`DATE: February 2022
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`CURRICULUM VITAE
`OREGON HEALTH & SCIENCE UNIVERSITY
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`Paul T. Spellman, Ph.D.
`NAME
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`I. PRESENT POSITION AND ADDRESS
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`Academic Rank:
`Professor with Tenure
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`Department/Division:
`Molecular & Medical Genetics
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`Professional Address:
`2730 S. Moody Ave. Portland, OR 97201
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`E-Mail Address:
`spellmap@ohsu.edu
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`II. EDUCATION
`
`Undergraduate and Graduate (Include Year, Degree, and Institution):
`S.B., Biology, Massachusetts Institute of Technology, 1995
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`Ph.D., Genetics, Stanford University Medical School, 2000
`Dissertation: “Generating and Analyzing Genome Scale Data”
`
`Postgraduate (Include Year, Degree, and Institution):
`N/A
`
`Certification (Include Board, Number, Date, and Recertification):
`N/A
`
`Licenses (Include State, Date, Status, Number, and Renewal Date):
`N/A
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`III. PROFESSIONAL EXPERIENCE
`
`Academic (Include Year, Position, and Institution):
`Administrative (Include Year, Position, and Institution):
`1995 – 2000
`Graduate Student Research Assistant, Stanford University School of
`Medicine, Drs. David Botstein and Patrick O. Brown Advisors
`Post-doctoral Fellow, UC Berkeley, Department of Molecular and Cellular
`Biology, Gerald M. Rubin Advisor
` Scientist, Lawrence Berkeley Lab, Life Science Division
` Staff Scientist, Lawrence Berkeley Lab, Life Science Division
` Special Assistant to the Deputy Director of the National Cancer Institute
`Associate Professor, Oregon Health Sciences University, Department of
`Molecular and Medical Genetics
`
`2003 – 2007
`2007 – 2011
`2011
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`2011 – 2013
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`2000 – 2003
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`00001
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`EX1003
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`2012 – 2017
`2013 –
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`Proposed Program Leader for Quantitative Oncology Knight Cancer Institute
`Professor, Oregon Health and Sciences University, Department of Molecular
`and Medical Genetics
`Interim Director, Program in Computational Biology
`Seminar Director, Program in Molecular and Cellular Biology
`Program Leader for Quantitative Oncology, Knight Cancer Institute
`Co-Director, CEDAR Center
`Interim Director, Program in Computational Biology
`
`2013 – 2014
`2013 – 2015
`2017 –
`2017 –
`2018 – 2020
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`
`Other (Include Year, Position, and Institution):
`
`IV. HONORS & AWARDS
`2018
` Penny and Phil Knight Endowed Professorship in Cancer Research Innovation
`2020
` AACR Team Science Award: THE CANCER GENOME ATLAS (TCGA)
`PILOT PROJECT
`
`
`V. SCHOLARSHIP
`
`Area(s) of Research/Scholarly Interest: Cancer Genomics
`
`Grants and Contracts:
`
`Federal (Include Title, Source, PI, Amount Period, and % Effort, timeframe)
`
`Systems-Based Predictions of Responses to Cancer Therapy. NIH/NCI U54 CA112970.
`$250,000 Role: Project 1 Leader. (Gray, Joe W.) 50% effort. 09/30/04-08/31/10
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`NIH/NHGRI P41 G003619-01. Role: Project Leader. (Ball). 20% effort. 8/1/2005-7/31/2008
`
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`Development of cost effective sequence-based technologies to identify genome. Department of
`Energy DE-AC02-05CH11231. Role: Co-Principal Investigator (Pennachio) 5% effort. 10/1/05-
`9/30/07
`
`Development of RPPA data modules for caArray. National Cancer Institute Y1-CO-6120-01.
`135,000. Role: Spellman, Paul T. 10% effort. 09/19/06-07/31/09
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`Univ. of Calif., San Francisco (NIH/NCI Prime) U24 CA126477 Role: Scientist (Fisher, Susan
`J.) 20% effort. 09/26/06-08/31/11
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`The Berkeley Cancer Genome Center NIH/NCI. U24 CA126551 $1,250,000 CoPI (Gray, Joe
`W.) 30% effort 09/28/06-08/31/10
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`
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`SPORE in Breast Cancer Univ. of Calif., San Francisco (NIH/NCI Prime) P50 CA058207.
