OHSU

Joe Gray

Gray, Joe-Profile Photo

Dr. Joe W. Gray, a physicist and an engineer by training, holds positions as the Gordon Moore Endowed Chair, Biomedical Engineering Department Chair; Director, Center for Spatial Systems Biomedicine; and Associate Director for Translational Research, Knight Cancer Institute at the Oregon Health & Science University. He is also Emeritus Professor, University of California San Francisco; and Senior Scientist, Lawrence Berkeley National Laboratory. He was a Staff Scientist in the Biomedical Sciences Division of the Lawrence Livermore National Laboratory (1972-1991), Professor of Laboratory Medicine at the University of California, San Francisco (1991-2011), and Associate Laboratory Director for Biosciences and Life Sciences Division Director at the Lawrence Berkeley National Laboratory (2003-2011). He is Principal Investigator of the National Cancer Institute /Integrative Cancer Biology Program (ICBP)Center for Cancer Systems Biology (CCSB) aimed at understanding and modeling of RTK signaling, PI of a DOD Innovator project aimed at improving early breast cancer detection, Co-investigator on human and mouse cancer genome atlas projects, and PI of a Keck Project to initiate development of image-based approaches that will allow architectural analyst of the nanoscale molecular assemblies that regulate information flow in cells.

Dr. Grays work is described in over 400 publications and in 73 US patents. He is a Fellow of the American Association for the Advancement of Science and the American Institute for Medical and Biological Engineering, an elected a member of the Institute of Medicine of the National Academy of Sciences and Chair of the National Institutes of Health, Frederick Advisory Committee to the Director of the National Cancer Institute.

Professional Associations
Dr. Gray is involved in several projects and collaborations with organizations outside of Oregon Health & Science University. View list

Sadanandam, A., Wang, X., Melo, F.d.S.E., Gray, J.W., Vermeulen, L., Hanahan, D., Medema, J.P. (2014) Reconciliation of classification systems defining molecular subtypes of colorectal cancer: Interrelationships and clinical implications. Cell Cycle, 13(3):353-7. PMC3956531

Wang, Y., Wen, M., Kwon, Y., Xu, Y., Liu, Y., Zhang, P., He, X., Wang, Q., Huang, Y., Jen, K.Y., LaBarge, M.A., You, L., Kogan, S.C., Gray, J.W., Mao, J.H., Wei, G. (2014) CUL4A induces epithelial-mesenchymal transition and promotes cancer metastasis by regulating ZEB1 expression. Cancer Res., 74(2):1-12. PMC3934357


Fan, Y., Ge, N., Wang, X., Sun, W., Mao, R., Bu, W., Creighton, C.J., Zheng, P., Vasudevan, S., An, L., Yang, J., Zhao, Y.J., Zhang, H., Li, X.N., Rao, P.H., Leung, E., Lu, Y.J., Gray, J.W., Schiff, R., Hilsenbeck, S.G., Osborne, C.K., Yang, J., and Zhang, H. (2013) Amplification and overexpression of MAP3K3 gene in human breast cancer promotes formation and survival of breast cancer cells. J. Pathol., 232(1):75-86. NIHMS561900

Lovci, M.T., Ghanem, D., Marr, H., Arnold, J., Gee, S., Parra, M., Liang, T.Y., Stark, T.J., Gehman, L.T., Hoon, S., Massirer, K.B., Pratt, G.A., Black, D.L., Gray, J.W., Conboy, J.G., Yeo, G.W. (2013) Rbfox proteins regulate alternative mRNA splicing via evolutionarily conserved RNA bridges. Nat. Struct. Mol. Biol., 20(12):1434-42. PMC3918504


Daemen, A., Griffith, O.L., Heiser, L.M., Wang, N.J., Enache, O.M., Sanborn, Z., Pepin, F., Durinck, S., Korkola, J.E., Griffith, M., Hur, J.S., Huh, N., Chung, J., Cope, L., Fackler, M.J., Umbricht, C., Sukumar, S., Seth, P. Sukhatme, V.P., Jakkula, L.R., Lu, Y., Mills, G.B., Cho, R.J., Collisson, E.A., van Nan, X., Collisson, E.A., Lewis, S., Huang, J., Tamg Griffith, O.L., Pepin, F., Enache, O.M., Heiser, L.M., Collisson, E.A., Spellman, P.T., Gray, J.W. (2013) A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Med., 5(10):92. [Epub ahead of print] PMID: 24112773

