OHSU

Lab Publications

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2014

  • Spellman PT, Gray JW. Detecting cancer by monitoring circulating tumor DNA. Nat Med. 2014 May;20(5):474-5. doi: 10.1038/nm.3564.
  • Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM.Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nat Genet. 2014 Apr;46(4):318-9. doi: 10.1038/ng.2932.
  • Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L. Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun. 2014;5:3156. doi: 10.1038/ncomms4156.

2013

  • Purdom E, Ho C, Grasso CS, Quist MJ, Cho RJ, Spellman P. Methods and challenges in timing chromosomal abnormalities within cancer samples. Bioinformatics. 2013 Dec 15;29(24):3113-20. doi: 10.1093/bioinformatics/btt546. Epub 2013 Sep 23.
  • Chang H, Nayak N, Spellman PT, Parvin B.Characterization of tissue histopathology via predictive sparse decomposition and spatial pyramid matching. Med Image Comput Comput Assist Interv. 2013;16(Pt 2):91-8.
  • Griffith OL, Pepin F, Enache OM, Heiser LM, Collisson EA, Spellman PT, Gray JW. A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Med. 2013.
  • Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M; Cancer Genome Atlas Research Network. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013.
  • Chang H, Han J, Borowsky A, Loss L, Gray JW, Spellman PT, Parvin B. Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association. IEEE Trans Med Imaging. 2013.
  • Daemen A, Griffith OL, Heiser LM, Wang NJ, Enache OM, Sanborn Z, Pepin F, Durinck S, Korkola JE, Griffith M, Hur JS, Huh N, Chung J, Cope L, Fackler MJ, Umbricht C, Sukumar S, Seth P, Sukhatme VP, Jakkula LR, Lu Y, Mills GB, Cho RJ, Collisson EA, Van't Veer LJ, Spellman PT, Gray JW. Modeling precision treatment of breast cancer. Genome Biol. 2013 Oct 31;14(10):R110.
  • Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-9. doi: 10.1038/nature12222.
  • C.W. Brennan, R.G. Verhaak, A. McKenna, B. Campos, H. Noushmehr, S.R. Salama, S. Zheng, D. Chakravarty, J.Z. Sanborn, S.H. Berman, R. Beroukhim, B. Bernard, C.J. Wu, G. Genovese, I. Shmulevich, J. Barnholtz-Sloan, L. Zou, R. Vegesna, S.A. Shukla, G.  Ciriello, W.K. Yung, W. Zhang, C. Sougnez, T. Mikkelsen, K. Aldape, D.D. Bigner, E.G. Van Meir, M. Prados, A. Sloan, K.L. Black, J. Eschbacher, G. Finocchiaro, W. Friedman, D.W. Andrews, A. Guha, M. Iacocca, B.P. O'Neill, G. Foltz, J. Myers, D.J. Weisenberger, R. Penny, R. Kucherlapati, C.M. Perou, D.N. Hayes, R. Gibbs, M, Marra, G.B. Mills, E. Lander, P. Spellman, R. Wilson, C. Sander, J. Weinstein, M. Meyerson, S. Gabriel, P.W. Laird, D. Haussler, G. Getz, L. Chin and TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell. 2013.
  • S.W. Luoh, B. Ramsey, A. Hanlon Newell, M. Troxell M, Z. Hu, K. Chin, P. Spellman, S. Olson, and E. Keenan. HER-2 gene amplification in human breast cancer without concurrent HER-2 over-expression. Springerplus 2013.
  • Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genetics 2013.
  • J.K. Rhee, K. Kim, H. Chae, J. Evans, P. Yan, B.T. Zhang, J. Gray, P. Spellman, T.H.  Huang, K.P. Nephew, and S. Kim. Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer. NAR 2013.
  • K.M. Kodigepalli, P. Anur P, P. Spellman, P.J. Sims, M. Nanjundan. Phospholipid Scramblase 1, an interferon-regulated gene located at 3q23, is regulated by SnoN/SkiL in ovarian cancer cells. Mol. Cancer 2013.
  • P.D. Pharoah, Y.Y. Tsai, S.J. Ramus, C.M. Phelan, et al. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet. 2013

