• 65064 Citations
  • 110 h-Index
1971 …2020
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Research Output 1971 2020

2013
81 Citations (Scopus)

CpG island shore methylation regulates caveolin-1 expression in breast cancer

Rao, X., Evans, J., Chae, H., Pilrose, J., Kim, S., Yan, P., Huang, R. L., Lai, H. C., Lin, H., Liu, Y., Miller, D., Rhee, J. K., Huang, Y. W., Gu, F., Gray, J., Huang, T. M. & Nephew, K. P., Sep 19 2013, In : Oncogene. 32, 38, p. 4519-4528 10 p.

Research output: Contribution to journalArticle

Caveolin 1
CpG Islands
Methylation
Breast Neoplasms
DNA Methylation
44 Citations (Scopus)

C-Src modulates estrogen-induced stress and apoptosis in estrogen-deprived breast cancer cells

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. & Jordan, V. C., Jul 15 2013, In : Cancer Research. 73, 14, p. 4510-4520 11 p.

Research output: Contribution to journalArticle

Estrogens
MCF-7 Cells
Apoptosis
Breast Neoplasms
Eukaryotic Initiation Factor-2
196 Citations (Scopus)

Glutamine Sensitivity Analysis Identifies the xCT Antiporter as a Common Triple-Negative Breast Tumor Therapeutic Target

Timmerman, L., Holton, T., Yuneva, M., Louie, R., Padró, M., Daemen, A., Hu, M., Chan, D., Ethier, S., van'tVeer, L., Polyak, K., McCormick, F. & Gray, J., Oct 14 2013, In : Cancer Cell. 24, 4, p. 450-465 16 p.

Research output: Contribution to journalArticle

Antiporters
Glutamine
Breast Neoplasms
Sulfasalazine
Neoplasms
27 Citations (Scopus)

Identification and quantification of AKT isoforms and phosphoforms in breast cancer using a novel nanofluidic immunoassay

Iacovides, D. C., Johnson, A. B., Wang, N., Boddapati, S., Korkola, J. & Gray, J., Nov 2013, In : Molecular and Cellular Proteomics. 12, 11, p. 3210-3220 11 p.

Research output: Contribution to journalArticle

Nanofluidics
Immunoassay
Protein Isoforms
Breast Neoplasms
Assays
43 Citations (Scopus)

Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer

Rhee, J. K., Kim, K., Chae, H., Evans, J., Yan, P., Zhang, B. T., Gray, J., Spellman, P., Huang, T. H. M., Nephew, K. P. & Kim, S., Oct 2013, In : Nucleic Acids Research. 41, 18, p. 8464-8474 11 p.

Research output: Contribution to journalArticle

DNA Methylation
Transcriptome
Genome
Breast Neoplasms
Gene Expression
60 Citations (Scopus)

Invariant delineation of nuclear architecture in glioblastoma multiforme for clinical and molecular association

Chang, H., Han, J., Borowsky, A., Loss, L., Gray, J., Spellman, P. & Parvin, B., 2013, In : IEEE Transactions on Medical Imaging. 32, 4, p. 670-682 13 p., 6374258.

Research output: Contribution to journalArticle

Glioblastoma
Tumors
Tissue
Neoplasms
Bioinformatics
140 Citations (Scopus)

Metrics other than potency reveal systematic variation in responses to cancer drugs

Fallahi-Sichani, M., Honarnejad, S., Heiser, L., Gray, J. & Sorger, P. K., Nov 2013, In : Nature Chemical Biology. 9, 11, p. 708-714 7 p.

Research output: Contribution to journalArticle

Pharmaceutical Preparations
Neoplasms
Single-Cell Analysis
Drug Delivery Systems
Phosphatidylinositol 3-Kinases
131 Citations (Scopus)

Modeling precision treatment of breast cancer.

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. & 7 others, Lu, Y., Mills, G. B., Cho, R. J., Collisson, E. A., van't Veer, L. J., Spellman, P. T. & Gray, J. W., 2013, In : Genome Biology. 14, 10

Research output: Contribution to journalArticle

breast neoplasms
cancer
Breast Neoplasms
therapeutics
modeling
261 Citations (Scopus)

