A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation
Fields, Alexander P., Rodriguez, Edwin H., Jovanovic, Marko, Stern-Ginossar, Noam, Haas, Brian J., Mertins, Philipp, Raychowdhury, Raktima, Hacohen, Nir, Carr, Steven A., Ingolia, Nicholas T., Regev, Aviv, Weissman, Jonathan S.
Published in Molecular cell (03.12.2015)
Published in Molecular cell (03.12.2015)
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High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
Rabani, Michal, Raychowdhury, Raktima, Jovanovic, Marko, Rooney, Michael, Stumpo, Deborah J., Pauli, Andrea, Hacohen, Nir, Schier, Alexander F., Blackshear, Perry J., Friedman, Nir, Amit, Ido, Regev, Aviv
Published in Cell (18.12.2014)
Published in Cell (18.12.2014)
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Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq
Fishman, Lior, Modak, Avani, Nechooshtan, Gal, Razin, Talya, Erhard, Florian, Regev, Aviv, Farrell, Jeffrey A., Rabani, Michal
Published in Nature communications (10.04.2024)
Published in Nature communications (10.04.2024)
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Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML
Puram, Rishi V., Kowalczyk, Monika S., de Boer, Carl G., Schneider, Rebekka K., Miller, Peter G., McConkey, Marie, Tothova, Zuzana, Tejero, Héctor, Heckl, Dirk, Järås, Marcus, Chen, Michelle C., Li, Hubo, Tamayo, Alfred, Cowley, Glenn S., Rozenblatt-Rosen, Orit, Al-Shahrour, Fatima, Regev, Aviv, Ebert, Benjamin L.
Published in Cell (07.04.2016)
Published in Cell (07.04.2016)
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Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming
Schiebinger, Geoffrey, Shu, Jian, Tabaka, Marcin, Cleary, Brian, Subramanian, Vidya, Solomon, Aryeh, Gould, Joshua, Liu, Siyan, Lin, Stacie, Berube, Peter, Lee, Lia, Chen, Jenny, Brumbaugh, Justin, Rigollet, Philippe, Hochedlinger, Konrad, Jaenisch, Rudolf, Regev, Aviv, Lander, Eric S.
Published in Cell (07.03.2019)
Published in Cell (07.03.2019)
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B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV
Scheid, Johannes F., Barnes, Christopher O., Eraslan, Basak, Hudak, Andrew, Keeffe, Jennifer R., Cosimi, Lisa A., Brown, Eric M., Muecksch, Frauke, Weisblum, Yiska, Zhang, Shuting, Delorey, Toni, Woolley, Ann E., Ghantous, Fadi, Park, Sung-Moo, Phillips, Devan, Tusi, Betsabeh, Huey-Tubman, Kathryn E., Cohen, Alexander A., Gnanapragasam, Priyanthi N.P., Rzasa, Kara, Hatziioanno, Theodora, Durney, Michael A., Gu, Xiebin, Tada, Takuya, Landau, Nathaniel R., West, Anthony P., Rozenblatt-Rosen, Orit, Seaman, Michael S., Baden, Lindsey R., Graham, Daniel B., Deguine, Jacques, Bieniasz, Paul D., Regev, Aviv, Hung, Deborah, Bjorkman, Pamela J., Xavier, Ramnik J.
Published in Cell (10.06.2021)
Published in Cell (10.06.2021)
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Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Ray, John P., de Boer, Carl G., Fulco, Charles P., Lareau, Caleb A., Kanai, Masahiro, Ulirsch, Jacob C., Tewhey, Ryan, Ludwig, Leif S., Reilly, Steven K., Bergman, Drew T., Engreitz, Jesse M., Issner, Robbyn, Finucane, Hilary K., Lander, Eric S., Regev, Aviv, Hacohen, Nir
Published in Nature communications (06.03.2020)
Published in Nature communications (06.03.2020)
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Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis
Ludwig, Leif S, Lareau, Caleb A, Bao, Erik L, Nandakumar, Satish K, Muus, Christoph, Ulirsch, Jacob C, Chowdhary, Kaitavjeet, Buenrostro, Jason D, Mohandas, Narla, An, Xiuli, Aryee, Martin J, Regev, Aviv, Sankaran, Vijay G
Published in Cell reports (Cambridge) (11.06.2019)
Published in Cell reports (Cambridge) (11.06.2019)
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Purine synthesis promotes maintenance of brain tumor initiating cells in glioma
Wang, Xiuxing, Yang, Kailin, Xie, Qi, Wu, Qiulian, Mack, Stephen C, Shi, Yu, Kim, Leo J Y, Prager, Briana C, Flavahan, William A, Liu, Xiaojing, Singer, Meromit, Hubert, Christopher G, Miller, Tyler E, Zhou, Wenchao, Huang, Zhi, Fang, Xiaoguang, Regev, Aviv, Suvà, Mario L, Hwang, Tae Hyun, Locasale, Jason W, Bao, Shideng, Rich, Jeremy N
Published in Nature neuroscience (01.05.2017)
Published in Nature neuroscience (01.05.2017)
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Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma
Jerby-Arnon, Livnat, Neftel, Cyril, Shore, Marni E., Weisman, Hannah R., Mathewson, Nathan D., McBride, Matthew J., Haas, Brian, Izar, Benjamin, Volorio, Angela, Boulay, Gaylor, Cironi, Luisa, Richman, Alyssa R., Broye, Liliane C., Gurski, Joseph M., Luo, Christina C., Mylvaganam, Ravindra, Nguyen, Lan, Mei, Shaolin, Melms, Johannes C., Georgescu, Christophe, Cohen, Ofir, Buendia-Buendia, Jorge E., Segerstolpe, Asa, Sud, Malika, Cuoco, Michael S., Labes, Danny, Gritsch, Simon, Zollinger, Daniel R., Ortogero, Nicole, Beechem, Joseph M., Petur Nielsen, G., Chebib, Ivan, Nguyen-Ngoc, Tu, Montemurro, Michael, Cote, Gregory M., Choy, Edwin, Letovanec, Igor, Cherix, Stéphane, Wagle, Nikhil, Sorger, Peter K., Haynes, Alex B., Mullen, John T., Stamenkovic, Ivan, Rivera, Miguel N., Kadoch, Cigall, Wucherpfennig, Kai W., Rozenblatt-Rosen, Orit, Suvà, Mario L., Riggi, Nicolò, Regev, Aviv
Published in Nature medicine (01.02.2021)
Published in Nature medicine (01.02.2021)
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Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing
Jasso, Guadalupe J, Jaiswal, Alok, Varma, Mukund, Laszewski, Tyler, Grauel, Angelo, Omar, Abdifatah, Silva, Nilsa, Dranoff, Glenn, Porter, Jeffrey A, Mansfield, Keith, Cremasco, Viviana, Regev, Aviv, Xavier, Ramnik J, Graham, Daniel B
Published in PLoS biology (27.01.2022)
Published in PLoS biology (27.01.2022)
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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Kellis, Manolis, Feldser, David, Cassady, John P, Amit, Ido, Lander, Eric S, Zuk, Or, Lin, Michael F, Carey, Bryce W, Garber, Manuel, Mikkelsen, Tarjei S, Jacks, Tyler, Hacohen, Nir, Guttman, Mitchell, French, Courtney, Cabili, Moran N, Huarte, Maite, Regev, Aviv, Rinn, John L, Jaenisch, Rudolf, Bernstein, Bradley E
Published in Nature (12.03.2009)
Published in Nature (12.03.2009)
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A human breast atlas integrating single-cell proteomics and transcriptomics
Gray, G. Kenneth, Li, Carman Man-Chung, Rosenbluth, Jennifer M., Selfors, Laura M., Girnius, Nomeda, Lin, Jia-Ren, Schackmann, Ron C.J., Goh, Walter L., Moore, Kaitlin, Shapiro, Hana K., Mei, Shaolin, D’Andrea, Kurt, Nathanson, Katherine L., Sorger, Peter K., Santagata, Sandro, Regev, Aviv, Garber, Judy E., Dillon, Deborah A., Brugge, Joan S.
Published in Developmental cell (06.06.2022)
Published in Developmental cell (06.06.2022)
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Chromatin signature of embryonic pluripotency is established during genome activation
Liu, X. Shirley, Schier, Alexander F, Vastenhouw, Nadine L, Zhang, Yong, Woods, Ian G, Imam, Farhad, Regev, Aviv, Rinn, John
Published in Nature (London) (08.04.2010)
Published in Nature (London) (08.04.2010)
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A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection
Shapira, Sagi D., Gat-Viks, Irit, Shum, Bennett O.V., Dricot, Amelie, de Grace, Marciela M., Wu, Liguo, Gupta, Piyush B., Hao, Tong, Silver, Serena J., Root, David E., Hill, David E., Regev, Aviv, Hacohen, Nir
Published in Cell (24.12.2009)
Published in Cell (24.12.2009)
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Comprehensive comparative analysis of 5′-end RNA-sequencing methods
Adiconis, Xian, Haber, Adam L., Simmons, Sean K., Levy Moonshine, Ami, Ji, Zhe, Busby, Michele A., Shi, Xi, Jacques, Justin, Lancaster, Madeline A., Pan, Jen Q., Regev, Aviv, Levin, Joshua Z.
Published in Nature methods (01.07.2018)
Published in Nature methods (01.07.2018)
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Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells
Ram, Oren, Goren, Alon, Amit, Ido, Shoresh, Noam, Yosef, Nir, Ernst, Jason, Kellis, Manolis, Gymrek, Melissa, Issner, Robbyn, Coyne, Michael, Durham, Timothy, Zhang, Xiaolan, Donaghey, Julie, Epstein, Charles B., Regev, Aviv, Bernstein, Bradley E.
Published in Cell (23.12.2011)
Published in Cell (23.12.2011)
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Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
Novershtern, Noa, Subramanian, Aravind, Lawton, Lee N., Mak, Raymond H., Haining, W. Nicholas, McConkey, Marie E., Habib, Naomi, Yosef, Nir, Chang, Cindy Y., Shay, Tal, Frampton, Garrett M., Drake, Adam C.B., Leskov, Ilya, Nilsson, Bjorn, Preffer, Fred, Dombkowski, David, Evans, John W., Liefeld, Ted, Smutko, John S., Chen, Jianzhu, Friedman, Nir, Young, Richard A., Golub, Todd R., Regev, Aviv, Ebert, Benjamin L.
Published in Cell (21.01.2011)
Published in Cell (21.01.2011)
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