2012

  • L.M. Heiser, A. Sadanandam, W.L. Kuo, S.C. Benz, T.C. Goldstein, S. Ng, W.J. Gibb, N.J. Wang, S. Ziyad, F. Tong, N. Bayani, Z Hu, J.I. Billig, A. Dueregger, S. Lewis, L. Jakkula, J.E. Korkola, S. Durinck, F. Pepin, Y. Guan, E. Purdom, P. Neuvial, H. Bengtsson, K.W. Wood, P.G. Smith, L.T. Vassilev, B.T. Hennessy, J. Greshock, K.E. Bachman, M.A. Hardwicke, J.W. Park, L.J. Marton, D.M. Wolf, E.A. Collisson, R.M. Neve, G.B. Mills, T.P. Speed, H.S. Feiler, R.F. Wooster, D. Haussler, J.M. Stuart, J.W. Gray, P.T. Spellman. Subtype and pathway specific responses to anti-cancer compounds in breast cancer. PNAS. 2012.
  • Daemen A, Wolf DM, Korkola JE, Griffith OL, Frankum JR, Brough R, Jakkula LR, Wang NJ, Natrajan R, Reis-Filho JS, Lord CJ, Ashworth A, Spellman PT, Gray JW, van't Veer LJ. Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib. Breast Cancer Res Treat. 2012.
  • Ordinario E, Han HJ, Furuta S, Heiser LM, Jakkula LR, Rodier F, Spellman PT, Campisi J, Gray JW, Bissell MJ, Kohwi Y, Kohwi-Shigematsu T. ATM supresses SATB1-induced malignant progression in breast epithelial cells. PLoS One. 2012.
  • Chang H, Han J, Spellman PT, Parvin B. Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme. IEEE Trans Med Imaging. 2012.
  • Petrillo LA, Wolf DM, Kapoun AM, Wang NJ, Barczak A, Xiao Y, Korkaya H, Baehner F, Lewicki J, Wicha M, Park JW, Spellman PT, Gray JW, van't Veer L, Esserman LJ. Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors. Breast Cancer Res Treat. 2012.
  • Hill SM, Lu Y, Molina J, Heiser LM, Spellman PT, Speed TP, Gray JW, Mills GB, Mukherjee S. Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics. 2012.
  • Collisson EA, Trejo CL, Silva JM, Gu S, Korkola JE, Heiser LM, Charles RP, Rabinovich BA, Hann B, Dankort D, Spellman PT, Phillips WA, Gray JW, McMahon M. A central role for RAF->MEK->ERK signaling in the genesis of pancreatic ductal adenocarcinoma. Cancer Discov. 2012.
  • Corless CL, Spellman PT. Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing. Cancer Discov. 2012.
  • Hill SM, Neve RM, Bayani N, Kuo WL, Ziyad S, Spellman PT, Gray JW, Mukherjee S. Integrating biological knowledge into variable selection: an emperical Bayes approach with an application in cancer biology. BMC Bioinformatics. 2012.
  • Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH; Cancer Genome Atlas Research Network. Integrated analyses of microRNAs demonstrated their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One. 2012.

