• 67731 Citations
  • 113 h-Index
1971 …2020

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Article
2016

Genome co-amplification upregulates a mitotic gene network activity that predicts outcome and response to mitotic protein inhibitors in breast cancer

Hu, Z., Mao, J. H., Curtis, C., Huang, G., Gu, S., Heiser, L., Lenburg, M. E., Korkola, J. E., Bayani, N., Samarajiwa, S., Seoane, J. A., Dane, M., Esch, A., Feiler, H. S., Wang, N. J., Hardwicke, M. A., Laquerre, S., Jackson, J., Wood, K., Weber, B. & 5 others, Spellman, P. T., Aparicio, S., Wooster, R., Caldas, C. & Gray, J. W., Jul 1 2016, In : Breast Cancer Research. 18, 1, 70.

Research output: Contribution to journalArticle

6 Scopus citations

IL-10 and integrin signaling pathways are associated with head and neck cancer progression

Bornstein, S., Schmidt, M., Choonoo, G., Levin, T., Gray, J., Thomas, C., Wong, M. & McWeeney, S., Jan 8 2016, In : BMC Genomics. 17, 1, 38.

Research output: Contribution to journalArticle

25 Scopus citations

Inferring causal molecular networks: Empirical assessment through a community-based effort

Hill, S. M., Heiser, L. M., Cokelaer, T., Linger, M., Nesser, N. K., Carlin, D. E., Zhang, Y., Sokolov, A., Paull, E. O., Wong, C. K., Graim, K., Bivol, A., Wang, H., Zhu, F., Afsari, B., Danilova, L. V., Favorov, A. V., Lee, W. S., Taylor, D., Hu, C. W. & 115 others, Long, B. L., Noren, D. P., Bisberg, A. J., Mills, G. B., Gray, J. W., Kellen, M., Norman, T., Friend, S., Qutub, A. A., Fertig, E. J., Guan, Y., Song, M., Stuart, J. M., Spellman, P. T., Koeppl, H., Stolovitzky, G., Saez-Rodriguez, J., Mukherjee, S., Al-Ouran, R., Anton, B., Arodz, T., Sichani, O. A., Bagheri, N., Berlow, N., Bohler, A., Bonet, J., Bonneau, R., Budak, G., Bunescu, R., Caglar, M., Cai, B., Cai, C., Carlon, A., Chen, L., Ciaccio, M. F., Cooper, G., Coort, S., Creighton, C. J., Daneshmand, S. M. H., De La Fuente, A., Di Camillo, B., Dutta-Moscato, J., Emmett, K., Evelo, C., Fassia, M. K. H., Finotello, F., Finkle, J. D., Gao, X., Garcia-Garcia, J., Ghosh, S., Giaretta, A., Großeholz, R., Guinney, J., Hafemeister, C., Hahn, O., Haider, S., Hase, T., Hodgson, J., Hoff, B., Hsu, C. H., Hu, Y., Huang, X., Jalili, M., Jiang, X., Kacprowski, T., Kaderali, L., Kang, M., Kannan, V., Kikuchi, K., Kim, D. C., Kitano, H., Knapp, B., Komatsoulis, G., Krämer, A., Kursa, M. B., Kutmon, M., Li, Y., Liang, X., Liu, Z., Liu, Y., Lu, S., Lu, X., Manfrini, M., Matos, M. R. A., Meerzaman, D., Min, W., Müller, C. L., Neapolitan, R. E., Oliva, B., Opiyo, S. O., Pal, R., Palinkas, A., Planas-Iglesias, J., Poglayen, D., Sambo, F., Sanavia, T., Sharifi-Zarchi, A., Slawek, J., Streck, A., Strunz, S., Tegnér, J., Thobe, K., Toffolo, G. M., Trifoglio, E., Unger, M., Wan, Q., Welch, L., Wu, J. J., Xue, A. Y., Yamanaka, R., Yan, C., Zairis, S., Zengerling, M., Zenil, H. & Zi, Z., Mar 30 2016, In : Nature Methods. 13, 4, p. 310-322 13 p.

Research output: Contribution to journalArticle

104 Scopus citations

Multiplexed imaging reveals heterogeneity of PI3K/MAPK network signaling in breast lesions of known PIK3CA genotype

Jacob, T., Gray, J., Troxell, M. & Vu, T. T., Oct 1 2016, In : Breast Cancer Research and Treatment. 159, 3, p. 575-583 9 p.

Research output: Contribution to journalArticle

4 Scopus citations

PI3 Kinase Pathway Mutations in Human Cancers

Gray, J., Dec 1 2016, In : JAMA oncology. 2, 12, p. 1543-1544 2 p.

