GenePattern Related Papers

Comparability and reproducibility of biomedical data

Yunda Huang and Raphael Gottardo Brief Bioinform (2013) 14 (4): 391-401 first published online November 27, 2012doi:10.1093/bib/bbs078

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ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems

Vivek Kaimal, Eric E. Bardes, Scott C. Tabar, Anil G. Jegga, and Bruce J. Aronow. Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W96-W102.

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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.

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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.

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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.)

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NuGO contributions to GenePattern

P.J. De Groot, C. Reiff, C. Mayer and M. Müller. Genes Nutr (2008) 3:143-146

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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

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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

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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.

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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.

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