Liudmila V Danilova

Research Associate

20012020

Research output per year

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Research Output

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2020

Multipanel mass cytometry reveals anti–PD-1 therapy–mediated B and T cell compartment remodeling in tumor-draining lymph nodes

Ho, W. J., Yarchoan, M., Charmsaz, S., Munday, R. M., Danilova, L., Sztein, M. B., Fertig, E. J. & Jaffee, E. M., Jan 30 2020, In : JCI Insight. 5, 2, e132286.

Research output: Contribution to journalArticle

Open Access

Revisiting the tumorigenesis timeline with a data-driven generative model

Lahouel, K., Younes, L., Danilova, L., Giardiello, F. M., Hruban, R. H., Groopman, J., Kinzler, K. W., Vogelstein, B., Geman, D. & Tomasetti, C., Jan 14 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 2, p. 857-864 8 p.

Research output: Contribution to journalArticle

Open Access
2019

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

Flam, E. L., Danilova, L., Kelley, D. Z., Stavrovskaya, E., Guo, T., Considine, M., Qian, J., Califano, J. A., Favorov, A., Fertig, E. J. & Gaykalova, D. A., Dec 1 2019, In : Scientific reports. 9, 1, 15034.

Research output: Contribution to journalArticle

Open Access

Integrated genomic and functional microRNA analysis identifies miR-30-5p as a tumor suppressor and potential therapeutic nanomedicine in head and neck cancer

Saleh, A. D., Cheng, H., Martin, S. E., Si, H., Ormanoglu, P., Carlson, S., Clavijo, P. E., Yang, X., Das, R., Cornelius, S., Couper, J., Chepeha, D., Danilova, L. V., Harris, T. M., Prystowsky, M. B., Childs, G. J., Smith, R. V., Gordon Robertson, A., Jones, S. J. M., Cherniack, A. D. & 6 others, Kim, S. S., Rait, A., Pirollo, K. F., Chang, E. H., Chen, Z. & Van Waes, C., Jan 1 2019, In : Clinical Cancer Research. 25, 9, p. 2860-2873 14 p.

Research output: Contribution to journalArticle

Major pathologic response on biopsy (MPRbx) in patients with advanced melanoma treated with anti-PD-1: evidence for an early, on-therapy biomarker of response

Stein, J. E., Soni, A., Danilova, L. V., Cottrell, T. R., Gajewski, T. F., Hodi, F. S., Bhatia, S., Urba, W. J., Sharfman, W., Wind-Rotolo, M., Edwards, R., Lipson, E. & Taube, J. M., Apr 1 2019, In : Annals of oncology : official journal of the European Society for Medical Oncology. 30, 4, p. 589-596 8 p.

Research output: Contribution to journalArticle

Open Access

Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma

Jafarnejad, M., Sové, R. J., Danilova, L. V., Mirando, A. C., Zhang, Y., Yarchoan, M., Tran, P. T., Pandey, N., Fertig, E. & Popel, A. S., Dec 1 2019, In : npj Systems Biology and Applications. 5, 1, 29.

Research output: Contribution to journalArticle

Open Access

Persistent mutant oncogene specific T cells in two patients benefitting from anti-PD-1

Smith, K. N., Llosa, N. J., Cottrell, T. R., Siegel, N., Fan, H., Suri, P., Chan, H. Y., Guo, H., Oke, T., Awan, A. H., Verde, F., Danilova, L., Anagnostou, V., Tam, A. J., Luber, B. S., Bartlett, B. R., Aulakh, L. K., Sidhom, J. W., Zhu, Q., Sears, C. L. & 21 others, Cope, L., Sharfman, W. H., Thompson, E. D., Riemer, J., Marrone, K. A., Naidoo, J., Velculescu, V. E., Forde, P. M., Vogelstein, B., Kinzler, K. W., Papadopoulos, N., Durham, J. N., Wang, H., Le, D. T., Justesen, S., Taube, J. M., Diaz, L. A., Brahmer, J. R., Pardoll, D. M., Anders, R. A. & Housseau, F., Feb 11 2019, In : Journal for immunotherapy of cancer. 7, 1, 40.

