globally distributed object identification for biological knowledgebases
  T. Clark, S. Martin, and T. Liefeld
  Briefings in Bioinformatics 5.1: 59-70 (2004)
• Consensus clustering: A resampling-based method for class discovery and visualization of gene expression microarray data
  S. Monti, P. Tamayo, J. Mesirov, and T.R. Golub
  Machine Learning Journal 52: 91-118 (2003)