Research Output 2004 2018

  • 33524 Citations
  • 42 h-Index
  • 58 Article
  • 3 Comment/debate
  • 1 Chapter
  • 1 Review article
2018

Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer

Siegel, M. B. , He, X. , Hoadley, K. A. , Hoyle, A. , Pearce, J. B. , Garrett, A. L. , Kumar, S. , Moylan, V. J. , Brady, C. M. , Van Swearingen, A. E. D. , Marron, D. , Gupta, G. P. , Thorne, L. B. , Kieran, N. , Livasy, C. , Mardis, E. R. , Parker, J. S. , Chen, M. , Anders, C. K. , Carey, L. A. & 1 others Perou, C. M. Apr 2 2018 In : Journal of Clinical Investigation. 128, 4, p. 1371-1383 13 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
DNA Sequence Analysis
Breast Neoplasms
Neoplasm Metastasis
Neoplasms

Pathological response in a triple-negative breast cancer cohort treated with neoadjuvant carboplatin and docetaxel according to Lehmann's refined classification

Echavarria, I. , Lopez-Tarruella, S. , Picornell, A. , García-Saenz, J. A. , Jerez, Y. , Hoadley, K. , Gomez, H. L. , Moreno, F. , Monte-Millan, M. D. , Marquez-Rodas, I. , Alvarez, E. , Ramos-Medina, R. , Gayarre, J. , Massarrah, T. , Ocaña, I. , Cebollero, M. , Fuentes, H. , Barnadas, A. , Ballesteros, A. I. , Bohn, U. & 2 others Perou, C. M. & Martin, M. Apr 15 2018 In : Clinical Cancer Research. 24, 8, p. 1845-1852 8 p.

Research output: Contribution to journalArticle

docetaxel
Triple Negative Breast Neoplasms
Carboplatin
Drug Therapy
Germ-Line Mutation

Racial Differences in PAM50 Subtypes in the Carolina Breast Cancer Study

Troester, M. A., Sun, X., Allott, E. H., Geradts, J., Cohen, S. M., Tse, C. K., Kirk, E. L., Thorne, L. B., Mathews, M., Li, Y., Hu, Z., Robinson, W. R., Hoadley, K. A., Olopade, O. I., Reeder-Hayes, K. E., Earp, H. S., Olshan, A. F., Carey, L. A. & Perou, C. M. Feb 1 2018 In : Journal of the National Cancer Institute. 110, 2, djx135

Research output: Contribution to journalArticle

Neoplasm RNA
ErbB-2 Receptor
Progesterone Receptors
Tumor Burden
Estrogen Receptors

Reproductive risk factor associations with lobular and ductal carcinoma in the Carolina Breast Cancer Study

Williams, L. A., Nichols, H. B., Hoadley, K. A., Tse, C. K., Geradts, J., Bell, M. E., Perou, C. M., Love, M. I., Olshan, A. F. & Troester, M. A. Jan 1 2018 In : Cancer Causes and Control. 29, 1, p. 25-32 8 p.

Research output: Contribution to journalArticle

Lobular Carcinoma
Ductal Carcinoma
Histology
Breast Neoplasms
Odds Ratio
2017
2 Citations

Age at diagnosis, obesity, smoking, and molecular subtypes in muscle-invasive bladder cancer

Sun, X., Hoadley, K. A., Kim, W. Y., Furberg, H., Olshan, A. F. & Troester, M. A. Jun 1 2017 In : Cancer Causes and Control. 28, 6, p. 539-544 6 p.

Research output: Contribution to journalArticle

Urinary Bladder Neoplasms
Obesity
Smoking
Muscles
Atlases
6 Citations

Use of molecular tools to identify patients with indolent breast cancers with ultralow risk over 2 decades

Esserman, L. J., Yau, C., Thompson, C. K., Van 't Veer, L. J., Borowsky, A. D., Hoadley, K. A., Tobin, N. P., Nordenskjöld, B., Fornander, T., Stål, O., Benz, C. C. & Lindström, L. S. Nov 1 2017 In : JAMA Oncology. 3, 11, p. 1503-1510 8 p.

