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ArticlesPeer ReviewedFull Text
A cell-free nanobody engineering platform rapidly generates SARS-CoV-2 neutralizing nanobodies
Author / Creator:Chen, Xun ; Gentili, Matteo ; Hacohen, Nir ; Regev, Aviv
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-09, Vol.12 (1), p.5506-5506, Article 5506
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Newsletter articlesFull Text
INTERNATIONAL PATENT: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION, HACOHEN, NIR FILES APPLICATION FOR "CHIMERIC AMPLICON ARRAY SEQUENCING"
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2021
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Newsletter articlesFull Text
INTERNATIONAL PATENT: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION, HACOHEN, NIR FILES APPLICATION FOR "SINGLE CELL COMBINATORIAL INDEXING FROM AM...
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2021
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INTERNATIONAL PATENT: HACOHEN, NIR, THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION FILES APPLICATION FOR "HIGH-THROUGHPUT ASSESSMENT OF EXOGENOUS PO...
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2022
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Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
Author / Creator:Ding, Jiarui ; Adiconis, Xian ; Simmons, Sean K. ; Kowalczyk, Monika S. ; Hession, Cynthia C. ; Marjanovic, Nemanja D. ; Hughes, Travis K. ; Wadsworth, Marc H. ; Burks, Tyler ; Nguyen, Lan T. ; Kwon, John Y. H. ; Barak, Boaz ; Ge, William ; Kedaigle, Amanda J. ; Carroll, Shaina ; Li, Shuqiang ; Hacohen, Nir ; Rozenblatt-Rosen, Orit ; Shalek, Alex K. ; Villani, Alexandra-Chloé ; Regev, Aviv ; Levin, Joshua Z.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2020-06, Vol.38 (6), p.737-746
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Newsletter articlesFull Text
INTERNATIONAL PATENT: THE GENERAL HOSPITAL CORPORATION , PRESIDENT AND FELLOWS OF HARVARD COLLEGE , HACOHEN, NIR FILES APPLICATION FOR "METHODS FOR PREDICTING OUTCOMES OF CHECKPOINT INHIBITION AND TRE...
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2021
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ArticlesPeer ReviewedFull Text
An immune-cell signature of bacterial sepsis
Author / Creator:Reyes, Miguel ; Filbin, Michael R. ; Bhattacharyya, Roby P. ; Billman, Kianna ; Eisenhaure, Thomas ; Hung, Deborah T. ; Levy, Bruce D. ; Baron, Rebecca M. ; Blainey, Paul C. ; Goldberg, Marcia B. ; Hacohen, Nir
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2020-03, Vol.26 (3), p.333-340
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ArticlesPeer ReviewedFull Text
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Author / Creator:Grabherr, Manfred G ; Haas, Brian J ; Yassour, Moran ; Levin, Joshua Z ; Thompson, Dawn A ; Amit, Ido ; Adiconis, Xian ; Fan, Lin ; Raychowdhury, Raktima ; Zeng, Qiandong ; Chen, Zehua ; Mauceli, Evan ; Hacohen, Nir ; Gnirke, Andreas ; Rhind, Nicholas ; di Palma, Federica ; Birren, Bruce W ; Nusbaum, Chad ; Lindblad-Toh, Kerstin ; Friedman, Nir ; Regev, Aviv
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2011-07, Vol.29 (7), p.644-652
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ArticlesPeer ReviewedFull Text
Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection
Author / Creator:Li, Bo ; Clohisey, Sara M. ; Chia, Bing Shao ; Wang, Bo ; Cui, Ang ; Eisenhaure, Thomas ; Schweitzer, Lawrence D. ; Hoover, Paul ; Parkinson, Nicholas J. ; Nachshon, Aharon ; Smith, Nikki ; Regan, Tim ; Farr, David ; Gutmann, Michael U. ; Bukhari, Syed Irfan ; Law, Andrew ; Sangesland, Maya ; Gat-Viks, Irit ; Digard, Paul ; Vasudevan, Shobha ; Lingwood, Daniel ; Dockrell, David H. ; Doench, John G. ; Baillie, J. Kenneth ; Hacohen, Nir
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-01, Vol.11 (1), p.164-18, Article 164
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Newsletter articlesFull Text
INTERNATIONAL PATENT: THE BROAD INSTITUTE, INC. , MASSACHUSETTS INSTITUTE OF TECHNOLOGY , THE GENERAL HOSPITAL CORPORATION , HACOHEN, NIR , BLAINEY, PAUL, C. , FILBIN, MICHAEL, R. , GOLDBERG, MARCIA,...
Publisher:Washington, D.C: HT Digital Streams Limited
Journal title:US Fed News Service, Including US State News, 2020
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ArticlesPeer ReviewedFull Text
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Author / Creator:Villani, Alexandra-Chloé ; Satija, Rahul ; Reynolds, Gary ; Sarkizova, Siranush ; Shekhar, Karthik ; Fletcher, James ; Griesbeck, Morgane ; Butler, Andrew ; Zheng, Shiwei ; Lazo, Suzan ; Jardine, Laura ; Dixon, David ; Stephenson, Emily ; Nilsson, Emil ; Grundberg, Ida ; McDonald, David ; Filby, Andrew ; Li, Weibo ; De Jager, Philip L. ; Rozenblatt-Rosen, Orit ; Lane, Andrew A. ; Haniffa, Muzlifah ; Regev, Aviv ; Hacohen, Nir
Publisher:United States: American Association for the Advancement of Science
Journal title:Science (American Association for the Advancement of Science), 2017-04, Vol.356 (6335), p.283-283
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ArticlesPeer ReviewedFull Text
A large peptidome dataset improves HLA class I epitope prediction across most of the human population
Author / Creator:Sarkizova, Siranush ; Klaeger, Susan ; Le, Phuong M. ; Li, Letitia W. ; Oliveira, Giacomo ; Keshishian, Hasmik ; Hartigan, Christina R. ; Zhang, Wandi ; Braun, David A. ; Ligon, Keith L. ; Bachireddy, Pavan ; Zervantonakis, Ioannis K. ; Rosenbluth, Jennifer M. ; Ouspenskaia, Tamara ; Law, Travis ; Justesen, Sune ; Stevens, Jonathan ; Lane, William J. ; Eisenhaure, Thomas ; Lan Zhang, Guang ; Clauser, Karl R. ; Hacohen, Nir ; Carr, Steven A. ; Wu, Catherine J. ; Keskin, Derin B.
