Paul Spellman

Professor

  • 66935 Citations
  • 61 h-Index
1992 …2021
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Research Output 1998 2019

1998
12298 Citations (Scopus)

Cluster analysis and display of genome-wide expression patterns

Eisen, M. B., Spellman, P., 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 journalArticle

Cluster Analysis
Genome
Genes
Gene Expression
Saccharomycetales
3655 Citations (Scopus)

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

Spellman, P., 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 journalArticle

cdc Genes
Saccharomyces cerevisiae
Cell Cycle
Yeasts
Cyclin G1
2000
3335 Citations (Scopus)

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

Gasch, A. P., Spellman, P., 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 journalArticle

Yeasts
Diamide
Vitamin K 3
Dithiothreitol
Reducing Agents
1719 Citations (Scopus)

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 journalArticle

Gene Expression
Cell Line
Neoplasms
Tumor Cell Line
Antitumor Drug Screening Assays
271 Citations (Scopus)

Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth

Gefeng, Z., Spellman, P., 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 journalArticle

cdc Genes
Yeasts
Growth
Cell Cycle
Transcription Factors
2001
16 Citations (Scopus)

Ceramic capillaries for use in microarray fabrication

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

Research output: Contribution to journalArticle

Ceramics
Printing
Steel
Stainless Steel
Oligonucleotide Array Sequence Analysis
527 Citations (Scopus)

Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays

De Gregorio, E., Spellman, P., 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 journalArticle

Oligonucleotide Array Sequence Analysis
Drosophila
Genome
Genes
Infection
3018 Citations (Scopus)

Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C. A., Causton, H. C., Gaasterland, T., Glenisson, P., Holstege, F. C. P., Kim, I. F., Markowitz, V., Matese, J. C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S. & 4 others, Stewart, J., Taylor, R., Vilo, J. & Vingron, M., 2001, In : Nature Genetics. 29, 4, p. 365-371 7 p.

Research output: Contribution to journalArticle

Gene Expression
Microarray Analysis
Databases
1 Citation (Scopus)

The future of publishing microarray data.

Spellman, P., Dec 2001, In : Briefings in Bioinformatics. 2, 4, p. 316-318 3 p.

Research output: Contribution to journalArticle

Nucleic Acid Databases
Microarrays
Oligonucleotide Array Sequence Analysis
2002
15 Citations (Scopus)

A guide to microarray experiments - An open letter to the scientific journals [1]

Ball, C. A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H. C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert, C. J., Stewart, J. E., Taylor, R., Brazma, A. & Quackenbush, J., Sep 28 2002, In : Lancet. 360, 9338, p. 1019 1 p.

Research output: Contribution to journalArticle

Protein Array Analysis
Oligonucleotide Array Sequence Analysis
Publications
340 Citations (Scopus)

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

Spellman, P., 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

Research output: Contribution to journalArticle

gene expression
Language
Gene Expression
Biota
information exchange
393 Citations (Scopus)

Evidence for large domains of similarly expressed genes in the Drosophila genome

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

Research output: Contribution to journalArticle

Drosophila
Genes
Genome
genome
genes
136 Citations (Scopus)

Standards for microarray data [1]

Ball, C. A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H. C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert, C. J., Stewart, J. E., Taylor, R., Brazma, A. & Quackenbush, J., Oct 18 2002, In : Science. 298, 5593, p. 539 1 p.

Research output: Contribution to journalArticle

Nucleic Acid Databases
Gene Expression Profiling
Oligonucleotide Array Sequence Analysis
Computational Biology
Research Design
498 Citations (Scopus)

The Toll and Imd pathways are the major regulators of the immune response in Drosophila

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

Research output: Contribution to journalArticle

Drosophila
Genes
Microarrays
Microbial Genes
Infection
38 Citations (Scopus)

The underlying principles of scientific publication.

Ball, C. A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H. C., Cavalieri, D., Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert, C. J., Stewart, J. E., Taylor, R., Brazma, A. & Quackenbush, J., Nov 2002, In : Bioinformatics (Oxford, England). 18, 11, p. 1409 1 p.

