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1.

Systems Immunology: Learning the Rules of the Immune System.

Villani, Alexandra-Chloé; Sarkizova, Siranush; Hacohen, Nir.

Annu Rev Immunol ; 36: 813-842, 2018 04 26.

Artículo Inglés | MEDLINE | ID: mdl-29677477

2.

Cytotoxic CD4⁺ T cells eliminate senescent cells by targeting cytomegalovirus antigen.

Hasegawa, Tatsuya; Oka, Tomonori; Son, Heehwa G; Oliver-García, Valeria S; Azin, Marjan; Eisenhaure, Thomas M; Lieb, David J; Hacohen, Nir; Demehri, Shadmehr.

Cell ; 186(7): 1417-1431.e20, 2023 03 30.

Artículo Inglés | MEDLINE | ID: mdl-37001502

3.

Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy.

Chen, Jonathan H; Nieman, Linda T; Spurrell, Maxwell; Jorgji, Vjola; Elmelech, Liad; Richieri, Peter; Xu, Katherine H; Madhu, Roopa; Parikh, Milan; Zamora, Izabella; Mehta, Arnav; Nabel, Christopher S; Freeman, Samuel S; Pirl, Joshua D; Lu, Chenyue; Meador, Catherine B; Barth, Jaimie L; Sakhi, Mustafa; Tang, Alexander L; Sarkizova, Siranush; Price, Colles; Fernandez, Nicolas F; Emanuel, George; He, Jiang; Van Raay, Katrina; Reeves, Jason W; Yizhak, Keren; Hofree, Matan; Shih, Angela; Sade-Feldman, Moshe; Boland, Genevieve M; Pelka, Karin; Aryee, Martin J; Mino-Kenudson, Mari; Gainor, Justin F; Korsunsky, Ilya; Hacohen, Nir.

Nat Immunol ; 25(4): 644-658, 2024 Apr.

Artículo Inglés | MEDLINE | ID: mdl-38503922

4.

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.

Weingarten-Gabbay, Shira; Klaeger, Susan; Sarkizova, Siranush; Pearlman, Leah R; Chen, Da-Yuan; Gallagher, Kathleen M E; Bauer, Matthew R; Taylor, Hannah B; Dunn, W Augustine; Tarr, Christina; Sidney, John; Rachimi, Suzanna; Conway, Hasahn L; Katsis, Katelin; Wang, Yuntong; Leistritz-Edwards, Del; Durkin, Melissa R; Tomkins-Tinch, Christopher H; Finkel, Yaara; Nachshon, Aharon; Gentili, Matteo; Rivera, Keith D; Carulli, Isabel P; Chea, Vipheaviny A; Chandrashekar, Abishek; Bozkus, Cansu Cimen; Carrington, Mary; Bhardwaj, Nina; Barouch, Dan H; Sette, Alessandro; Maus, Marcela V; Rice, Charles M; Clauser, Karl R; Keskin, Derin B; Pregibon, Daniel C; Hacohen, Nir; Carr, Steven A; Abelin, Jennifer G; Saeed, Mohsan; Sabeti, Pardis C.

Cell ; 184(15): 3962-3980.e17, 2021 07 22.

Artículo Inglés | MEDLINE | ID: mdl-34171305

5.

Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps.

Chen, Bob; Scurrah, Cherie' R; McKinley, Eliot T; Simmons, Alan J; Ramirez-Solano, Marisol A; Zhu, Xiangzhu; Markham, Nicholas O; Heiser, Cody N; Vega, Paige N; Rolong, Andrea; Kim, Hyeyon; Sheng, Quanhu; Drewes, Julia L; Zhou, Yuan; Southard-Smith, Austin N; Xu, Yanwen; Ro, James; Jones, Angela L; Revetta, Frank; Berry, Lynne D; Niitsu, Hiroaki; Islam, Mirazul; Pelka, Karin; Hofree, Matan; Chen, Jonathan H; Sarkizova, Siranush; Ng, Kimmie; Giannakis, Marios; Boland, Genevieve M; Aguirre, Andrew J; Anderson, Ana C; Rozenblatt-Rosen, Orit; Regev, Aviv; Hacohen, Nir; Kawasaki, Kenta; Sato, Toshiro; Goettel, Jeremy A; Grady, William M; Zheng, Wei; Washington, M Kay; Cai, Qiuyin; Sears, Cynthia L; Goldenring, James R; Franklin, Jeffrey L; Su, Timothy; Huh, Won Jae; Vandekar, Simon; Roland, Joseph T; Liu, Qi; Coffey, Robert J.

