Paul Spellman

Professor

  • Source: Scopus
  • Calculated based on no. of publications stored in Pure and citations from Scopus
1992 …2021

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  • 1998

    Cluster analysis and display of genome-wide expression patterns

    Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D., Dec 8 1998, In: Proceedings of the National Academy of Sciences of the United States of America. 95, 25, p. 14863-14868 6 p.

    Research output: Contribution to journalArticlepeer-review

    12831 Scopus citations
  • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

    Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D. & Futcher, B., Dec 1998, In: Molecular biology of the cell. 9, 12, p. 3273-3297 25 p.

    Research output: Contribution to journalArticlepeer-review

    3799 Scopus citations
  • 2000

    Genomic expression programs in the response of yeast cells to environmental changes

    Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D. & Brown, P. O., 2000, In: Molecular biology of the cell. 11, 12, p. 4241-4257 17 p.

    Research output: Contribution to journalArticlepeer-review

    3582 Scopus citations
  • Systematic variation in gene expression patterns in human cancer cell lines

    Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., Van De Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C. F., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D. & Brown, P. O., Mar 2000, In: Nature genetics. 24, 3, p. 227-235 9 p.

    Research output: Contribution to journalArticlepeer-review

    1768 Scopus citations
  • Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

    Gefeng, Z., Spellman, P. T., Volpe, T., Brown, P. O., Botstein, D., Davis, T. N. & Futcher, B., Jul 6 2000, In: Nature. 406, 6791, p. 90-94 5 p.

    Research output: Contribution to journalArticlepeer-review

    282 Scopus citations
  • 2001

    Ceramic capillaries for use in microarray fabrication

    George, R. A., Woolley, J. P. & Spellman, P. T., 2001, In: Genome Research. 11, 10, p. 1780-1783 4 p.

    Research output: Contribution to journalArticlepeer-review

    16 Scopus citations
  • Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays

    De Gregorio, E., Spellman, P. T., Rubin, G. M. & Lemaitre, B., Oct 23 2001, In: Proceedings of the National Academy of Sciences of the United States of America. 98, 22, p. 12590-12595 6 p.

    Research output: Contribution to journalArticlepeer-review

    560 Scopus citations
  • 2002

    Design and implementation of microarray gene expression markup language (MAGE-ML).

    Spellman, P. T., Miller, M., Stewart, J., Troup, C., Sarkans, U., Chervitz, S., Bernhart, D., Sherlock, G., Ball, C., Lepage, M., Swiatek, M., Marks, W. L., Goncalves, J., Markel, S., Iordan, D., Shojatalab, M., Pizarro, A., White, J., Hubley, R., Deutsch, E. & 6 others, Senger, M., Aronow, B. J., Robinson, A., Bassett, D., Stoeckert, C. J. & Brazma, A., Aug 23 2002, In: Genome biology. 3, 9, p. RESEARCH0046

    Research output: Contribution to journalArticlepeer-review

    351 Scopus citations
  • Evidence for large domains of similarly expressed genes in the Drosophila genome

    Spellman, P. T. & Rubin, G. M., Dec 1 2002, In: Journal of Biology. 1, 1, 5.

    Research output: Contribution to journalArticlepeer-review

    397 Scopus citations
  • The Toll and Imd pathways are the major regulators of the immune response in Drosophila

    De Gregorio, E., Spellman, P. T., Tzou, P., Rubin, G. M. & Lemaitre, B., Jun 3 2002, In: EMBO Journal. 21, 11, p. 2568-2579 12 p.

    Research output: Contribution to journalArticlepeer-review

    572 Scopus citations
  • 2003

    The SIN3 deacetylase complex represses genes encoding mitochondrial proteins: Implications for the regulation of energy metabolism

    Pile, L. A., Spellman, P. T., Katzenberger, R. J. & Wassarman, D. A., Sep 26 2003, In: Journal of Biological Chemistry. 278, 39, p. 37840-37848 9 p.

    Research output: Contribution to journalArticlepeer-review

    64 Scopus citations
  • 2004

    Final words: Cell age and cell cycle are unlinked

    Spellman, P. T. & Sherlock, G., Jun 2004, In: Trends in biotechnology. 22, 6, p. 277-278 2 p.

    Research output: Contribution to journalArticlepeer-review

    10 Scopus citations
  • Reply: Whole-culture synchronization - Effective tools for cell cycle studies

    Spellman, P. T. & Sherlock, G., Jun 2004, In: Trends in biotechnology. 22, 6, p. 270-273 4 p.

    Research output: Contribution to journalArticlepeer-review

    19 Scopus citations
  • 2005

    Drosophila host defense after oral infection by an entomopathogenic Pseudomonas species

    Vodovar, N., Vinals, M., Liehl, P., Basset, A., Degrouard, J., Spellman, P., Boccard, F. & Lemaitre, B., Aug 9 2005, In: Proceedings of the National Academy of Sciences of the United States of America. 102, 32, p. 11414-11419 6 p.