Research output: Contribution to journalArticle

Cooperative Behavior
Computational Biology
Nucleic Acid Databases
Gene Expression Profiling
Oligonucleotide Array Sequence Analysis
2003
56 Citations (Scopus)

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

Pile, L. A., Spellman, P., 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 journalArticle

Sin3 Histone Deacetylase and Corepressor Complex
Gene encoding
Mitochondrial Proteins
Energy Metabolism
Genes
2004
10 Citations (Scopus)

Final words: Cell age and cell cycle are unlinked

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

Research output: Contribution to journalArticle

Cell Cycle
Cells
Batch Cell Culture Techniques
Cell culture
Conservation
22 Citations (Scopus)

Microarray data standards: An open letter

Ball, C., Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J. C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, S. A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J. & Winergarden, N., Aug 2004, In : Environmental Health Perspectives. 112, 12

Research output: Contribution to journalArticle

Toxicogenetics
Genetic Databases
International Cooperation
Research Ethics Committees
Oligonucleotide Array Sequence Analysis
19 Citations (Scopus)

Reply: Whole-culture synchronization - Effective tools for cell cycle studies

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

Research output: Contribution to journalArticle

Cell culture
Cell Cycle
Synchronization
Cells
Age Distribution
96 Citations (Scopus)

Submission of microarray data to public repositories

Ball, C. A., Brazma, A., Causton, H., Chervitz, S., Edgar, R., Hingamp, P., Matese, J. C., Parkinson, H., Quackenbush, J., Ringwald, M., Sansone, S. A., Sherlock, G., Spellman, P., Stoeckert, C., Tateno, Y., Taylor, R., White, J. & Winegarden, N., Sep 2004, In : PLoS Biology. 2, 9

Research output: Contribution to journalArticle

Database Management Systems
Software Design
Genetic Databases
Information Storage and Retrieval
information systems
2005
4 Citations (Scopus)

A status report on mage

Spellman, P., Sep 1 2005, In : Bioinformatics. 21, 17, p. 3459-3460 2 p.

Research output: Contribution to journalArticle

Program documentation
Organizational Objectives
User-Computer Interface
Genetic Databases
Information dissemination
245 Citations (Scopus)

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 journalArticle

Pseudomonas Infections
Drosophila
Pseudomonas
Larva
Genes
2006
1978 Citations (Scopus)

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

Neve, R. M., Chin, K-Y., Fridlyand, J., Yeh, J., Baehner, F. L., Fevr, T., Clark, L., Bayani, N., Coppe, J. P., Tong, F., Speed, T., Spellman, P., 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., Dec 2006, In : Cancer Cell. 10, 6, p. 515-527 13 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Cell Line
Neoplasms
Epigenomics
Genes
143 Citations (Scopus)

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Rayner, T. F., Rocca-Serra, P., Spellman, P., 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 journalArticle

Spreadsheet
Spreadsheets
Microarrays
Microarray Data
Computational Biology
25 Citations (Scopus)

FuGE: Functional Genomics Experiment Object Model

Jones, A. R., Pizarro, A., Spellman, P. & Miller, M., 2006, In : OMICS A Journal of Integrative Biology. 10, 2, p. 179-184 6 p.

Research output: Contribution to journalArticle

Genomics
Experiments
Software
Workflow
Microarrays
909 Citations (Scopus)

Genomic and transcriptional aberrations linked to breast cancer pathophysiologies

Chin, K-Y., DeVries, S., Fridlyand, J., Spellman, P., 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., Dec 2006, In : Cancer Cell. 10, 6, p. 529-541 13 p.

