Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259

PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer

Hartkopf, A. D., Taran, F., Wallwiener, M., Walter, C. B., Krämer, B., Grischke, E., & Brucker, S. Y. (2016) · Breast Care · doi:10.1159/000453569 · Cited by 30,989

Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review

Wanchoo, R., Karam, S., Uppal, N. N., Barta, V. S., Deray, G., Devoe, C., Launay‐Vacher, V., Jhaveri, K. D., & on behalf of Cancer and Kidney International Network Workgroup on Immune Checkpoint Inhibitors (2017) · American Journal of Nephrology · doi:10.1159/000455014 · Cited by 15,320

Robust enumeration of cell subsets from tissue expression profiles

Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., & Alizadeh, A. A. (2015) · Nature Methods · doi:10.1038/nmeth.3337 · Cited by 13,224

Safety, activity, and immune correlates of anti–PD-1 antibody in cancer

Topalian, S. L., Hodi, F. S., Brahmer, J. R., Gettinger, S. N., Smith, D. C., McDermott, D. F., Powderly, J. D., Carvajal, R. D., Sosman, J. A., Atkins, M. B., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1200690 · Cited by 12,628

Inferring tumour purity and stromal and immune cell admixture from expression data

Yoshihara, K., Shahmoradgoli, M., Martínez, E., Vegesna, R., Kim, H., Torres-Garcia, W., Treviño, V., Shen, H., Laird, P. W., Levine, D. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms3612 · Cited by 9,778

Signatures of mutational processes in human cancer

Initiative, A. P. C. G., Alexandrov, L. B., ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, PedBrain, I., Nik-Zainal, S., Wedge, D. C., Aparicio, S. A. J. R., Behjati, S., Biankin, A. V., et al. (2013) · Nature · doi:10.1038/nature12477 · Cited by 9,660

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

Le, D. T., Uram, J. N., Wang, H., Bartlett, B. R., Kemberling, H., Eyring, A. D., Skora, A. D., Luber, B. S., Azad, N. S., Laheru, D., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1500596 · Cited by 9,377

Nivolumab versus Docetaxel in Advanced Squamous-Cell Non–Small-Cell Lung Cancer

Brahmer, J., Reckamp, K. L., Baas, P., Crinò, L., Eberhardt, W. E. E., Poddubskaya, E., Antonia, S., Pluzanski, A., Vokes, E. E., Holgado, E., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1504627 · Cited by 8,447

Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer

Rizvi, N. A., Hellmann, M. D., Snyder, A., Kvistborg, P., Makarov, V., Havel, J. J., Lee, W., Yuan, J., Wong, P., Ho, T. S., et al. (2015) · Science · doi:10.1126/science.aaa1348 · Cited by 7,802

PD-1 blockade induces responses by inhibiting adaptive immune resistance

Tumeh, P. C., Harview, C. L., Yearley, J. H., Shintaku, I. P., Taylor, E. J. M., Robert, L., Chmielowski, B., Spasic, M., Henry, G., Ciobanu, V., et al. (2014) · Nature · doi:10.1038/nature13954 · Cited by 6,609

Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma

Motzer, R. J., Escudier, B., McDermott, D. F., George, S., Hammers, H. J., Srinivas, S., Tykodi, S. S., Sosman, J. A., Procopio, G., Plimack, E. R., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1510665 · Cited by 5,807

Nivolumab in Previously Untreated Melanoma without BRAF Mutation

Robert, C., Long, G. V., Brady, B., Dutriaux, C., Maio, M., Mortier, L., Hassel, J. C., Rutkowski, P., McNeil, C., Kalinka-Warzocha, E., et al. (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1412082 · Cited by 5,519

Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients

Herbst, R. S., Soria, J.-C., Kowanetz, M., Fine, G. D., Hamid, O., Gordon, M. S., Sosman, J. A., McDermott, D. F., Powderly, J. D., Gettinger, S. N., et al. (2014) · Nature · doi:10.1038/nature14011 · Cited by 5,231

Nivolumab for Recurrent Squamous-Cell Carcinoma of the Head and Neck

Ferris, R. L., Blumenschein, G., Fayette, J., Guigay, J., Colevas, A. D., Licitra, L., Harrington, K., Kasper, S., Vokes, E. E., Even, C., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1602252 · Cited by 5,101