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2020-02, Vol.38 (2), p.199-209
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ArticlesPeer ReviewedFull Text
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
Author / Creator:Ouspenskaia, Tamara ; Law, Travis ; Clauser, Karl R. ; Klaeger, Susan ; Sarkizova, Siranush ; Aguet, François ; Li, Bo ; Christian, Elena ; Knisbacher, Binyamin A. ; Le, Phuong M. ; Hartigan, Christina R. ; Keshishian, Hasmik ; Apffel, Annie ; Oliveira, Giacomo ; Zhang, Wandi ; Chen, Sarah ; Chow, Yuen Ting ; Ji, Zhe ; Jungreis, Irwin ; Shukla, Sachet A. ; Justesen, Sune ; Bachireddy, Pavan ; Kellis, Manolis ; Getz, Gad ; Hacohen, Nir ; Keskin, Derin B. ; Carr, Steven A. ; Wu, Catherine J. ; Regev, Aviv
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2022-02, Vol.40 (2), p.209-217
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ArticlesPeer ReviewedFull Text
Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma
Author / Creator:Hu, Zhuting ; Leet, Donna E. ; Allesøe, Rosa L. ; Oliveira, Giacomo ; Li, Shuqiang ; Luoma, Adrienne M. ; Liu, Jinyan ; Forman, Juliet ; Huang, Teddy ; Iorgulescu, J. Bryan ; Holden, Rebecca ; Sarkizova, Siranush ; Gohil, Satyen H. ; Redd, Robert A. ; Sun, Jing ; Elagina, Liudmila ; Giobbie-Hurder, Anita ; Zhang, Wandi ; Peter, Lauren ; Ciantra, Zoe ; Rodig, Scott ; Olive, Oriol ; Shetty, Keerthi ; Pyrdol, Jason ; Uduman, Mohamed ; Lee, Patrick C. ; Bachireddy, Pavan ; Buchbinder, Elizabeth I. ; Yoon, Charles H. ; Neuberg, Donna ; Pentelute, Bradley L. ; Hacohen, Nir ; Livak, Kenneth J. ; Shukla, Sachet A. ; Olsen, Lars Rønn ; Barouch, Dan H. ; Wucherpfennig, Kai W. ; Fritsch, Edward F. ; Keskin, Derin B. ; Wu, Catherine J. ; Ott, Patrick A.
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2021-03, Vol.27 (3), p.515-525
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ArticlesPeer ReviewedFull Text
Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq
Author / Creator:Li, Bo ; Gould, Joshua ; Yang, Yiming ; Sarkizova, Siranush ; Tabaka, Marcin ; Ashenberg, Orr ; Rosen, Yanay ; Slyper, Michal ; Kowalczyk, Monika S. ; Villani, Alexandra-Chloé ; Tickle, Timothy ; Hacohen, Nir ; Rozenblatt-Rosen, Orit ; Regev, Aviv
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2020-08, Vol.17 (8), p.793-798
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Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes
Author / Creator:Shukla, Sachet A ; Rooney, Michael S ; Rajasagi, Mohini ; Tiao, Grace ; Dixon, Philip M ; Lawrence, Michael S ; Stevens, Jonathan ; Lane, William J ; Dellagatta, Jamie L ; Steelman, Scott ; Sougnez, Carrie ; Cibulskis, Kristian ; Kiezun, Adam ; Hacohen, Nir ; Brusic, Vladimir ; Wu, Catherine J ; Getz, Gad
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2015-11, Vol.33 (11), p.1152-1158
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Extranuclear DNA accumulates in aged cells and contributes to senescence and inflammation
Author / Creator:Lan, Yuk Yuen ; Heather, James M. ; Eisenhaure, Thomas ; Garris, Christopher Stuart ; Lieb, David ; Raychowdhury, Raktima ; Hacohen, Nir
Publisher:England: John Wiley & Sons, Inc
Journal title:Aging cell, 2019-04, Vol.18 (2), p.e12901-n/a
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PD-1 blockade in subprimed CD8 cells induces dysfunctional PD-1+CD38hi cells and anti-PD-1 resistance
Author / Creator:Verma, Vivek ; Shrimali, Rajeev K ; Ahmad, Shamim ; Dai, Winjie ; Wang, Hua ; Lu, Sumin ; Nandre, Rahul ; Gaur, Pankaj ; Lopez, Jose ; Sade-Feldman, Moshe ; Yizhak, Keren ; Bjorgaard, Stacey L. ; Flaherty, Keith T. ; Wargo, Jennifer A. ; Boland, Genevieve M. ; Sullivan, Ryan J. ; Getz, Gad ; Hammond, Scott A. ; Tan, Ming ; Qi, Jingjing ; Wong, Phillip ; Merghoub, Taha ; Wolchok, Jedd ; Hacohen, Nir ; Janik, John E. ; Mkrtichyan, Mikayel ; Gupta, Seema ; Khleif, Samir N.
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2019-09, Vol.20 (9), p.1231-1243
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ArticlesPeer ReviewedFull Text
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Author / Creator:Shalek, Alex K. ; Satija, Rahul ; Adiconis, Xian ; Gertner, Rona S. ; Gaublomme, Jellert T. ; Raychowdhury, Raktima ; Schwartz, Schraga ; Yosef, Nir ; Malboeuf, Christine ; Lu, Diana ; Trombetta, John J. ; Gennert, Dave ; Gnirke, Andreas ; Goren, Alon ; Hacohen, Nir ; Levin, Joshua Z. ; Park, Hongkun ; Regev, Aviv
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2013-06, Vol.498 (7453), p.236-240
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Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis
Author / Creator:Mizoguchi, Fumitaka ; Slowikowski, Kamil ; Wei, Kevin ; Marshall, Jennifer L. ; Rao, Deepak A. ; Chang, Sook Kyung ; Nguyen, Hung N. ; Noss, Erika H. ; Turner, Jason D. ; Earp, Brandon E. ; Blazar, Philip E. ; Wright, John ; Simmons, Barry P. ; Donlin, Laura T. ; Kalliolias, George D. ; Goodman, Susan M. ; Bykerk, Vivian P. ; Ivashkiv, Lionel B. ; Lederer, James A. ; Hacohen, Nir ; Nigrovic, Peter A. ; Filer, Andrew ; Buckley, Christopher D. ; Raychaudhuri, Soumya ; Brenner, Michael B.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2018-02, Vol.9 (1), p.789-11, Article 789
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A cell-free nanobody engineering platform rapidly generates SARS-CoV-2 neutralizing nanobodies