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma

Verhaak, R. G. W., Tamayo, P., Yang, J. Y., Hubbard, D., Zhang, H., Creighton, C. J., Fereday, S., Lawrence, M., Carter, S. L., Mermel, C. H., Kostic, A. D., Etemadmoghadam, D., Saksena, G., Cibulskis, K., Duraisamy, S., Levanon, K., Sougnez, C., Tsherniak, A., Gomez, S., Onofrio, R. & 21 others, Gabriel, S., Chin, L., Zhang, N., Spellman, P., Zhang, Y., Akbani, R., Hoadley, K. A., Kahn, A., Köbel, M., Huntsman, D., Soslow, R. A., Defazio, A., Birrer, M. J., Gray, J., Weinstein, J. N., Bowtell, D. D., Drapkin, R., Mesirov, J. P., Getz, G., Levine, D. A. & Meyerson, M., Jan 2 2013, In : Journal of Clinical Investigation. 123, 1, p. 517-525 9 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Carcinoma
Genes
Platinum
Survival
119 Citations (Scopus)

Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges

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., Conboy, J. G. & Yeo, G. W., Dec 2013, In : Nature Structural and Molecular Biology. 20, 12, p. 1434-1442 9 p.

Research output: Contribution to journalArticle

Alternative Splicing
RNA
Exons
Messenger RNA
Proteins
87 Citations (Scopus)

Single-molecule superresolution imaging allows quantitative analysis of RAF multimer formation and signaling

Nan, X., Collisson, E. A., Lewis, S., Huang, J., Tamgüney, T. M., Liphardt, J. T., McCormick, F., Gray, J. & Chu, S., Nov 12 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 46, p. 18519-18524 6 p.

Research output: Contribution to journalArticle

Microscopy
Spatial Analysis
Membrane Fusion
Protein-Serine-Threonine Kinases
Neoplasms
42 Citations (Scopus)

Targeting uPAR with antagonistic recombinant human antibodies in aggressive breast cancer

Le Beau, A. M., Duriseti, S., Murphy, S. T., Pepin, F., Hann, B., Gray, J., Van Brocklin, H. F. & Craik, C. S., Apr 1 2013, In : Cancer Research. 73, 7, p. 2070-2081 12 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Antibodies
Triple Negative Breast Neoplasms
Plasminogen
Heterografts
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
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
189 Citations (Scopus)

Chemotherapy response and recurrence-free survival in Neoadjuvant breast cancer depends on biomarker profiles: Results from the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657)

Esserman, L. J., Berry, D. A., Cheang, M. C. U., Yau, C., Perou, C. M., Carey, L., De Michele, A., Gray, J., Conway-Dorsey, K., Lenburg, M. E., Buxton, M. B., Davis, S. E., Van't Veer, L. J., Hudis, C., Chin, K-Y., Wolf, D., Krontiras, H., Montgomery, L., Tripathy, D., Lehman, C. & 14 others, Liu, M. C., Olopade, O. I., Rugo, H. S., Carpenter, J. T., Livasy, C., Dressler, L., Chhieng, D., Singh, B., Mies, C., Rabban, J., Chen, Y. Y., Giri, D., Au, A. & Hylton, N., Apr 2012, In : Breast Cancer Research and Treatment. 132, 3, p. 1049-1062 14 p.

Research output: Contribution to journalArticle

Biomarkers
Breast Neoplasms
Recurrence
Drug Therapy
Survival
44 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
17 Citations (Scopus)

Elevated levels of proliferating and recently migrated tumor-associated macrophages confer increased aggressiveness and worse outcomes in breast cancer

Mukhtar, R. A., Moore, A. P., Tandon, V. J., Nseyo, O., Twomey, P., Adisa, C. A., Eleweke, N., Au, A., Baehner, F. L., Moore, D. H., McGrath, M. S., Olopade, O. I., Gray, J., Campbell, M. J. & Esserman, L. J., Nov 2012, In : Annals of Surgical Oncology. 19, 12, p. 3979-3986 8 p.

Research output: Contribution to journalArticle

Proliferating Cell Nuclear Antigen
Macrophages
Breast Neoplasms
Neoplasms
Hormones
15 Citations (Scopus)

Genetic Differences in Transcript Responses to Low-Dose Ionizing Radiation Identify Tissue Functions Associated with Breast Cancer Susceptibility

Snijders, A. M., Marchetti, F., Bhatnagar, S., Duru, N., Han, J., Hu, Z., Mao, J. H., Gray, J. & Wyrobek, A. J., Oct 15 2012, In : PLoS One. 7, 10, e45394.

Research output: Contribution to journalArticle

Ionizing radiation
Ionizing Radiation
ionizing radiation
breast neoplasms
Dosimetry
24 Citations (Scopus)

Genome wide DNA copy number analysis of serous type ovarian carcinomas identifies genetic markers predictive of clinical outcome

Engler, D. A., Gupta, S., Growdon, W. B., Drapkin, R. I., Nitta, M., Sergent, P. A., Allred, S. F., Gross, J., Deavers, M. T., Kuo, W. L., Karlan, B. Y., Rueda, B. R., Orsulic, S., Gershenson, D. M., Birrer, M. J., Gray, J. & Mohapatra, G., Feb 15 2012, In : PLoS One. 7, 2, e30996.