2011

  • N. Nabavizadeh, C. Klifa, D. Newitt, Y. Lu, Y.Y. Chen, H. Hsu, C. Fisher, T. Tokayasu, A.B. Olshen, P. Spellman, J.W. Gray, N. Hylton, and C.C. Park. Topographic enhancement mapping of the cancer-associated breast stroma usine breast MRI. Integr. Biol. 2011
  • X.V. Wang, R.G. Verhaak, E. Purdom, P.T. Spellman, and T.P. Speed. Unifying gene expression measures from multiple platforms using factor analysis. PLoS ONE. 2011
  • E.A. Collisson, A. Sadanandam, P. Olson, W.J. Gibb, M. Truitt, S. Gu, J. Cooc, J. Weinkle, G.E. Kim, L. Jakkula, H.S. Feiler, A.H. Koh, A.B. Olshen, K.L. Danenberg, M.A. Tempero, P.T. Spellman, D. Hanahan, and J.W. Gray. Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy. Nat. Med. 2011
  • TCGA Network, P.T. Spellman corresponding author. Integrative Genomic Analyses of Ovarian Carcinoma. Nature. 2011.
  • A.B. Olshen, H. Bengtsson, P. Neuvial, P. Spellman, R.A. Olshen, V.E. Seshan. Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics.  2011.
  • S. Durinck, C. Ho, N.J. Wang, W. Liao, L.R. Jakkula, E.A. Collisson, J. Pons, S.W. Chan, E.T. Lam, C. Chu, K. Park, S.W. Hong, J.S. Hur, N. Huh, I.M. Neuhaus, S.S. Yu, R.T. Grekin, T.M. Mauro, J.E. Cleaver, P.Y. Kwok, P.E. LeBoit, G. Getz, K. Cibulskis, J.C. Aster, H. Huang, E. Purdom, J. Li, L. Bolund, S. Arron, J.W. Gray, P.T. Spellman*, R.J. Cho* (*corresponding authors). Temporal Dissection of Tumorigenesis in Primary Cancers. Cancer Discovery. 2011.
  • Ju Han, Hang Chang, Leandro A. Loss, Kai Zhang, Fredrick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin: Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma mulitforme. ISBI 2011: 711-714
  • Chang H, Fontenay GV, Han J, Cong G, Baehner FL, Gray JW, Spellman PT, Parvin B: Morphometic Analysis of TCGA Glioblastoma Muliforme. BMC Bioinformatics. 2011 Dec 20; 12(1):484. [Epub ahead of print] PMID: 22185703.

2010

  • R.G. Verhaak, K.A. Hoadley, E. Purdom, V. Wang, Y. Qi, M.D. Wilkerson, C.R. Miller, L. Ding, T. Golub, J.P. Mesirov, G. Alexe, M. Lawrence, M. O’Kelly, P. Tamayo, B.A. Weir, S. Gabriel, W. Winckler, S. Gupta, L. Jakkula, H.S. Feiler, J.G. Hodgson, C.D. James, J.N. Sarkaria, C. Brennan, A. Kahn, P.T. Spellman, R. K. Wilson, T.P. Speed, J.W. Gray, M. Meyerson, G. Getz, C.M. Perou, D.N. Hayes, Cancer Genome Atlas Network. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010.
  • International Cancer Genome Consortium. International network of cancer genome projects. Nature. 2010.
  • L.A. Loss, A. Sadanandam, S. Durinck, S. Nautiya, D. Flaucher, V.E. Carlton, M. Moorhead, Y. Lu, J.W. Gray, M. Faham, P. Spellman, B. Parvin. Prediction of epigenetically regulated genes in breast cancer cell lines. BMC Bioinformatics. 2010.
  • A. Lapuk, H. Marr, L. Jakkula, H. Pedro, S. Bhattacharya, E. Purdom, Z. Hu, K. Simpson, L. Pachter, N. Wang, B. Parvin, G. Fontenay, T. Speed, J. Garbe, M. Stampfer, H. Bayandorian, S. Dorton, T.A. Clark, A. Schweitzer, A. Wyrobek, H. Feiler, P. Spellman, J. Conboy, and J.W. Gray. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res. 2010.
  • S. Nautiyal, V.E. Carlton, Y. Lu, J.S. Ireland, M. Moorhead, J.W. Gray, P. Spellman, M. Mindrinos, P. Berg, and M. Faham. High-throughput method for analyzing methylation of CpGs in targeted genomic regions. PNAS. 2010

