• 65500 Citations
  • 111 h-Index
1971 …2020
If you made any changes in Pure, your changes will be visible here soon.

Research Output 1971 2020

2009
72 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
19 Citations (Scopus)

Immutable functional attributes of histologic grade revealed by context-independent gene expression in primary breast cancer cells

Dairkee, S. H., Sayeed, A., Luciani, G., Champion, S., Zhenhang, M., Jakkula, L. R., Feiler, H., Gray, J. & Moore, D. H., Oct 1 2009, In : Cancer Research. 69, 19, p. 7826-7834 9 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Gene Expression
Neoplasms
Genes
Phenotype
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
95 Citations (Scopus)

Integrative analysis of cyclin protein levels identifies cyclin B1 as a classifier and predictor of outcomes in breast cancer

Agarwal, R., Gonzalez-Angulo, A. M., Myhre, S., Carey, M., Lee, J. S., Overgaard, J., Alsner, J., Stemke-Hale, K., Lluch, A., Neve, R. M., Kuo, W. L., Sorlie, T., Sahin, A., Valero, V., Keyomarsi, K., Gray, J., Borresen-Dale, A. L., Mills, G. & Hennessy, B. T., Jun 1 2009, In : Clinical Cancer Research. 15, 11, p. 3654-3662 9 p.

Research output: Contribution to journalArticle

Cyclin B1
Cyclins
Cyclin D1
Breast Neoplasms
Proteins
17 Citations (Scopus)

LARG at chromosome 11q23 has functional characteristics of a tumor suppressor in human breast and colorectal cancer

Ong, D. C. T., Ho, Y. M., Rudduck, C., Chin, K-Y., Kuo, W. L., Lie, D. K. H., Chua, C. L. M., Tan, P. H., Eu, K. W., Seow-Choen, F., Wong, C. Y., Hong, G. S., Gray, J. & Lee, A. S. G., Nov 2009, In : Oncogene. 28, 47, p. 4189-4200 12 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Chromosomes
Breast Neoplasms
Neoplasms
decitabine
1 Citation (Scopus)

Morphometric subtyping for a panel of breast cancer cell lines

Han, J., Chang, H., Fontenay, G., Wang, N. J., Gray, J. & Parvin, B., 2009, Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009. p. 791-794 4 p. 5193168

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

Cells
Breast Neoplasms
Cell Line
Assays
Pipelines
137 Citations (Scopus)

Picomolar sensitivity MRI and photoacoustic imaging of cobalt nanoparticles

Bouchard, L. S., Anwar, M. S., Liu, G. L., Hann, B., Xie, Z. H., Gray, J., Wang, X., Pines, A. & Chen, F. F., Mar 17 2009, In : Proceedings of the National Academy of Sciences of the United States of America. 106, 11, p. 4085-4089 5 p.

Research output: Contribution to journalArticle

Cobalt
Nanoparticles
Tomography
Gold
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
41 Citations (Scopus)

Yin Yang 1 modulates taxane response in epithelial ovarian cancer

Matsumura, N., Huang, Z., Baba, T., Lee, P. S., Barnett, J. C., Mori, S., Chang, J. T., Kuo, W. L., Gusberg, A. H., Whitaker, R. S., Gray, J., Fujii, S., Berchuck, A. & Murphy, S. K., Feb 1 2009, In : Molecular Cancer Research. 7, 2, p. 210-220 11 p.

Research output: Contribution to journalArticle

Yin-Yang
Ovarian Neoplasms
Microtubules
Taxoids
Cell Line
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
141 Citations (Scopus)

A technical assessment of the utility of reverse phase protein arrays for the study of the functional proteome in non-microdissected human breast cancers

Hennessy, B. T., Lu, Y., Gonzalez-Angulo, A. M., Carey, M. S., Myhre, S., Ju, Z., Davies, M. A., Liu, W., Coombes, K., Meric-Bernstam, F., Bedrosian, I., McGahren, M., Agarwal, R., Zhang, F., Overgaard, J., Alsner, J., Neve, R. M., Kuo, W. L., Gray, J., Borresen-Dale, A. L. & 1 others, Mills, G., Dec 2010, In : Clinical Proteomics. 6, 4, p. 129-151 23 p.

Research output: Contribution to journalArticle

Protein Array Analysis
Proteome
Breast Neoplasms
Antibodies
Tumors
37 Citations (Scopus)

Breast cancer genomes - form and function

Korkola, J. & Gray, J., Feb 2010, In : Current Opinion in Genetics and Development. 20, 1, p. 4-14 11 p.

Research output: Contribution to journalArticle

Genome
Breast Neoplasms
Epigenomics
Neoplasm Metastasis
Technology
10 Citations (Scopus)

Cancer: Genomics of metastasis

Gray, J., Apr 15 2010, In : Nature. 464, 7291, p. 989-990 2 p.

Research output: Contribution to journalArticle

Neoplasm Transplantation
DNA Mutational Analysis
DNA Copy Number Variations
alpha Catenin
disease prevalence
4 Citations (Scopus)

ERBB receptor regulation of ESX/ELF3 promotes invasion in breast epithelial cells

Coppe, J. P., Amend, C., Semeiks, J., Baehner, F. L., Bayani, N., Campisi, J., Benz, C. C., Gray, J. & Neve, R. M., 2010, In : Open Cancer Journal. 3, SPEC. ISSUE 1, p. 89-100 12 p.