Cell ; 184(26): 6262-6280.e26, 2021 12 22.

Artículo Inglés | MEDLINE | ID: mdl-34910928

6.

Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro.

Dolan, Michael-John; Therrien, Martine; Jereb, Sasa; Kamath, Tushar; Gazestani, Vahid; Atkeson, Trevor; Marsh, Samuel E; Goeva, Aleksandrina; Lojek, Neal M; Murphy, Sarah; White, Cassandra M; Joung, Julia; Liu, Bingxu; Limone, Francesco; Eggan, Kevin; Hacohen, Nir; Bernstein, Bradley E; Glass, Christopher K; Leinonen, Ville; Blurton-Jones, Mathew; Zhang, Feng; Epstein, Charles B; Macosko, Evan Z; Stevens, Beth.

Nat Immunol ; 24(8): 1382-1390, 2023 08.

Artículo Inglés | MEDLINE | ID: mdl-37500887

7.

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Johnstone, Sarah E; Reyes, Alejandro; Qi, Yifeng; Adriaens, Carmen; Hegazi, Esmat; Pelka, Karin; Chen, Jonathan H; Zou, Luli S; Drier, Yotam; Hecht, Vivian; Shoresh, Noam; Selig, Martin K; Lareau, Caleb A; Iyer, Sowmya; Nguyen, Son C; Joyce, Eric F; Hacohen, Nir; Irizarry, Rafael A; Zhang, Bin; Aryee, Martin J; Bernstein, Bradley E.

Cell ; 182(6): 1474-1489.e23, 2020 09 17.

Artículo Inglés | MEDLINE | ID: mdl-32841603

8.

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.

Wells, Daniel K; van Buuren, Marit M; Dang, Kristen K; Hubbard-Lucey, Vanessa M; Sheehan, Kathleen C F; Campbell, Katie M; Lamb, Andrew; Ward, Jeffrey P; Sidney, John; Blazquez, Ana B; Rech, Andrew J; Zaretsky, Jesse M; Comin-Anduix, Begonya; Ng, Alphonsus H C; Chour, William; Yu, Thomas V; Rizvi, Hira; Chen, Jia M; Manning, Patrice; Steiner, Gabriela M; Doan, Xengie C; Merghoub, Taha; Guinney, Justin; Kolom, Adam; Selinsky, Cheryl; Ribas, Antoni; Hellmann, Matthew D; Hacohen, Nir; Sette, Alessandro; Heath, James R; Bhardwaj, Nina; Ramsdell, Fred; Schreiber, Robert D; Schumacher, Ton N; Kvistborg, Pia; Defranoux, Nadine A.

Cell ; 183(3): 818-834.e13, 2020 10 29.

Artículo Inglés | MEDLINE | ID: mdl-33038342

9.

In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer.

Dubrot, Juan; Du, Peter P; Lane-Reticker, Sarah Kate; Kessler, Emily A; Muscato, Audrey J; Mehta, Arnav; Freeman, Samuel S; Allen, Peter M; Olander, Kira E; Ockerman, Kyle M; Wolfe, Clara H; Wiesmann, Fabius; Knudsen, Nelson H; Tsao, Hsiao-Wei; Iracheta-Vellve, Arvin; Schneider, Emily M; Rivera-Rosario, Andrea N; Kohnle, Ian C; Pope, Hans W; Ayer, Austin; Mishra, Gargi; Zimmer, Margaret D; Kim, Sarah Y; Mahapatra, Animesh; Ebrahimi-Nik, Hakimeh; Frederick, Dennie T; Boland, Genevieve M; Haining, W Nicholas; Root, David E; Doench, John G; Hacohen, Nir; Yates, Kathleen B; Manguso, Robert T.

Nat Immunol ; 23(10): 1495-1506, 2022 10.

Artículo Inglés | MEDLINE | ID: mdl-36151395

10.

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.

Ludwig, Leif S; Lareau, Caleb A; Ulirsch, Jacob C; Christian, Elena; Muus, Christoph; Li, Lauren H; Pelka, Karin; Ge, Will; Oren, Yaara; Brack, Alison; Law, Travis; Rodman, Christopher; Chen, Jonathan H; Boland, Genevieve M; Hacohen, Nir; Rozenblatt-Rosen, Orit; Aryee, Martin J; Buenrostro, Jason D; Regev, Aviv; Sankaran, Vijay G.