Nan, X., Collisson, E.A., Lewis, S., Huang, J., Tamgüney, T.M., Liphardt, J.T., McCormick, F., Gray, J.W., and Chu, S. (2013) Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling. Proc. Natl. Acad. Sci. USA, 110(46):18519-24. PMC3831949

Griffith, O.L., Pepin, F., Enache, O.M., Heiser, L.M., Collisson, E.A., Spellman, P.T., Gray, J.W. (2013) A robust prognostic signature for hormone-positive node-negative breast cancer. Genome Med., 5(10):92. [Epub ahead of print] PMID: 24112773

Timmerman, L.A., Holton, T., Yuneva, M., Louie, R.J., Padr Fallahi-Sichani, M., Honarnejad, S., Heiser, L.M., Gray, J.W., Sorger, P.K. (2013) Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat. Chem. Biol., 9(11):708-14. PMID: 24013279 Iacovides, D.C., Johnson, A.B., Wang, N., Boddapati, S., Korkola, J., Gray, J.W. (2013) Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay. Mol. Cell. Proteomics, 12(11):3210-20. PMC1418244

Timmerman, L.A., Holton, T., Yuneva, M., Louie, R.J., Padró, M., Daemen, A., Hu, M., Chan, D.A., Ethier, S.P., van ‘t Veer, L.J., Polyak, K., McCormick, F., Gray, J.W. (2013) Glutamine sensitivity analysis identifies the xCT antiporter as a common triple-negative breast tumor therapeutic target. Cancer Cell, 24(4):450-65. PMC3931310

Fallahi-Sichani, M., Honarnejad, S., Heiser, L.M., Gray, J.W., Sorger, P.K. (2013) Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat. Chem. Biol., 9(11):708-14. PMC3947796

Iacovides, D.C., Johnson, A.B., Wang, N., Boddapati, S., Korkola, J., Gray, J.W. (2013) Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay. Mol. Cell. Proteomics, 12(11):3210-20. PMC1418244

Rhee, J.-K., Kim, K., Chae, H., Evans, J., Yan, P., Zhang, B.-T., Gray, J., Spellman, P., Huang, T.H., Nephew, K.P., Kim, S. (2013) Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer. Nucleic Acids Res., 41(18):8464-74. PMC3794600

Fan, P., Griffith, O.L., Agboke, F.A., Anur, P., Zou, X., McDaniel, R.E., Creswell, K., Kim, S.H., Katzenellenbogen, J.A., Gray, J.W., Jordan, V.C. (2013) c-Src modulates estrogen-induced stress and apoptosis in estrogen-deprived breast cancer cells. Cancer Res., 73(14):4510-20. PMC3715569

Sadanandam, A., Lyssiotis, C.A., Homicsko, K., Collisson, E.A., Gibb, W.J., Wullschleger, S., Ostos, L.C., Lannon, W.A., Grotzinger, C., Del Rio, M., Lhermitte, B., Olshen, A.B., Wiedenmann, B., Cantley, L.C., Gray, J.W., Hanahan, D. (2013) A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat. Med., 19(5)619 LeBeau, A.M., Duriseti, S., Murphy, S.T., Pepin, F., Hann, B., Gray, J.W., VanBrocklin, H.F., Craik, C.S. (2013) Targeting uPAR with antagonistic recombinant human antibodies in aggressive breast cancer. Cancer Res., 73(7)2070

Sadanandam, A., Lyssiotis, C.A., Homicsko, K., Collisson, E.A., Gibb, W.J., Wullschleger, S., Ostos, L.C., Lannon, W.A., Grotzinger, C., Del Rio, M., Lhermitte, B., Olshen, A.B., Wiedenmann, B., Cantley, L.C., Gray, J.W., Hanahan, D. (2013) A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat. Med., 19(5)619

LeBeau, A.M., Duriseti, S., Murphy, S.T., Pepin, F., Hann, B., Gray, J.W., VanBrocklin, H.F., Craik, C.S. (2013) Targeting uPAR with antagonistic recombinant human antibodies in aggressive breast cancer. Cancer Res., 73(7)2070

