Research output per year
Research output per year
- 1 - 50 out of 164 results
Search results
-
2024
Association between pathologic response and survival after neoadjuvant therapy in lung cancer
Deutsch, J. S., Cimino-Mathews, A., Thompson, E., Provencio, M., Forde, P. M., Spicer, J., Girard, N., Wang, D., Anders, R. A., Gabrielson, E., Illei, P., Jedrych, J., Danilova, L., Sunshine, J., Kerr, K. M., Tran, M., Bushong, J., Cai, J., Devas, V., Neely, J., & 4 others, Jan 2024, In: Nature medicine. 30, 1, p. 218-228 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Entinostat, nivolumab and ipilimumab for women with advanced HER2-negative breast cancer: a phase Ib trial
Roussos Torres, E. T., Ho, W. J., Danilova, L., Tandurella, J. A., Leatherman, J., Rafie, C., Wang, C., Brufsky, A., LoRusso, P., Chung, V., Yuan, Y., Downs, M., O’Connor, A., Shin, S. M., Hernandez, A., Engle, E. L., Piekarz, R., Streicher, H., Talebi, Z., Rudek, M., & 7 others, 2024, (Accepted/In press) In: Nature Cancer.Research output: Contribution to journal › Article › peer-review
-
MLL1 regulates cytokine-driven cell migration and metastasis
Nair, P. R., Danilova, L., Gómez-De-Mariscal, E., Kim, D., Fan, R., Muñoz-Barrutia, A., Fertig, E. J. & Wirtz, D., Mar 15 2024, In: Science Advances. 10, 11, eadk0785.Research output: Contribution to journal › Article › peer-review
-
2023
Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (Nature Genetics, (2020), 52, 3, (306-319), 10.1038/s41588-019-0562-0)
PCAWG Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1080 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)
PCAWG Consortium, May 2023, In: Nature genetics. 55, 5, p. 892 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6)
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E39Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (Nature Genetics, (2020), 52, 3, (331-341), 10.1038/s41588-019-0576-7)
PCAWG Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1076 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: The landscape of viral associations in human cancers (Nature Genetics, (2020), 52, 3, (320-330), 10.1038/s41588-019-0558-9)
PCAWG Pathogens & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1077 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)
PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1078 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (Nature Genetics, (2020), 52, 3, (294-305), 10.1038/s41588-019-0564-y)
PCAWG Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1079 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Combinatorial biomarker for predicting outcomes to anti-PD-1 therapy in patients with metastatic clear cell renal cell carcinoma
Deutsch, J. S., Lipson, E. J., Danilova, L., Topalian, S. L., Jedrych, J., Baraban, E., Ged, Y., Singla, N., Choueiri, T. K., Gupta, S., Motzer, R. J., McDermott, D., Signoretti, S., Atkins, M. & Taube, J. M., Feb 21 2023, In: Cell Reports Medicine. 4, 2, 100947.Research output: Contribution to journal › Article › peer-review
Open Access -
Erratum: Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces (Cell Systems (2023) 14(4) (285–301.e4), (S2405471223000807), (10.1016/j.cels.2023.03.004))
Deshpande, A., Loth, M., Sidiropoulos, D. N., Zhang, S., Yuan, L., Bell, A. T. F., Zhu, Q., Ho, W. J., Santa-Maria, C., Gilkes, D. M., Williams, S. R., Uytingco, C. R., Chew, J., Hartnett, A., Bent, Z. W., Favorov, S., Popel, A. S., Yarchoan, M., Kiemen, A., Wu, P. H., & 10 others, Aug 16 2023, In: Cell Systems. 14, 8, p. 722 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Myo1e overexpression in lung adenocarcinoma is associated with increased risk of mortality
Jusue-Torres, I., Tiv, R., Ricarte-Filho, J. C., Mallisetty, A., Contreras-Vargas, L., Godoy-Calderon, M. J., Khaddour, K., Kennedy, K., Valyi-Nagy, K., David, O., Menchaca, M., Kottorou, A., Koutras, A., Dimitrakopoulos, F., Abdelhady, K. M., Massad, M., Rubinstein, I., Feldman, L., Stewart, J., Shimamura, T., & 2 others, Dec 2023, In: Scientific reports. 13, 1, 4107.Research output: Contribution to journal › Article › peer-review