Research output: Contribution to journalArticle

Open Access

PTPRT epigenetic silencing defines lung cancer with STAT3 activation and can direct STAT3 targeted therapies

Sen, M., Kindsfather, A., Danilova, L., Zhang, F., Colombo, R., LaPorte, M. G., Kurland, B. F., Huryn, D. M., Wipf, P. & Herman, J. G., Jan 1 2019, (Accepted/In press) In : Epigenetics.

Research output: Contribution to journalArticle

2018

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 690-705.e9

Research output: Contribution to journalArticle

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 400-416.e11

Research output: Contribution to journalArticle

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 386-399.e12

Research output: Contribution to journalArticle

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

The Cancer Genome Atlas Network, Apr 5 2018, In : Cell. 173, 2, p. 291-304.e6

Research output: Contribution to journalArticle

Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 721-735.e8

Research output: Contribution to journalArticle

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

The Cancer Genome Atlas Research Network, Aug 13 2018, In : Cancer Cell. 34, 2, p. 211-224.e6

Research output: Contribution to journalArticle

Comprehensive Characterization of Cancer Driver Genes and Mutations

The MC3 Working Group & The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 371-385.e18

Research output: Contribution to journalArticle

Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

The Cancer Genome Atlas Research Network, Oct 30 2018, In : Cell Reports. 25, 5, p. 1304-1317.e5

Research output: Contribution to journalArticle

Detection and localization of surgically resectable cancers with a multi-analyte blood test

Cohen, J. D., Li, L., Wang, Y., Thoburn, C., Afsari, B., Danilova, L. V., Douville, C., Javed, A. A., Wong, F., Mattox, A., Hruban, R. H., Wolfgang, C., Goggins, M. S., Molin, M. D., Wang, T-L., Roden, R. S., Klein, A., Ptak, J., Dobbyn, L., Schaefer, J. & 22 others, Silliman, N., Popoli, M., Vogelstein, J. T., Browne, J. D., Schoen, R. E., Brand, R. E., Tie, J., Gibbs, P., Wong, H. L., Mansfield, A. S., Jen, J., Hanash, S. M., Falconi, M., Allen, P. J., Zhou, S., Bettegowda, C., Diaz, L. A., Tomasetti, C., Kinzler, K. W., Vogelstein, B., O'Broin-Lennon, A. M. & Papadopoulos, N., Feb 23 2018, In : Science. 359, 6378, p. 926-930 5 p.

Research output: Contribution to journalArticle

Diagnostic utility of telomere length testing in a hospital-based setting

Alder, J., Hanumanthu, V. S., Strong, M. A., Dezern, A., Stanley, S. E., Takemoto, C. M., Danilova, L. V., Applegate, C. D., Bolton, S. G., Mohr, D. W., Brodsky, R. A., Casella, J. F., Greider, C. W., Brooks Jackson, J. & Armanios, M., Mar 6 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 10, p. E2358-E2365

Research output: Contribution to journalArticle

Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma

Ren, S., Gaykalova, D., Wang, J., Guo, T., Danilova, L. V., Favorov, A., Fertig, E., Bishop, J., Khan, Z., Flam, E., Wysocki, P. T., DeJong, P., Ando, M., Liu, C., Sakai, A., Fukusumi, T., Haft, S., Sadat, S. & Califano, J. A., Jan 1 2018, (Accepted/In press) In : International Journal of Cancer.