Research output: Contribution to journalArticle

Genetic Markers
carcinoma
Tumors
Genes
Genome
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
32 Citations (Scopus)

Genomics: The breast cancer landscape

Gray, J. & Druker, B., Jun 21 2012, In : Nature. 486, 7403, p. 328-329 2 p.

Research output: Contribution to journalArticle

Neoplastic Gene Expression Regulation
Neoplastic Cell Transformation
DNA Copy Number Variations
Genetic Translocation
Aromatase Inhibitors
58 Citations (Scopus)

Identification of PADI2 as a potential breast cancer biomarker and therapeutic target

McElwee, J. L., Mohanan, S., Griffith, O. L., Breuer, H. C., Anguish, L. J., Cherrington, B. D., Palmer, A. M., Howe, L. R., Subramanian, V., Causey, C. P., Thompson, P. R., Gray, J. & Coonrod, S. A., Oct 30 2012, In : BMC Cancer. 12, 500.

Research output: Contribution to journalArticle

Tumor Biomarkers
Breast Neoplasms
Cell Line
cdc Genes
Neoplasms
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
40 Citations (Scopus)

Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers

Drake, P. M., Schilling, B., Niles, R. K., Prakobphol, A., Li, B., Jung, K., Cho, W., Braten, M., Inerowicz, H. D., Williams, K., Albertolle, M., Held, J. M., Iacovides, D., Sorensen, D. J., Griffith, O. L., Johansen, E., Zawadzka, A. M., Cusack, M. P., Allen, S., Gormley, M. & 6 others, Hall, S. C., Witkowska, H. E., Gray, J., Regnier, F., Gibson, B. W. & Fisher, S. J., Apr 6 2012, In : Journal of Proteome Research. 11, 4, p. 2508-2520 13 p.

Research output: Contribution to journalArticle

Workflow
Biomarkers
Chromatography
Lectins
Mass spectrometry
26 Citations (Scopus)

Loss of cell-surface laminin anchoring promotes tumor growth and is associated with poor clinical outcomes

Akhavan, A., Griffith, O. L., Soroceanu, L., Leonoudakis, D., Luciani-Torres, M. G., Daemen, A., Gray, J. & Muschler, J., May 15 2012, In : Cancer Research. 72, 10, p. 2578-2588 11 p.

Research output: Contribution to journalArticle

Laminin
Growth
Neoplasms
Brain Neoplasms
Disease Progression
30 Citations (Scopus)

Omics and therapy - A basis for precision medicine

Garay, J. P. & Gray, J., Apr 2012, In : Molecular Oncology. 6, 2, p. 128-139 12 p.

Research output: Contribution to journalArticle

Precision Medicine
Genome
Neoplasms
Disease Management
Therapeutics
4 Citations (Scopus)

Optimization-based inference for temporally evolving networks with applications in biology

Chang, Y. H., Gray, J. & Tomlin, C., Dec 1 2012, In : Journal of Computational Biology. 19, 12, p. 1307-1323 17 p.

Research output: Contribution to journalArticle

Genetic Network
Biological Networks
Biology
Research Design
Costs and Cost Analysis
246 Citations (Scopus)

Pathologic complete response predicts recurrence-free survival more effectively by cancer subset: Results from the I-SPY 1 TRIAL - CALGB 150007/150012, ACRIN 6657

Esserman, L. J., Berry, D. A., DeMichele, A., Carey, L., Davis, S. E., Buxton, M., Hudis, C., Gray, J., Perou, C., Yau, C., Livasy, C., Krontiras, H., Montgomery, L., Tripathy, D., Lehman, C., Liu, M. C., Olopade, O. I., Rugo, H. S., Carpenter, J. T., Dressler, L. & 8 others, Chhieng, D., Singh, B., Mies, C., Rabban, J., Chen, Y. Y., Giri, D., Van't Veer, L. & Hylton, N., Sep 10 2012, In : Journal of Clinical Oncology. 30, 26, p. 3242-3249 8 p.

Research output: Contribution to journalArticle

Recurrence
Survival
Hormones
Neoplasms
Breast Neoplasms
45 Citations (Scopus)

Rab25 increases cellular ATP and glycogen stores protecting cancer cells from bioenergetic stress

Cheng, K. W., Agarwal, R., Mitra, S., Lee, J. S., Carey, M., Gray, J. & Mills, G., Feb 2012, In : EMBO Molecular Medicine. 4, 2, p. 125-141 17 p.