    Research output: Contribution to journalArticlepeer-review

    285 Scopus citations
  • 2006

    A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

    Neve, R. M., Chin, K., Fridlyand, J., Yeh, J., Baehner, F. L., Fevr, T., Clark, L., Bayani, N., Coppe, J. P., Tong, F., Speed, T., Spellman, P. T., DeVries, S., Lapuk, A., Wang, N. J., Kuo, W. L., Stilwell, J. L., Pinkel, D., Albertson, D. G., Waldman, F. M. & 7 others, McCormick, F., Dickson, R. B., Johnson, M. D., Lippman, M., Ethier, S., Gazdar, A. & Gray, J. W., Dec 2006, In: Cancer Cell. 10, 6, p. 515-527 13 p.

    Research output: Contribution to journalArticlepeer-review

    2252 Scopus citations
  • A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

    Rayner, T. F., Rocca-Serra, P., Spellman, P. T., Causton, H. C., Farne, A., Holloway, E., Irizarry, R. A., Liu, J., Maier, D. S., Miller, M., Petersen, K., Quackenbush, J., Sherlock, G., Stoeckert, C. J., White, J., Whetzel, P. L., Wymore, F., Parkinson, H., Sarkans, U., Ball, C. A. & 1 others, Brazma, A., Nov 6 2006, In: BMC bioinformatics. 7, 489.

    Research output: Contribution to journalArticlepeer-review

    155 Scopus citations
  • Genomic and transcriptional aberrations linked to breast cancer pathophysiologies

    Chin, K., DeVries, S., Fridlyand, J., Spellman, P. T., Roydasgupta, R., Kuo, W. L., Lapuk, A., Neve, R. M., Qian, Z., Ryder, T., Chen, F., Feiler, H., Tokuyasu, T., Kingsley, C., Dairkee, S., Meng, Z., Chew, K., Pinkel, D., Jain, A., Ljung, B. M. & 4 others, Esserman, L., Albertson, D. G., Waldman, F. M. & Gray, J. W., Dec 2006, In: Cancer Cell. 10, 6, p. 529-541 13 p.

    Research output: Contribution to journalArticlepeer-review

    977 Scopus citations
  • The MAPKKK Mekk1 regulates the expression of Turandot stress genes in response to septic injury in Drosophila

    Brun, S., Vidal, S., Spellman, P., Takahashi, K., Tricoire, H. & Lemaitre, B., Apr 2006, In: Genes to Cells. 11, 4, p. 397-407 11 p.

    Research output: Contribution to journalArticlepeer-review

    60 Scopus citations
  • 2007

    Analysis of molecular inversion probe performance for allele copy number determination

    Wang, Y., Moorhead, M., Karlin-Neumann, G., Wang, N. J., Ireland, J., Lin, S., Chen, C., Heiser, L. M., Chin, K., Esserman, L., Gray, J. W., Spellman, P. T. & Faham, M., Nov 20 2007, In: Genome biology. 8, 11, R246.

    Research output: Contribution to journalArticlepeer-review

    50 Scopus citations
  • The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression

    Kenny, P. A., Lee, G. Y., Myers, C. A., Neve, R. M., Semeiks, J. R., Spellman, P. T., Lorenz, K., Lee, E. H., Barcellos-Hoff, M. H., Petersen, O. W., Gray, J. W. & Bissell, M. J., Jun 2007, In: Molecular Oncology. 1, 1, p. 84-96 13 p.

    Research output: Contribution to journalArticlepeer-review

    682 Scopus citations
  • 2008

    Amplification of 11q13 in ovarian carcinoma

    Brown, L. A., Kalloger, S. E., Miller, M. A., Shih, L. M., McKinney, S. E., Santos, J. L., Swenerton, K., Spellman, P. T., Gray, J., Gilks, C. B. & Huntsman, D. G., Jun 2008, In: Genes Chromosomes and Cancer. 47, 6, p. 481-489 9 p.