Research output: Contribution to journalArticle

Hormonal Antineoplastic Agents
Predictive Value of Tests
Adjuvant Radiotherapy
Segmental Mastectomy
Mastectomy
2016
33 Citations
B-Lymphocytes
Confidence Intervals
Neoplasms
Melanoma
Survival
72 Citations

Molecular heterogeneity and response to neoadjuvant human epidermal growth factor receptor 2 targeting in CALGB 40601, a randomized phase III trial of paclitaxel plus trastuzumab with or without lapatinib

Carey, L. A., Berry, D. A., Cirrincione, C. T., Barry, W. T., Pitcher, B. N., Harris, L. N., Ollila, D. W., Krop, I. E., Henry, N. L., Weckstein, D. J., Anders, C. K., Singh, B., Hoadley, K. A., Iglesia, M., Cheang, M. C. U., Perou, C. M., Winer, E. P. & Hudis, C. A. Feb 20 2016 In : Journal of Clinical Oncology. 34, 6, p. 542-549 8 p.

Research output: Contribution to journalArticle

Paclitaxel
Tumor Microenvironment
Gene Expression
Arm
Hormones
2015
553 Citations

Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas

Brat, D. J. , Verhaak, R. G. W. , Aldape, K. D. , Yung, W. K. A. , Salama, S. R. , Cooper, L. A. D. , Rheinbay, E. , Miller, C. R. , Vitucci, M. , Morozova, O. , Robertson, A. G. , Noushmehr, H. , Laird, P. W. , Cherniack, A. D. , Akbani, R. , Huse, J. T. , Ciriello, G. , Poisson, L. M. , Barnholtz-Sloan, J. S. , Berger, M. S. & 30 others Brennan, C., Colen, R. R., Colman, H., Flanders, A. E., Giannini, C., Grifford, M., Iavarone, A., Jain, R., Joseph, I., Kim, J., Kasaian, K., Mikkelsen, T., Murray, B. A., O'Neill, B. P., Pachter, L., Parsons, D. W., Sougnez, C., Sulman, E. P., Vandenberg, S. R., Van Meir, E. G., Von Deimling, A., Zhang, H., Crain, D., Lau, K., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, T. & Sherman, M. Jun 25 2015 In : New England Journal of Medicine. 372, 26, p. 2481-2498 18 p.

Research output: Contribution to journalArticle

Glioma
Mutation
Glioblastoma
DNA Methylation
Exome
764 Citations

Comprehensive genomic characterization of head and neck squamous cell carcinomas

The Cancer Genome Atlas Network Jan 29 2015 In : Nature. 517, 7536, p. 576-582 7 p.

Research output: Contribution to journalArticle

Mutation
Neoplasms
TNF Receptor-Associated Factor 3
cdc Genes
Atlases
295 Citations

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

Ciriello, G. , Gatza, M. L. , Beck, A. H. , Wilkerson, M. D. , Rhie, S. K. , Pastore, A. , Zhang, H. , McLellan, M. , Yau, C. , Kandoth, C. , Bowlby, R. , Shen, H. , Hayat, S. , Fieldhouse, R. , Lester, S. C. , Tse, G. M. K. , Factor, R. E. , Collins, L. C. , Allison, K. H. , Chen, Y. Y. & 30 others Jensen, K., Johnson, N. B., Oesterreich, S., Mills, G. B., Cherniack, A. D., Robertson, G., Benz, C., Sander, C., Laird, P. W., Hoadley, K. A., King, T. A., Akbani, R., Auman, J. T., Balasundaram, M., Balu, S., Barr, T., Benz, S., Berrios, M., Beroukhim, R., Bodenheimer, T., Boice, L., Bootwalla, M. S., Bowen, J., Brooks, D., Chin, L., Cho, J., Chudamani, S., Davidsen, T., Demchok, J. A. & Dennison, J. B. Oct 8 2015 In : Cell. 163, 2, p. 506-519 14 p.

Research output: Contribution to journalArticle

Lobular Carcinoma
Breast Neoplasms
Phosphorylation
Cadherins
Tumors
526 Citations

Genomic Classification of Cutaneous Melanoma

The Cancer Genome Atlas Network Jun 20 2015 In : Cell. 161, 7, p. 1681-1696 16 p.

Research output: Contribution to journalArticle

Melanoma
Skin
T-cells
Lymphocytes
Pathology
5 Citations

Proteomic profiling of patient-derived glioblastoma xenografts identifies a subset with activated EGFR: Implications for drug development

Brown, K. E., Chagoya, G., Kwatra, S. G., Yen, T., Keir, S. T., Cooter, M., Hoadley, K. A., Rasheed, A., Lipp, E. S., McLendon, R., Ali-Osman, F., Bigner, D. D., Sampson, J. H. & Kwatra, M. M. Jun 1 2015 In : Journal of Neurochemistry. 133, 5, p. 730-738 9 p.