Cell ; 176(6): 1325-1339.e22, 2019 03 07.

Artículo Inglés | MEDLINE | ID: mdl-30827679

11.

Differentiation of exhausted CD8⁺ T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory.

Tonnerre, Pierre; Wolski, David; Subudhi, Sonu; Aljabban, Jihad; Hoogeveen, Ruben C; Damasio, Marcos; Drescher, Hannah K; Bartsch, Lea M; Tully, Damien C; Sen, Debattama R; Bean, David J; Brown, Joelle; Torres-Cornejo, Almudena; Robidoux, Maxwell; Kvistad, Daniel; Alatrakchi, Nadia; Cui, Ang; Lieb, David; Cheney, James A; Gustafson, Jenna; Lewis-Ximenez, Lia L; Massenet-Regad, Lucile; Eisenhaure, Thomas; Aneja, Jasneet; Haining, W Nicholas; Chung, Raymond T; Hacohen, Nir; Allen, Todd M; Kim, Arthur Y; Lauer, Georg M.

Nat Immunol ; 22(8): 1030-1041, 2021 08.

Artículo Inglés | MEDLINE | ID: mdl-34312544

12.

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

Sade-Feldman, Moshe; Yizhak, Keren; Bjorgaard, Stacey L; Ray, John P; de Boer, Carl G; Jenkins, Russell W; Lieb, David J; Chen, Jonathan H; Frederick, Dennie T; Barzily-Rokni, Michal; Freeman, Samuel S; Reuben, Alexandre; Hoover, Paul J; Villani, Alexandra-Chloé; Ivanova, Elena; Portell, Andrew; Lizotte, Patrick H; Aref, Amir R; Eliane, Jean-Pierre; Hammond, Marc R; Vitzthum, Hans; Blackmon, Shauna M; Li, Bo; Gopalakrishnan, Vancheswaran; Reddy, Sangeetha M; Cooper, Zachary A; Paweletz, Cloud P; Barbie, David A; Stemmer-Rachamimov, Anat; Flaherty, Keith T; Wargo, Jennifer A; Boland, Genevieve M; Sullivan, Ryan J; Getz, Gad; Hacohen, Nir.

Cell ; 175(4): 998-1013.e20, 2018 11 01.

Artículo Inglés | MEDLINE | ID: mdl-30388456

13.

Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade.

Shukla, Sachet A; Bachireddy, Pavan; Schilling, Bastian; Galonska, Christina; Zhan, Qian; Bango, Clyde; Langer, Rupert; Lee, Patrick C; Gusenleitner, Daniel; Keskin, Derin B; Babadi, Mehrtash; Mohammad, Arman; Gnirke, Andreas; Clement, Kendell; Cartun, Zachary J; Van Allen, Eliezer M; Miao, Diana; Huang, Ying; Snyder, Alexandra; Merghoub, Taha; Wolchok, Jedd D; Garraway, Levi A; Meissner, Alexander; Weber, Jeffrey S; Hacohen, Nir; Neuberg, Donna; Potts, Patrick R; Murphy, George F; Lian, Christine G; Schadendorf, Dirk; Hodi, F Stephen; Wu, Catherine J.

Cell ; 173(3): 624-633.e8, 2018 04 19.

Artículo Inglés | MEDLINE | ID: mdl-29656892

14.

Heavy Metal Enlightens Tumor Immunity.

Chen, Jonathan H; Pelka, Karin; Hacohen, Nir.

Cell ; 169(4): 567-569, 2017 05 04.

Artículo Inglés | MEDLINE | ID: mdl-28475889

15.

Author Correction: PD-1 blockade in subprimed CD8 cells induces dysfunctional PD-1⁺CD38^hi cells and anti-PD-1 resistance.

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.

Nat Immunol ; 20(11): 1555, 2019 Nov.

Artículo Inglés | MEDLINE | ID: mdl-31551574

16.

PD-1 blockade in subprimed CD8 cells induces dysfunctional PD-1⁺CD38^hi cells and anti-PD-1 resistance.

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.

Nat Immunol ; 20(9): 1231-1243, 2019 09.

Artículo Inglés | MEDLINE | ID: mdl-31358999

17.

The immune cell landscape in kidneys of patients with lupus nephritis.