Research output: Contribution to journalArticle

I-kappa B Kinase
Breast Neoplasms
Neoplasms
Genome
RNA
49 Citations (Scopus)

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 journalArticle

MAP Kinase Kinase Kinases
Drosophila
Wounds and Injuries
Genes
Paraquat
12 Citations (Scopus)

Top-down standards will not serve systems biology [1]

Quackenbush, J., Stoeckert, C., Ball, C., Brazma, A., Gentleman, R., Huber, W., Irizarry, R., Salit, M., Sherlock, G., Spellman, P. & Winegarden, N., Mar 2 2006, In : Nature. 440, 7080, p. 24 1 p.

Research output: Contribution to journalArticle

Systems Biology
2007
46 Citations (Scopus)

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., Chin, K-Y., Esserman, L., Gray, J., Spellman, P. & Faham, M., Nov 20 2007, In : Genome Biology. 8, 11, R246.

Research output: Contribution to journalArticle

Molecular Probes
allele
Alleles
probe
alleles

Spectral decomposition of signaling networks

Parvin, B., Ghosh, N., Heiser, L., Knapp, M., Talcott, C., Laderoute, K., Gray, J. & Spellman, P., 2007, 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology, CIBCB 2007. p. 76-81 6 p. 4221207

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Decomposition
Proteins
Petri nets
Directed graphs
Cells
75 Citations (Scopus)

The Functional Genomics Experiment model (FuGE): An extensible framework for standards in functional genomics

Jones, A. R., Miller, M., Aebersold, R., Apweiler, R., Ball, C. A., Brazma, A., DeGreef, J., Hardy, N., Hermjakob, H., Hubbard, S. J., Hussey, P., Igra, M., Jenkins, H., Julian, R. K., Laursen, K., Oliver, S. G., Paton, N. W., Sansone, S. A., Sarkans, U., Stoeckert, C. J. & 5 others, Taylor, C. F., Whetzel, P. L., White, J. A., Spellman, P. & Pizarro, A., Oct 2007, In : Nature Biotechnology. 25, 10, p. 1127-1133 7 p.

Research output: Contribution to journalArticle

Genomics
Experiments
Workflow
Metabolomics
Systems Biology
577 Citations (Scopus)

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., Lorenz, K., Lee, E. H., Barcellos-Hoff, M. H., Petersen, O. W., Gray, J. & Bissell, M. J., Jun 2007, In : Molecular Oncology. 1, 1, p. 84-96 13 p.

Research output: Contribution to journalArticle

Transcriptome
Breast Neoplasms
Cell Line
Cell Culture Techniques
Cultured Tumor Cells
2008
92 Citations (Scopus)

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., 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 journalArticle

Oncogenes
Ovarian Neoplasms
Carcinoma
Genes
Histology

Cancer Genomics

Spellman, P., Costello, J. F. & Gray, J., 2008, The Molecular Basis of Cancer. Elsevier Inc., p. 267-282 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Genomics
Neoplasms
4455 Citations (Scopus)

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., 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., Speed, T. P., Gray, J., 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 journalArticle

Glioblastoma
Atlases
Genes
DNA Methylation
Neoplasms
220 Citations (Scopus)

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., 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 journalArticle

Epigenomics
Carcinoma
Mutation
Loss of Heterozygosity
Ovarian Neoplasms
2009
30 Citations (Scopus)

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 journalArticle

Genes
Genome
Estimate
Microarrays
Atlases
24 Citations (Scopus)

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., Sadanandam, A., Fontenay, G. V., Hu, Z., Wang, N. J., Bayani, N., Feiler, H., Neve, R. M., Wyrobek, A. J., Spellman, P., Marton, L. J. & Gray, J., Dec 14 2009, In : BMC Medicine. 7, 77.

Research output: Contribution to journalArticle

Polyamines
Systems Analysis
Breast Neoplasms
Cell Line
Breast
265 Citations (Scopus)

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

Research output: Contribution to journalArticle

1-Phosphatidylinositol 4-Kinase
Mitogen-Activated Protein Kinase Kinases
Extracellular Signal-Regulated MAP Kinases
Phosphotransferases
Breast Neoplasms
83 Citations (Scopus)

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., Gray, J., Spellman, P., 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 journalArticle

Gene Dosage
Glioblastoma
Heterografts
Messenger RNA
Neoplasms
45 Citations (Scopus)

GenomeGraphs: integrated genomic data visualization with R.

