Photo of Joe W. Gray, Ph.D.

Joe W. Gray Ph.D.

The Gray Laboratory explores mechanisms by which genomic, transcriptional and proteomic abnormalities occur in selected cancers, elucidates how these abnormalities contribute to cancer pathophysiologies and assesses the ways in which these abnormalities influence responses to gene targeted therapies. Current studies focus on developing: (a) integrated analyses of the spectrum of recurrent abnormalities that influence cancer behavior (b) mathematical models that describe how cancer-associated molecular abnormalities influence individual responses to therapeutic inhibitors (c) novel therapeutic approaches to treat breast or ovarian cancer subpopulations that do not respond well to current aggressive chemotherapeutic strategies (d) proteomic strategies for early detection of breast cancer related proteins in blood (e) automated functional assessment of genes deregulated by genomic abnormalities in cancers, and (f) molecular imaging for early detection of metastasis prone breast cancer. Integrated analysis We are assessing abnormalities associated with clinical outcome in breast cancers using a combination of comparative genomic hybridization (CGH), massively parallel sequencing (whole exome sequencing and RNA sequencing) and reverse phase protein lysate arrays to assess allele specific genome copy number, RNA expression, and protein and phosphoprotein levels in cancer related genes. These studies are supported by the NCI Bay Area Breast Cancer SPORE and The Cancer Genome Altas project. Mathematical models We are developing mathematical methods to predict individual responses to therapeutic agents using information on responses to these agents in a collection of cell lines grown in vitro. Major emphasis in this project is on breast cancer. Current emphasis is on development of statistical, Bayesian and ODE models of Her-family signaling. Work in this area is supported by an NCI Center for Cancer Systems Biology award. Novel therapeutic approaches We are using advanced genomic analysis and high content, high throughput imaging to assess responses to NCI and private sector compounds for our collection of ~100 breast, ovary, prostate and pancreas cancer cell lines. 


  • "Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis." Cell Reports In: , Vol. 19, No. 1, 04.04.2017, p. 203-217.
  • "Targeted treatment of metastatic breast cancer by PLK1 siRNA delivered by an antioxidant nanoparticle platform." Molecular Cancer Therapeutics  In: , Vol. 16, No. 4, 01.04.2017, p. 763-772.
  • "Erratum to : "Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer", [Breast Cancer Research, 19, (2017) (17)] DOI: 10.1186/s13058-017-0809-6." Breast Cancer Research In: , Vol. 19, No. 1, 17, 09.02.2017.
  • "Circulating-tumor DNA as an early detection and diagnostic tool." Current Opinion in Genetics and Development  In: , Vol. 42, 01.02.2017, p. 14-21.
  • "Epigenomic inactivation of RasGAPs activates RAS signaling in a subset of luminal B breast cancers." Cancer Discovery In: , Vol. 7, No. 2, 01.02.2017, p. 131-133.
  • "Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling." Cell Systems In: , Vol. 4, No. 1, 25.01.2017, p. 73-83.e10.
  • "Bayesian network inference modeling identifies TRIB1 as a novel regulator of cell-cycle progression and survival in cancer cells." Cancer Research  In: , Vol. 77, No. 7, 2017, p. 1575-1585.
  • "A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow." Methods in Cell Biology In: , 2017.
  • "PI3 Kinase Pathway Mutations in Human Cancers." JAMA oncology In: , Vol. 2, No. 12, 01.12.2016, p. 1543-1544.
  • "Characterizing the immune microenvironment in high-risk ductal carcinoma in situ of the breast." Breast Cancer Research and Treatment  In: , 26.10.2016, p. 1-12.
  • "FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer." Proceedings of the National Academy of Sciences of the United States of America  In: , Vol. 113, No. 43, 25.10.2016, p. E6600-E6609.
  • "Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics."  2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016. Vol. 2016-October Institute of Electrical and Electronics Engineers Inc., 2016. p. 1175-1178 7590914.
  • "Multiplexed imaging reveals heterogeneity of PI3K/MAPK network signaling in breast lesions of known PIK3CA genotype." Breast Cancer Research and Treatment In: , Vol. 159, No. 3, 01.10.2016, p. 575-583.
  • "A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds." Cell  In: , Vol. 167, No. 1, 22.09.2016, p. 260-274.e22.
  • "Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer." Breast Cancer Research In: , Vol. 18, No. 1, 70, 01.07.2016.
  • "Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices." IEEE/ACM Transactions on Computational Biology and Bioinformatics In: , Vol. 13, No. 4, 7182286, 01.07.2016, p. 767-777.
  • "The ErbB2ΔEx16 splice variant is a major oncogenic driver in breast cancer that promotes a pro-metastatic tumor microenvironment." Oncogene In: , 09.05.2016.
  • "Current development of targeted oligonucleotide-based cancer therapies : Perspective on HER2-positive breast cancer treatment." Cancer Treatment Reviews  In: , Vol. 45, 01.04.2016, p. 19-29.
  • "Inferring causal molecular networks : Empirical assessment through a community-based effort." Nature Methods  In: , Vol. 13, No. 4, 30.03.2016, p. 310-318.
  • "Therapeutic siRNA for drug-resistant HER2-positive breast cancer." Oncotarget  In: , Vol. 7, No. 12, 22.03.2016, p. 14727-14741.
  • "Functional proteomics identifies miRNAs to target a p27/Myc/phospho-Rb signature in breast and ovarian cancer." Oncogene In: , Vol. 35, No. 6, 11.02.2016, p. 691-701.
  • "Erratum : Functional proteomics identifies miRNAs to target a p27/Myc/phospho-Rb signature in breast and ovarian cancer (Oncogene (2016) 35 (691-701) DOI:10.1038/onc.2014.469)." Oncogene In: , Vol. 35, No. 6, 11.02.2016, p. 801.
  • "Retrieving common dynamics of gene regulatory networks under various perturbations."  Proceedings of the IEEE Conference on Decision and Control. Vol. 2016-February Institute of Electrical and Electronics Engineers Inc., 2016. p. 2531-2536 7402597.
  • "ARTIK-52 induces replication-dependent DNA damage and p53 activation exclusively in cells of prostate and breast cancer origin." Cell Cycle  In: , Vol. 15, No. 3, 01.02.2016, p. 455-470.
  • "IL-10 and integrin signaling pathways are associated with head and neck cancer progression." BMC Genomics  In: , Vol. 17, No. 1, 38, 08.01.2016.
  • "Tumor-derived cell lines as molecular models of cancer pharmacogenomics." Molecular Cancer Research In: , Vol. 14, No. 1, 01.01.2016, p. 3-13.
  • "Functional oncogene signatures guide rationally designed combination therapies to synergistically induce breast cancer cell death." Oncotarget In: , Vol. 7, No. 24, 2016, p. 36138-36153.
  • "Large-scale drug screens support precision medicine." Cancer Discovery In: , Vol. 5, No. 11, 01.11.2015, p. 1130-1132.
  • "The consensus molecular subtypes of colorectal cancer." Nature Medicine  In: , Vol. 21, No. 11, 01.11.2015, p. 1350-1356.
  • "Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway." Nature Genetics In: , Vol. 47, No. 10, 29.09.2015, p. 1194-1199.

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