Research output: Contribution to journalArticle

4 Scopus citations

Reconstruction of Gene Regulatory Networks Based on Repairing Sparse Low-Rank Matrices

Chang, Y. H., Dobbe, R., Bhushan, P., Gray, J. & Tomlin, C. J., Jul 1 2016, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 13, 4, p. 767-777 11 p., 7182286.

Research output: Contribution to journalArticle

The ErbB2ΔEx16 splice variant is a major oncogenic driver in breast cancer that promotes a pro-metastatic tumor microenvironment

Turpin, J., Ling, C., Crosby, E. J., Hartman, Z. C., Simond, A. M., Chodosh, L. A., Rennhack, J. P., Andrechek, E. R., Ozcelik, J., Hallett, M., Mills, G. B., Cardiff, R. D., Gray, J. W., Griffith, O. L. & Muller, W. J., Nov 24 2016, In : Oncogene. 35, 47, p. 6053-6064 12 p.

Research output: Contribution to journalArticle

21 Scopus citations

Therapeutic siRNA for drug-resistant HER2-positive breast cancer

Gu, S., Hu, Z., Ngamcherdtrakul, W., Castro, D. J., Morry, J., Reda, M. M., Gray, J. W. & Yantasee, W., Mar 22 2016, In : Oncotarget. 7, 12, p. 14727-14741 15 p.

Research output: Contribution to journalArticle

15 Scopus citations
2017

Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes

Rahman, M., MacNeil, S. M., Jenkins, D. F., Shrestha, G., Wyatt, S. R., McQuerry, J. A., Piccolo, S. R., Heiser, L. M., Gray, J. W., Johnson, W. E. & Bild, A. H., Apr 26 2017, In : Genome Medicine. 9, 1, 40.

Research output: Contribution to journalArticle

5 Scopus citations

A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow

López, C. S., Bouchet-Marquis, C., Arthur, C. P., Riesterer, J. L., Heiss, G., Thibault, G., Pullan, L., Kwon, S. & Gray, J. W., 2017, In : Methods in cell biology. 140, p. 149-164 16 p.

Research output: Contribution to journalArticle

8 Scopus citations

Bayesian network inference modeling identifies TRIB1 as a novel regulator of cell-cycle progression and survival in cancer cells

Gendelman, R., Xing, H., Mirzoeva, O. K., Sarde, P., Curtis, C., Feiler, H., McDonagh, P., Gray, J., Khalil, I. & Korn, W. M., 2017, In : Cancer Research. 77, 7, p. 1575-1585 11 p.

Research output: Contribution to journalArticle

26 Scopus citations

Characterizing the immune microenvironment in high-risk ductal carcinoma in situ of the breast

Campbell, M. J., Baehner, F., O’Meara, T., Ojukwu, E., Han, B., Mukhtar, R., Tandon, V., Endicott, M., Zhu, Z., Wong, J., Krings, G., Au, A., Gray, J. W. & Esserman, L., Jan 1 2017, In : Breast Cancer Research and Treatment. 161, 1, p. 17-28 12 p.

Research output: Contribution to journalArticle

40 Scopus citations

Combating subclonal evolution of resistant cancer phenotypes

Brady, S. W., McQuerry, J. A., Qiao, Y., Piccolo, S. R., Shrestha, G., Jenkins, D. F., Layer, R. M., Pedersen, B. S., Miller, R. H., Esch, A., Selitsky, S. R., Parker, J. S., Anderson, L. A., Dalley, B. K., Factor, R. E., Reddy, C. B., Boltax, J. P., Li, D. Y., Moos, P. J., Gray, J. W. & 8 others, Heiser, L. M., Buys, S. S., Cohen, A. L., Johnson, W. E., Quinlan, A. R., Marth, G., Werner, T. L. & Bild, A. H., Dec 1 2017, In : Nature communications. 8, 1, 1231.

Research output: Contribution to journalArticle

34 Scopus citations

Combinatorial Microenvironments Impose a Continuum of Cellular Responses to a Single Pathway-Targeted Anti-cancer Compound

Lin, C. H., Jokela, T., Gray, J. & LaBarge, M. A., Oct 10 2017, In : Cell Reports. 21, 2, p. 533-545 13 p.