    Research output: Contribution to journalArticlepeer-review

    106 Scopus citations
  • Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    McLendon, R., Friedman, A., Bigner, D., Van Meir, E. G., Brat, D. J., Mastrogianakis, G. M., Olson, J. J., Mikkelsen, T., Lehman, N., Aldape, K., Yung, W. K. A., Bogler, O., Weinstein, J. N., VandenBerg, S., Berger, M., Prados, M., Muzny, D., Morgan, M., Scherer, S., Sabo, A. & 211 others, Nazareth, L., Lewis, L., Hall, O., Zhu, Y., Ren, Y., Alvi, O., Yao, J., Hawes, A., Jhangiani, S., Fowler, G., San Lucas, A., Kovar, C., Cree, A., Dinh, H., Santibanez, J., Joshi, V., Gonzalez-Garay, M. L., Miller, C. A., Milosavljevic, A., Donehower, L., Wheeler, D. A., Gibbs, R. A., Cibulskis, K., Sougnez, C., Fennell, T., Mahan, S., Wilkinson, J., Ziaugra, L., Onofrio, R., Bloom, T., Nicol, R., Ardlie, K., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., McLellan, M. D., Wallis, J., Larson, D. E., Shi, X., Abbott, R., Fulton, L., Chen, K., Koboldt, D. C., Wendl, M. C., Meyer, R., Tang, Y., Lin, L., Osborne, J. R., Dunford-Shore, B. H., Miner, T. L., Delehaunty, K., Markovic, C., Swift, G., Courtney, W., Pohl, C., Abbott, S., Hawkins, A., Leong, S., Haipek, C., Schmidt, H., Wiechert, M., Vickery, T., Scott, S., Dooling, D. J., Chinwalla, A., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Getz, G., Winckler, W., Verhaak, R. G. W., Lawrence, M. S., O'Kelly, M., Robinson, J., Alexe, G., Beroukhim, R., Carter, S., Chiang, D., Gould, J., Gupta, S., Korn, J., Mermel, C., Mesirov, J., Monti, S., Nguyen, H., Parkin, M., Reich, M., Stransky, N., Weir, B. A., Garraway, L., Golub, T., Meyerson, M., Chin, L., Protopopov, A., Zhang, J., Perna, I., Aronson, S., Sathiamoorthy, N., Ren, G., Yao, J., Wiedemeyer, W. R., Kim, H., Sek, W. K., Xiao, Y., Kohane, I. S., Seidman, J., Park, P. J., Kucherlapati, R., Laird, P. W., Cope, L., Herman, J. G., Weisenberger, D. J., Pan, F., Van Den Berg, D., Van Neste, L., Joo, M. Y., Schuebel, K. E., Baylin, S. B., Absher, D. M., Li, J. Z., Southwick, A., Brady, S., Aggarwal, A., Chung, T., Sherlock, G., Brooks, J. D., Myers, R. M., Spellman, P. T., Purdom, E., Jakkula, L. R., Lapuk, A. V., Marr, H., Dorton, S., Yoon, G. C., Han, J., Ray, A., Wang, V., Durinck, S., Robinson, M., Wang, N. J., Vranizan, K., Peng, V., Van Name, E., Fontenay, G. V., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Brennan, C., Socci, N. D., Olshen, A., Taylor, B. S., Lash, A., Schultz, N., Reva, B., Antipin, Y., Stukalov, A., Gross, B., Cerami, E., Wei, Q. W., Qin, L. X., Seshan, V. E., Villafania, L., Cavatore, M., Borsu, L., Viale, A., Gerald, W., Sander, C., Ladanyi, M., Perou, C. M., Hayes, D. N., Topal, M. D., Hoadley, K. A., Qi, Y., Balu, S., Shi, Y., Wu, J., Penny, R., Bittner, M., Shelton, T., Lenkiewicz, E., Morris, S., Beasley, D., Sanders, S., Kahn, A., Sfeir, R., Chen, J., Nassau, D., Feng, L., Hickey, E., Barker, A., Gerhard, D. S., Vockley, J., Compton, C., Vaught, J., Fielding, P., Ferguson, M. L., Schaefer, C., Zhang, J., Madhavan, S., Buetow, K. H., Collins, F., Good, P., Guyer, M., Ozenberger, B., Peterson, J. & Thomson, E., Oct 23 2008, In: Nature. 455, 7216, p. 1061-1068 8 p.

    Research output: Contribution to journalArticlepeer-review

    5255 Scopus citations
  • Ovarian carcinomas with genetic and epigenetic BRCA1 loss have distinct molecular abnormalities

    Press, J. Z., De Luca, A., Boyd, N., Young, S., Troussard, A., Ridge, Y., Kaurah, P., Kalloger, S. E., Blood, K. A., Smith, M., Spellman, P. T., Wang, Y., Miller, D. M., Horsman, D., Faham, M., Gilks, C. B., Gray, J. & Huntsman, D. G., Jan 22 2008, In: BMC cancer. 8, 17.

    Research output: Contribution to journalArticlepeer-review

    231 Scopus citations
  • 2009

    A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods

    Bengtsson, H., Ray, A., Spellman, P. & Speed, T. P., 2009, In: Bioinformatics. 25, 7, p. 861-867 7 p.

    Research output: Contribution to journalArticlepeer-review

    30 Scopus citations
  • A systems analysis of the chemosensitivity of breast cancer cells to the polyamine analogue PG-11047

    Kuo, W. L., Das, D., Ziyad, S., Bhattacharya, S., Gibb, W. J., Heiser, L. M., Sadanandam, A., Fontenay, G. V., Hu, Z., Wang, N. J., Bayani, N., Feiler, H. S., Neve, R. M., Wyrobek, A. J., Spellman, P. T., Marton, L. J. & Gray, J. W., Dec 14 2009, In: BMC Medicine. 7, 77.

    Research output: Contribution to journalArticlepeer-review

    28 Scopus citations
  • Basal subtype and MAPK/ERK kinase (MEK)-phosphoinositide 3-kinase feedback signaling determine susceptibility of breast cancer cells to MEK inhibition

    Mirzoeva, O. K., Das, D., Heiser, L. M., Bhattacharya, S., Siwak, D., Gendelman, R., Bayani, N., Wang, N. J., Neve, R. M., Guan, Y., Hu, Z., Knight, Z., Feiler, H. S., Gascard, P., Parvin, B., Spellman, P. T., Shokat, K. M., Wyrobek, A. J., Bissell, M. J., McCormick, F. & 4 others, Kuo, W. L., Mills, G. B., Gray, J. W. & Korn, W. M., Jan 15 2009, In: Cancer Research. 69, 2, p. 565-572 8 p.