Research output: Contribution to journalArticle

Glioblastoma
Heterografts
Proteomics
Pharmaceutical Preparations
Genes
22 Citations

Response and survival of breast cancer intrinsic subtypes following multi-agent neoadjuvant chemotherapy

Prat, A., Fan, C., Fernández, A., Hoadley, K. A., Martinello, R., Vidal, M., Viladot, M., Pineda, E., Arance, A., Muñoz, M., Paré, L., Cheang, M. C. U., Adamo, B. & Perou, C. M. Dec 18 2015 In : BMC Medicine. 13, 1, 303

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
Breast Neoplasms
Drug Therapy
Survival
Recurrence
2 Citations

The Cancer Genome Atlas Project on Muscle-invasive Bladder Cancer

Lerner, S. P., Weinstein, J., Kwiatkowski, D., Kim, J., Robertson, G., Hoadley, K. A., Akbani, R., Creighton, C. & on behalf of the TCGA Muscle Invasive Bladder Cancer Analysis Working Group Jan 1 2015 In : European Urology Focus. 1, 1, p. 94-95 2 p.

Research output: Contribution to journalArticle

Atlases
Urinary Bladder Neoplasms
Genome
Muscles
Neoplasms
390 Citations

The Molecular Taxonomy of Primary Prostate Cancer

Abeshouse, A. , Ahn, J. , Akbani, R. , Ally, A. , Amin, S. , Andry, C. D. , Annala, M. , Aprikian, A. , Armenia, J. , Arora, A. , Auman, J. T. , Balasundaram, M. , Balu, S. , Barbieri, C. E. , Bauer, T. , Benz, C. C. , Bergeron, A. , Beroukhim, R. , Berrios, M. , Bivol, A. & 30 others Bodenheimer, T., Boice, L., Bootwalla, M. S., Borges Dos Reis, R., Boutros, P. C., Bowen, J., Bowlby, R., Boyd, J., Bradley, R. K., Breggia, A., Brimo, F., Bristow, C. A., Brooks, D., Broom, B. M., Bryce, A. H., Bubley, G., Burks, E., Butterfield, Y. S. N., Button, M., Canes, D., Carlotti, C. G., Carlsen, R., Carmel, M., Carroll, P. R., Carter, S. L., Cartun, R., Carver, B. S., Chan, J. M., Chang, M. T. & Chen, Y. Nov 5 2015 In : Cell. 163, 4, p. 1011-1025 15 p.

Research output: Contribution to journalArticle

Taxonomies
Prostatic Neoplasms
Genes
Androgen Receptors
Tumors
178 Citations

Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma

Moffitt, R. A., Marayati, R., Flate, E. L., Volmar, K. E., Loeza, S. G. H., Hoadley, K. A., Rashid, N. U., Williams, L. A., Eaton, S. C., Chung, A. H., Smyla, J. K., Anderson, J. M., Kim, H. J., Bentrem, D. J., Talamonti, M. S., Iacobuzio-Donahue, C. A., Hollingsworth, M. A. & Yeh, J. J. Jan 1 2015 In : Nature Genetics. 47, 10, p. 1168-1178 11 p.

Research output: Contribution to journalArticle

Microdissection
Adenocarcinoma
Neoplasms
Gene Expression
Urinary Bladder Neoplasms
2014
82 Citations
RNA Sequence Analysis
Poly A
Oligonucleotide Array Sequence Analysis
Paraffin
Formaldehyde
953 Citations

Comprehensive molecular characterization of urothelial bladder carcinoma

Weinstein, J. N. , Akbani, R. , Broom, B. M. , Wang, W. , Verhaak, R. G. W. , McConkey, D. , Lerner, S. , Morgan, M. , Creighton, C. J. , Smith, C. , Cherniack, A. D. , Kim, J. , Pedamallu, C. S. , Noble, M. S. , Al-Ahmadie, H. A. , Reuter, V. E. , Rosenberg, J. E. , F.Bajorin, D. , Bochner, B. H. , Solit, D. B. & 30 others Koppie, T., Robinson, B., Gordenin, D. A., Fargo, D., Klimczak, L. J., Roberts, S. A., Au, J., Laird, P. W., Hinoue, T., Schultz, N., Ramirez, R., Hansel, D., Hoadley, K. A., Kim, W. Y., Damrauer, J. S., Baylin, S. B., Mungall, A. J., Robertson, A. G., Chu, A., Kwiatkowski, D. J., Sougnez, C., Cibulskis, K., Lichtenstein, L., Sivachenko, A., Stewart, C., Lawrence, M. S., Getz, G., Lander, E., Gabrie, S. B. & Donehower, L. Jan 1 2014 In : Nature. 507, 7492, p. 315-322 8 p.