Research output: Contribution to journalArticle

11 Scopus citations

Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling

Hill, S. M., Nesser, N. K., Johnson-Camacho, K., Jeffress, M., Johnson, A., Boniface, C., Spencer, S. E. F., Lu, Y., Heiser, L. M., Lawrence, Y., Pande, N. T., Korkola, J. E., Gray, J. W., Mills, G. B., Mukherjee, S. & Spellman, P. T., Jan 25 2017, In : Cell Systems. 4, 1, p. 73-83.e10

Research output: Contribution to journalArticle

12 Scopus citations

Epigenomic inactivation of RasGAPs activates RAS signaling in a subset of luminal B breast cancers

Sears, R. & Gray, J., Feb 1 2017, In : Cancer Discovery. 7, 2, p. 131-133 3 p.

Research output: Contribution to journalArticle

8 Scopus citations

HER2 reactivation through acquisition of the HER2 L755S mutation as a mechanism of acquired resistance to HER2-targeted therapy in HER2+ breast cancer

Xu, X., De Angelis, C., Burke, K. A., Nardone, A., Hu, H., Qin, L., Veeraraghavan, J., Sethunath, V., Heiser, L., Wang, N., Ng, C. K. Y., Chen, E. S., Renwick, A., Wang, T., Nanda, S., Shea, M., Mitchell, T., Rajendran, M., Waters, I., Zabransky, D. J. & 14 others, Scott, K. L., Gutierrez, C., Nagi, C., Geyer, F. C., Chamness, G. C., Park, B. H., Shaw, C. A., Hilsenbeck, S. G., Rimawi, M. F., Gray, J., Weigelt, B., Reis-Filho, J. S., Osborne, C. K. & Schiff, R., Sep 1 2017, In : Clinical Cancer Research. 23, 17, p. 5123-5134 12 p.

Research output: Contribution to journalArticle

33 Scopus citations

Pathway-enriched gene signature associated with 53BP1 response to PARP inhibition in triple-negative breast cancer

Hassan, S., Esch, A., Liby, T., Gray, J. & Heiser, L., Dec 1 2017, In : Molecular Cancer Therapeutics. 16, 12, p. 2892-2901 10 p.

Research output: Contribution to journalArticle

10 Scopus citations

Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics

Hafner, M., Heiser, L., Williams, E. H., Niepel, M., Wang, N. J., Korkola, J., Gray, J. & Sorger, P. K., Nov 7 2017, In : Scientific data. 4, 170166.

Research output: Contribution to journalArticle

10 Scopus citations

Quantitating morphological changes in biological samples during scanning electron microscopy sample preparation with correlative super-resolution microscopy

Zhang, Y., Huang, T., Jorgens, D. M., Nickerson, A., Lin, L. J., Pelz, J., Gray, J. W., López, C. S. & Nan, X., May 2017, In : PloS one. 12, 5, e0176839.

Research output: Contribution to journalArticle

17 Scopus citations

Quantitative, in situ analysis of mRNAs and proteins with subcellular resolution

Kwon, S., Chin, K-Y., Nederlof, M. & Gray, J., Dec 1 2017, In : Scientific Reports. 7, 1, 16459.

Research output: Contribution to journalArticle

2 Scopus citations

Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

Tsujikawa, T., Kumar, S., Borkar, R. N., Azimi, V., Thibault, G., Chang, Y. H., Balter, A., Kawashima, R., Choe, G., Sauer, D., El Rassi, E., Clayburgh, D., Kulesz-Martin, M., Lutz, E. R., Zheng, L., Jaffee, E. M., Leyshock, P., Margolin, A., Mori, M. T., Gray, J. & 2 others, Flint, P. & Coussens, L., Apr 4 2017, In : Cell Reports. 19, 1, p. 203-217 15 p.

Research output: Contribution to journalArticle

128 Scopus citations

Targeted treatment of metastatic breast cancer by PLK1 siRNA delivered by an antioxidant nanoparticle platform

Morry, J., Ngamcherdtrakul, W., Gu, S., Reda, M., Castro, D. J., Sangvanich, T., Gray, J. W. & Yantasee, W., Apr 2017, In : Molecular cancer therapeutics. 16, 4, p. 763-772 10 p.

Research output: Contribution to journalArticle

20 Scopus citations
2018

CCR5 Governs DNA damage repair and breast cancer stem cell expansion

Jiao, X., Velasco-Velazquez, M. A., Wang, M., Li, Z., Rui, H., Peck, A. R., Korkola, J. E., Chen, X., Xu, S., DuHadaway, J. B., Guerrero-Rodriguez, S., Addya, S., Sicoli, D., Mu, Z., Zhang, G., Stucky, A., Zhang, X., Cristofanilli, M., Fatatis, A., Gray, J. W. & 3 others, Zhong, J. F., Prendergast, G. C. & Pestell, R. G., Apr 1 2018, In : Cancer Research. 78, 7, p. 1657-1671 15 p.