    Research output: Contribution to journalArticlepeer-review

    296 Scopus citations
  • Comparative analyses of gene copy number and mRNA expression in glioblastoma multiforme tumors and xenografts

    Hodgson, J. G., Yeh, R. F., Ray, A., Wang, N. J., Smirnov, I., Yu, M., Hariono, S., Silber, J., Feiler, H. S., Gray, J. W., Spellman, P. T., Vandenberg, S. R., Berger, M. S. & James, C. D., Oct 2009, In: Neuro-Oncology. 11, 5, p. 477-487 11 p.

    Research output: Contribution to journalArticlepeer-review

    95 Scopus citations
  • GenomeGraphs: integrated genomic data visualization with R.

    Durinck, S., Bullard, J., Spellman, P. T. & Dudoit, S., 2009, In: BMC bioinformatics. 10, p. 2 1 p., 2.

    Research output: Contribution to journalArticlepeer-review

    50 Scopus citations
  • High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    Wang, Y., Carlton, V. E., Karlin-Neumann, G., Sapolsky, R., Zhang, L., Moorhead, M., Wang, Z. C., Richardson, A. L., Warren, R., Walther, A., Bondy, M., Sahin, A., Krahe, R., Tuna, M., Thompson, P. A., Spellman, P. T., Gray, J. W., Mills, G. B. & Faham, M., 2009, In: BMC Medical Genomics. 2, 8.

    Research output: Contribution to journalArticlepeer-review

    78 Scopus citations
  • Integrated analysis of breast cancer cell lines reveals unique signaling pathways

    Heiser, L. M., Wang, N. J., Talcott, C. L., Laderoute, K. R., Knapp, M., Guan, Y., Hu, Z., Ziyad, S., Weber, B. L., Laquerre, S., Jackson, J. R., Wooster, R. F., Kuo, W., Gray, J. W. & Spellman, P. T., Mar 25 2009, In: Genome biology. 10, 3, R31.

    Research output: Contribution to journalArticlepeer-review

    53 Scopus citations
  • Mapping identifiers for the integration of genomic datasets with the R/ Bioconductor package biomaRt

    Durinck, S., Spellman, P. T., Birney, E. & Huber, W., 2009, In: Nature protocols. 4, 8, p. 1184-1191 8 p.

    Research output: Contribution to journalArticlepeer-review

    1167 Scopus citations
  • Sparse combinatorial inference with an application in cancer biology

    Mukherjee, S., Pelech, S., Neve, R. M., Kuo, W. L., Ziyad, S., Spellman, P. T., Gray, J. W. & Speed, T. P., Jan 2009, In: Bioinformatics. 25, 2, p. 265-271 7 p.

    Research output: Contribution to journalArticlepeer-review

    18 Scopus citations
  • 2010

    Exon-level microarray analyses identify alternative splicing programs in breast cancer

    Lapuk, A., Marr, H., Jakkula, L., Pedro, H., Bhattacharya, S., Purdom, E., Hu, Z., Simpson, K., Pachter, L., Durinck, S., Wang, N., Parvin, B., Fontenay, G., Speed, T., Garbe, J., Stampfer, M., Bayandorian, H., Dorton, S., Clark, T. A., Schweitzer, A. & 5 others, Wyrobek, A., Feiler, H., Spellman, P., Conboy, J. & Gray, J. W., Jul 2010, In: Molecular Cancer Research. 8, 7, p. 961-974 14 p.

    Research output: Contribution to journalArticlepeer-review

    91 Scopus citations
  • High-throughput method for analyzing methylation of CpGs in targeted genomic regions

    Nautiyal, S., Carlton, V. E. H., Lu, Y., Ireland, J. S., Flaucher, D., Moorhead, M., Gray, J. W., Spellman, P., Mindrinos, M., Berg, P. & Faham, M., Jul 13 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 28, p. 12587-12592 6 p.

    Research output: Contribution to journalArticlepeer-review

    29 Scopus citations
  • Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

    Verhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., Alexe, G., Lawrence, M., O'Kelly, M., Tamayo, P., Weir, B. A., Gabriel, S., Winckler, W., Gupta, S., Jakkula, L., Feiler, H. S. & 13 others, Hodgson, J. G., James, C. D., Sarkaria, J. N., Brennan, C., Kahn, A., Spellman, P. T., Wilson, R. K., Speed, T. P., Gray, J. W., Meyerson, M., Getz, G., Perou, C. M. & Hayes, D. N., Jan 19 2010, In: Cancer Cell. 17, 1, p. 98-110 13 p.

    Research output: Contribution to journalArticlepeer-review

    4351 Scopus citations
  • Prediction of epigenetically regulated genes in breast cancer cell lines

    Loss, L. A., Sadanandam, A., Durinck, S., Nautiyal, S., Flaucher, D., Carlton, V. E. H., Moorhead, M., Lu, Y., Gray, J. W., Faham, M., Spellman, P. & Parvin, B., Jun 4 2010, In: BMC bioinformatics. 11, 305.

