• 65500 Citations
  • 111 h-Index
1971 …2020
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Research Output 1971 2020

2017
101 Citations (Scopus)

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

Tumors
Immunohistochemistry
Tissue
Biomarkers
Papillomaviridae
20 Citations (Scopus)

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. & Yantasee, W., Apr 1 2017, In : Molecular Cancer Therapeutics. 16, 4, p. 763-772 10 p.

Research output: Contribution to journalArticle

Triple Negative Breast Neoplasms
Nanoparticles
Small Interfering RNA
Antioxidants
Breast Neoplasms
70 Citations (Scopus)

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

Keenan, A. B., Jenkins, S. L., Jagodnik, K. M., Koplev, S., He, E., Torre, D., Wang, Z., Dohlman, A. B., Silverstein, M. C., Lachmann, A., Kuleshov, M. V., Ma'ayan, A., Stathias, V., Terryn, R., Cooper, D., Forlin, M., Koleti, A., Vidovic, D., Chung, C., Schürer, S. C. & 87 others, Vasiliauskas, J., Pilarczyk, M., Shamsaei, B., Fazel, M., Ren, Y., Niu, W., Clark, N. A., White, S., Mahi, N., Zhang, L., Kouril, M., Reichard, J. F., Sivaganesan, S., Medvedovic, M., Meller, J., Koch, R. J., Birtwistle, M. R., Iyengar, R., Sobie, E. A., Azeloglu, E. U., Kaye, J., Osterloh, J., Haston, K., Kalra, J., Finkbiener, S., Li, J., Milani, P., Adam, M., Escalante-Chong, R., Sachs, K., Lenail, A., Ramamoorthy, D., Fraenkel, E., Daigle, G., Hussain, U., Coye, A., Rothstein, J., Sareen, D., Ornelas, L., Banuelos, M., Mandefro, B., Ho, R., Svendsen, C. N., Lim, R. G., Stocksdale, J., Casale, M. S., Thompson, T. G., Wu, J., Thompson, L. M., Dardov, V., Venkatraman, V., Matlock, A., Van Eyk, J. E., Jaffe, J. D., Papanastasiou, M., Subramanian, A., Golub, T. R., Erickson, S. D., Fallahi-Sichani, M., Hafner, M., Gray, N. S., Lin, J. R., Mills, C. E., Muhlich, J. L., Niepel, M., Shamu, C. E., Williams, E. H., Wrobel, D., Sorger, P. K., Heiser, L., Gray, J., Korkola, J., Mills, G., LaBarge, M., Feiler, H., Dane, M. A., Bucher, E., Nederlof, M., Sudar, D., Gross, S., Kilburn, D. F., Smith, R., Devlin, K., Margolis, R., Derr, L., Lee, A. & Pillai, A., Jan 1 2017, (Accepted/In press) In : Cell Systems.

Research output: Contribution to journalArticle

Cataloging
Libraries
Inborn Genetic Diseases
Molecular Imaging
Neurodegenerative Diseases
2018
20 Citations (Scopus)

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., 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. & 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

Neoplastic Stem Cells
DNA Repair
DNA Damage
Breast Neoplasms
Epithelial Cells
24 Citations (Scopus)

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., Shasthri, V., Iizuka, S., Flynn, P., Watson, S., Korkola, J., Courtneidge, S., Fischer, J. & 8 others, Jaboin, J., Billingsley, K., Lopez, C., Burchard, J., Gray, J., Coussens, L., Sheppard, B. & Wong, M., Sep 12 2018, In : Science advances. 4, 9, eaat7828.

Research output: Contribution to journalArticle

Cell Fusion
Hybrid Cells
Survival
Neoplasms
Biomarkers
17 Citations (Scopus)

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-Y., Aswani, A. J., Wang, N. J., Califano, A., Lewis, M. T., Tomlin, C. J., Spellman, P., Adey, A., Gray, J. & 1 others, Sears, R., Dec 1 2018, In : Nature Communications. 9, 1, 3815.

Research output: Contribution to journalArticle

plastic properties
breast
chromatin
Plasticity
drugs

Erratum: Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes (Nature communications (2017) 8 1 (1231))

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. & 8 others, Heiser, L., Buys, S. S., Cohen, A. L., Johnson, W. E., Quinlan, A. R., Marth, G., Werner, T. L. & Bild, A. H., Feb 5 2018, In : Nature Communications. 9, 1, 1 p.

Research output: Contribution to journalComment/debate

phenotype
cancer
communication
Communication
document markup languages
2 Citations (Scopus)
Oncology
Biopsy
Genes
Tumors
Testing
3 Citations (Scopus)

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. & Yantasee, W., Jun 1 2018, In : PLoS One. 13, 6, e0198141.