Research output: Contribution to journalArticle

Urinary Bladder
Carcinoma
Chromatin
RNA Sequence Analysis
Neoplasms
1223 Citations

Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network

Collisson, E. A. , Campbell, J. D. , Brooks, A. N. , Berger, A. H. , Lee, W. , Chmielecki, J. , Beer, D. G. , Cope, L. , Creighton, C. J. , Danilova, L. , Ding, L. , Getz, G. , Hammerman, P. S. , Hayes, D. N. , Hernandez, B. , Herman, J. G. , Heymach, J. V. , Jurisica, I. , Kucherlapati, R. , Kwiatkowski, D. & 30 others Ladanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M. S., Travis, W. D., Weinstein, J. N., Wigle, D. A., Wilkerson, M. D., Chu, A., Cherniack, A. D., Hadjipanayis, A., Rosenberg, M., Weisenberger, D. J., Laird, P. W., Radenbaugh, A., Ma, S., Stuart, J. M., Byers, L. A., Baylin, S. B., Govindan, R., Meyerson, M., Gabriel, S. B., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L. & Lander, E. S. Jan 1 2014 In : Nature. 511, 7511, p. 543-550 8 p.

Research output: Contribution to journalArticle

Atlases
Genome
Mutation
Research
Neoplasms

Erratum: Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes (PLoS ONE (2014) 9:1 DOI: 10.1371/annotation/e9ad5950-a048-4a44-8e26-d8b07a9d4bb8)

Walter, V. , Yin, X. , Wilkerson, M. D. , Cabanski, C. R. , Zhao, N. , Du, Y. , Ang, M. K. , Hayward, M. C. , Salazar, A. H. , Hoadley, K. A. , Fritchie, K. , Sailey, C. G. , Weissler, M. C. , Shockley, W. W. , Zanation, A. M. , Hackman, T. , Thorne, L. B. , Funkhouser, W. D. , Muldrew, K. L. , Olshan, A. F. & 4 others Randell, S. H., Wright, F. A., Shores, C. G. & Hayes, D. N. Jan 16 2014 In : PLoS ONE. 9, 1, 1315

Research output: Contribution to journalComment/debate

Neoplasm Genes
Head and Neck Neoplasms
neoplasms
genes
head and neck neoplasms
575 Citations

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

Agrawal, N. , Akbani, R. , Aksoy, B. A. , Ally, A. , Arachchi, H. , Asa, S. L. , Auman, J. T. , Balasundaram, M. , Balu, S. , Baylin, S. B. , Behera, M. , Bernard, B. , Beroukhim, R. , Bishop, J. A. , Black, A. D. , Bodenheimer, T. , Boice, L. , Bootwalla, M. S. , Bowen, J. , Bowlby, R. & 30 others Bristow, C. A., Brookens, R., Brooks, D., Bryant, R., Buda, E., Butterfield, Y. S. N., Carling, T., Carlsen, R., Carter, S. L., Carty, S. E., Chan, T. A., Chen, A. Y., Cherniack, A. D., Cheung, D., Chin, L., Cho, J., Chu, A., Chuah, E., Cibulskis, K., Ciriello, G., Clarke, A., Clayman, G. L., Cope, L., Copland, J. A., Covington, K., Danilova, L., Davidsen, T., Demchok, J. A., DiCara, D. & Dhalla, N. Oct 23 2014 In : Cell. 159, 3, p. 676-690 15 p.