    Research output: Contribution to journalArticlepeer-review

    31 Scopus citations
  • 2011

    A new treasure in the breast cancer gene hunt

    Spellman, P. & Gray, J., Apr 2011, In: Nature medicine. 17, 4, p. 422-423 2 p.

    Research output: Contribution to journalArticlepeer-review

    13 Scopus citations
  • Integrated genomic analyses of ovarian carcinoma

    Bell, D., Berchuck, A., Birrer, M., Chien, J., Cramer, D. W., Dao, F., Dhir, R., Disaia, P., Gabra, H., Glenn, P., Godwin, A. K., Gross, J., Hartmann, L., Huang, M., Huntsman, D. G., Iacocca, M., Imielinski, M., Kalloger, S., Karlan, B. Y., Levine, D. A. & 240 others, Mills, G. B., Morrison, C., Mutch, D., Olvera, N., Orsulic, S., Park, K., Petrelli, N., Rabeno, B., Rader, J. S., Sikic, B. I., Smith-Mccune, K., Sood, A. K., Bowtell, D., Penny, R., Testa, J. R., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Gunaratne, P., Hawes, A. C., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Santibanez, J., Reid, J. G., Trevino, L. R., Wu, Y. Q., Wang, M., Muzny, D. M., Wheeler, D. A., Gibbs, R. A., Getz, G., Lawrence, M. S., Cibulskis, K., Sivachenko, A. Y., Sougnez, C., Voet, D., Wilkinson, J., Bloom, T., Ardlie, K., Fennell, T., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., Koboldt, D. C., McLellan, M. D., Wylie, T., Walker, J., O'Laughlin, M., Dooling, D. J., Fulton, L., Abbott, R., Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M., Schierding, W., Shen, D., Harris, C. C., Schmidt, H., Kalicki, J., Delehaunty, K. D., Fronick, C. C., Demeter, R., Cook, L., Wallis, J. W., Lin, L., Magrini, V. J., Hodges, J. S., Eldred, J. M., Smith, S. M., Pohl, C. S., Vandin, F., Raphael, B. J., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Meyerson, M., Winckler, W., Verhaak, R. G. W., Carter, S. L., Mermel, C. H., Saksena, G., Nguyen, H., Onofrio, R. C., Hubbard, D., Gupta, S., Crenshaw, A., Ramos, A. H., Chin, L., Protopopov, A., Zhang, J., Kim, T. M., Perna, I., Xiao, Y., Zhang, H., Ren, G., Sathiamoorthy, N., Park, R. W., Lee, E., Park, P. J., Kucherlapati, R., Absher, D. M., Waite, L., Sherlock, G., Brooks, J. D., Li, J. Z., Xu, J., Myers, R. M., Laird, P. W., Cope, L., Herman, J. G., Shen, H., Weisenberger, D. J., Noushmehr, H., Pan, F., Triche, T., Berman, B. P., Van Den Berg, D. J., Buckley, J., Baylin, S. B., Spellman, P. T., Purdom, E., Neuvial, P., Bengtsson, H., Jakkula, L. R., Durinck, S., Han, J., Dorton, S., Marr, H., Choi, Y. G., Wang, V., Wang, N. J., Ngai, J., Conboy, J. G., Parvin, B., Feiler, H. S., Speed, T. P., Gray, J. W., Socci, N. D., Liang, Y., Taylor, B. S., Schultz, N., Borsu, L., Lash, A. E., Brennan, C., Viale, A., Sander, C., Ladanyi, M., Hoadley, K. A., Meng, S., Du, Y., Shi, Y., Li, L., Turman, Y. J., Zang, D., Helms, E. B., Balu, S., Zhou, X., Wu, J., Topal, M. D., Hayes, D. N., Perou, C. M., Wu, C. J., Shukla, S., Sivachenko, A., Jing, R., Liu, Y., Noble, M., Carter, H., Kim, D., Karchin, R., Korkola, J. E., Heiser, L. M., Cho, R. J., Hu, Z., Cerami, E., Olshen, A., Reva, B., Antipin, Y., Shen, R., Mankoo, P., Sheridan, R., Ciriello, G., Chang, W. K., Bernanke, J. A., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Sanborn, J. Z., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Wilkerson, M. D., Zhang, N., Akbani, R., Baggerly, K. A., Yung, W. K., Weinstein, J. N., Shelton, T., Grimm, D., Hatfield, M., Morris, S., Yena, P., Rhodes, P., Sherman, M., Paulauskis, J., Millis, S., Kahn, A., Greene, J. M., Sfeir, R., Jensen, M. A., Chen, J., Whitmore, J., Alonso, S., Jordan, J., Chu, A., Barker, A., Compton, C., Eley, G., Ferguson, M., Fielding, P., Gerhard, D. S., Myles, R., Schaefer, C., Mills Shaw, K. R., Vaught, J., Vockley, J. B., Good, P. J., Guyer, M. S., Ozenberger, B., Peterson, J. & Thomson, E., Jun 30 2011, In: Nature. 474, 7353, p. 609-615 7 p.

