Paul Spellman

Professor

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

2013
1778 Citations (Scopus)

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N., Collisson, E. A., Mills, G., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Sander, C., Stuart, J. M., Chang, K., Creighton, C. J., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chu, A., Chuah, E. & 316 others, Chun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T., Oct 2013, In : Nature Genetics. 45, 10, p. 1113-1120 8 p.

Research output: Contribution to journalArticle

Atlases
Genome
Neoplasms
Epigenomics
RNA
1664 Citations (Scopus)

The somatic genomic landscape of glioblastoma

TCGA Research Network, Oct 10 2013, In : Cell. 155, 2

Research output: Contribution to journalArticle

Glioblastoma
Tumors
Telomerase
Biomarkers
Neoplasms
2012
132 Citations (Scopus)

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., Heiser, L., Charles, R. P., Rabinovich, B. A., Hann, B., Dankort, D., Spellman, P., Phillips, W. A., Gray, J. & McMahon, M., Aug 2012, In : Cancer Discovery. 2, 8, p. 685-693 9 p.

Research output: Contribution to journalArticle

Adenocarcinoma
Maintenance
Cell Line
Mutation
1-Phosphatidylinositol 4-Kinase
16 Citations (Scopus)

ATM Suppresses SATB1-Induced Malignant Progression in Breast Epithelial Cells

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

Research output: Contribution to journalArticle

Automatic teller machines
breasts
Breast
epithelial cells
Epithelial Cells
8 Citations (Scopus)

Batch-invariant nuclear segmentation in whole mount histology sections

Chang, H., Loss, L. A., Spellman, P., Borowsky, A. & Parvin, B., 2012, Proceedings - International Symposium on Biomedical Imaging. p. 856-859 4 p. 6235683

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

Histology
Atlases
Tumors
Neoplasms
Color
59 Citations (Scopus)

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

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

Research output: Contribution to journalArticle

Bayesian inference
Network Topology
Cancer
Cells
Topology
3687 Citations (Scopus)

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 journalArticle

Rectal Neoplasms
Colonic Neoplasms
Colorectal Neoplasms
Mutation
Genome
5254 Citations (Scopus)

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., Lu, Y., Liu, W., Verhaak, R. R. G., Mills, G., 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 journalArticle

Breast Neoplasms
Mutation
Exome
Protein Array Analysis
p53 Genes
42 Citations (Scopus)

Cross-platform pathway-based analysis identifies markers of response to the PARP inhibitor olaparib

Daemen, A., Wolf, D. M., Korkola, J., Griffith, O. L., Frankum, J. R., Brough, R., Jakkula, L. R., Wang, N. J., Natrajan, R., Reis-Filho, J. S., Lord, C. J., Ashworth, A., Spellman, P., Gray, J. & Van'T Veer, L. J., Sep 2012, In : Breast Cancer Research and Treatment. 135, 2, p. 505-517 13 p.

Research output: Contribution to journalArticle

DNA Repair
Cell Line
Genes
Breast Neoplasms
BRCA1 Gene
12 Citations (Scopus)

Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: Field cancerization or contaminating tumor cells?

Sadanandam, A., Lal, A., Benz, S. C., Eppenberger-Castori, S., Scott, G., Gray, J., Spellman, P., Waldman, F. & Benz, C. C., Dec 2012, In : Breast Cancer Research and Treatment. 136, 3, p. 693-703 11 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Neoplasms
Breast
Segmental Mastectomy
erbB-2 Genes
76 Citations (Scopus)

Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma

Creighton, C. J., Hernandez-Herrera, A., Jacobsen, A., Levine, D. A., Mankoo, P., Schultz, N., Du, Y., Zhang, Y., Larsson, E., Sheridan, R., Xiao, W., Spellman, P., Getz, G., Wheeler, D. A., Perou, C. M., Gibbs, R. A., Sander, C., Hayes, D. N. & Gunaratne, P. H., Mar 29 2012, In : PLoS One. 7, 3, e34546.

Research output: Contribution to journalArticle

MicroRNAs
microRNA
Gene expression
carcinoma
Carcinoma
13 Citations (Scopus)

Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology

Hill, S. M., Neve, R. M., Bayani, N., Kuo, W. L., Ziyad, S., Spellman, P., Gray, J. & Mukherjee, S., May 11 2012, In : BMC Bioinformatics. 13, 1, 94.