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

Cibulskis, K., Lawrence, M. S., Carter, S. L., Sivachenko, A., Jaffe, D. B., Sougnez, C. L., Gabriel, S., Meyerson, M. M., Lander, E. S., & Getz, G. A. (2013) · Nature Biotechnology · doi:10.1038/nbt.2514 · Cited by 4,965

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingPreprint

Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,954

Neoantigens in cancer immunotherapy

Schumacher, T. N., & Schreiber, R. D. (2015) · Science · doi:10.1126/science.aaa4971 · Cited by 4,783

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

Snyder, A., Makarov, V., Merghoub, T., Yuan, J., Zaretsky, J. M., Desrichard, A., Walsh, L. A., Postow, M. A., Wong, P., Ho, T. S., et al. (2014) · New England Journal of Medicine · doi:10.1056/nejmoa1406498 · Cited by 4,286

Molecular and genetic properties of tumors associated with local immune cytolytic activity

Rooney, M. S., Shukla, S. A., Wu, C. J., Getz, G., & Hacohen, N. (2015) · Cell · doi:10.1016/j.cell.2014.12.033 · Cited by 3,825

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial

Rosenberg, J. E., Hoffman-Censits, J., Powles, T., van der Heijden, M. S., Balar, A. V., Necchi, A., Dawson, N., O'Donnell, P. H., Balmanoukian, A., Loriot, Y., et al. (2016) · The Lancet · doi:10.1016/s0140-6736(16)00561-4 · Cited by 3,669

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

Hugo, W., Zaretsky, J. M., Sun, L., Song, C., Moreno, B. H., Hu-Lieskovan, S., Berent-Maoz, B., Pang, J., Chmielowski, B., Cherry, G., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.065 · Cited by 3,448

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

Zaretsky, J. M., Garcia-Diaz, A., Shin, D. S., Escuin-Ordinas, H., Hugo, W., Hu-Lieskovan, S., Torrejon, D. Y., Abril-Rodriguez, G., Sandoval, S., Barthly, L., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1604958 · Cited by 3,237

Guidelines for the Evaluation of Immune Therapy Activity in Solid Tumors: Immune-Related Response Criteria

Wolchok, J. D., Hoos, A., O'Day, S. J., Weber, J. S., Hamid, O., Lebbé, C., Maio, M., Binder, M., Bohnsack, O., Nichol, G. M., et al. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-09-1624 · Cited by 3,214

Genomic classification of cutaneous melanoma

Akbani, R., Akdemir, K. C., Aksoy, B. A., Albert, M., Ally, A., Amin, S. B., Arachchi, H., Arora, A., Auman, J. T., Ayala, B., et al. (2015) · Cell · doi:10.1016/j.cell.2015.05.044 · Cited by 3,151

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

McGranahan, N., Furness, A. J. S., Rosenthal, R., Ramskov, S., Lyngaa, R., Saini, S. K., Jamal-Hanjani, M., Wilson, G. A., Birkbak, N. J., Hiley, C. T., et al. (2016) · Science · doi:10.1126/science.aaf1490 · Cited by 3,065

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

Van Allen, E. M., Miao, D., Schilling, B., Shukla, S. A., Blank, C., Zimmer, L., Sucker, A., Hillen, U., Geukes Foppen, M. H., Goldinger, S. M., et al. (2015) · Science · doi:10.1126/science.aad0095 · Cited by 2,839

Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity

Spranger, S., Bao, R., & Gajewski, T. F. (2015) · Nature · doi:10.1038/nature14404 · Cited by 2,830

Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy

Topalian, S. L., Taube, J. M., Anders, R. A., & Pardoll, D. M. (2016) · Nature Reviews Cancer · doi:10.1038/nrc.2016.36 · Cited by 2,733

T cell exclusion, immune privilege, and the tumor microenvironment

Joyce, J. A., & Fearon, D. T. (2015) · Science · doi:10.1126/science.aaa6204 · Cited by 2,539

PD-1 expression by tumour-associated macrophages inhibits phagocytosis and tumour immunity

Gordon, S. R., Maute, R. L., Dulken, B. W., Hutter, G., George, B. M., McCracken, M. N., Gupta, R., Tsai, J. M., Sinha, R., Corey, D., et al. (2017) · Nature · doi:10.1038/nature22396 · Cited by 2,247