    Research output: Contribution to journalArticlepeer-review

    4669 Scopus citations
  • Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma

    Wang, N. J., Sanborn, Z., Arnett, K. L., Bayston, L. J., Liao, W., Proby, C. M., Leigh, I. M., Collisson, E. A., Gordon, P. B., Jakkula, L., Pennypacker, S., Zou, Y., Sharma, M., North, J. P., Vemula, S. S., Mauro, T. M., Neuhaus, I. M., LeBoit, P. E., Hur, J. S., Park, K. & 13 others, Huh, N., Kwok, P. Y., Arron, S. T., Massion, P. P., Bale, A. E., Haussler, D., Cleaver, J. E., Gray, J. W., Spellman, P. T., South, A. P., Aster, J. C., Blacklow, S. C. & Cho, R. J., Oct 25 2011, In: Proceedings of the National Academy of Sciences of the United States of America. 108, 43, p. 17761-17766 6 p.

    Research output: Contribution to journalArticlepeer-review

    306 Scopus citations
  • Morphometic analysis of TCGA glioblastoma multiforme

    Chang, H., Fontenay, G. V., Han, J., Cong, G., Baehner, F. L., Gray, J. W., Spellman, P. T. & Parvin, B., Dec 20 2011, In: BMC bioinformatics. 12, 484.

    Research output: Contribution to journalArticlepeer-review

    36 Scopus citations
  • Parent-specific copy number in paired tumor-normal studies using circular binary segmentation

    Olshen, A. B., Bengtsson, H., Neuvial, P., Spellman, P. T., Olshen, R. A. & Seshan, V. E., Aug 2011, In: Bioinformatics. 27, 15, p. 2038-2046 9 p., btr329.

    Research output: Contribution to journalArticlepeer-review

    68 Scopus citations
  • Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

    Collisson, E. A., Sadanandam, A., Olson, P., Gibb, W. J., Truitt, M., Gu, S., Cooc, J., Weinkle, J., Kim, G. E., Jakkula, L., Feiler, H. S., Ko, A. H., Olshen, A. B., Danenberg, K. L., Tempero, M. A., Spellman, P. T., Hanahan, D. & Gray, J. W., Apr 2011, In: Nature medicine. 17, 4, p. 500-503 4 p.

    Research output: Contribution to journalArticlepeer-review

    846 Scopus citations
  • Temporal dissection of tumorigenesis in primary cancers

    Durinck, S., Ho, C., Wang, N. J., Liao, W., Jakkula, L. R., Collisson, E. A., Pons, J., Chan, S. W., Lam, E. T., Chu, C., Park, K., Hong, S. W., Hur, J. S., Huh, N., Neuhaus, I. M., Yu, S. S., Grekin, R. C., Mauro, T. M., Cleaver, J. E., Kwok, P. Y. & 12 others, LeBoit, P. E., Getz, G., Cibulskis, K., Aster, J. C., Huang, H., Purdom, E., Li, J., Bolund, L., Arron, S. T., Gray, J. W., Spellman, P. T. & Cho, R. J., Jun 29 2011, In: Cancer discovery. 1, 2, p. 137-143 7 p.

    Research output: Contribution to journalArticlepeer-review

    177 Scopus citations
  • Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI

    Nabavizadeh, N., Klifa, C., Newitt, D., Lu, Y., Chen, Y. Y., Hsu, H., Fisher, C., Tokayasu, T., Olshen, A. B., Spellman, P., Gray, J. W., Hylton, N. & Park, C. C., Apr 2011, In: Integrative Biology. 3, 4, p. 490-496 7 p.

    Research output: Contribution to journalArticlepeer-review

    14 Scopus citations
  • Unifying gene expression measures from multiple platforms using factor analysis

    Wang, X. V., Verhaak, R. G. W., Purdom, E., Spellman, P. T. & Speed, T. P., 2011, In: PloS one. 6, 3, e17691.

    Research output: Contribution to journalArticlepeer-review

    12 Scopus citations
  • 2012

    A Central role for RAF→MEK→ERK signaling in the genesis of pancreatic ductal adenocarcinoma

    Collisson, E. A., Trejo, C. L., Silva, J. M., Gu, S., Korkola, J. E., Heiser, L. M., Charles, R. P., Rabinovich, B. A., Hann, B., Dankort, D., Spellman, P. T., Phillips, W. A., Gray, J. W. & McMahon, M., Aug 2012, In: Cancer discovery. 2, 8, p. 685-693 9 p.

    Research output: Contribution to journalArticlepeer-review

    181 Scopus citations
  • ATM Suppresses SATB1-Induced Malignant Progression in Breast Epithelial Cells

    Ordinario, E., Han, H. J., Furuta, S., Heiser, L. M., Jakkula, L. R., Rodier, F., Spellman, P. T., Campisi, J., Gray, J. W., Bissell, M. J., Kohwi, Y. & Kohwi-Shigematsu, T., Dec 10 2012, In: PloS one. 7, 12, e51786.