Research output: Contribution to journalArticle

Glycogen
Energy Metabolism
Adenosine Triphosphate
Neoplasms
Autophagy
264 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
37 Citations (Scopus)

The transcription factor ZNF217 Is a prognostic biomarker and therapeutic target during breast cancer progression

Littlepage, L. E., Adler, A. S., Kouros-Mehr, H., Huang, G., Chou, J., Krig, S. R., Griffi th, O. L., Korkola, J., Qu, K., Lawson, D. A., Xue, Q., Sternlicht, M. D., Dijkgraaf, G. J. P., Yaswen, P., Rugo, H. S., Sweeney, C. A., Collins, C. C., Gray, J., Chang, H. Y. & Werb, Z., Jul 2012, In : Cancer Discovery. 2, 7, p. 638-651 14 p.

Research output: Contribution to journalArticle

triciribine
Transcription Factors
Biomarkers
Breast Neoplasms
Neoplasms
32 Citations (Scopus)

What are we learning from the cancer genome?

Collisson, E. A., Cho, R. J. & Gray, J., Nov 2012, In : Nature Reviews Clinical Oncology. 9, 11, p. 621-630 10 p.

Research output: Contribution to journalArticle

Learning
Genome
Neoplasms
Technology
Precision Medicine
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

Hormone-Dependent Neoplasms
Neoplasm Invasiveness
Chromosomes, Human, Pair 8
Gene Amplification
Neoplasm Genes
22 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
133 Citations (Scopus)

Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence

Fackler, M. J., Umbricht, C. B., Williams, D., Argani, P., Cruz, L. A., Merino, V. F., Teo, W. W., Zhang, Z., Huang, P., Visvananthan, K., Marks, J., Ethier, S., Gray, J., Wolff, A. C., Cope, L. M. & Sukumar, S., Oct 1 2011, In : Cancer Research. 71, 19, p. 6195-6207 13 p.

Research output: Contribution to journalArticle

Estrogen Receptors
Methylation
Genome
Hormones
Breast Neoplasms
3666 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
249 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
43 Citations (Scopus)

Lrig1 is an estrogen-regulated growth suppressor and correlates with longer relapse-free survival in ERα-positive breast cancer

Krig, S. R., Frietze, S., Simion, C., Miller, J. K., Fry, W. H. D., Rafidi, H., Kotelawala, L., Qi, L., Griffith, O. L., Gray, J., Carraway, K. L. & Sweeney, C., Oct 2011, In : Molecular Cancer Research. 9, 10, p. 1406-1417 12 p.

Research output: Contribution to journalArticle

Estrogen Receptors
Estrogens
Breast Neoplasms
Recurrence
Growth
33 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
13 Citations (Scopus)

'Omic approaches to preventing or managing metastatic breast cancer

Griffith, O. L. & Gray, J., Dec 8 2011, In : Breast Cancer Research. 13, 6, 230.

Research output: Contribution to journalArticle

Breast Neoplasms
Residual Neoplasm
Genome
Neoplasm Metastasis
Technology
4 Citations (Scopus)

Optimization-based inference for temporally evolving Boolean networks with applications in biology

Chang, Y. H., Gray, J. & Tomlin, C., 2011, Proceedings of the American Control Conference. p. 4129-4134 6 p. 5991347

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

Cost functions
Systems Biology
549 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
140 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

Magnetic resonance imaging
2010
54 Citations (Scopus)

Activity of the kinesin spindle protein inhibitor ispinesib (SB-715992) in models of breast cancer

Purcell, J. W., Davis, J., Reddy, M., Martin, S., Samayoa, K., Vo, H., Thomsen, K., Bean, P., Kuo, W. L., Ziyad, S., Billig, J., Feiler, H., Gray, J., Wood, K. W. & Cases, S., Jan 15 2010, In : Clinical Cancer Research. 16, 2, p. 566-576 11 p.

Research output: Contribution to journalArticle

Kinesin
Breast Neoplasms
Proteins
Mitosis
ispinesib
3 Citations (Scopus)

An ODE model for the HER2/3-AKT signaling pathway in cancers that overexpress HER2

Itani, S., Gray, J. & Tomlin, C. J., 2010, Proceedings of the 2010 American Control Conference, ACC 2010. p. 1235-1241 7 p. 5531034

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

Drug therapy
Oncology
Mathematical models
Epidermal Growth Factor