Open Access -
Profiling of syngeneic mouse HCC tumor models as a framework to understand anti-PD-1 sensitive tumor microenvironments
Zabransky, D. J., Danilova, L., Leatherman, J. M., Lopez-Vidal, T. Y., Sanchez, J., Charmsaz, S., Gross, N. E., Shin, S., Yuan, X., Hernandez, A., Yang, H., Xavier, S., Shu, D., Saeed, A., Munjal, K., Kamdar, Z., Kagohara, L. T., Jaffee, E. M., Yarchoan, M. & Ho, W. J., May 2023, In: Hepatology. 77, 5, p. 1566-1579 14 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)
PCAWG Consortium, May 2023, In: Nature genetics. 55, 5, p. 893 1 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence
Zhang, S., Yuan, L., Danilova, L., Mo, G., Zhu, Q., Deshpande, A., Bell, A. T. F., Elisseeff, J., Popel, A. S., Anders, R. A., Jaffee, E. M., Yarchoan, M., Fertig, E. J. & Kagohara, L. T., Dec 2023, In: Genome Medicine. 15, 1, 72.Research output: Contribution to journal › Article › peer-review
Open Access -
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces
Deshpande, A., Loth, M., Sidiropoulos, D. N., Zhang, S., Yuan, L., Bell, A. T. F., Zhu, Q., Ho, W. J., Santa-Maria, C., Gilkes, D. M., Williams, S. R., Uytingco, C. R., Chew, J., Hartnett, A., Bent, Z. W., Favorov, A. V., Popel, A. S., Yarchoan, M., Kiemen, A., Wu, P. H., & 10 others, Apr 19 2023, In: Cell Systems. 14, 4, p. 285-301.e4Research output: Contribution to journal › Article › peer-review
Open Access -
2022
Accurate Nonendoscopic Detection of Esophageal Squamous Cell Carcinoma Using Methylated DNA Biomarkers
Esophageal Squamous Cell Carcinoma Consortium, Aug 2022, In: Gastroenterology. 163, 2, p. 507-509.e2Research output: Contribution to journal › Short survey › peer-review
Open Access -
Author Correction: Inferring structural variant cancer cell fraction (Nature Communications, (2020), 11, 1, (730), 10.1038/s41467-020-14351-8)
PCAWG Evolution and Heterogeneity Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7568.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (Nature Communications, (2020), 11, 1, (736), 10.1038/s41467-019-13885-w)
PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7572.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Nature Communications, (2020), 11, 1, (733), 10.1038/s41467-019-13824-9)
PCAWG Structural Variation Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7574.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes (Nature Communications, (2020), 11, 1, (729), 10.1038/s41467-020-14367-0)
PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7566.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours (Nature Communications, (2020), 11, 1, (737), 10.1038/s41467-019-14052-x)
PCAWG Consortium, Dec 2022, In: Nature communications. 13, 1, 7569.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns (Nature Communications, (2020), 11, 1, (728), 10.1038/s41467-019-13825-8)
PCAWG Tumor Subtypes and Clinical Translation Working Group & PCAWG Consortium, Dec 2022, In: Nature communications. 13, 1, 7573.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig (Nature Communications, (2020), 11, 1, (731), 10.1038/s41467-020-14352-7)
PCAWG Evolution and Heterogeneity Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7567.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower (Nature Communications, (2020), 11, 1, (734), 10.1038/s41467-019-13929-1)
PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7571.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Author Correction: Integrative pathway enrichment analysis of multivariate omics data (Nature Communications, (2020), 11, 1, (735), 10.1038/s41467-019-13983-9)
PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2022, In: Nature communications. 13, 1, 7570.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