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INTERNATIONAL PATENT: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION, HACOHEN, NIR FILES APPLICATION FOR "CHIMERIC AMPLICON ARRAY SEQUENCING"

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INTERNATIONAL PATENT: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION, HACOHEN, NIR FILES APPLICATION FOR "SINGLE CELL COMBINATORIAL INDEXING FROM AM...

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INTERNATIONAL PATENT: HACOHEN, NIR, THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY, THE GENERAL HOSPITAL CORPORATION FILES APPLICATION FOR "HIGH-THROUGHPUT ASSESSMENT OF EXOGENOUS PO...

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

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INTERNATIONAL PATENT: THE GENERAL HOSPITAL CORPORATION , PRESIDENT AND FELLOWS OF HARVARD COLLEGE , HACOHEN, NIR FILES APPLICATION FOR "METHODS FOR PREDICTING OUTCOMES OF CHECKPOINT INHIBITION AND TRE...

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An immune-cell signature of bacterial sepsis

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

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Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection

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INTERNATIONAL PATENT: THE BROAD INSTITUTE, INC. , MASSACHUSETTS INSTITUTE OF TECHNOLOGY , THE GENERAL HOSPITAL CORPORATION , HACOHEN, NIR , BLAINEY, PAUL, C. , FILBIN, MICHAEL, R. , GOLDBERG, MARCIA,...

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

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A large peptidome dataset improves HLA class I epitope prediction across most of the human population

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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

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Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

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Cumulus provides cloud-based data analysis for large-scale single-cell and single-nucleus RNA-seq

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Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

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Extranuclear DNA accumulates in aged cells and contributes to senescence and inflammation

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PD-1 blockade in subprimed CD8 cells induces dysfunctional PD-1+CD38hi cells and anti-PD-1 resistance

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

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Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis

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