Research output: Contribution to journalArticle

Epidermal Growth Factor
Breast
Proto-Oncogene Proteins c-ets
Epithelial Cells
Breast Neoplasms
85 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
186 Citations (Scopus)

HER2 signaling pathway activation and response of breast cancer cells to HER2-targeting agents is dependent strongly on the 3D microenvironment

Weigelt, B., Lo, A. T., Park, C. C., Gray, J. & Bissell, M. J., Jul 2010, In : Breast Cancer Research and Treatment. 122, 1, p. 35-43 9 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Cell Line
Extracellular Matrix
Antibodies, Monoclonal, Humanized
Laminin
28 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
3512 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
27 Citations (Scopus)

Linking changes in epithelial morphogenesis to cancer mutations using computational modeling

Rejniak, K. A., Wang, S. E., Bryce, N. S., Chang, H., Parvin, B., Jourquin, J., Estrada, L., Gray, J., Arteaga, C. L., Weaver, A. M., Quaranta, V. & Anderson, A. R. A., Aug 2010, In : PLoS Computational Biology. 6, 8, e1000900.

Research output: Contribution to journalArticle

Morphogenesis
Computational Modeling
morphogenesis
tumor
Linking
57 Citations (Scopus)

Molecular predictors of 3D morphogenesis by breast cancer cell lines in 3D culture

Han, J., Chang, H., Giricz, O., Lee, G. Y., Baehner, F. L., Gray, J., Bissell, M. J., Kenny, P. A. & Parvin, B., Feb 2010, In : PLoS Computational Biology. 6, 2, e1000684.

Research output: Contribution to journalArticle

Morphogenesis
morphogenesis
Breast Cancer
Cell culture
Phenotype
7 Citations (Scopus)

p27Kip1 mediates addiction of ovarian cancer cells to MYCC (c-MYC) and their dependence on MYC paralogs

Prathapam, T., Aleshin, A., Guan, Y., Gray, J. & Martin, G. S., Oct 15 2010, In : Journal of Biological Chemistry. 285, 42, p. 32529-32538 10 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Cells
Cyclin A
Small Interfering RNA
Cell Aging
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
151 Citations (Scopus)

Proteomic and transcriptomic profiling reveals a link between the PI3K pathway and lower estrogen-receptor (ER) levels and activity in ER+ breast cancer

Creighton, C. J., Fu, X., Hennessy, B. T., Casa, A. J., Zhang, Y., Gonzalez-Angulo, A. M., Lluch, A., Gray, J., Brown, P. H., Hilsenbeck, S. G., Osborne, C. K., Mills, G., Lee, A. V. & Schiff, R., Jun 22 2010, In : Breast Cancer Research. 12, 3, R40.

Research output: Contribution to journalArticle

Phosphatidylinositol 3-Kinase
Estrogen Receptors
Proteomics
Breast Neoplasms
Growth Factor Receptors
12 Citations (Scopus)

Radiosensitivity profiles from a panel of ovarian cancer cell lines exhibiting genetic alterations in p53 and disparate DNA-dependent protein kinase activities

Langland, G. T., Yannone, S. M., Langland, R. A., Nakao, A., Guan, Y., Long, S. B. T., Vonguyen, L., Chen, D. J., Gray, J. & Chen, F., Apr 2010, In : Oncology Reports. 23, 4, p. 1021-1026 6 p.

Research output: Contribution to journalArticle

DNA-Activated Protein Kinase
Radiation Tolerance
Ovarian Neoplasms
Cell Line
Radiation
229 Citations (Scopus)

Restriction of receptor movement alters cellular response: Physical force sensing by EphA2

Salaita, K., Nair, P. M., Petit, R. S., Neve, R. M., Das, D., Gray, J. & Groves, J. T., Mar 12 2010, In : Science. 327, 5971, p. 1380-1385 6 p.

Research output: Contribution to journalArticle

Ephrin-A1
Ligands
EphA2 Receptor
Disintegrins
Architectural Accessibility
21 Citations (Scopus)

Sparse multitask regression for identifying common mechanism of response to therapeutic targets

Zhang, K., Gray, J. & Parvin, B., Jun 1 2010, In : Bioinformatics. 26, 12, btq181.

Research output: Contribution to journalArticle

Cell Cycle
Regression
Cells
Synthetic Data
Gene Expression
70 Citations (Scopus)

The expression level of HJURP has an independent prognostic impact and predicts the sensitivity to radiotherapy in breast cancer

Hu, Z., Huang, G., Sadanandam, A., Gu, S., Lenburg, M. E., Pai, M., Bayani, N., Blakely, E. A., Gray, J. & Mao, J. H., Mar 8 2010, In : Breast Cancer Research. 12, 2, R18.

Research output: Contribution to journalArticle

Cruciform DNA
Radiotherapy
Breast Neoplasms
Proteins
Messenger RNA
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
134 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
3714 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
253 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
14 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
561 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
142 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
2012
135 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
62 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
191 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