DNA-methylation for the detection and distinction of 19 human malignancies
Danilova, L., Wrangle, J., Herman, J. G. & Cope, L., 2022, In: Epigenetics. 17, 2, p. 191-201 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Genome-Wide Analysis of DNA Methylation in Cd4+ T Lymphocytes of Patients with Primary Progressive Multiple Sclerosis Indicates Involvement of This Epigenetic Process in the Disease Immunopathogenesis
Kiselev, I. S., Kulakova, O. G., Danilova, L. V., Baturina, O. A., Kabilov, M. R., Popova, E. V., Boyko, A. N. & Favorova, O. O., Jun 2022, In: Molecular Biology. 56, 3, p. 417-423 7 p.Research output: Contribution to journal › Article › peer-review
-
Genome-wide DNA methylation profiling identifies epigenetic changes in CD4+ and CD14+ cells of multiple sclerosis patients
Kiselev, I., Danilova, L., Baulina, N., Baturina, O., Kabilov, M., Boyko, A., Kulakova, O. & Favorova, O., Apr 2022, In: Multiple Sclerosis and Related Disorders. 60, 103714.Research output: Contribution to journal › Article › peer-review
Open Access -
Integrated T cell cytometry metrics for immune-monitoring applications in immunotherapy clinical trials
Sidiropoulos, D. N., Stein-O'Brien, G. L., Danilova, L., Gross, N. E., Charmsaz, S., Xavier, S., Leatherman, J., Wang, H., Yarchoan, M., Jaffee, E. M., Fertig, E. J. & Ho, W. J., Oct 10 2022, In: JCI Insight. 7, 19, e160398.Research output: Contribution to journal › Article › peer-review
Open Access -
Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy
Li, K., Tandurella, J. A., Gai, J., Zhu, Q., Lim, S. J., Thomas, D. L., Xia, T., Mo, G., Mitchell, J. T., Montagne, J., Lyman, M., Danilova, L. V., Zimmerman, J. W., Kinny-Köster, B., Zhang, T., Chen, L., Blair, A. B., Heumann, T., Parkinson, R., Durham, J. N., & 11 others, Nov 14 2022, In: Cancer cell. 40, 11, p. 1374-1391.e7Research output: Contribution to journal › Article › peer-review
Open Access -
Novel Genes Involved in Hypertrophic Cardiomyopathy: Data of Transcriptome and Methylome Profiling
Kiselev, I., Kozin, M., Baulina, N., Pisklova, M., Danilova, L., Zotov, A., Chumakova, O., Zateyshchikov, D. & Favorova, O., Dec 2022, In: International journal of molecular sciences. 23, 23, 15280.Research output: Contribution to journal › Article › peer-review
Open Access -
2021
Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade
Berry, S., Giraldo, N. A., Green, B. F., Cottrell, T. R., Stein, J. E., Engle, E. L., Xu, H., Ogurtsova, A., Roberts, C., Wang, D., Nguyen, P., Zhu, Q., Soto-Diaz, S., Loyola, J., Braunstein, I., Wong, P. F., Jessel, S., Doyle, J., Signer, D., Wilton, R., & 17 others, Jun 11 2021, In: Science. 372, 6547, eaba2609.Research output: Contribution to journal › Article › peer-review
Open Access -
Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways
Ho, W. J., Erbe, R., Danilova, L., Phyo, Z., Bigelow, E., Stein-O’Brien, G., Thomas, D. L., Charmsaz, S., Gross, N., Woolman, S., Cruz, K., Munday, R. M., Zaidi, N., Armstrong, T. D., Sztein, M. B., Yarchoan, M., Thompson, E. D., Jaffee, E. M. & Fertig, E. J., Dec 2021, In: Genome biology. 22, 1, 154.Research output: Contribution to journal › Article › peer-review
Open Access -
Neoadjuvant cabozantinib and nivolumab convert locally advanced hepatocellular carcinoma into resectable disease with enhanced antitumor immunity
Ho, W. J., Zhu, Q., Durham, J., Popovic, A., Xavier, S., Leatherman, J., Mohan, A., Mo, G., Zhang, S., Gross, N., Charmsaz, S., Lin, D., Quong, D., Wilt, B., Kamel, I. R., Weiss, M., Philosophe, B., Burkhart, R., Burns, W. R., Shubert, C., & 11 others, Sep 2021, In: Nature Cancer. 2, 9, p. 891-903 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Proteogenomic characterization of pancreatic ductal adenocarcinoma
Clinical Proteomic Tumor Analysis Consortium, Sep 16 2021, In: Cell. 184, 19, p. 5031-5052.e26Research output: Contribution to journal › Article › peer-review