`$53,820. Role: Co-investigator (van’t Veer, L). 8% effort. 09/30/07-11/30/12
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`TCGA Data Analysis Center at Berkeley NIH/NCI U24 CA143799. $537,280. Role: PI
`(Spellman, Paul T. et al.) 20% effort. 09/30/09-07/31/14
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`Model-based Predictions of Responses to RTK Pathway Therapies. NIH/NCI. U54 CA112970
`$520,700 Role: Project 1 PI and Data & Model Repository Core PI. (Gray, Joe W.) 17% effort.
`09/1/10-02/28/15.
`
`Enhancing the Breadth and Efficacy of Therapeutic Vaccines for Breast Cancer. DoD
`BC100597P1. $383,443. Role: PI (Spellman, Paul T.) 30% effort 9/30/11-9/29/15
`
`Complications During Long-duration Space Missions NSBRI/Baylor CA04201. $232,073. (PI:
`Lindner) 0.36 calendar months 06/01/15-05/31/17.
`
`
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`Extrinsic Perturbations of Cell Physiology and Associated Regulatory Networks NIH/NHGRI
`U54HG008100. $1,396,812. (PI: Gray). 0.6 calendar months 09/10/14-06/30/20
`
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`Intratumor heterogeneity underlying treatment resistance in HER2+ breast tumors NIH/NCI
`U01CA195469). $165,999. (PI: Gray, Michor, Polyak, Spellman – Multip-PI) 0.84 calendar
`months 06/01/15-05/31/20
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`Control of genetic and epigenetic instabilities by lincRNA genes NIH/NIHMS R01GM114162
`$192,500. (PI:Thayer) 0.6 calendar months 09/17/15-06/30/19
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`Integrative approach to heterogeneity in breast metastasis. UCSF/NIH U01CA199315
`$166,414. (PI: Werb and Spellman) 1.8 calendar months 06/01/16-05/31/21
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`OHSU Center for Specialized Data Analysis as part of the GDAN NIH/NCI U24CA210957).
`$273,900. (PI: Spellman / Margolin – Multi-PI 2.4 calendar months 09/13/16-08/31/21
`
`Molecular Changes Associated with Initial Steps of Breast Cancer Metastasis for Risk
`Stratification and Therapy Development DOD/BCRP BC151431P1 $148,059. (PI: Spellman).
`0.48 calendar months 09/30/16-08/31/19
`
`Quantitative Oncology NIH/NCI 5P30CA069533. $190,837 total cost. (PI Spellman). 0.9
`calendar months 07/01/17-06/30/22
`
`Evaluation of Population Based Testing for HBOC and Lynch Syndromes $4,627,812 direct
`costs. (MPI Spellman / Shannon). 1.2 cal. 06/10/2020-05/31/2025
`
`OHSU Center for Specialized Data Analysis as part of the GDAN U24CA264007. $369,600/year
`total cost. PI: Spellman / Ellrott – Multi-PI 2.4 calendar months 09/01/21-08/31/26
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`State and Local (Include Title, Source, PI, Amount Period, and % Effort)
`N/A
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`Other Support (Include Title, Source, PI, Amount Period, and % Effort)
`
`Molecular Predictors of Drug Response in Breast Cancer SmithKline Beecham Corporation
`Role: Scientist (Gray, Joe W.) 5% effort 01/27/06-01/26/10
`
`MIPS Analysis The Buck Institute Role: PI (Spellman, Paul T.) 2% effort. 05/01/07-04/30/08
`
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`An Integrated Approach to Targeting Breast Cancer Molecular Subtypes and Their 'Resistance'
`Phenotypes University of California at Los Angeles (American Association for Cancer
`Research/Stand Up To Cancer, Prime) SU2C-AACR-DT0409. $915,164 Role: Co-Investigator
`10% effort (PI: Slamon, Dennis J. and Gray, Joe W.) 10/01/09 – 09/30/12
`
`The development of the ovarian cancer genome Anna Fuller Fund $100,000. Role: PI (Spellman,
`Paul T.) 0% effort 03/01/12-02/28/14
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`Identification of breast cancer-specific antigen targets for development of anti-cancer vaccines
`National Philanthropic Trust National Breast Cancer Coalition – Artemis Project. $129,714.