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

Research output: Contribution to journalArticle

Data visualization
Data Visualization
Software packages
Genomics
Visualization
69 Citations (Scopus)

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., Gray, J., Mills, G. & Faham, M., 2009, In : BMC Medical Genomics. 2, 8.

Research output: Contribution to journalArticle

Molecular Probes
Paraffin
Formaldehyde
Genotype
DNA
51 Citations (Scopus)

Integrated analysis of breast cancer cell lines reveals unique signaling pathways

Heiser, L., 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. & Spellman, P., Mar 25 2009, In : Genome Biology. 10, 3, R31.

Research output: Contribution to journalArticle

breast neoplasms
cancer
cell lines
Breast Neoplasms
Cell Line
532 Citations (Scopus)

Mapping identifiers for the integration of genomic datasets with the R/ Bioconductor package biomaRt

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

Research output: Contribution to journalArticle

Computational Biology
DNA Copy Number Variations
Databases
Bioinformatics
Proteins
16 Citations (Scopus)

Sparse combinatorial inference with an application in cancer biology

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

Research output: Contribution to journalArticle

Boolean functions
Boolean Functions
Biology
Cancer
Statistical Models
2010
84 Citations (Scopus)

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., Jul 2010, In : Molecular Cancer Research. 8, 7, p. 961-974 14 p.

Research output: Contribution to journalArticle

Alternative Splicing
Microarray Analysis
Exons
Breast Neoplasms
Protein Isoforms
27 Citations (Scopus)

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., 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 journalArticle

Methylation
Essential Genes
DNA Methylation
Genetic Promoter Regions
Base Pairing
3392 Citations (Scopus)

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. & 13 others, Hodgson, J. G., James, C. D., Sarkaria, J. N., Brennan, C., Kahn, A., Spellman, P., Wilson, R. K., Speed, T. P., Gray, J., 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 journalArticle

Glioblastoma
Gene Expression
Atlases
Genome
Mutation
1221 Citations (Scopus)