Verhaak, R., Tamayo, P., Creighton, C.J., Yang, J.Y., Hubbard, D., Zhang, H., Fereday, S., Lawrence, M., Carter, S.L., Mermel, C., Kostic, A.D., Etemadmoghadam, D., Saksena, G., Cibulskis, K., Duraisamy, S., Levanon, K., Sougnez, C., Tsherniak, A., Gomez, S., Onofrio, R.C., Gabriel, S.B., Chin, L., Zhang, N., Spellman, P.T., Zhang, Y., Akbani, R., Hoadley, K.A., Kahn, A., K Chang, H., Han, J., Borowsky, A.D., Loss, L., Gray, J.W., Spellman, P.T., Parvin, B. (2013) Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association. IEEE Trans. Med. Imaging., 32(4):670-82. PMC3728287 Köbel, M., Huntsman, D.G., Soslow, R.A., deFazio, A., Birrer, M.J., Gray, J.W., Weinstein, J.N., Bowtell, D.D., Drapkin, R.I., Mesirov, J., Getz, G., Levine, D.A., and Meyerson M. (2013) Prognostically relevant gene expression signatures of high grade serous ovarian carcinoma. J. Clin. Invest., 123(1):517-25. PMC3533304

Issued United States Patents

Finding leaks in a tandem Van de Graff accelerator

  • Gray, J.W., Hartnell, G.W., and Legg, J.C. Method of locating defects in a high-voltage insulating tube. U.S. Patent #3,76l,720 (1974)
Flow cytometry and sorting
  • Gray, J.W., Alger, T.W., and Lord, D. Fluidic assembly for an ultra-high-speed chromosome flow sorter. U.S. Patent #4,361,400 (1982)
  • Gray, J.W., Hirschfeld, T.B., and Norgren, R.M. Method and apparatus for fringe-scanning chromosome analysis. U.S. Patent #4,596,036 (1986)
BrdUrd/DNA analysis
  • Dolbeare, F. and Gray, J.W. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine. U.S. Patents #4,585,736 (1986); #4,780,406 (1988); #4,812,394 (1989)
Fluorescence in situ hybridization (FISH)
  • Gray, J.W. and Pinkel, D. Methods of preparing and applying single stranded DNA probes to double stranded target DNAs in situ. U.S. Patent #5,028,525 (1991)
  • Gray, J.W. and Pinkel, D. Methods for chromosome-specific staining. U.S. Patents #5,447,841 (1995); #6,596,479 (1995); #6,607,877 (2003); #6,872,817 (2005)
  • Gray, J.W., Pinkel, D., and Tkachuk, D. Method of detecting genetic translocations identified with chromosomal abnormalities (BCR/ABL translocation). U.S. Patent #6,280,929 (2001)
  • Gray, J.W. and Pinkel, D. Methods of biological dosimetry employing chromosome-specific staining. U.S. Patent #6,132,961 (2000)
  • Gray, J.W., Pinkel, D., Kallioniemi, O.-P., Kallioniemi, A., and Sakamoto, M. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes. U.S. Patent #7,115,709 (2006)
  • Pinkel, D., Kallioniemi, O.-P., Kallioniemi, A., Waldman, F., Gray, J.W., and Sakamoto, M. Genomic probing. U.S. Patent #5,856,097 (1995)
  • Weier, H.-U. and Gray, J.W. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using. U.S. Patent #5,427,932 (1995)
  • Gray, J.W., Stokke, T., and Pinkel, D. Detection of amplified or deleted chromosomal regions. U.S. Patents #5,472,842 (1995); #5,633,365 (1997).
  • Gray, J.W. and Weier, H.-U. Y-Chromosome specific nucleic acid probe and method for determining the y-chromosome in situ. U.S. Patents #5,840,482 (1998); #5,888,730 (1999); #6,300,066 (2001)
  • Gray, J. and Weier, H.-U. Quantitative DNA fiber mapping. U.S. Patent #5,851,769 (1998)
Comparative genomic hybridization (CGH)
  • Pinkel, D., Gray, J.W., Kallioniemi, A., Kallioniemi, O.-P., and Waldman, F. Comparative genomic hybridization (CGH). U.S. Patent #5,665,549 (1997); #5,721,098 (1998); #5,965,362 (1999); #5,976,790 (1999); #6,159,685 (2000); #6,335,167 (2002); #7,238,484 (2007), #7,537,895 (2009)