Arazi, Arnon; Rao, Deepak A; Berthier, Celine C; Davidson, Anne; Liu, Yanyan; Hoover, Paul J; Chicoine, Adam; Eisenhaure, Thomas M; Jonsson, A Helena; Li, Shuqiang; Lieb, David J; Zhang, Fan; Slowikowski, Kamil; Browne, Edward P; Noma, Akiko; Sutherby, Danielle; Steelman, Scott; Smilek, Dawn E; Tosta, Patti; Apruzzese, William; Massarotti, Elena; Dall'Era, Maria; Park, Meyeon; Kamen, Diane L; Furie, Richard A; Payan-Schober, Fernanda; Pendergraft, William F; McInnis, Elizabeth A; Buyon, Jill P; Petri, Michelle A; Putterman, Chaim; Kalunian, Kenneth C; Woodle, E Steve; Lederer, James A; Hildeman, David A; Nusbaum, Chad; Raychaudhuri, Soumya; Kretzler, Matthias; Anolik, Jennifer H; Brenner, Michael B; Wofsy, David; Hacohen, Nir; Diamond, Betty.

Nat Immunol ; 20(7): 902-914, 2019 07.

Artículo Inglés | MEDLINE | ID: mdl-31209404

18.

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry.

Zhang, Fan; Wei, Kevin; Slowikowski, Kamil; Fonseka, Chamith Y; Rao, Deepak A; Kelly, Stephen; Goodman, Susan M; Tabechian, Darren; Hughes, Laura B; Salomon-Escoto, Karen; Watts, Gerald F M; Jonsson, A Helena; Rangel-Moreno, Javier; Meednu, Nida; Rozo, Cristina; Apruzzese, William; Eisenhaure, Thomas M; Lieb, David J; Boyle, David L; Mandelin, Arthur M; Boyce, Brendan F; DiCarlo, Edward; Gravallese, Ellen M; Gregersen, Peter K; Moreland, Larry; Firestein, Gary S; Hacohen, Nir; Nusbaum, Chad; Lederer, James A; Perlman, Harris; Pitzalis, Costantino; Filer, Andrew; Holers, V Michael; Bykerk, Vivian P; Donlin, Laura T; Anolik, Jennifer H; Brenner, Michael B; Raychaudhuri, Soumya.

Nat Immunol ; 20(7): 928-942, 2019 07.

Artículo Inglés | MEDLINE | ID: mdl-31061532

19.

Publisher Correction: The immune cell landscape in kidneys of patients with lupus nephritis.

Arazi, Arnon; Rao, Deepak A; Berthier, Celine C; Davidson, Anne; Liu, Yanyan; Hoover, Paul J; Chicoine, Adam; Eisenhaure, Thomas M; Jonsson, A Helena; Li, Shuqiang; Lieb, David J; Zhang, Fan; Slowikowski, Kamil; Browne, Edward P; Noma, Akiko; Sutherby, Danielle; Steelman, Scott; Smilek, Dawn E; Tosta, Patti; Apruzzese, William; Massarotti, Elena; Dall'Era, Maria; Park, Meyeon; Kamen, Diane L; Furie, Richard A; Payan-Schober, Fernanda; Pendergraft, William F; McInnis, Elizabeth A; Buyon, Jill P; Petri, Michelle A; Putterman, Chaim; Kalunian, Kenneth C; Woodle, E Steve; Lederer, James A; Hildeman, David A; Nusbaum, Chad; Raychaudhuri, Soumya; Kretzler, Matthias; Anolik, Jennifer H; Brenner, Michael B; Wofsy, David; Hacohen, Nir; Diamond, Betty.

Nat Immunol ; 20(10): 1404, 2019 Oct.

Artículo Inglés | MEDLINE | ID: mdl-31409923

20.

Parsing the Interferon Transcriptional Network and Its Disease Associations.

Mostafavi, Sara; Yoshida, Hideyuki; Moodley, Devapregasan; LeBoité, Hugo; Rothamel, Katherine; Raj, Towfique; Ye, Chun Jimmie; Chevrier, Nicolas; Zhang, Shen-Ying; Feng, Ting; Lee, Mark; Casanova, Jean-Laurent; Clark, James D; Hegen, Martin; Telliez, Jean-Baptiste; Hacohen, Nir; De Jager, Philip L; Regev, Aviv; Mathis, Diane; Benoist, Christophe.

Cell ; 164(3): 564-78, 2016 Jan 28.

Artículo Inglés | MEDLINE | ID: mdl-26824662

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