Hacohen, Nir

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature

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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

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An immunogenic personal neoantigen vaccine for patients with melanoma

Ott, P. A., Hu, Z., Keskin, D. B., Shukla, S. A., Sun, J., Bozym, D. J., Zhang, W., Luoma, A., Giobbie-Hurder, A., Peter, L., et al. (2017) · Nature

Immunotherapy and Immune ResponsesCancer Immunotherapy and Biomarkers

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B cells and tertiary lymphoid structures promote immunotherapy response

Helmink, B. A., Reddy, S. M., Gao, J., Zhang, S., Basar, R., Thakur, R., Yizhak, K., Sade-Feldman, M., Blando, J., Han, G., et al. (2020) · Nature

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

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Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

Villani, A.-C., Satija, R., Reynolds, G., Sarkizova, S., Shekhar, K., Fletcher, J., Griesbeck, M., Butler, A., Zheng, S., Lazo, S., et al. (2017) · Science

Single-cell and spatial transcriptomicsImmunotherapy and Immune Responses

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The human cell atlas

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

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Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

Sade-Feldman, M., Yizhak, K., Bjorgaard, S. L., Ray, J. P., de Boer, C. G., Jenkins, R. W., Lieb, D. J., Chen, J. H., Frederick, D. T., Barzily-Rokni, M., et al. (2018) · Cell

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

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CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

Platt, R. J., Chen, S., Zhou, Y., Yim, M. J., Swiech, L., Kempton, H. R., Dahlman, J. E., Parnas, O., Eisenhaure, T. M., Jovanovic, M., et al. (2014) · Cell

CRISPR and Genetic EngineeringVirus-based gene therapy research

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Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

Keskin, D. B., Anandappa, A. J., Sun, J., Tirosh, I., Mathewson, N. D., Li, S., Oliveira, G., Giobbie-Hurder, A., Felt, K., Gjini, E., et al. (2019) · Nature

Cancer Immunotherapy and BiomarkersImmunotherapy and Immune Responses

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Evolution and impact of subclonal mutations in chronic lymphocytic leukemia

Landau, D. A., Carter, S. L., Stojanov, P., McKenna, A., Stevenson, K., Lawrence, M. S., Sougnez, C., Stewart, C., Sivachenko, A., Wang, L., et al. (2013) · Cell

Chronic Lymphocytic Leukemia ResearchCancer Genomics and Diagnostics

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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature

Single-cell and spatial transcriptomicsRNA Research and Splicing

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Landscape of X chromosome inactivation across human tissues

GTEx Consortium, Tukiainen, T., Villani, A.-C., Yen, A., Rivas, M. A., Marshall, J. L., Satija, R., Aguirre, M., Gauthier, L., Fleharty, M., et al. (2017) · Nature

Genetic and Clinical Aspects of Sex Determination and Chromosomal AbnormalitiesGenomics and Chromatin Dynamics

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Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Sade-Feldman, M., Jiao, Y. J., Chen, J. H., Rooney, M. S., Barzily-Rokni, M., Eliane, J.-P., Bjorgaard, S. L., Hammond, M. R., Vitzthum, H., Blackmon, S. M., et al. (2017) · Nature Communications

Cancer Immunotherapy and BiomarkersImmunotherapy and Immune Responses

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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

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Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Ding, J., Adiconis, X., Simmons, S. K., Kowalczyk, M. S., Hession, C. C., Marjanovic, N. D., Hughes, T. K., Wadsworth, M. H., Burks, T., Nguyen, L. T., et al. (2020) · Nature Biotechnology

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Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity

Shrock, E., Fujimura, E., Kula, T., Timms, R. T., Lee, I.-H., Leng, Y., Robinson, M. L., Sie, B. M., Li, M. Z., Chen, Y., et al. (2020) · Science

SARS-CoV-2 and COVID-19 ResearchSARS-CoV-2 detection and testing

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Genome-wide enhancer maps link risk variants to disease genes

Nasser, J., Bergman, D. T., Fulco, C. P., Guckelberger, P., Doughty, B. R., Patwardhan, T. A., Jones, T. R., Nguyen, T. H., Ulirsch, J. C., Lekschas, F., et al. (2021) · Nature

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

Rabani, M., Levin, J. Z., Fan, L., Adiconis, X., Raychowdhury, R., Garber, M., Gnirke, A., Nusbaum, C., Hacohen, N., Friedman, N., et al. (2011) · Nature Biotechnology

RNA Research and SplicingRNA and protein synthesis mechanisms

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Key parameters of tumor epitope immunogenicity revealed through a consortium approach improve neoantigen prediction

Wells, D. K., van Buuren, M. M., Dang, K. K., Hubbard-Lucey, V. M., Sheehan, K. C. F., Campbell, K. M., Lamb, A., Ward, J. P., Sidney, J., Blazquez, A. B., et al. (2020) · Cell

vaccines and immunoinformatics approachesCancer Immunotherapy and Biomarkers

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Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

Raj, T., Rothamel, K., Mostafavi, S., Ye, C., Lee, M. N., Replogle, J. M., Feng, T., Lee, M., Asinovski, N., Frohlich, I., et al. (2014) · Science

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

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Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J. K., Li, W., Zuk, O., et al. (2009) · Science

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

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Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science

Advanced Proteomics Techniques and ApplicationsGene Regulatory Network Analysis

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A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., Przybylski, D., Platt, R. J., Tirosh, I., Sanjana, N. E., et al. (2015) · Cell

Immune Response and InflammationCRISPR and Genetic Engineering

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Aryl hydrocarbon receptor Controls Monocyte Differentiation into dendritic Cells versus Macrophages

Goudot, C., Coillard, A., Villani, A.-C., Gueguen, P., Cros, A., Sarkizova, S., Tang-Huau, T.-L., Bohec, M., Baulande, S., Hacohen, N., et al. (2017) · Immunity

Immunotherapy and Immune ResponsesImmune cells in cancer

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