Research output: Contribution to journalArticle

Thyroid Neoplasms
Factor IX
Methylation
Pathology
Gene expression
35 Citations

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors

Wilkerson, M. D., Cabanski, C. R., Sun, W., Hoadley, K. A., Walter, V., Mose, L. E., Troester, M. A., Hammerman, P. S., Parker, J. S., Perou, C. M. & Hayes, D. N. Jan 1 2014 In : Nucleic acids research. 42, 13

Research output: Contribution to journalArticle

RNA Sequence Analysis
Exome
DNA Sequence Analysis
Mutation
DNA
216 Citations

Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology

Damrauer, J. S., Hoadley, K. A., Chism, D. D., Fan, C., Tiganelli, C. J., Wobker, S. E., Yeh, J. J., Milowsky, M. I., Iyer, G., Parker, J. S. & Kim, W. Y. Feb 25 2014 In : Proceedings of the National Academy of Sciences of the United States of America. 111, 8, p. 3110-3115 6 p.

Research output: Contribution to journalArticle

Urinary Bladder Neoplasms
Breast Neoplasms
Gene Expression
Microarray Analysis
Standard of Care
14 Citations

Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status

Prat, A., Cruz, C., Hoadley, K. A., Díez, O., Perou, C. M. & Balmaña, J. Jan 1 2014 In : Breast Cancer Research and Treatment. 147, 1, p. 185-191 7 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Mutation
DNA Methylation
Neoplasms
MicroRNAs
443 Citations

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

The Cancer Genome Atlas Research Network Aug 14 2014 In : Cell. 158, 4, p. 929-944 16 p.

Research output: Contribution to journalArticle

Tissue
Urinary Bladder Neoplasms
Neoplasms
Genes
Data Mining
19 Citations

Overexpression of miR-146a in basal-like breast cancer cells confers enhanced tumorigenic potential in association with altered p53 status

Sandhu, R., Rein, J., D'Arcy, M., Herschkowitz, J. I., Hoadley, K. A. & Troester, M. A. Nov 1 2014 In : Carcinogenesis. 35, 11, p. 2567-2575 9 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Neoplasms
Up-Regulation
Down-Regulation
Mutation Rate
52 Citations
Ovarian Neoplasms
B-Lymphocytes
Breast Neoplasms
Messenger RNA
Neoplasms
2013
9 Citations

BreakTrans: Uncovering the genomic architecture of gene fusions

Chen, K., Navin, N. E., Wang, Y., Schmidt, H. K., Wallis, J. W., Niu, B., Fan, X., Zhao, H., McLellan, M. D., Hoadley, K. A., Mardis, E. R., Ley, T. J., Perou, C. M., Wilson, R. K. & Ding, L. Aug 23 2013 In : Genome Biology. 14, 8, R87

Research output: Contribution to journalArticle

gene fusion
Gene Fusion
cancer
genomics
gene
1030 Citations

Comprehensivemolecular characterization of clear cell renal cell carcinoma

Creighton, C. J. , Morgan, M. , Gunaratne, P. H. , Wheeler, D. A. , Gibbs, R. A. , Robertson, G. , Chu, A. , Beroukhim, R. , Cibulskis, K. , Signoretti, S. , Vandin, F. , Wu, H. T. , Raphael, B. J. , Verhaak, R. G. W. , Tamboli, P. , Torres-Garcia, W. , Akbani, R. , Weinstein, J. N. , Reuter, V. , Hsieh, J. J. & 30 others Brannon, A. R., Hakimi, A. A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C. J., Linehan, W. M., Stuart, J. M., Rathmell, W. K., Hui, S., Laird, P. W., Muzny, D., Davis, C., Liu, X., Chang, K., Kakkar, N., Treviño, L. R., Benton, S., Reid, J. G., Morton, D., Doddapaneni, H., Yi, H., Lewis, L., Huyen, D., Kovar, C., Zhu, Y., Santibanez, J., Min, W., Hale, W. & Kalra, D. Aug 28 2013 In : Nature. 499, 7456, p. 43-49 7 p.

Research output: Contribution to journalArticle

Renal Cell Carcinoma
Genes
PTEN Phosphohydrolase
Acetyl-CoA Carboxylase
Pentose Phosphate Pathway
3 Citations

Erratum: Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes (PLoS ONE (2013) 8:7 DOI:10.1371/annotation/b42f61c5-cb7e-49ca-8cd6-6e1f7903ad08)

Walter, V. , Yin, X. , Wilkerson, M. D. , Cabanski, C. R. , Zhao, N. , Du, Y. , Ang, M. K. , Hayward, M. C. , Salazar, A. H. , Hoadley, K. A. , Fritchie, K. , Sailey, C. J. , Weissler, M. C. , Shockley, W. W. , Zanation, A. M. , Hackman, T. , Thorne, L. B. , Funkhouser, W. D. , Muldrew, K. L. , Olshan, A. F. & 4 others Randell, S. H., Wright, F. A., Shores, C. G. & Hayes, D. N. Jul 16 2013 In : PLoS ONE. 8, 7, A2275