Research output: Contribution to journalArticle

nanoparticles
small interfering RNA
breast neoplasms
Nanoparticles
Small Interfering RNA
7 Citations (Scopus)

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

Cells
Breast Neoplasms
Ligands
Cell Line
Peptides
7 Citations (Scopus)

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

Protein-Tyrosine Kinases
Breast Neoplasms
Ligands
Cell Line
Hepatocyte Growth Factor
6 Citations (Scopus)

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

High-Throughput Nucleotide Sequencing
Genetic Translocation
sequencing
chromosomes
Computational Biology
3 Citations (Scopus)

SHIFT: Speedy histopathological-To-immunofluorescent translation of whole slide images using conditional generative adversarial networks

Burlingame, E. A., Margolin, A., Gray, J. & Chang, Y. H., Jan 1 2018, Medical Imaging 2018: Digital Pathology. SPIE, Vol. 10581. 1058105

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

Hematoxylin
Eosine Yellowish-(YS)
chutes
Coloring Agents
Imaging techniques
9 Citations (Scopus)

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

Lasers
Cell Tracking
Biological Phenomena
Photons
Calibration
13 Citations (Scopus)

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. & 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

Epidermis
Skin
Keratinocytes
RNA Sequence Analysis
Macrophages
2019
2 Citations (Scopus)

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., Apr 1 2019, In : Cold Spring Harbor molecular case studies. 5, 2

Research output: Contribution to journalArticle

Open Access
Chemotherapy
Tumors
Assays
Breast Neoplasms
Drug Therapy

cmIF: A Python Library for Scalable Multiplex Imaging Pipelines

Eng, J., Bucher, E., Gray, E., Campbell, L. G., Thibault, G., Heiser, L., Gibbs, S., Gray, J. W., Chin, K. & Chang, Y. H., Jan 1 2019, Mathematical and Computational Oncology - 1st International Symposium, ISMCO 2019, Proceedings. Bebis, G., Benos, T., Chen, K., Jahn, K. & Lima, E. (eds.). Springer, p. 37-43 7 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11826 LNCS).

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

Python
Pipelines
Imaging
Imaging techniques
Reproducibility

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
Monomeric GTP-Binding Proteins
Phenotype
Mutation
Growth
Neoplasms
7 Citations (Scopus)

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., Sheppard, B., Korkola, J., Muschler, J., Thibault, G., Chang, Y. H., Gray, J., Presnell, S. C., Nguyen, D. G. & Sears, R., Jan 15 2019, In : Cell Reports. 26, 3, p. 608-623.e6

Research output: Contribution to journalArticle

Bioprinting
Tumors
Tissue
Phenotype
Scaffolds

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

Radiation-Sensitizing Agents
Epidermal Growth Factor Receptor
Non-Small Cell Lung Carcinoma
Nanoparticles
Neoplasms
1 Citation (Scopus)

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., Gray, J., Coussens, L. & Chang, Y. H., Jan 1 2019, In : Cytometry Part A.

Research output: Contribution to journalArticle

Image Cytometry
Th17 Cells
Papillomaviridae
Immunohistochemistry
Biomarkers

Signal removal methods for highly multiplexed immunofluorescent staining using antibody conjugated oligonucleotides

McMahon, N., Jones, J., Eng, J., Kwon, S., Chang, Y. H., Thibault, G., Chin, K-Y., Nederlof, M., Gray, J. & Gibbs, S., Jan 1 2019, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII. Farkas, D. L., Tarnok, A. & Leary, J. F. (eds.). SPIE, 108810X. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10881).

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

oligonucleotides
Oligonucleotides
staining
antibodies
Antibodies
2 Citations (Scopus)

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. & Spellman, P., Mar 1 2019, In : PloS one. 14, 3, e0205623.

Research output: Contribution to journalArticle

Open Access
Mitochondria
Assays
mitochondria
therapeutics
neoplasms
3 Citations (Scopus)

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., Nov 1 2019, In : Molecular cancer research : MCR. 17, 11, p. 2318-2330 13 p.

Research output: Contribution to journalArticle

Mevalonic Acid
Breast Neoplasms
zoledronic acid
Hydroxymethylglutaryl-CoA Reductase Inhibitors
simvastatin acid
1 Citation (Scopus)

Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers

Heiser, L., Mills, G. & Gray, J., Mar 18 2019, In : Cancer Cell. 35, 3, p. 341-343 3 p.

Research output: Contribution to journalShort survey

Triple Negative Breast Neoplasms
Decision Trees
Population
Therapeutics
Neoplasms

Variational autoencoding tissue response to microenvironment perturbation

Schau, G. F., Thibault, G., Dane, M. A., Gray, J., Heiser, L. & Chang, Y. H., Jan 1 2019, Medical Imaging 2019: Image Processing. Landman, B. A., Angelini, E. D., Angelini, E. D. & Angelini, E. D. (eds.). SPIE, 109491M. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10949).

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

learning
Learning
Tissue
annotations
perturbation
2020
1 Citation (Scopus)
Single-Cell Analysis
Tumor-Infiltrating Lymphocytes
Fluorescent Antibody Technique
Breast Neoplasms
Neoplasms