Spellman Lab Publications
The Spellman Lab - Publications
1. P.T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9: 3273-97, 1998.
2. 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.
3. G. Zhu, P.T. Spellman, T. Volpe, P. O. Brown, D. Botstein, T. N. Davis and B. Futcher. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406: 90-4, 2000.
4. 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.
5. 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.
6. G. Sherlock, T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J. C. Matese, S. S. Dwight, M. Kaloper, S. Weng, H. Jin, C. A. Ball, M. B. Eisen, P. T. Spellman, P. O. Brown, D. Botstein and J. M. Cherry. The Stanford Microarray Database. Nucleic Acids Research 29: 152-5, 2001.
7. R. A. George, J. P. Woolley and P. T. Spellman. Ceramic capillaries for use in microarray fabrication. Genome Research 11: 1780-3, 2001.
8. 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.
9. 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.
10. P. T. Spellman and G. M. Rubin. Evidence for large domains of similarly expressed genes in the Drosophila genome. Journal of Biology 1: 5, 2002.
11. 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.
12. 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.
13. 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.
14. 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
15. 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
16. A.R. Jones, A. Pizarro, P. Spellman, M. Miller. FuGE: Functional Genomics Object Model. Omics 10:179-84. 2006
17. 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
18. 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
19. 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
20. 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
21. 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
22. 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
23. 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
24. 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
25. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008
26. 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
27. S. Durinck, J. Bullard, P.T. Spellman, S. Dudoit. GenomeGraphs: Integrated genomic visualization with R. BMC Bioinformatics. 2009
28. 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
29. 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
30. 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
31. 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
32. 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. Genome Biology. 2009
33. S. Durinck, P.T. Spellman, W. Huber. Mapping Identifiers for the Integration of Genomic Datasets with the R/Bioconductor package biomaRt. Nature Protocols. 2009
34. 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.
35. 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.
36. International Cancer Genome Consortium. International network of cancer genome projects. Nature. 2010.
37. 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.
38. 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.
39. 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
40. 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
41. 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
42. 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
43. TCGA Network, P.T. Spellman corresponding author. Integrative Genomic Analyses of Ovarian Carcinoma. Nature. 2011.
44. 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.
45. 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.
46. 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, in press.
47. 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
48. 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.