Open Access -
Spatial UMAP and image cytometry for topographic immuno-oncology biomarker discovery
Giraldo, N. A., Berry, S., Becht, E., Ates, D., Schenk, K. M., Engle, E. L., Green, B., Nguyen, P., Soni, A., Stein, J. E., Succaria, F., Ogurtsova, A., Xu, H., Gottardo, R., Anders, R. A., Lipson, E. J., Danilova, L., Baras, A. S. & Taube, J. M., Nov 2021, In: Cancer Immunology Research. 9, 11, p. 1262-1269 8 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer
Afsari, B., Kuo, A., Zhang, Y., Li, L., Lahouel, K., Danilova, L., Favorov, A., Rosenquist, T., Grollman, A. P., Kinzler, K. W., Cope, L., Vogelstein, B. & Tomasetti, C., Jan 2021, In: eLife. 10, p. 1-71 71 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Systemic inhibition of PTPN22 augments anticancer immunity
Ho, W. J., Croessmann, S., Lin, J., Phyo, Z. H., Charmsaz, S., Danilova, L., Mohan, A. A., Gross, N. E., Chen, F., Dong, J., Aggarwal, D., Bai, Y., Wang, J., He, J., Leatherman, J. M., Yarchoan, M., Armstrong, T. D., Zaidi, N., Fertig, E. J., Denny, J. C., & 3 others, Sep 1 2021, In: Journal of Clinical Investigation. 131, 17, e146950.Research output: Contribution to journal › Article › peer-review
Open Access -
Transfer learning between preclinical models and human tumors identifies a conserved NK cell activation signature in anti-CTLA-4 responsive tumors
Davis-Marcisak, E. F., Fitzgerald, A. A., Kessler, M. D., Danilova, L., Jaffee, E. M., Zaidi, N., Weiner, L. M. & Fertig, E. J., Dec 2021, In: Genome Medicine. 13, 1, 129.Research output: Contribution to journal › Article › peer-review
Open Access -
2020
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
PCAWG Tumor Subtypes and Clinical Translation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 728.Research output: Contribution to journal › Article › peer-review
Open Access -
Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y)
MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 6232.Research output: Contribution to journal › Comment/debate › peer-review
Open Access -
Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma
Guo, T., Zambo, K. D. A., Zamuner, F. T., Ou, T., Hopkins, C., Kelley, D. Z., Wulf, H. A., Winkler, E., Erbe, R., Danilova, L., Considine, M., Sidransky, D., Favorov, A., Florea, L., Fertig, E. J. & Gaykalova, D. A., Sep 1 2020, In: Epigenetics. 15, 9, p. 959-971 13 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Combined burden and functional impact tests for cancer driver discovery using DriverPower
PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 734.Research output: Contribution to journal › Article › peer-review
Open Access -
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
PCAWG Structural Variation Working Group & PCAWG Consortium, Mar 1 2020, In: Nature genetics. 52, 3, p. 331-341 11 p.Research output: Contribution to journal › Article › peer-review
Open Access76 Scopus citations -
Comprehensive molecular characterization of mitochondrial genomes in human cancers
PCAWG Consortium, Mar 1 2020, In: Nature genetics. 52, 3, p. 342-352 11 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy
Malone, M. K., Smrekar, K., Park, S., Blakely, B., Walter, A., Nasta, N., Park, J., Considine, M., Danilova, L. V., Pandey, N. B., Fertig, E. J., Popel, A. S. & Jin, K., Jun 2 2020, In: Cancer Biology and Therapy. 21, 6, p. 560-569 10 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
PCAWG Structural Variation Working Group & PCAWG Consortium, Mar 1 2020, In: Nature genetics. 52, 3, p. 294-305 12 p.Research output: Contribution to journal › Article › peer-review
Open Access32 Scopus citations -
Divergent mutational processes distinguish hypoxic and normoxic tumours
PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 737.Research output: Contribution to journal › Article › peer-review
Open Access