GenePattern Related Papers

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

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Neighborhood-Based Clustering of Gene-Gene Interactions

Norberto Díaz–Díaz, Domingo S. Rodríguez–Baena, Isabel Nepomuceno, and Jesús S. Aguilar–Ruiz. Proceeding IDEAL'06 Proceedings of the 7th international conference on Intelligent Data Engineering and Automated Learning. Pages 1111-1120, Springer-Verlag Berlin, Heidelberg 2006

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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)

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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)

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Comparative Gene Marker Selection Suite

Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P. Mesirov. Bioinformatics 2006 Aug 1;22(15):1924-5. Epub 2006 May 18.

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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)

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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)

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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)

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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)

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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)

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