Research output: Contribution to journalComment/debate

Neoplasm Genes
Head and Neck Neoplasms
neoplasms
genes
head and neck neoplasms
1424 Citations

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

Ley, T. J. , Miller, C. , Ding, L. , Raphael, B. J. , Mungall, A. J. , Robertson, G. , Hoadley, K. , Triche, T. J. , Laird, P. W. , Baty, J. D. , Fulton, L. L. , Fulton, R. , Heath, S. E. , Kalicki-Veizer, J. , Kandoth, C. , Klco, J. M. , Koboldt, D. C. , Kanchi, K. L. , Kulkarni, S. , Lamprecht, T. L. & 30 others Larson, D. E., Lin, G., Lu, C., McLellan, M. D., McMichael, J. F., Payton, J., Schmidt, H., Spencer, D. H., Tomasson, M. H., Wallis, J. W., Wartman, L. D., Watson, M. A., Welch, J., Wendl, M. C., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chiu, R., Chu, A., Chuah, E., Chun, H. J., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A. & Jones, S. May 30 2013 In : New England Journal of Medicine. 368, 22, p. 2059-2074 16 p.

Research output: Contribution to journalArticle

Acute Myeloid Leukemia
Epigenomics
Genes
Mutation
Genome
46 Citations

Impact of tumor microenvironment and epithelial phenotypes on metabolism in breast cancer

Brauer, H. A., Makowski, L., Hoadley, K. A., Casbas-Hernandez, P., Lang, L. J., Romàn-Pèrez, E., D'Arcy, M., Freemerman, A. J., Perou, C. M. & Troester, M. A. Feb 1 2013 In : Clinical Cancer Research. 19, 3, p. 571-585 15 p.

Research output: Contribution to journalArticle

Tumor Microenvironment
Breast Neoplasms
Phenotype
Hepatocyte Growth Factor
Neoplasms
1139 Citations

Integrated genomic characterization of endometrial carcinoma

Getz, G. , Gabriel, S. B. , Cibulskis, K. , Lander, E. , Sivachenko, A. , Sougnez, C. , Lawrence, M. , Kandoth, C. , Dooling, D. , Fulton, R. , Fulton, L. , Kalicki-Veizer, J. , McLellan, M. D. , O'Laughlin, M. , Schmidt, H. , Wilson, R. K. , Ye, K. , Li, D. , Ally, A. , Balasundaram, M. & 30 others Birol, I., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H. J. E., Dhalla, N., Guin, R., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Plettner, P., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R. J., Gordon Robertson, A., Cherniack, A. D., Pashtan, I., Saksena, G., Onofrio, R. C., Schumacher, S. E. & Tabak, B. May 13 2013 In : Nature. 497, 7447, p. 67-73 7 p.

Research output: Contribution to journalArticle

Endometrial Neoplasms
Mutation
Neoplasms
Microsatellite Instability
Chromatin Assembly and Disassembly
54 Citations

Joint and individual variation explained (JIVE) for integrated analysis of multiple data types

Lock, E. F., Hoadley, K. A., Marron, J. S. & Nobel, A. B. Mar 1 2013 In : Annals of Applied Statistics. 7, 1, p. 523-542 20 p.

Research output: Contribution to journalArticle

Tumors
Genes
Decomposition
Gene expression
Principal component analysis
95 Citations

Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes

Walter, V. , Yin, X. , Wilkerson, M. D. , Cabanski, C. R. , Zhao, N. , Du, Y. , Ang, M. K. , Hayward, M. C. , Salazar, A. H. , Hoadley, K. A. , Fritchie, K. , Sailey, C. G. , Weissler, M. C. , Shockley, W. W. , Zanation, A. M. , Hackman, T. , Thorne, L. B. , Funkhouser, W. D. , Muldrew, K. L. , Olshan, A. F. & 4 others Randell, S. H., Wright, F. A., Shores, C. G. & Hayes, D. N. Feb 22 2013 In : PLoS ONE. 8, 2, e56823

Research output: Contribution to journalArticle

Papillomaviridae
papilloma
Neoplasm Genes
squamous cell carcinoma
Head and Neck Neoplasms
194 Citations