    Research output: Contribution to journalArticlepeer-review

    17 Scopus citations
  • Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

    Hill, S. M., Lu, Y., Molina, J., Heiser, L. M., Spellman, P. T., Speed, T. P., Gray, J. W., Mills, G. B. & Mukherjee, S., Nov 2012, In: Bioinformatics. 28, 21, p. 2804-2810 7 p.

    Research output: Contribution to journalArticlepeer-review

    73 Scopus citations
  • Comprehensive molecular characterization of human colon and rectal cancer

    Muzny, D. M., Bainbridge, M. N., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Reid, J. G., Santibanez, J., Shinbrot, E., Trevino, L. R., Wu, Y. Q., Wang, M., Gunaratne, P., Donehower, L. A., Creighton, C. J., Wheeler, D. A. & 293 others, Gibbs, R. A., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Ding, L., Fulton, R. S., Koboldt, D. C., Wylie, T., Walker, J., Dooling, D. J., Fulton, L., Delehaunty, K. D., Fronick, C. C., Demeter, R., Mardis, E. R., Wilson, R. K., Chu, A., Chun, H. J. E., Mungall, A. J., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Bass, A. J., Ramos, A. H., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Pho, N. H., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Meyerson, M., Protopopov, A., Hadjipanayis, A., Lee, E., Xi, R., Yang, L., Ren, X., Sathiamoorthy, N., Chen, P. C., Haseley, P., Xiao, Y., Lee, S., Seidman, J., Chin, L., Park, P. J., Kucherlapati, R., Todd Auman, J., Hoadley, K. A., Du, Y., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Prins, J. F., Chiang, D. Y., Neil Hayes, D., Perou, C. M., Hinoue, T., Weisenberger, D. J., Maglinte, D. T., Pan, F., Berman, B. P., Van Den Berg, D. J., Shen, H., Triche, T., Baylin, S. B., Laird, P. W., Getz, G., Noble, M., Voat, D., Gehlenborg, N., Dicara, D., Zhang, J., Zhang, H., Wu, C. J., Liu, S. Y., Shukla, S., Zhou, L., Lin, P., Park, R. W., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Thorsson, V., Reynolds, S. M., Bernard, B., Kreisberg, R., Lin, J., Iype, L., Bressler, R., Erkkilä, T., Gundapuneni, M., Liu, Y., Norberg, A., Robinson, T., Yang, D., Zhang, W., Shmulevich, I., De Ronde, J. J., Schultz, N., Cerami, E., Ciriello, G., Goldberg, A. P., Gross, B., Jacobsen, A., Gao, J., Kaczkowski, B., Sinha, R., Arman Aksoy, B., Antipin, Y., Reva, B., Shen, R., Taylor, B. S., Ladanyi, M., Sander, C., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Hamilton, S. R., Craig Cason, R., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Zachary Sanborn, J., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Ellrott, K., Collisson, E., Cozen, A. E., Zerbino, D., Wilks, C., Craft, B., Spellman, P., Penny, R., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Gastier-Foster, J. M., Bowen, J., Ramirez, N. C., Black, A., Pyatt, R., Wise, L., White, P., Bertagnolli, M., Brown, J., Chan, T. A., Chu, G. C., Czerwinski, C., Denstman, F., Dhir, R., Dörner, A., Fuchs, C. S., Guillem, J. G., Iacocca, M., Juhl, H., Kaufman, A., Iii, B. K., Van Le, X., Mariano, M. C., Medina, E. N., Meyers, M., Nash, G. M., Paty, P. B., Petrelli, N., Rabeno, B., Richards, W. G., Solit, D., Swanson, P., Temple, L., Tepper, J. E., Thorp, R., Vakiani, E., Weiser, M. R., Willis, J. E., Witkin, G., Zeng, Z., Zinner, M. J., Zornig, C., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Ayala, B., Backus, M., Walton, J., Whitmore, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Shaw, K. R. M., Dillon, L. A. L., Buetow, K., Davidsen, T., Demchok, J. A., Eley, G., Ferguson, M., Fielding, P., Schaefer, C., Sheth, M., Yang, L., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J. & Thomson., E., Jul 19 2012, In: Nature. 487, 7407, p. 330-337 8 p.