Colocalization of Inflammatory Response with B7-H1 Expression in Human Melanocytic Lesions Supports an Adaptive Resistance Mechanism of Immune Escape

Taube, J. M., Anders, R. A., Young, G. D., Xu, H., Sharma, R., McMiller, T. L., Chen, S., Klein, A. P., Pardoll, D. M., Topalian, S. L., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003689 · Cited by 2,157

Absolute quantification of somatic DNA alterations in human cancer

Carter, S. L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T. I., Laird, P. W., Onofrio, R. C., Winckler, W., Weir, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2203 · Cited by 2,031

Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses

Chiappinelli, K. B., Strissel, P. L., Desrichard, A., Li, H., Henke, C., Akman, B., Hein, A., Rote, N. S., Cope, L. M., Snyder, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.011 · Cited by 2,022

Up-Regulation of PD-L1, IDO, and T regs in the Melanoma Tumor Microenvironment Is Driven by CD8 + T Cells

Spranger, S., Spaapen, R. M., Zha, Y., Williams, J., Meng, Y., Ha, T. T., & Gajewski, T. F. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3006504 · Cited by 1,677

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

Saunders, C. T., Wong, W. S. W., Swamy, S., Becq, J., Murray, L. J., & Cheetham, R. K. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts271 · Cited by 1,589

Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma

Johnson, B. E., Mazor, T., Hong, C., Barnes, M., Aihara, K., McLean, C. Y., Fouse, S. D., Yamamoto, S., Ueda, H., Tatsuno, K., et al. (2014) · Science · doi:10.1126/science.1239947 · Cited by 1,362

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

Davoli, T., Uno, H., Wooten, E. C., & Elledge, S. J. (2017) · Science · doi:10.1126/science.aaf8399 · Cited by 1,347

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

Shen, R., & Seshan, V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw520 · Cited by 1,263

PI3Kγ is a molecular switch that controls immune suppression

Kaneda, M. M., Messer, K. S., Ralainirina, N., Li, H., Leem, C. J., Gorjestani, S., Woo, G., Nguyen, A. V., Figueiredo, C. C., Foubert, P., et al. (2016) · Nature · doi:10.1038/nature19834 · Cited by 1,224

deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution

Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S., & Swanton, C. (2016) · Genome biology · doi:10.1186/s13059-016-0893-4 · Cited by 1,178

Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells

Robins, H. S., Campregher, P. V., Srivastava, S. K., Wacher, A., Turtle, C. J., Kahsai, O., Riddell, S. R., Warren, E. H., & Carlson, C. S. (2009) · Blood · doi:10.1182/blood-2009-04-217604 · Cited by 1,122

Mutations driving CLL and their evolution in progression and relapse

Landau, D. A., Tausch, E., Taylor-Weiner, A. N., Stewart, C., Reiter, J. G., Bahlo, J., Kluth, S., Božić, I., Lawrence, M. S., Böttcher, S., et al. (2015) · Nature · doi:10.1038/nature15395 · Cited by 1,081

Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations

Nielsen, M., Lundegaard, C., Worning, P., Lauemøller, S. L., Lamberth, K., Buus, S., Brunak, S., & Lund, O. (2003) · Protein Science · doi:10.1110/ps.0239403 · Cited by 1,075

PyClone: statistical inference of clonal population structure in cancer

Roth, A. J. L., Khattra, J. S., Yap, D., Wan, A. N. C., Laks, E., Biele, J., Ha, G., Aparicio, S. A. J. R., Bouchard‐Côté, A., & Shah, S. P. (2014) · Nature Methods · doi:10.1038/nmeth.2883 · Cited by 1,002

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

Chen, P.-L., Roh, W., Reuben, A., Cooper, Z. A., Spencer, C. N., Prieto, P. A., Miller, J. P., Bassett, R. L., Gopalakrishnan, V., Wani, K., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-15-1545 · Cited by 988

A Direct Estimate of the Human αβ T Cell Receptor Diversity

Arstila, T. P., Casrouge, A., Baron, V., Even, J., Kanellopoulos, J., & Kourilsky, P. (1999) · Science · doi:10.1126/science.286.5441.958 · Cited by 931

Clonal evolution of glioblastoma under therapy

Wang, J., Cazzato, E., Ladewig, E., Frattini, V., Rosenbloom, D. I. S., Zairis, S., Abate, F., Liu, Z., Elliott, O., Shin, Y.-J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3590 · Cited by 720