`Role: PI 10% effort (Spellman, Paul T.) 8/1/12-7/31/13
`
`Restoring hormone sensitivity of late recurrences in breast cancer patients. Promise Grant
`(O’Malley, Bert W) Susan G. Komen Foundation / Baylor College of Medicine. $134,838.
`Role: Co-investigator (Gray) 2% effort 09/13/12-09/12/17
`
`Accelerator-Rich Architectures with Applications to Healthcare Intel/UCLA. $25,974 (PI: Cong)
`0.6 calendar months 01/01/14-08/31/17
`
`ctDNA profiling to detect early recurrence Prospect Creek Foundation $238,096. (PI: Gray) 0.6
`calendar months 10/01/15-09/30/17
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`
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`OHSU Center for Specialized Data Analysis as part of the GDAN. NIH/NCI U24CA210957.
`$273,900 (Spellman/Margolin) 2.4 cal 09/13/16-08/31/21
`
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`Molecular Changes Associated with Initial Steps of Breast Cancer Metastasis for Risk
`Stratification and Therapy Development DOD/U.S. Army Medical Research & Materiel
`Command BC151431P1.$149,691 (Spellman) .48 cal mos. 09/30/16-09/29/19
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`Integrative approach to heterogeneity in breast metastasis. NIH/NCI U01CA199315 $166,414.
`(Werb / Spellman – Multi-PI) 1.8 cal mos. 06/01/16-05/31/21
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`OHSU Knight Cancer Institute NIH/NCI P30CA069533 $1,500,000. (Druker) 0.9 cal. Mos.
`07/01/17-06/30/22.
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`Intratumor heterogeneity underlying treatment resistance in HER2+ breast tumors NIH/NCI
`U01CA195469 $165,999 (Gray, Michor, Polyak, Spellman – multi-PI) 0.84 cal. mos. 06/01/15-
`05/31/20
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`ctDNA profiling to detect early recurrence Prospect Creek Foundation $158,730. (Gray) 0.6 cal.
`mos. 10/01/15-09/30/18
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`Widespread Testing for Cancer Risk Syndromes Knight Cancer Institute $311,373. (Spellman).
`09/01/17-08/31/18
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`
`Publications/Creative Work:
`Peer-reviewed
`1. P.T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O.
`Brown, D. Botstein and B. Futcher. Comprehensive identification of cell cycle-regulated
`genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular
`Biology of the Cell. 9: 3273-97. 1998
`2. M. B. Eisen, P.T. Spellman, P. O. Brown and D. Botstein. Cluster analysis and display
`of genome-wide expression patterns. Proceedings of the National Academy of Sciences,
`U.S.A. 95: 14863-8. 1998
`3. G. Zhu, P.T. Spellman, T. Volpe, P. O. Brown, D. Botstein, T. N. Davis and B. Futcher.
`Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature. 406:
`90-4. 2000
`4. D. T. Ross, U. Scherf, M. B. Eisen, C. M. Perou, C. Rees, P. Spellman, V. Iyer, S. S.
`Jeffrey, M. Van de Rijn, M. Waltham, A. Pergamenschikov, J. C. Lee, D. Lashkari, D.
`Shalon, T. G. Myers, J. N. Weinstein, D. Botstein and P. O. Brown. Systematic variation
`in gene expression patterns in human cancer cell lines. Nature Genetics. 24: 227-35. 2000
`5. P. Gasch, P. T. Spellman, C. M. Kao, O. Carmel-Harel, M. B. Eisen, G. Storz, D.
`Botstein and P. O. Brown. Genomic expression programs in the response of yeast cells to
`environmental changes. Molecular Biology of the Cell. 11: 4241-57. 2000
`6. G. Sherlock, T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J. C. Matese, S. S.