2009

  • S. Mukherjee, S. Pelech, R.M. Neve, W.L. Kuo, S. Ziyad, P.T. Spellman, J.W. Gray, T.P. Speed. Sparse combinatorial inference with an application in cancer biology. Bioinformtics. 2009
  • S. Durinck, J. Bullard, P.T. Spellman, S. Dudoit. GenomeGraphs: Integrated genomic visualization with R. BMC Bioinformatics. 2009
  • J.G. Hodgson, R.F. Yeh, A. Ray, N.J. Wang, I. Smirnov, M. Yu, S. Hariono, J. Silber, H.S. Feiler, J.W. Gray, P.T. Spellman, S.R. Vandenberg, M.S. Berger, C.D. James. Comparitive analysis of gene copy number and mRNA expression in GBM tumors and GBM xenografts. Neuro Oncology. 2009
  • O.K. Mirzoeva, D. Das, L.M. Heiser, S. Bhattacharya, D. Siwak, R. Gendelman, N. Bayani, N.J. Wang, R.M. Neve, Y. Guan, Z. Hu, Z. Knight, H.S. Feiler, P. Gascard, B. Parvin, P.T. Spellman, K.M. Shokat, A.J. Wyrobek, M.J. Bissell, F. McCormick, W.L. Kuo, G.B. Mills, J.W. Gray, W.M. Korn. Cancer Research. 2009
  • Y. Wang, V.E.H. Carlton, G. Karlin-Neumann, R. Sapolsky, L. Zhang, M. Moorhead, Z.C. Wang, A.L. Richardson, R. Warren, A. Walther, M. Bondy, A Sahin, R. Krahe, M. Tuna, P.A. Thompson, P.T. Spellman, J.W. Gray, G.B. Mills, M. Faham. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays. BMC Medical Genomics. 2009
  • H. Bengtsson, A. Ray, P. Spellman, T.P. Speed. A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinformatics. 2009
  • L.M. Heiser, N.J. Wang, C.L. Talcott, K.R. Laderoute, M. Knapp, Y. Guan, Z. Hu, S. Ziyad, B.L. Weber, S Laquerre, J.R. Jackson, R.F. Wooster, W.L. Kuo, J.W. Gray, P.T. Spellman.Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biology. 2009
  • S. Durinck, P.T. Spellman, W. Huber. Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor package biomaRt. Nature Protocols. 2009
  • W.L. Kuo, D. Das, S. Ziyad, S. Battacharya, W.J. Gibb, L.M. Heiser, A. Sadanandam, G.V. Fontenay, Z. Hu, N.J. Wang, N. Bayani, H.S. Feiler, R.M. Neve, A.J. Wyrobek, P.T. Spellman, L.J. Marton and J.W. Gray. A Systems Analysis of the Chemosensitivity of Breast Cancer Cells to the Polyamine Analogue PG-11047. BMC Medicine. 2009.

2008

  • L.A. Brown, S.E. Kalloger, M.A. Miller, I.M. Shih, S.E. McKinney,  J.L. Santos, K. Swenerton, P.T. Spellman, J. Gray, C.B. Gilks, D.G. Huntsman. Amplification of 11q13 in ovarian carcinoma. Genes Chromosomes Cancer. 47:481-9. 2008
  • J.Z. Press, A. De Luca, N. Boyd, S. Young, A. Troussard, Y. Ridge, P. Kaurah, S.E. Kalloger, K.A. Blood, M. Smith, P.T. Spellman, Y. Yang, D.M. Miller, D. Horsman, M. Faham, C.B. Gilks, J. Gray, D.G. Huntsman. Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities. BMC Cancer. 22:17. 2008
  • The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008

2007

  • A.R. Jones, M. Miller, R. Aebersold, R. Apweiler, C.A. Ball, A. Brazma, J. Degreef, N. Hardy, H. Hermjakob, S.J. Hubbard, P. Hussey, M. Igra, H. Jenkins, R.K. Julian, K. Laursen, S.G. Oliver, N.W. Paton, S.A. Sansone, U. Sarkans, C.J. Stoeckert, C.F. Taylor, P.L. Whetzel, J.A. White, P. Spellman, A. Pizarro. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat. Biotechnology. 25:1127-33. 2007
  • Y. Wang, M. Moorhead, G. Karlin-Neumann, N. Wang, J. Ireland, S. Lin, C. Chen, L.M. Heiser, K. Chin, L. Esserman, J.W. Gray, P.T. Spellman. M. Faham. Performance of Molecular Inversion Probes (MIP) in Allele Copy Number Determination. Genome Biology. 8:R246. 2007
  • P.A. Kenny, G.Y. Lee, C.A. Myers, R.M. Neve, J.R. Semeiks, P.T. Spellman, K. Lorenz, E.H. Lee, M.H. Barcellos-Hoff, O.W. Petersen, J.W. Gray, M.J. Bissell. The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression. Mol Oncol. 1:84-96. 2007