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

McGranahan, N., Favero, F., de Bruin, E. C., Birkbak, N. J., Szallasi, Z., & Swanton, C. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa1408 · Cited by 685

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

Fisher, S., Barry, A. J., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r1 · Cited by 676

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

Larson, D. E., Harris, C. C., Chen, K., Koboldt, D. C., Abbott, T. E., Dooling, D. J., Ley, T. J., Mardis, E. R., Wilson, R. K., & Ding, L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr665 · Cited by 658

Standardizing methods to address clonality in population studies

Arnaud‐Haond, S., Duarte, C. M., Alberto, F., & Serrão, E. Á. (2007) · Molecular Ecology · doi:10.1111/j.1365-294x.2007.03535.x · Cited by 654

Using synthetic templates to design an unbiased multiplex PCR assay

Carlson, C. S., Emerson, R., Sherwood, A., Desmarais, C., Chung, M., Parsons, J. M., Steen, M. S., LaMadrid-Herrmannfeldt, M., Williamson, D. W., Livingston, R. J., et al. (2013) · Nature Communications · doi:10.1038/ncomms3680 · Cited by 568

Overall Survival in Patients With Advanced Melanoma Who Received Nivolumab Versus Investigator’s Choice Chemotherapy in CheckMate 037: A Randomized, Controlled, Open-Label Phase III Trial

Larkin, J., Minor, D. R., D’Angelo, S. P., Neyns, B., Smylie, M., Miller, W. H., Gutzmer, R., Linette, G. P., Chmielowski, B., Lao, C. D., et al. (2017) · Journal of Clinical Oncology · doi:10.1200/jco.2016.71.8023 · Cited by 522

Combination Therapy with Anti–CTLA-4 and Anti–PD-1 Leads to Distinct Immunologic Changes In Vivo

Das, R., Verma, R., Sznol, M., Boddupalli, C. S., Gettinger, S. N., Kluger, H. M., Callahan, M. K., Wolchok, J. D., Halaban, R., Dhodapkar, M. V., et al. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1401686 · Cited by 473

Neoantigen landscape dynamics during human melanoma–T cell interactions

Verdegaal, E. M. E., de Miranda, N. F. C. C., Visser, M., Harryvan, T. J., van Buuren, M. M., Andersen, R. S., Hadrup, S. R., van der Minne, C. E., Schotte, R., Spits, H., et al. (2016) · Nature · doi:10.1038/nature18945 · Cited by 464

Molecular Drivers of the Non–T-cell-Inflamed Tumor Microenvironment in Urothelial Bladder Cancer

Sweis, R. F., Spranger, S., Bao, R., Paner, G. P., Stadler, W. M., Steinberg, G. D., & Gajewski, T. F. (2016) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-15-0274 · Cited by 356

Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival

Morris, L. G. T., Riaz, N., Desrichard, A., Şenbabaoğlu, Y., Hakimi, A. A., Makarov, V., Reis-Filho, J. S., & Chan, T. A.-T. (2016) · Oncotarget · doi:10.18632/oncotarget.7067 · Cited by 307

Differential Expression of Immune-Regulatory Genes Associated with PD-L1 Display in Melanoma: Implications for PD-1 Pathway Blockade

Taube, J. M., Young, G. D., McMiller, T. L., Chen, S., Salas, J. T., Pritchard, T. S., Xu, H., Meeker, A. K., Fan, J., Cheadle, C., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-0244 · Cited by 252

Phase I/II Study of Metastatic Melanoma Patients Treated with Nivolumab Who Had Progressed after Ipilimumab

Weber, J., Gibney, G., Kudchadkar, R., Yu, B., Cheng, P., Martinez, A. J., Kroeger, J., Richards, A., McCormick, L., Moberg, V., et al. (2016) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-15-0193 · Cited by 248

The Past, Present, and Future of Immune Repertoire Biology – The Rise of Next-Generation Repertoire Analysis

Six, A., Mariotti‐Ferrandiz, E., Chaara, W., Magadán, S., Pham, H., Lefranc, M., Mora, T., Thomas‐Vaslin, V., Walczak, A. M., & Boudinot, P. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00413 · Cited by 181

Estimating the Diversity, Completeness, and Cross-Reactivity of the T Cell Repertoire