`Dwight, M. Kaloper, S. Weng, H. Jin, C. A. Ball, M. B. Eisen, P. T. Spellman, P. O.
`Brown, D. Botstein and J. M. Cherry. The Stanford Microarray Database. Nucleic Acids
`Research. 29: 152-5. 2001
`7. R. A. George, J. P. Woolley and P. T. Spellman. Ceramic capillaries for use in
`microarray fabrication. Genome Research. 11: 1780-3. 2001
`8. E. De Gregorio, P. T. Spellman, G. M. Rubin and B. Lemaitre. Genome-wide analysis
`of the Drosophila immune response by using oligonucleotide microarrays. Proceedings of
`the National Academy of Sciences, U.S.A. 98: 12590-5. 2001
`9. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach,
`W. Ansorge, C. A. Ball, H. C. Causton, T. Gaasterland, P. Glenisson, F. C. Holstege, I. F.
`Kim, V. Markowitz, J. C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-
`Kremer, J. Stewart, R. Taylor, J. Vilo and M. Vingron. Minimum information about a
`microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics.
`29: 365-71. 2001
`10. P. T. Spellman and G. M. Rubin. Evidence for large domains of similarly expressed
`genes in the Drosophila genome. Journal of Biology. 1: 5. 2002
`11. P. T. Spellman, M. Miller, J. Stewart, C. Troup, U. Sarkans, S. Chervitz, D. Bernhart, G.
`Sherlock, C. Ball, M. Lepage, M. Swiatek, W. L. Marks, J. Goncalves, S. Markel, D.
`Iordan, M. Shojatalab, A. Pizarro, J. White, R. Hubley, E. Deutsch, M. Senger, B. J.
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`Aronow, A. Robinson, D. Bassett, C. J. Stoeckert, Jr. and A. Brazma. Design and
`implementation of microarray gene expression markup language (MAGE-ML). Genome
`Biology 3: RESEARCH. 0046. 2002
`12. E. De Gregorio, P. T. Spellman, P. Tzou, G. M. Rubin and B. Lemaitre. The Toll and
`Imd pathways are the major regulators of the immune response in Drosophila. Embo
`Journal. 21: 2568-79. 2002
`13. L. A. Pile, P. T. Spellman, R. J. Katzenberger and D. A. Wassarman. The SIN3
`deacetylase complex represses genes encoding mitochondrial proteins: implications for
`the regulation of energy metabolism. J Biol Chem. 278: 37840-8. 2003
`14. N. Vodovar, M. Vinal, P. Liehl, A. Basset, J. Degrouard, P. Spellman, F. Boccard, B
`Lemaitre. Drosophila host defense after oral infection by an entomopathogenic
`Pseudomonas species. PNAS. 102:11414-9. 2005
`15. S. Brun, S. Vidal, P. Spellman, K. Takahashi, H. Tricoire, B. Lemaitre. The MAPKKK
`Mekk1 regulates the expression of Turandot stress genes in response to septic injury in
`Drosophila. Genes Cells. 11:397-407. 2006
`16. A.R. Jones, A. Pizarro, P. Spellman, M. Miller. FuGE: Functional Genomics Object
`Model. Omics. 10:179-84. 2006
`17. K. Chin K, S. DeVries, J. Fridlyand, P.T. Spellman, R. Roydasgupta, W.L. Kuo, A.
`Lapuk, R.M. Neve, Z. Qian, T. Ryder, F. Chen, H. Feiler, T. Tokuyasu, C. Kingsley, S.
`Daikree, Z. Meng, K. Chew, D. Pinkel, A. Jain, B.M. Ljung, L. Esserman, D.G.
`Albertson, F.M. Waldman, J.W. Gray. Genomic and transcriptional aberrations linked to
`breast cancer pathophysiologies. Cancer Cell. 6:529-41. 2006
`18. R.M. Neve, K. Chin, J. Fridlyand, J. Yeh, F.L. Baehner, T. Fevr, L. Clark, N. Bayani, J.P.
`Coppe JP, F. Tong, T. Speed, P.T. Spellman, S. DeVries, A. Lapuk, N.J. Wang, W.L.