  • Pinkel, D., Albertson, D., and Gray, J.W. Comparative fluorescence hybridization to nucleic acid arrays. U.S. Patents #5,830,645 (1998); #6,562,565 (2003)
  • Pinkel, D. and Gray, J.W. High density array fabrication and readout method for a fiber optic biosensor. U.S. Patents #5,690,894 (1997); #6,146,593 (2000); #6,417,506 (2002)
  • Pinkel, D., Albertson, D.G., and Gray, J.W. Array-based detection of genetic alterations associated with disease. U.S. Patents #6,210,878 (2001); #7,267,947 (2007)
  • Gray, J.W., Pinkel, D., Albertson, D., Collins, C.C., and Baldocchi, R. Comparative fluorescence hybridization to oligonucleotide microarrays. U.S. Patent #6,465,182 (2002)
  • Pinkel, D., Albertson, D.G., Gray, J.W., Hamilton, G., Brown, N.W., and Clark, S.M. High-efficiency microarray printing device. U.S. Patent #6,855,538 (2005)
  • Albertson, D., Pinkel, D., Fridyland, J., Huey, B., Snijders, A., Gray, J.W., Kallioniemi, A., Kallioniemi, O., Waldman, F. Detection of nucleic acid differences by comparative genomic hybridization. U.S. Patent #7,534,567 (2009)
Diagnostic markers
  • Christman, M.F., Gray, J.W., Levin, N.A., Brzoska, P., and Nakamura, H. Genetic alterations that correlate with lung carcinomas. U.S. Patent #5,670,314 (1997)
  • Gray, J.W., Pinkel, D. Collins, C., Kallioniemi, O.-P., and Tanner, M. Amplification of chromosomal region 20q13 as prognostic indicator in breast cancer. U.S. Patents #5,801,021 (1998); #6,268,184 (2001)
  • Gray, J., Collins, C., Godfrey, T., Kowbel, D., Hwang, S., and Rommens, J. Genes from the 20Q13 amplicon and their uses. U.S. Patents #5,892,010 (1999); # 6,808,878 (2005); # 7,049,424 (2006); # 7,413,899 (2008)
  • Shayesteh, L. and Gray, J.W. Genetic aberrations associated with cancer (PIK3CA). U.S. Patents #6,110,673 (2000); #6,277,563 (2001); #6,475,732 (2002); #6,537,761 (2003); # 7,670,767 (2010)
  • Gray, J.W., Pinkel, D., Kallioniemi, O.-P., Kallioniemi, A., and Sakamoto, M. Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17. U.S. Patents #6,475,720 (2002); #6,344,315 (2002); #RE40,929 (2009)
  • Gray, J.W., Pinkel, D., Tkachuk, D., and Westbrook, C. Chromosome specific staining to detect genetic rearrangements. U.S. Patent Application #09/765,291 (2001, amendment filed 2007)
  • Gray, J.W. and Pinkel, D. Methods and compositions for chromosome 21-specific staining. U.S. Patent #6,500,612 (2002)
  • Albertson, D.G., Pinkel, D., Collins, C., and Gray, J.W. Amplicon in the 20q13 region of human chromosome 20 and uses thereof. U.S. Patent #6,664,057 (2003)
  • Giacomini, K.M., Gray, J.W., Lapuk, A.V., and Zhang, S. Use of organic cation transporters for cancer diagnosis and therapy. U.S. Provisional Patent Application #60/793,803 (2006)
  • Albertson, D., Pinkel, D., Collins, C., Gray, J.W., Ystra, B. Detecting CYP24 expression level as a marker for predisposition to cancer. U.S. Patent #7,648,826 (2010)
End sequence profiling (ESP)
  • Collins, C., Volik, S., and Gray, J.W. End sequence profiling. U.S. Patent #6,785,614 (2004)
Mass spectrometric imaging of mass tag labeled specimens
  • Felton, James S., Wu, Kuang Jen J., Knize, Mark G., Kulp, Kristen S., Gray, Joe W. Imaging mass spectrometer with mass tags. US Patent #7,728,287 (2010)
Others
  • Ginzinger, D., Godfrey, T., Jensen, R., and Gray, J.W. Quantitative PCR method to enumerate DNA copy number. U.S. Patent #6,180,349 (2001)
  • Fulwyler, M.J. and Gray, J.W. Capillary array and related methods. US Patents #6,610,499 (2003); #6,818,184 (2005); #6,898,237 (2006); #7,741,104 (2010)