Research output: Contribution to journalArticle

29 Scopus citations

Cell fusion potentiates tumor heterogeneity and reveals circulating hybrid cells that correlate with stage and survival

Gast, C. E., Silk, A. D., Zarour, L., Riegler, L., Burkhart, J. G., Gustafson, K. T., Parappilly, M. S., Roh-Johnson, M., Goodman, J. R., Olson, B., Schmidt, M., Swain, J. R., Davies, P. S., Shasthri, V., Iizuka, S., Flynn, P., Watson, S., Korkola, J., Courtneidge, S. A., Fischer, J. M. & 8 others, Jaboin, J., Billingsley, K. G., Lopez, C. D., Burchard, J., Gray, J., Coussens, L. M., Sheppard, B. C. & Wong, M. H., Sep 12 2018, In : Science Advances. 4, 9, eaat7828.

Research output: Contribution to journalArticle

43 Scopus citations

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

Risom, T., Langer, E. M., Chapman, M. P., Rantala, J., Fields, A. J., Boniface, C., Alvarez, M. J., Kendsersky, N. D., Pelz, C. R., Johnson-Camacho, K., Dobrolecki, L. E., Chin, K., Aswani, A. J., Wang, N. J., Califano, A., Lewis, M. T., Tomlin, C. J., Spellman, P. T., Adey, A., Gray, J. W. & 1 others, Sears, R. C., Dec 1 2018, In : Nature communications. 9, 1, 3815.

Research output: Contribution to journalArticle

29 Scopus citations
7 Scopus citations

Lack of acquired resistance in HER2-positive breast cancer cells after long-term HER2 siRNA nanoparticle treatment

Gu, S., Ngamcherdtrakul, W., Reda, M., Hu, Z., Gray, J. W. & Yantasee, W., Jun 2018, In : PloS one. 13, 6, e0198141.

Research output: Contribution to journalArticle

3 Scopus citations

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection

Rozanov, D., Rozanov, N. D., Chiotti, K. E., Reddy, A., Wilmarth, P., David, L., Cha, S. W., Woo, S., Pevzner, P., Bafna, V., Burrows, G. G., Rantala, J. K., Levin, T., Anur, P., Johnson-Camacho, K., Tabatabaei, S., Munson, D. J., Bruno, T. C., Slansky, J. E., Kappler, J. W. & 9 others, Hirano, N., Boegel, S., Fox, B. A., Egelston, C., Simons, D. L., Jimenez, G., Lee, P. P., Gray, J. & Spellman, P., Mar 30 2018, In : Journal of Proteomics. 176, p. 13-23 11 p.

Research output: Contribution to journalArticle

8 Scopus citations

Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes

Watson, S. S., Dane, M., Chin, K-Y., Tatarova, Z., Liu, M., Liby, T., Thompson, W., Smith, R., Nederlof, M., Bucher, E., Kilburn, D., Whitman, M., Sudar, D., Mills, G., Heiser, L., Jonas, O., Gray, J. & Korkola, J., Jan 1 2018, (Accepted/In press) In : Cell Systems.

Research output: Contribution to journalArticle

13 Scopus citations

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells

Cornforth, M. N., Anur, P., Wang, N., Robinson, E., Ray, F. A., Bedford, J. S., Loucas, B. D., Williams, E. S., Peto, M., Spellman, P., Kollipara, R., Kittler, R., Gray, J. & Bailey, S. M., Jul 1 2018, In : Radiation Research. 190, 1, p. 88-97 10 p.

Research output: Contribution to journalArticle

6 Scopus citations

Simultaneous Multicolor Single-Molecule Tracking with Single-Laser Excitation via Spectral Imaging

Huang, T., Phelps, C., Wang, J., Lin, L. J., Bittel, A., Scott, Z., Jacques, S., Gibbs, S., Gray, J. & Nan, X., Jan 23 2018, In : Biophysical Journal. 114, 2, p. 301-310 10 p.

Research output: Contribution to journalArticle

16 Scopus citations

Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution

Cheng, J. B., Sedgewick, A. J., Finnegan, A. I., Harirchian, P., Lee, J., Kwon, S., Fassett, M. S., Golovato, J., Gray, M., Ghadially, R., Liao, W., Perez White, B. E., Mauro, T. M., Mully, T., Kim, E. A., Sbitany, H., Neuhaus, I. M., Grekin, R. C., Yu, S. S., Gray, J. W. & 6 others, Purdom, E., Paus, R., Vaske, C. J., Benz, S. C., Song, J. S. & Cho, R. J., Oct 23 2018, In : Cell Reports. 25, 4, p. 871-883 13 p.