    Research output: Contribution to journalArticlepeer-review

    5038 Scopus citations
  • Comprehensive molecular portraits of human breast tumours

    Koboldt, D. C., Fulton, R. S., McLellan, M. D., Schmidt, H., Kalicki-Veizer, J., McMichael, J. F., Fulton, L. L., Dooling, D. J., Ding, L., Mardis, E. R., Wilson, R. K., Ally, A., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H. J. E., Coope, R. J. N. & 323 others, Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Pleasance, E., Robertson, A. G., Schein, J. E., Shafiei, A., Sipahimalani, P., Slobodan, J. R., Stoll, D., Tam, A., Thiessen, N., Varhol, R. J., Wye, N., Zeng, T., Zhao, Y., Birol, I., Jones, S. J. M., Marra, M. A., Cherniack, A. D., Saksena, G., Onofrio, R. C., Pho, N. H., Carter, S. L., Schumacher, S. E., Tabak, B., Hernandez, B., Gentry, J., Nguyen, H., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Getz, G., Gabriel, S. B., Meyerson, M., Chin, L., Kucherlapati, R., Hoadley, K. A., Auman, J. T., Fan, C., Turman, Y. J., Shi, Y., Li, L., Topal, M. D., He, X., Chao, H. H., Prat, A., Silva, G. O., Iglesia, M. D., Zhao, W., Usary, J., Berg, J. S., Adams, M., Booker, J., Wu, J., Gulabani, A., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Mose, L. E., Jefferys, S. R., Balu, S., Parker, J. S., Hayes, D. N., Perou, C. M., Malik, S., Mahurkar, S., Shen, H., Weisenberger, D. J., Triche, T., Lai, P. H., Bootwalla, M. S., Maglinte, D. T., Berman, B. P., Van Den Berg, D. J., Baylin, S. B., Laird, P. W., Creighton, C. J., Donehower, L. A., Noble, M., Voet, D., Gehlenborg, N., Di Cara, D., Zhang, J., Zhang, H., Wu, C. J., Yingchun Liu, S., Lawrence, M. S., Zou, L., Sivachenko, A., Lin, P., Stojanov, P., Jing, R., Cho, J., Sinha, R., Park, R. W., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Park, P. J., Reynolds, S., Kreisberg, R. B., Bernard, B., Bressler, R., Erkkila, T., Lin, J., Thorsson, V., Zhang, W., Shmulevich, I., Ciriello, G., Weinhold, N., Schultz, N., Gao, J., Cerami, E., Gross, B., Jacobsen, A., Sinha, R., Aksoy, B. A., Antipin, Y., Reva, B., Shen, R., Taylor, B. S., Ladanyi, M., Sander, C., Anur, P., Spellman, P. T., Lu, Y., Liu, W., Verhaak, R. R. G., Mills, G. B., Akbani, R., Zhang, N., Broom, B. M., Casasent, T. D., Wakefield, C., Unruh, A. K., Baggerly, K., Coombes, K., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Zhu, J., Szeto, C. C., Scott, G. K., Yau, C., Paull, E. O., Carlin, D., Wong, C., Sokolov, A., Thusberg, J., Mooney, S., Ng, S., Goldstein, T. C., Ellrott, K., Grifford, M., Wilks, C., Ma, S., Craft, B., Yan, C., Hu, Y., Meerzaman, D., Gastier-Foster, J. M., Bowen, J., Ramirez, N. C., Black, A. D., Pyatt, R. E., White, P., Zmuda, E. J., Frick, J., Lichtenberg, T. M., Brookens, R., George, M. M., Gerken, M. A., Harper, H. A., Leraas, K. M., Wise, L. J., Tabler, T. R., McAllister, C., Barr, T., Hart-Kothari, M., Tarvin, K., Saller, C., Sandusky, G., Mitchell, C., Iacocca, M. V., Brown, J., Rabeno, B., Czerwinski, C., Petrelli, N., Dolzhansky, O., Abramov, M., Voronina, O., Potapova, O., Marks, J. R., Suchorska, W. M., Murawa, D., Kycler, W., Ibbs, M., Korski, K., Spychała, A., Murawa, P., Brzeziński, J. J., Perz, H., Łaźniak, R., Teresiak, M., Tatka, H., Leporowska, E., Bogusz-Czerniewicz, M., Malicki, J., Mackiewicz, A., Wiznerowicz, M., Van Le, X., Kohl, B., Viet Tien, N., Thorp, R., Van Bang, N., Sussman, H., Phu, B. D., Hajek, R., Hung, N. P., Phuong, T. V. T., Thang, H. Q., Khan, K. Z., Penny, R., Mallery, D., Curley, E., Shelton, C., Yena, P., Ingle, J. N., Couch, F. J., Lingle, W. L., King, T. A., Gonzalez-Angulo, A. M., Dyer, M. D., Liu, S., Meng, X., Patangan, M., Waldman, F., Stöppler, H., Rathmell, W. K., Thorne, L., Huang, M., Boice, L., Hill, A., Morrison, C., Gaudioso, C., Bshara, W., Daily, K., Egea, S. C., Pegram, M. D., Gomez-Fernandez, C., Dhir, R., Bhargava, R., Brufsky, A., Shriver, C. D., Hooke, J. A., Campbell, J. L., Mural, R. J., Hu, H., Somiari, S., Larson, C., Deyarmin, B., Kvecher, L., Kovatich, A. J., Ellis, M. J., Stricker, T., White, K., Olopade, O., Luo, C., Chen, Y., Bose, R., Chang, L. W., Beck, A. H., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Chu, A., Kothiyal, P., Wang, Z., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J. A., Shaw, K. R. M., Yang, L., Eley, G., Ferguson, M. L., Tarnuzzer, R. W., Zhang, J., Dillon, L. A. L., Buetow, K., Fielding, P., Ozenberger, B. A., Guyer, M. S., Sofia, H. J. & Palchik, J. D., Oct 4 2012, In: Nature. 490, 7418, p. 61-70 10 p.

    Research output: Contribution to journalArticlepeer-review

    7059 Scopus citations