Research output: Contribution to journalArticle

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

The Fusion Analysis Working Group & The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 227-238.e3

Research output: Contribution to journalArticle

Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers

Wang, Y., Li, L., Douville, C., Cohen, J. D., Yen, T. T., Kinde, I., Sundfelt, K., Kjær, S. K., Hruban, R. H., Shih, I. M., Wang, T-L., Kurman, R. J., Springer, S., Ptak, J., Popoli, M., Schaefer, J., Silliman, N., Dobbyn, L., Tanner, E. J., Angarita, A. & 17 others, Lycke, M., Jochumsen, K., Afsari, B., Danilova, L. V., Levine, D. A., Jardon, K., Zeng, X., Arseneau, J., Fu, L., Diaz, L. A., Karchin, R., Tomasetti, C., Kinzler, K. W., Vogelstein, B., Nickles Fader, A. N., Gilbert, L. & Papadopoulos, N., Mar 21 2018, In : Science Translational Medicine. 10, 433, 8793.

Research output: Contribution to journalArticle

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

Kelley, D. Z., Flam, E. L., Guo, T., Danilova, L. V., Zamuner, F. T., Bohrson, C., Considine, M., Windsor, E. J., Bishop, J. A., Zhang, C., Koch, W. M., Sidransky, D., Westra, W. H., Chung, C. H., Califano, J. A., Wheelan, S., Favorov, A., Florea, L. D., Fertig, E. & Gaykalova, D., Jan 1 2018, (Accepted/In press) In : Translational Research.

Research output: Contribution to journalArticle

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 194-212.e6

Research output: Contribution to journalArticle

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 676-689.e3

Research output: Contribution to journalArticle

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 239-254.e6

Research output: Contribution to journalArticle

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 213-226.e3

Research output: Contribution to journalArticle

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance

Stein-O'Brien, G., Tsukamoto Kagohara, L., Li, S., Thakar, M., Ranaweera, R., Ozawa, H., Cheng, H., Considine, M., Schmitz, S., Favorov, A., Danilova, L. V., Califano, J. A., Izumchenko, E., Gaykalova, D., Chung, C. H. & Fertig, E., May 23 2018, In : Genome Medicine. 10, 1, 37.

Research output: Contribution to journalArticle

Integrative molecular characterization of malignant pleural mesothelioma

TCGA Research Network, Dec 1 2018, In : Cancer Discovery. 8, 12, p. 1549-1565 17 p.

Research output: Contribution to journalArticle

lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

The Cancer Genome Atlas Research Network, Apr 9 2018, In : Cancer Cell. 33, 4, p. 706-720.e9

Research output: Contribution to journalArticle

Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 172-180.e3

Research output: Contribution to journalArticle

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 338-354.e15

Research output: Contribution to journalArticle

Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 255-269.e4

Research output: Contribution to journalArticle

Multidimensional, quantitative assessment of PD-1/PD-L1 expression in patients with Merkel cell carcinoma and association with response to pembrolizumab 11 Medical and Health Sciences 1107 Immunology

Giraldo, N. A., Nguyen, P., Engle, E. L., Kaunitz, G. J., Cottrell, T. R., Berry, S., Green, B., Soni, A., Cuda, J. D., Stein, J. E., Sunshine, J. C., Succaria, F., Xu, H., Ogurtsova, A., Danilova, L. V., Church, C. D., Miller, N. J., Fling, S., Lundgren, L., Ramchurren, N. & 7 others, Yearley, J. H., Lipson, E., Cheever, M., Anders, R. A., Nghiem, P. T., Topalian, S. & Taube, J. M., Oct 1 2018, In : Journal for ImmunoTherapy of Cancer. 6, 1, 99.

Research output: Contribution to journalArticle

MVisAGe identifies concordant and discordant genomic alterations of driver genes in squamous tumors

Walter, V., Du, Y., Danilova, L. V., Hayward, M. C. & Hayes, D. N., Jun 15 2018, In : Cancer Research. 78, 12, p. 3375-3385 11 p.