Research output: Contribution to journalArticle

26 Scopus citations
2019

Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer

Butler, T. M., Boniface, C. T., Johnson-Camacho, K., Tabatabaei, S., Melendez, D., Kelley, T., Gray, J., Corless, C. L. & Spellman, P. T., 2019, In : Cold Spring Harbor Molecular Case Studies. 5, 2, a003772.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

DIRAS3 (ARHI) Blocks RAS/MAPK Signaling by Binding Directly to RAS and Disrupting RAS Clusters

Sutton, M. N., Lu, Z., Li, Y. C., Zhou, Y., Huang, T., Reger, A. S., Hurwitz, A. M., Palzkill, T., Logsdon, C., Liang, X., Gray, J. W., Nan, X., Hancock, J., Wahl, G. M. & Bast, R. C., Dec 10 2019, In : Cell Reports. 29, 11, p. 3448-3459.e6

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

High-throughput single-particle tracking reveals 1 nested membrane domains that dictate krasg12d 2 diffusion and trafficking

Lee, Y., Phelps, C., Huang, T., Mostofian, B., Wu, L., Zhang, Y., Tao, K., Chang, Y. H., Stork, P. J. S., Gray, J. W., Zuckerman, D. M. & Nan, X., Nov 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting

Langer, E. M., Allen-Petersen, B. L., King, S. M., Kendsersky, N. D., Turnidge, M. A., Kuziel, G. M., Riggers, R., Samatham, R., Amery, T. S., Jacques, S. L., Sheppard, B. C., Korkola, J. E., Muschler, J. L., Thibault, G., Chang, Y. H., Gray, J. W., Presnell, S. C., Nguyen, D. G. & Sears, R. C., Jan 15 2019, In : Cell Reports. 26, 3, p. 608-623.e6

Research output: Contribution to journalArticle

18 Scopus citations

PLK1 and EGFR targeted nanoparticle as a radiation sensitizer for non-small cell lung cancer

Reda, M., Ngamcherdtrakul, W., Gu, S., Bejan, D. S., Siriwon, N., Gray, J. W. & Yantasee, W., Dec 28 2019, In : Cancer Letters. 467, p. 9-18 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity

Tsujikawa, T., Thibault, G., Azimi, V., Sivagnanam, S., Banik, G., Means, C., Kawashima, R., Clayburgh, D. R., Gray, J. W., Coussens, L. M. & Chang, Y. H., Apr 2019, In : Cytometry Part A. 95, 4, p. 389-398 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Targeting mitochondria in cancer therapy could provide a basis for the selective anticancer activity

Rozanov, D., Cheltsov, A., Nilsen, A., Boniface, C., Forquer, I., Korkola, J., Gray, J., Tyner, J., Tognon, C. E., Mills, G. B. & Spellman, P., Mar 2019, In : PloS one. 14, 3, e0205623.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Targeting the mevalonate pathway to overcome acquired anti-HER2 treatment resistance in breast cancer

Sethunath, V., Hu, H., De Angelis, C., Veeraraghavan, J., Qin, L., Wang, N., Simon, L. M., Wang, T., Fu, X., Nardone, A., Pereira, R., Nanda, S., Griffith, O. L., Tsimelzon, A., Shaw, C., Chamness, G. C., Reis-Filho, J. S., Weigelt, B., Heiser, L. M., Hilsenbeck, S. G. & 5 others, Huang, S., Rimawi, M. F., Gray, J. W., Osborne, C. K. & Schiff, R., 2019, In : Molecular Cancer Research. 17, 11, p. 2318-2330 13 p.

Research output: Contribution to journalArticle

4 Scopus citations
2020
2 Scopus citations

Oligonucleotide conjugated antibodies permit highly multiplexed immunofluorescence for future use in clinical histopathology

Mcmahon, N. P., Jones, J. A., Kwon, S., Chin, K., Nederlof, M. A., Gray, J. W. & Gibbs, S. L., May 1 2020, In : Journal of biomedical optics. 25, 5, 056004.

Research output: Contribution to journalArticle

Open Access

Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin

Schau, G. F., Burlingame, E. A., Thibault, G., Anekpuritanang, T., Wang, Y., Gray, J. W., Corless, C. & Chang, Y. H., Jan 1 2020, In : Journal of Medical Imaging. 7, 1, 012706.

Research output: Contribution to journalArticle

RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging

Chang, Y. H., Chin, K., Thibault, G., Eng, J., Burlingame, E. & Gray, J. W., Dec 1 2020, In : Communications Biology. 3, 1, 111.

Research output: Contribution to journalArticle

Open Access