Research output: Contribution to journalArticle

Empirical Bayes
Variable Selection
Biology
Cancer
Specifications
23 Citations (Scopus)

Learning invariant features of tumor signatures

Le, Q. V., Han, J., Gray, J., Spellman, P., Borowsky, A. & Parvin, B., 2012, Proceedings - International Symposium on Biomedical Imaging. p. 302-305 4 p. 6235544

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

Tumors
Learning
Tissue
Network layers
Neoplasms
3 Citations (Scopus)

Molecular bases of morphometric composition in Glioblastoma multiforme

Han, J., Chang, H., Fontenay, G. V., Spellman, P., Borowsky, A. & Parvin, B., 2012, Proceedings - International Symposium on Biomedical Imaging. p. 1631-1634 4 p. 6235889

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

Base Composition
Glioblastoma
Genes
Histology
Chemical analysis
14 Citations (Scopus)

Multireference level set for the characterization of nuclear morphology in glioblastoma multiforme

Chang, H., Han, J., Spellman, P. & Parvin, B., 2012, In : IEEE Transactions on Biomedical Engineering. 59, 12, p. 3460-3467 8 p., 6298001.

Research output: Contribution to journalArticle

Tissue
Pixels
Histology
Tumors
256 Citations (Scopus)

Subtype and pathway specific responses to anticancer compounds in breast cancer

Heiser, L., Sadanandam, A., Kuo, W. L., Benz, S. C., Goldstein, T. C., Ng, S., Gibb, W. J., Wang, N. J., Ziyad, S., Tong, F., Bayani, N., Hu, Z., Billig, J. I., Dueregger, A., Lewis, S., Jakkula, L., Korkola, J., Durinck, S., Pepin, F., Guan, Y. & 23 others, Purdom, E., Neuvial, P., Bengtsson, H., Wood, K. W., Smith, P. G., Vassilev, L. T., Hennessy, B. T., Greshock, J., Bachman, K. E., Hardwicke, M. A., Park, J. W., Marton, L. J., Wolf, D. M., Collisson, E. A., Neve, R. M., Mills, G., Speed, T. P., Feiler, H., Richard, F. W., Haussler, D., Stuart, J. M., Gray, J. & Spellman, P., Feb 21 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 8, p. 2724-2729 6 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Cell Line
Pharmaceutical Preparations
Therapeutics
Neoplasms
16 Citations (Scopus)

Tackling formalin-fixed, paraffin-embedded tumor tissue with next-generation sequencing

Corless, C. & Spellman, P., Jan 2012, In : Cancer Discovery. 2, 1, p. 23-24 2 p.

Research output: Contribution to journalArticle

Paraffin
Formaldehyde
High-Throughput Nucleotide Sequencing
Neoplasms
Data Accuracy
28 Citations (Scopus)

Xenografts faithfully recapitulate breast cancer-specific gene expression patterns of parent primary breast tumors

Petrillo, L. A., Wolf, D. M., Kapoun, A. M., Wang, N. J., Barczak, A., Xiao, Y., Korkaya, H., Baehner, F., Lewicki, J., Wicha, M., Park, J. W., Spellman, P., Gray, J., Van'T Veer, L. & Esserman, L. J., Oct 2012, In : Breast Cancer Research and Treatment. 135, 3, p. 913-922 10 p.

Research output: Contribution to journalArticle

Neoplasm Genes
Heterografts
Breast Neoplasms
Gene Expression
Neoplasms
2011
13 Citations (Scopus)

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 journalArticle

Estrogen Receptors
Carrier Proteins
Genes
Gene Amplification
21 Citations (Scopus)

Comparison of sparse coding and kernel methods for histopathological classification of gliobastoma multiforme

Han, J., Chang, H., Loss, L., Zhang, K., Baehner, F. L., Gray, J., Spellman, P. & Parvin, B., 2011, Proceedings - International Symposium on Biomedical Imaging. p. 711-714 4 p. 5872505

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

Histology
Discriminant analysis
Glossaries
Restoration
Support vector machines
3579 Citations (Scopus)