`Kuo, J.L. Stilwell, D. Pinkel, D.G. Albertson, F.M. Waldman, F. McCormick, R.B.
`Dickson, M.D. Johnson, M. Lippman, S. Ethier, A. Gazdar, J.W. Gray. A collection of
`breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell.
`6:515-27. 2006
`19. T.F. Rayner, P. Rocca-Serra, P.T. Spellman, H.C. Causton, A. Farne, E. Holloway, R.A.
`Irizarry, J. Liu, D.S. Maier, M. Miller, K. Petersen, J. Quackenbush, G. Sherlock, C.J.
`Stoeckert, J. White, P.L. Whetzel, F. Wymore, H. Parkinson, U. Sarkans, C.A. Ball, A.
`Brazma. A simple spreadsheet-based, MIAME-supportive format for microarray data:
`MAGE-TAB. BMC Bioinformatics. 7:489. 2006
`20. A.R. Jones, M. Miller, R. Aebersold, R. Apweiler, C.A. Ball, A. Brazma, J. Degreef, N.
`Hardy, H. Hermjakob, S.J. Hubbard, P. Hussey, M. Igra, H. Jenkins, R.K. Julian, K.
`Laursen, S.G. Oliver, N.W. Paton, S.A. Sansone, U. Sarkans, C.J. Stoeckert, C.F. Taylor,
`P.L. Whetzel, J.A. White, P. Spellman, A. Pizarro. The Functional Genomics
`Experiment model (FuGE): an extensible framework for standards in functional
`genomics. Nat. Biotechnology. 25:1127-33. 2007
`21. Y. Wang, M. Moorhead, G. Karlin-Neumann, N. Wang, J. Ireland, S. Lin, C. Chen, L.M.
`Heiser, K. Chin, L. Esserman, J.W. Gray, P.T. Spellman. M. Faham. Performance of
`Molecular Inversion Probes (MIP) in Allele Copy Number Determination. Genome
`Biology. 8: R246. 2007
`22. P.A. Kenny, G.Y. Lee, C.A. Myers, R.M. Neve, J.R. Semeiks, P.T. Spellman, K.
`Lorenz, E.H. Lee, M.H. Barcellos-Hoff, O.W. Petersen, J.W. Gray, M.J. Bissell. The
`morphologies of breast cancer cell lines in three-dimensional assays correlate with their
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`profiles of gene expression. Mol Oncol. 1:84-96. 2007
`23. L.A. Brown, S.E. Kalloger, M.A. Miller, I.M. Shih, S.E. McKinney, J.L. Santos, K.
`Swenerton, P.T. Spellman, J. Gray, C.B. Gilks, D.G. Huntsman. Amplification of 11q13
`in ovarian carcinoma. Genes Chromosomes Cancer. 47:481-9, 2008
`24. J.Z. Press, A. De Luca, N. Boyd, S. Young, A. Troussard, Y. Ridge, P. Kaurah, S.E.
`Kalloger, K.A. Blood, M. Smith, P.T. Spellman, Y. Yang, D.M. Miller, D. Horsman, M.
`Faham, C.B. Gilks, J. Gray, D.G. Huntsman. Ovarian carcinomas with genetic and
`epigenetic BRCA1 loss have distinct molecular abnormalities. BMC Cancer. 22:17. 2008
`25. The Cancer Genome Atlas Research Network. Comprehensive genomic
`characterization defines human glioblastoma genes and core pathways. Nature. 2008
`26. S. Mukherjee, S. Pelech, R.M. Neve, W.L. Kuo, S. Ziyad, P.T. Spellman, J.W. Gray,
`T.P. Speed. Sparse combinatorial inference with an application in cancer biology.
`Bioinformatics. 2009
`27. S. Durinck, J. Bullard, P.T. Spellman, S. Dudoit. Integrated genomic visualization with
`R. BMC Bioinformatics. GenomeGraphs. 2009
`28. J.G. Hodgson, R.F. Yeh, A. Ray, N.J. Wang, I. Smirnov, M. Yu, S. Hariono, J. Silber,
`H.S. Feiler, J.W. Gray, P.T. Spellman, S.R. Vandenberg, M.S. Berger, C.D. James.