Research output: Contribution to journalArticle

Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy

Springer, S. U., Chen, C. H., Del Carmen Rodriguez Pena, M., Li, L., Douville, C., Wang, Y., Cohen, J. D., Taheri, D., Silliman, N., Schaefer, J., Ptak, J., Dobbyn, L., Papoli, M., Kinde, I., Afsari, B., Tregnago, A. C., Bezerra, S. M., VandenBussche, C., Fujita, K., Ertoy, D. & 20 others, Cunha, I. W., Yu, L., Bivalacqua, T., Grollman, A. P., Diaz, L. A., Karchin, R., Danilova, L. V., Huang, C. Y., Shun, C. T., Turesky, R. J., Yun, B. H., Rosenquist, T. A., Pu, Y. S., Hruban, R. H., Tomasetti, C., Papadopoulos, N., Kinzler, K. W., Vogelstein, B., Dickman, K. G. & Netto, G. J., Mar 20 2018, In : eLife. 7, e32143.

Research output: Contribution to journalArticle

Oncogenic Signaling Pathways in The Cancer Genome Atlas

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 321-337.e10

Research output: Contribution to journalArticle

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

The Cancer Genome Atlas Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 282-300.e2

Research output: Contribution to journalArticle

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 297-312.e12

Research output: Contribution to journalArticle

Pathogenic Germline Variants in 10,389 Adult Cancers

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 355-370.e14

Research output: Contribution to journalArticle

Pathologic features of response to neoadjuvant anti-PD-1 in resected non-small-cell lung carcinoma: A proposal for quantitative immune-related pathologic response criteria (irPRC)

Cottrell, T. R., Thompson, E., Forde, P., Stein, J. E., Duffield, A. S., Anagnostou, V., Rekhtman, N., Anders, R. A., Cuda, J. D., Illei, P. B., Gabrielson, E., Askin, F. B., Niknafs, N., Smith, K., Velez, M. J., Sauter, J. L., Isbell, J. M., Jones, D. R., Battafarano, R. J., Yang, S. C. & 10 others, Danilova, L. V., Wolchok, J. D., Topalian, S., Velculescu, V. E., Pardoll, A. M., Brahmer, J., Hellmann, M. D., Chaft, J. E., Cimino-Mathews, A. M. & Taube, J. M., Jan 1 2018, In : Annals of Oncology. 29, 8, p. 1853-1860 8 p.

Research output: Contribution to journalArticle

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas Research Network, Apr 5 2018, In : Cell. 173, 2, p. 305-320.e10

Research output: Contribution to journalArticle

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 271-281.e7

Research output: Contribution to journalArticle

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 282-296.e4

Research output: Contribution to journalArticle

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 181-193.e7

Research output: Contribution to journalArticle

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 270-281.e3

Research output: Contribution to journalArticle

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

The Cancer Genome Atlas Research Network, Apr 3 2018, In : Cell Reports. 23, 1, p. 313-326.e5

Research output: Contribution to journalArticle

The Immune Landscape of Cancer

The Cancer Genome Atlas Research Network, Apr 17 2018, In : Immunity. 48, 4, p. 812-830.e14

Research output: Contribution to journalArticle

The Integrated Genomic Landscape of Thymic Epithelial Tumors

The Cancer Genome Atlas Network, Feb 12 2018, In : Cancer Cell. 33, 2, p. 244-258.e10

Research output: Contribution to journalArticle

The mutation-associated neoantigen functional expansion of specific T cells (MANAFEST) assay: A sensitive platform for monitoring antitumor immunity

Danilova, L. V., Anagnostou, V., Caushi, J. X., Sidhom, J. W., Guo, H., Chan, H. Y., Suri, P., Tam, A., Zhang, J., Asmar, M. E., Marrone, K., Naidoo, J., Brahmer, J., Forde, P., Baras, A., Cope, L., Velculescu, V. E., Pardoll, A. M., Housseau, F. & Smith, K., Aug 1 2018, In : Cancer immunology research. 6, 8, p. 888-899 12 p.

Research output: Contribution to journalArticle