Zarnitsyna, V. I., Evavold, B. D., Schoettle, L. N., Blattman, J. N., & Antia, R. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00485 · Cited by 180

The role of neoantigens in response to immune checkpoint blockade

Riaz, N., Morris, L. G. T., Havel, J. J., Makarov, V., Desrichard, A., & Chan, T. A.-T. (2016) · International Immunology · doi:10.1093/intimm/dxw019 · Cited by 178

Dynamics of the Cytotoxic T Cell Response to a Model of Acute Viral Infection

DeWitt, W. S., Emerson, R., Lindau, P., Vignali, M., Snyder, T. M., Desmarais, C., Sanders, C. M., Utsugi, H., Warren, E. H., McElrath, M. J., et al. (2015) · Journal of Virology · doi:10.1128/jvi.03474-14 · Cited by 161

Recurrent SERPINB3 and SERPINB4 mutations in patients who respond to anti-CTLA4 immunotherapy

Riaz, N., Havel, J. J., Kendall, S. M., Makarov, V., Walsh, L. A., Desrichard, A., Weinhold, N., & Chan, T. A.-T. (2016) · Nature Genetics · doi:10.1038/ng.3677 · Cited by 151

Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire

Sims, J. S., Grinshpun, B., Feng, Y., Ung, T. H., Neira, J. A., Samanamud, J. L., Canoll, P., Shen, Y., Sims, P. A., & Bruce, J. N. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601012113 · Cited by 103

Human melanomas and ovarian cancers overexpressing mechanical barrier molecule genes lack immune signatures and have increased patient mortality risk

Salerno, E. P., Bedognetti, D., Mauldin, I. S., Deacon, D. H., Shea, S. M., Pinczewski, J., Obeid, J. M., Coukos, G., Wang, E., Gajewski, T. F., et al. (2016) · OncoImmunology · doi:10.1080/2162402x.2016.1240857 · Cited by 98

Abstract CT001: Durable, long-term survival in previously treated patients with advanced melanoma (MEL) who received nivolumab (NIVO) monotherapy in a phase I trial

Hodi, F. S., Kluger, H. M., Sznol, M., Carvajal, R. D., Lawrence, D. P., Atkins, M. B., Powderly, J. D., Sharfman, W. H., Puzanov, I. J., Smith, D., et al. (2016) · Cancer Research · doi:10.1158/1538-7445.am2016-ct001 · Cited by 80

Estimating the ratio of CD4+ to CD8+ T cells using high-throughput sequence data

Emerson, R., Sherwood, A., Desmarais, C., Malhotra, S., Phippard, D., & Robins, H. S. (2013) · Journal of Immunological Methods · doi:10.1016/j.jim.2013.02.002 · Cited by 72

HLA Typing by SSO and SSP Methods

Dunckley, H. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-842-9_2 · Cited by 61

MAC: identifying and correcting annotation for multi-nucleotide variations

Wei, L., Liu, L. T., Conroy, J., Hu, Q., Conroy, J. M., Morrison, C. D., Johnson, C. S., Wang, J., & Liu, S. (2015) · BMC Genomics · doi:10.1186/s12864-015-1779-7 · Cited by 56

OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes

Yau, C. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt416 · Cited by 48

Baseline tumor T cell receptor (TcR) sequencing analysis and neo antigen load is associated with benefit in melanoma patients receiving sequential nivolumab and ipilimumab

Weber, J. S., Horak, C. E., Hodi, F. S., Chang, H., Woods, D. M., Sanders, C. M., Robins, H. S., & Yusko, E. C. (2016) · Annals of Oncology · doi:10.1093/annonc/mdw378.01 · Cited by 13

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

Jiang, P., Gu, S., Pan, D., Fu, J., Sahu, A., Hu, X., Li, Z., Traugh, N., Bu, X., Li, B., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0136-1 · Cited by 5,179

Inflammation and cancer: triggers, mechanisms, and consequences

Greten, F. R., & Grivennikov, S. I. (2019) · Immunity · doi:10.1016/j.immuni.2019.06.025 · Cited by 3,806

Approaches to treat immune hot, altered and cold tumours with combination immunotherapies

Galon, J., & Bruni, D. (2019) · Nature Reviews Drug Discovery · doi:10.1038/s41573-018-0007-y · Cited by 3,520

CD8+ T cells regulate tumour ferroptosis during cancer immunotherapy

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