`Comparitive analysis of gene copy number and mRNA expression in GBM tumors and
`GBM xenografts. Neuro Oncology. 2009
`29. O.K. Mirzoeva, D. Das, L.M. Heiser, S. Bhattacharya, D. Siwak, R. Gendelman, N.
`Bayani, N.J. Wang, R.M. Neve, Y. Guan, Z. Hu, Z. Knight, H.S. Feiler, P. Gascard, B.
`Parvin, P.T. Spellman, K.M. Shokat, A.J. Wyrobek, M.J. Bissell, F. McCormick, W.L.
`Kuo, G.B. Mills, J.W. Gray, W.M. Korn. Cancer Research, 2009
`30. Y. Wang, V.E.H. Carlton, G. Karlin-Neumann, R. Sapolsky, L. Zhang, M. Moorhead,
`Z.C. Wang, A.L. Richardson, R. Warren, A. Walther, M. Bondy, A Sahin, R. Krahe, M.
`Tuna, P.A. Thompson, P.T. Spellman, J.W. Gray, G.B. Mills, M. Faham. High quality
`copy number and genotype data from FFPE samples using Molecular Inversion Probe
`(MIP) microarrays. BMC Medical Genomics. 2009
`31. H. Bengtsson, A. Ray, P. Spellman, T.P. Speed. A single-sample method for normalizing
`and combining full-resolution copy numbers from multiple platforms, labs and analysis
`methods. Bioinformatics. 2009
`32. L.M. Heiser, N.J. Wang, C.L. Talcott, K.R. Laderoute, M. Knapp, Y. Guan, Z. Hu, S.
`Ziyad, B.L. Weber, S Laquerre, J.R. Jackson, R.F. Wooster, W.L. Kuo, J.W. Gray, P.T.
`Spellman. Genome Biology. 2009
`33. S. Durinck, P.T. Spellman, W. Huber. Mapping Identifiers for the Integration of
`Genomic Datasets with the R/Bioconductor package biomaRt. Nature Protocols. 2009
`34. W.L. Kuo, D. Das, S. Ziyad, S. Battacharya, W.J. Gibb, L.M. Heiser, A. Sadanandam,
`G.V. Fontenay, Z. Hu, N.J. Wang, N. Bayani, H.S. Feiler, R.M. Neve, A.J. Wyrobek,
`P.T. Spellman, L.J. Marton and J.W. Gray. A Systems Analysis of the Chemosensitivity
`of Breast Cancer Cells to the Polyamine Analogue PG-11047. BMC Medicine. 2009
`35. R.G. Verhaak, K.A. Hoadley, E. Purdom, V. Wang, Y. Qi, M.D. Wilkerson, C.R. Miller,
`L. Ding, T. Golub, J.P. Mesirov, G. Alexe, M. Lawrence, M. O’Kelly, P. Tamayo, B.A.
`Weir, S. Gabriel, W. Winckler, S. Gupta, L. Jakkula, H.S. Feiler, J.G. Hodgson, C.D.
`James, J.N. Sarkaria, C. Brennan, A. Kahn, P.T. Spellman, R. K. Wilson, T.P. Speed,
`J.W. Gray, M. Meyerson, G. Getz, C.M. Perou, D.N. Hayes, Cancer Genome Atlas
`Network. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of
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`Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1.
`Cancer Cell. 2010
`36. International Cancer Genome Consortium. International network of cancer genome
`projects. Nature. 2010
`37. L.A. Loss, A. Sadanandam, S. Durinck, S. Nautiya, D. Flaucher, V.E. Carlton, M.
`Moorhead, Y. Lu, J.W. Gray, M. Faham, P. Spellman, B. Parvin. Prediction of
`epigenetically regulated genes in breast cancer cell lines. BMC Bioinformatics. 2010
`38. A. Lapuk, H. Marr, L. Jakkula, H. Pedro, S. Bhattacharya, E. Purdom, Z. Hu, K.