2006

  • S. Brun, S. Vidal, P. Spellman, K. Takahashi, H. Tricoire, B. Lemaitre.  The MAPKKK Mekk1 regulates the expression of Turandot stress genes in response to septic injury in Drosophila.  Genes Cells 11:397-407, 2006
  • A.R. Jones, A. Pizarro, P. Spellman, M. Miller. FuGE: Functional Genomics Object Model. Omics 10:179-84. 2006
  • K. Chin K, S. DeVries, J. Fridlyand, P.T. Spellman, R. Roydasgupta, W.L. Kuo, A. Lapuk, R.M. Neve, Z. Qian, T. Ryder, F. Chen, H. Feiler, T. Tokuyasu, C. Kingsley, S. Daikree, Z. Meng, K. Chew, D. Pinkel, A. Jain, B.M. Ljung, L. Esserman, D.G. Albertson, F.M. Waldman, J.W. Gray. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 6:529-41. 2006
  • R.M. Neve, K. Chin, J. Fridlyand, J. Yeh, F.L. Baehner, T. Fevr, L. Clark, N. Bayani, J.P. Coppe JP, F. Tong, T. Speed, P.T. Spellman, S. DeVries, A. Lapuk, N.J. Wang, W.L. Kuo, J.L. Stilwell, D. Pinkel, D.G. Albertson, F.M. Waldman, F. McCormick, R.B. Dickson, M.D. Johnson, M. Lippman, S. Ethier, A. Gazdar, J.W. Gray. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 6:515-27. 2006
  • T.F. Rayner, P. Rocca-Serra, P.T. Spellman, H.C. Causton, A. Farne, E. Holloway, R.A. Irizarry, J. Liu, D.S. Maier, M. Miller, K. Petersen, J. Quackenbush, G. Sherlock, C.J. Stoeckert, J. White, P.L. Whetzel, F. Wymore, H. Parkinson, U. Sarkans, C.A. Ball, A. Brazma. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 7:489. 2006

2005

  • N. Vodovar, M. Vinal, P. Liehl, A. Basset, J. Degrouard, P. Spellman, F. Boccard, B Lemaitre. Drosophila host defense after oral infection by an entomopathogenic Pseudomonas species. PNAS 102:11414-9, 2005

2003

  • L. A. Pile, P. T. Spellman, R. J. Katzenberger and D. A. Wassarman. The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: implications for the regulation of energy metabolism. J Biol Chem 278: 37840-8, 2003.

2002

  • P. T. Spellman, M. Miller, J. Stewart, C. Troup, U. Sarkans, S. Chervitz, D. Bernhart, G. Sherlock, C. Ball, M. Lepage, M. Swiatek, W. L. Marks, J. Goncalves, S. Markel, D. Iordan, M. Shojatalab, A. Pizarro, J. White, R. Hubley, E. Deutsch, M. Senger, B. J. Aronow, A. Robinson, D. Bassett, C. J. Stoeckert, Jr. and A. Brazma. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology 3: RESEARCH0046, 2002.
  • E. De Gregorio, P. T. Spellman, P. Tzou, G. M. Rubin and B. Lemaitre. The Toll and Imd pathways are the major regulators of the immune response in Drosophila. Embo Journal 21: 2568-79, 2002.

2001

  • R. A. George, J. P. Woolley and P. T. Spellman. Ceramic capillaries for use in microarray fabrication. Genome Research 11: 1780-3, 2001.
  • E. De Gregorio, P. T. Spellman, G. M. Rubin and B. Lemaitre. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proceedings of the National Academy of Sciences, U.S.A. 98: 12590-5, 2001.
  • Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C. A. Ball, H. C. Causton, T. Gaasterland, P. Glenisson, F. C. Holstege, I. F. Kim, V. Markowitz, J. C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo and M. Vingron. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29: 365-71, 2001.

2000

  •  D. T. Ross, U. Scherf, M. B. Eisen, C. M. Perou, C. Rees, P. Spellman, V. Iyer, S. S. Jeffrey, M. Van de Rijn, M. Waltham, A. Pergamenschikov, J. C. Lee, D. Lashkari, D. Shalon, T. G. Myers, J. N. Weinstein, D. Botstein and P. O. Brown. Systematic variation in gene expression patterns in human cancer cell lines. Nature Genetics 24: 227-35, 2000.
  • P. Gasch, P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D. Botstein and P. O. Brown. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11: 4241-57, 2000.

1998

  • M. B. Eisen, P.T. Spellman, P. O. Brown and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences, U.S.A. 95: 14863-8, 1998