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. T., Zhang, Y., Akbani, R., Hoadley, K. A., Kahn, A., Köbel, M., Huntsman, D., Soslow, R. A., Defazio, A., Birrer, M. J., Gray, J. W., 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
1107 Citations

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N. , Collisson, E. A. , Mills, G. B. , Shaw, K. R. M. , Ozenberger, B. A. , Ellrott, K. , Sander, C. , Stuart, J. M. , Chang, K. , Creighton, C. J. , Davis, C. , Donehower, L. , Drummond, J. , Wheeler, D. , Ally, A. , Balasundaram, M. , Birol, I. , Butterfield, Y. S. N. , Chu, A. , Chuah, E. & 30 others Chun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I. & Pedamallu, C. S. Oct 1 2013 In : Nature Genetics. 45, 10, p. 1113-1120 8 p.

Research output: Contribution to journalReview article

Atlases
Genome
Neoplasms
Epigenomics
RNA
46 Citations

The molecular diversity of Luminal A breast tumors

Ciriello, G., Sinha, R., Hoadley, K. A., Jacobsen, A. S., Reva, B., Perou, C. M., Sander, C. & Schultz, N. Oct 1 2013 In : Breast Cancer Research and Treatment. 141, 3, p. 409-420 12 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Mutation
Aurora Kinases
Chromosomes, Human, Pair 16
Co-Repressor Proteins
1161 Citations

The somatic genomic landscape of glioblastoma

TCGA Research Network Oct 10 2013 In : Cell. 155, 2

Research output: Contribution to journalArticle

Glioblastoma
Tumors
Telomerase
Biomarkers
Neoplasms
2012
1592 Citations

Comprehensive genomic characterization of squamous cell lung cancers

Hammerman, P. S. , Voet, D. , Lawrence, M. S. , Voet, D. , Jing, R. , Cibulskis, K. , Sivachenko, A. , Stojanov, P. , McKenna, A. , Lander, E. S. , Gabriel, S. , Getz, G. , Imielinski, M. , Helman, E. , Hernandez, B. , Pho, N. H. , Meyerson, M. , Chu, A. , Hye-Chun, J. E. , Mungall, A. J. & 30 others Pleasance, E., Robertson, A. G., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, K., Nip, K. M., Olshen, A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T. & Zhao, Y. Sep 27 2012 In : Nature. 489, 7417, p. 519-525 7 p.

Research output: Contribution to journalArticle

Squamous Cell Neoplasms
Lung Neoplasms
Mutation
Neoplasms
Genes
2838 Citations

Comprehensive molecular characterization of human colon and rectal cancer

Muzny, D. M. , Bainbridge, M. N. , Chang, K. , Dinh, H. H. , Drummond, J. A. , Fowler, G. , Kovar, C. L. , Lewis, L. R. , Morgan, M. B. , Newsham, I. F. , Reid, J. G. , Santibanez, J. , Shinbrot, E. , Trevino, L. R. , Wu, Y. Q. , Wang, M. , Gunaratne, P. , Donehower, L. A. , Creighton, C. J. , Wheeler, D. A. & 30 others Gibbs, R. A., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Ding, L., Fulton, R. S., Koboldt, D. C., Wylie, T., Walker, J., Dooling, D. J., Fulton, L., Delehaunty, K. D., Fronick, C. C., Demeter, R., Mardis, E. R., Wilson, R. K., Chu, A., Chun, H. J. E., Mungall, A. J., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M. & Birol, I. Jul 19 2012 In : Nature. 487, 7407, p. 330-337 8 p.

Research output: Contribution to journalArticle

Rectal Neoplasms
Colonic Neoplasms
Colorectal Neoplasms
Mutation
Genome
4061 Citations

Comprehensive molecular portraits of human breast tumours

Koboldt, D. C. , Fulton, R. S. , McLellan, M. D. , Schmidt, H. , Kalicki-Veizer, J. , McMichael, J. F. , Fulton, L. L. , Dooling, D. J. , Ding, L. , Mardis, E. R. , Wilson, R. K. , Ally, A. , Balasundaram, M. , Butterfield, Y. S. N. , Carlsen, R. , Carter, C. , Chu, A. , Chuah, E. , Chun, H. J. E. , Coope, R. J. N. & 30 others Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Pleasance, E., Robertson, A. G., Schein, J. E., Shafiei, A., Sipahimalani, P., Slobodan, J. R., Stoll, D., Tam, A., Thiessen, N., Varhol, R. J., Wye, N., Zeng, T., Zhao, Y., Birol, I., Jones, S. J. M., Marra, M. A., Cherniack, A. D., Saksena, G., Onofrio, R. C. & Pho, N. H. Oct 4 2012 In : Nature. 490, 7418, p. 61-70 10 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Mutation
Exome
Protein Array Analysis
p53 Genes
302 Citations

Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer

Duncan, J. S. , Whittle, M. C. , Nakamura, K. , Abell, A. N. , Midland, A. A. , Zawistowski, J. S. , Johnson, N. L. , Granger, D. A. , Jordan, N. V. , Darr, D. B. , Usary, J. , Kuan, P. F. , Smalley, D. M. , Major, B. , He, X. , Hoadley, K. A. , Zhou, B. , Sharpless, N. E. , Perou, C. M. , Kim, W. Y. & 7 others Gomez, S. M., Chen, X., Jin, J., Frye, S. V., Earp, H. S., Graves, L. M. & Johnson, G. L. Apr 13 2012 In : Cell. 149, 2, p. 307-321 15 p.

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
Mitogen-Activated Protein Kinase Kinases
Receptor Protein-Tyrosine Kinases
Corrosion inhibitors
Drug Resistance
90 Citations

MiR-181d: Predictive glioblastoma biomarker that downregulates MGMT expression

Zhang, W., Zhang, J., Hoadley, K., Kushwaha, D., Ramakrishnan, V., Li, S., Kang, C., You, Y., Jiang, C., Song, S. W., Jiang, T. & Chen, C. C. Jun 1 2012 In : Neuro-Oncology. 14, 6, p. 712-719 8 p.

Research output: Contribution to journalArticle

temozolomide
Guanine
Glioblastoma
Transferases
Down-Regulation
231 Citations

TBCRC 001: Randomized phase II study of cetuximab in combination with carboplatin in stage IV triple-negative breast cancer

Carey, L. A., Rugo, H. S., Marcom, P. K., Mayer, E. L., Esteva, F. J., Ma, C. X., Liu, M. C., Storniolo, A. M., Rimawi, M. F., Forero-Torres, A., Wolff, A. C., Hobday, T. J., Ivanova, A., Chiu, W. K., Ferraro, M., Burrows, E., Bernard, P. S., Hoadley, K. A., Perou, C. M. & Winer, E. P. Jul 20 2012 In : Journal of Clinical Oncology. 30, 21, p. 2615-2623 9 p.

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
Carboplatin
Epidermal Growth Factor Receptor
Therapeutics
Survival
2011

Correction: An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer

Bild, A. H., Parker, J. S., Gustafson, A. M., Acharya, C. R., Hoadley, K. A., Anders, C., Marcom, P. K., Carey, L. A., Potti, A., Nevins, J. R. & Perou, C. M. Jul 12 2011 In : Breast Cancer Research. 13, 4, 406

Research output: Contribution to journalComment/debate

Breast Neoplasms
Gene Expression
Therapeutics
2899 Citations

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. & 30 others Mills, G. B., 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. Jun 30 2011 In : Nature. 474, 7353, p. 609-615 7 p.

Research output: Contribution to journalArticle

Ovarian Neoplasms
Carcinoma
Neoplasms
MicroRNAs
Methylation
2010
1171 Citations

Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma

Noushmehr, H. , Weisenberger, D. J. , Diefes, K. , Phillips, H. S. , Pujara, K. , Berman, B. P. , Pan, F. , Pelloski, C. E. , Sulman, E. P. , Bhat, K. P. , Verhaak, R. G. W. , Hoadley, K. A. , Hayes, D. N. , Perou, C. M. , Schmidt, H. K. , Ding, L. , Wilson, R. K. , Van Den Berg, D. , Shen, H. , Bengtsson, H. & 7 others Neuvial, P., Cope, L. M., Buckley, J., Herman, J. G., Baylin, S. B., Laird, P. W. & Aldape, K. May 18 2010 In : Cancer Cell. 17, 5, p. 510-522 13 p.

Research output: Contribution to journalArticle

CpG Islands
Glioma
Phenotype
Atlases
Neoplasms
2787 Citations

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. S. & 13 others Hodgson, J. G., James, C. D., Sarkaria, J. N., Brennan, C., Kahn, A., Spellman, P. T., Wilson, R. K., Speed, T. P., Gray, J. W., 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