`Simpson, L. Pachter, N. Wang, B. Parvin, G. Fontenay, T. Speed, J. Garbe, M. Stampfer,
`H. Bayandorian, S. Dorton, T.A. Clark, A. Schweitzer, A. Wyrobek, H. Feiler, P.
`Spellman, J. Conboy, and J.W. Gray. Exon-level microarray analyses identify alternative
`splicing programs in breast cancer. Mol Cancer Res. 2010
`39. S. Nautiyal, V.E. Carlton, Y. Lu, J.S. Ireland, M. Moorhead, J.W. Gray, P. Spellman, M.
`Mindrinos, P. Berg, and M. Faham. High-throughput method for analyzing methylation
`of CpGs in targeted genomic regions. PNAS. 2010
`40. N. Nabavizadeh, C. Klifa, D. Newitt, Y. Lu, Y.Y. Chen, H. Hsu, C. Fisher, T. Tokayasu,
`A.B. Olshen, P. Spellman, J.W. Gray, N. Hylton, and C.C. Park. Topographic
`enhancement mapping of the cancer-associated breast stroma usine breast MRI. Integr.
`Biol. 2011
`41. X.V. Wang, R.G. Verhaak, E. Purdom, P.T. Spellman, and T.P. Speed. Unifying gene
`expression measures from multiple platforms using factor analysis. PLoS ONE. 2011
`42. E.A. Collisson, A. Sadanandam, P. Olson, W.J. Gibb, M. Truitt, S. Gu, J. Cooc, J.
`Weinkle, G.E. Kim, L. Jakkula, H.S. Feiler, A.H. Koh, A.B. Olshen, K.L. Danenberg,
`M.A. Tempero, P.T. Spellman, D. Hanahan, and J.W. Gray. Subtypes of pancreatic
`ductal adenocarcinoma and their differing responses to therapy. Nat. Med. 2011
`43. TCGA Network, P.T. Spellman corresponding author. Integrative Genomic Analyses of
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`51. C.J. Creighton, A. Hernandez-Herrera, A. Jacobsen, D.A. Levine, P. Mankoo, N.
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`52. Collisson EA, Trejo CL, Silva JM, Gu S, Korkola JE, Heiser LM, Charles RP,
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`53. The Cancer Genome Atlas. Comprehensive Molecular Characterization of Human
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`56. L.A. Patrillo, D.M. Wolf, A.M. Kapoun, N.J. Wang, A. Barczak, Y. Xiao, H. Korkaya, F.
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`57. H. Chang, J. Han, P. Spellman, B. Parvin. Multi-Reference Level Set for
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`58. The Cancer Genome Atlas. Comprehensive molecular portraits of human breast tumors.
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`59. A. Sadanandam, A Lal, S.C. Benz, S. Eppenberger-Castori, G. Scott, J.W. Gray, P.
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`60. H. Chang, J. Han, A. Borowsky, L. Loss, J.W. Gray, P.T. Spellman, B. Parvin.
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` 61. E. Ordinario, H.J. Han, S. Furuta, L.M. Heiser, L.R. Jakkula, F. Rodier, P.T. Spellman,
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` 62. R.G. Verhaak, P. Tamayo, J.Y. Yang, D. Hubbard, H. Zhang, C.J. Creighton, S. Fereday,
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`66. J.K. Rhee, K. Kim, H. Chae, J. Evans, P. Yan, B.T. Zhang, J. Gray, P. Spellman, T.H.
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`68. Cancer Genome Atlas Research Network. The Cancer Genome Atlas Pan-Cancer
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`69. S.W. Luoh, B. Ramsey, A. Hanlon Newell, M. Troxell M, Z. Hu, K. Chin, P. Spellman,
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`76. K.L. Kanchi, K.J. Johnson, C. Lu, M.D. McLellan, M.D. Leiserson, M.C. Wendl, Q.
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`78. P.C. Boutros, A.D. Ewing, K. Ellrott, T.C. Norman, K.K. Dang, Y. Hu, M.R. Kellen, C.
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`79. X, Fu, C.J. Creighton, N.C. Biswal, V. Kumar, M .Shea, S. Herrera, A. Contreras, C.
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