International network of cancer genome projects

Hudson, T. J., Anderson, W., Aretz, A., Barker, A. D., Bell, C., Bernabé, R. R., Bhan, M. K., Calvo, F., Eerola, I., Gerhard, D. S., Guttmacher, A., Guyer, M., Hemsley, F. M., Jennings, J. L., Kerr, D., Klatt, P., Kolar, P., Kusuda, J., Lane, D. P., Laplace, F. & 241 others, Lu, Y., Nettekoven, G., Ozenberger, B., Peterson, J., Rao, T. S., Remacle, J., Schafer, A. J., Shibata, T., Stratton, M. R., Vockley, J. G., Watanabe, K., Yang, H., Yuen, M. M. F., Knoppers, B. M., Bobrow, M., Cambon-Thomsen, A., Dressler, L. G., Dyke, S. O. M., Joly, Y., Kato, K., Kennedy, K. L., Nicolás, P., Parker, M. J., Rial-Sebbag, E., Romeo-Casabona, C. M., Shaw, K. M., Wallace, S., Wiesner, G. L., Zeps, N., Lichter, P., Biankin, A. V., Chabannon, C., Chin, L., Clément, B., Alava, E. D., Degos, F., Ferguson, M. L., Geary, P., Hayes, D. N., Johns, A. L., Kasprzyk, A., Nakagawa, H., Penny, R., Piris, M. A., Sarin, R., Scarpa, A., De Vijver, M. V., Futreal, P. A., Aburatani, H., Bayés, M., Bowtell, D. D. L., Campbel, P. J., Estivill, X., Grimmond, S. M., Gut, I., Hirst, M., López-Otý́n, C., Majumder, P., Marra, M., McPherson, J. D., Ning, Z., Puente, X. S., Ruan, Y., Stunnenberg, H. G., Swerdlow, H., Velculescu, V. E., Wilson, R. K., Xue, H. H., Yang, L., Spellman, P., Bader, G. D., Boutros, P. C., Flicek, P., Getz, G., Guigó, R., Guo, G., Haussler, D., Heath, S., Hubbard, T. J., Jiang, T., Jones, S. M., Li, Q., López-Bigas, N., Luo, R., Muthuswamy, L., Ouellette, B. F. F., Pearson, J. V., Quesada, V., Raphael, B. J., Sander, C., Speed, T. P., Stein, L. D., Stuart, J. M., Teague, J. W., Totoki, Y., Tsunoda, T., Valencia, A., Wheeler, D. A., Wu, H., Zhao, S., Zhou, G., Lathrop, M., Thomas, G., Yoshida, T., Axton, M., Gunter, C., Miller, L. J., Zhang, J., Haider, S. A., Wang, J., Yung, C. K., Cross, A., Liang, Y., Gnaneshan, S., Guberman, J., Hsu, J., Chalmers, D. R. C., Hasel, K. W., Kaan, T. S. H., Lowrance, W. W., Masui, T., Rodriguez, L. L., Vergely, C., Bowtel, D. D. L., Cloonan, N., DeFazio, A., Eshleman, J. R., Etemadmoghadam, D., Gardiner, B. A., Kench, J. G., Sutherland, R. L., Tempero, M. A., Waddell, N. J., Wilson, P. J., Gallinger, S., Tsao, M. S., Shaw, P. A., Petersen, G. M., Mukhopadhyay, D., DePinho, R. A., Thayer, S., Shazand, K., Beck, T., Sam, M., Timms, L., Ballin, V., Ji, J., Zhang, X., Chen, F., Hu, X., Yang, Q., Tian, G., Zhang, L., Xing, X., Li, X., Zhu, Z., Yu, Y., Yu, J., Tost, J., Brennan, P., Holcatova, I., Zaridze, D., Brazma, A., Egevad, L., Prokhortchouk, E., Banks, R. E., Uhlén, M., Viksna, J., Ponten, F., Skryabin, K., Futrea, P. A., Birney, E., Borg, A., Børresen-Dale, A. L., Caldas, C., Foekens, J. A., Martin, S., Reis-Filho, J. S., Richardson, A. L., Sotiriou, C., Veer, L. V. T., Birnbaum, D., Blanche, H., Boucher, P., Boyault, S., Masson-Jacquemier, J. D., Pauporté, I., Pivot, X., Vincent-Salomon, A., Tabone, E., Theillet, C., Treilleux, I., Bioulac-Sage, P., Decaens, T., OiseDegos, F., Franco, D., Gut, M., Samuel, D., Zucman-Rossi, J., Eils, R., Brors, B., Korbe, J. O., Korshunov, A., Landgraf, P., Lehrach, H., Pfister, S., Radlwimmer, B., Reifenberger, G., Taylor, M. D., Kalle, C. V., Majumder, P. P., Rao, T. S., Pederzoli, P., Lawlor, R. T., Delledonne, M., Bardelli, A., Gress, T., Klimstra, D., Zamboni, G., Nakamura, Y., Miyano, S., Fujimoto, A., Campo, E., Sanjosé, S. D., Montserrat, E., González-Dý́az, M., Jares, P., Himmelbaue, H., Bea, S., Aparicio, S., Easton, D. F., Collins, F. S., Compton, C. C., Lander, E. S., Burke, W., Green, A. R., Hamilton, S. R., Kallioniemi, O. P., Ley, T. J., Liu, E. T. & Wainwright, B. J., Apr 15 2010, In : Nature. 464, 7291, p. 993-998 6 p.

Research output: Contribution to journalArticle

Genome
Neoplasms
Epigenomics
Mutation
Therapeutics
28 Citations (Scopus)

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., Faham, M., Spellman, P. & Parvin, B., Jun 4 2010, In : BMC Bioinformatics. 11, 305.

Research output: Contribution to journalArticle

Methylation
Breast Cancer
Genes
Cells
Breast Neoplasms