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. & 277 others, Mills, G., 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., Getz, G., Verhaak, R. G. W., Carter, S. L., Mermel, C. H., Saksena, G., Nguyen, H., Onofrio, R. C., Lawrence, M. S., Hubbard, D., Gupta, S., Crenshaw, A., Ramos, A. H., Ardlie, K., 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., Spellman, P., 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., Feiler, H., Conboy, J. G., Gray, J., Feiler, H. S., Speed, T. P., Gray, J. W., Levine, D. A., 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., Getz, G., Voet, D., Saksena, G., Zhang, J., Zhang, H., Korkola, J., Heiser, L., Cibulskis, K., Hu, Z., Sivachenko, A., Jing, R., Park, R. W., Liu, Y., Park, P. J., Noble, M., Chin, L., Carter, H., Kim, D., Karchin, R., Spellman, P. T., Purdom, E., Neuvial, P., Bengtsson, H., Durinck, S., Han, J., Korkola, J. E., Heiser, L. M., Cho, R. J., Hu, Z., Parvin, B., Speed, T. P., Gray, J. W., Schultz, N., Cerami, E., Taylor, B. S., Olshen, A., Reva, B., Antipin, Y., Shen, R., Mankoo, P., Sheridan, R., Ciriello, G., Chang, W. K., Bernanke, J. A., Borsu, L., Levine, D. A., Ladanyi, M., Sander, C., 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., Hoadley, K. A., Du, Y., Balu, S., Hayes, D. N., Perou, C. M., Wilkerson, M. D., Zhang, N., Akbani, R., Baggerly, K. A., Yung, W. K., Mills, G. B., Weinstein, J. N., Penny, R., 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., Zhang, J., 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 journalArticle

Ovarian Neoplasms
Carcinoma
Neoplasms
MicroRNAs
Methylation
245 Citations (Scopus)

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., Spellman, P., 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 journalArticle

Notch Receptors
Squamous Cell Carcinoma
Lung
Skin
Mutation
32 Citations (Scopus)

Morphometic analysis of TCGA glioblastoma multiforme

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

Research output: Contribution to journalArticle

Atlases
Atlas
Glioblastoma
Cellularity
Tumors
60 Citations (Scopus)

Parent-specific copy number in paired tumor-normal studies using circular binary segmentation

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

Research output: Contribution to journalArticle

Tumors
Tumor
Segmentation
Loss of Heterozygosity
Glioblastoma
533 Citations (Scopus)

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., Ko, A. H., Olshen, A. B., Danenberg, K. L., Tempero, M. A., Spellman, P., Hanahan, D. & Gray, J., Apr 2011, In : Nature Medicine. 17, 4, p. 500-503 4 p.

Research output: Contribution to journalArticle

Tumors
Adenocarcinoma
Neoplasms
Therapeutics
Genes
137 Citations (Scopus)

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., Spellman, P. & Cho, R. J., Jun 29 2011, In : Cancer Discovery. 1, 2, p. 137-143 7 p.

Research output: Contribution to journalArticle

Dissection
Carcinogenesis
Neoplasms
Mutation
Oncogenes
12 Citations (Scopus)

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., Hylton, N. & Park, C. C., Apr 2011, In : Integrative Biology. 3, 4, p. 490-496 7 p.

Research output: Contribution to journalArticle

Magnetic resonance
Breast
Magnetic Resonance Imaging
Tissue
Breast Neoplasms

Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI (Integrative Biology (2011) 3 (910-921) DOI: 10.1039/C1IB00043H)

Nabavizadeh, N., Klifa, C., Newitt, D., Lu, Y., Chen, Y. Y., Hsu, H., Fisher, C., Tokuyasu, T., Olshen, A. B., Spellman, P., Gray, J., Hylton, N. & Park, C. C., Dec 2011, In : Integrative Biology. 3, 12, p. 1233 1 p.

Research output: Contribution to journalArticle

Breast
Breast Neoplasms
11 Citations (Scopus)

Unifying gene expression measures from multiple platforms using factor analysis

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

Research output: Contribution to journalArticle

Factor analysis
Gene expression
Statistical Factor Analysis
Genes
Atlases
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
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
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
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