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1.

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.

Replogle, Joseph M; Saunders, Reuben A; Pogson, Angela N; Hussmann, Jeffrey A; Lenail, Alexander; Guna, Alina; Mascibroda, Lauren; Wagner, Eric J; Adelman, Karen; Lithwick-Yanai, Gila; Iremadze, Nika; Oberstrass, Florian; Lipson, Doron; Bonnar, Jessica L; Jost, Marco; Norman, Thomas M; Weissman, Jonathan S.

Cell ; 185(14): 2559-2575.e28, 2022 07 07.

Article in English | MEDLINE | ID: mdl-35688146

2.

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.

Yang, Dian; Jones, Matthew G; Naranjo, Santiago; Rideout, William M; Min, Kyung Hoi Joseph; Ho, Raymond; Wu, Wei; Replogle, Joseph M; Page, Jennifer L; Quinn, Jeffrey J; Horns, Felix; Qiu, Xiaojie; Chen, Michael Z; Freed-Pastor, William A; McGinnis, Christopher S; Patterson, David M; Gartner, Zev J; Chow, Eric D; Bivona, Trever G; Chan, Michelle M; Yosef, Nir; Jacks, Tyler; Weissman, Jonathan S.

Cell ; 185(11): 1905-1923.e25, 2022 05 26.

Article in English | MEDLINE | ID: mdl-35523183

3.

Mapping transcriptomic vector fields of single cells.

Qiu, Xiaojie; Zhang, Yan; Martin-Rufino, Jorge D; Weng, Chen; Hosseinzadeh, Shayan; Yang, Dian; Pogson, Angela N; Hein, Marco Y; Hoi Joseph Min, Kyung; Wang, Li; Grody, Emanuelle I; Shurtleff, Matthew J; Yuan, Ruoshi; Xu, Song; Ma, Yian; Replogle, Joseph M; Lander, Eric S; Darmanis, Spyros; Bahar, Ivet; Sankaran, Vijay G; Xing, Jianhua; Weissman, Jonathan S.

Cell ; 185(4): 690-711.e45, 2022 02 17.

Article in English | MEDLINE | ID: mdl-35108499

4.

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.

Nuñez, James K; Chen, Jin; Pommier, Greg C; Cogan, J Zachery; Replogle, Joseph M; Adriaens, Carmen; Ramadoss, Gokul N; Shi, Quanming; Hung, King L; Samelson, Avi J; Pogson, Angela N; Kim, James Y S; Chung, Amanda; Leonetti, Manuel D; Chang, Howard Y; Kampmann, Martin; Bernstein, Bradley E; Hovestadt, Volker; Gilbert, Luke A; Weissman, Jonathan S.

Cell ; 184(9): 2503-2519.e17, 2021 04 29.

Article in English | MEDLINE | ID: mdl-33838111

5.

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control.

Hickey, Kelsey L; Dickson, Kimberley; Cogan, J Zachery; Replogle, Joseph M; Schoof, Michael; D'Orazio, Karole N; Sinha, Niladri K; Hussmann, Jeffrey A; Jost, Marco; Frost, Adam; Green, Rachel; Weissman, Jonathan S; Kostova, Kamena K.

Mol Cell ; 79(6): 950-962.e6, 2020 09 17.

Article in English | MEDLINE | ID: mdl-32726578

6.

A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens.

Guna, Alina; Page, Katharine R; Replogle, Joseph M; Esantsi, Theodore K; Wang, Maxine L; Weissman, Jonathan S; Voorhees, Rebecca M.

BMC Genomics ; 24(1): 651, 2023 Oct 30.

Article in English | MEDLINE | ID: mdl-37904134

7.

Rheumatoid arthritis-associated RBPJ polymorphism alters memory CD4+ T cells.

Orent, William; Mchenry, Allison R; Rao, Deepak A; White, Charles; Klein, Hans-Ulrich; Bassil, Ribal; Srivastava, Gyan; Replogle, Joseph M; Raj, Towfique; Frangieh, Michael; Cimpean, Maria; Cuerdon, Nicole; Chibnik, Lori; Khoury, Samia J; Karlson, Elizabeth W; Brenner, Michael B; De Jager, Philip; Bradshaw, Elizabeth M; Elyaman, Wassim.

Hum Mol Genet ; 25(2): 404-17, 2016 Jan 15.

Article in English | MEDLINE | ID: mdl-26604133

8.

Interindividual variation in human T regulatory cells.

Ferraro, Alessandra; D'Alise, Anna Morena; Raj, Towfique; Asinovski, Natasha; Phillips, Roxanne; Ergun, Ayla; Replogle, Joseph M; Bernier, Angelina; Laffel, Lori; Stranger, Barbara E; De Jager, Philip L; Mathis, Diane; Benoist, Christophe.

Proc Natl Acad Sci U S A ; 111(12): E1111-20, 2014 Mar 25.

Article in English | MEDLINE | ID: mdl-24610777

9.

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility.

Raj, Towfique; Ryan, Katie J; Replogle, Joseph M; Chibnik, Lori B; Rosenkrantz, Laura; Tang, Anna; Rothamel, Katie; Stranger, Barbara E; Bennett, David A; Evans, Denis A; De Jager, Philip L; Bradshaw, Elizabeth M.

Hum Mol Genet ; 23(10): 2729-36, 2014 May 15.

Article in English | MEDLINE | ID: mdl-24381305

10.

Common risk alleles for inflammatory diseases are targets of recent positive selection.

Raj, Towfique; Kuchroo, Manik; Replogle, Joseph M; Raychaudhuri, Soumya; Stranger, Barbara E; De Jager, Philip L.

Am J Hum Genet ; 92(4): 517-29, 2013 Apr 04.

Article in English | MEDLINE | ID: mdl-23522783

11.

A TREM1 variant alters the accumulation of Alzheimer-related amyloid pathology.

Replogle, Joseph M; Chan, Gail; White, Charles C; Raj, Towfique; Winn, Phoebe A; Evans, Denis A; Sperling, Reisa A; Chibnik, Lori B; Bradshaw, Elizabeth M; Schneider, Julie A; Bennett, David A; De Jager, Philip L.

Ann Neurol ; 77(3): 469-77, 2015 Mar.

Article in English | MEDLINE | ID: mdl-25545807

12.

A pharmacogenetic study implicates SLC9a9 in multiple sclerosis disease activity.

Esposito, Federica; Sorosina, Melissa; Ottoboni, Linda; Lim, Elaine T; Replogle, Joseph M; Raj, Towfique; Brambilla, Paola; Liberatore, Giuseppe; Guaschino, Clara; Romeo, Marzia; Pertel, Thomas; Stankiewicz, James M; Martinelli, Vittorio; Rodegher, Mariaemma; Weiner, Howard L; Brassat, David; Benoist, Christophe; Patsopoulos, Nikolaos A; Comi, Giancarlo; Elyaman, Wassim; Martinelli Boneschi, Filippo; De Jager, Philip L.

Ann Neurol ; 78(1): 115-27, 2015 Jul.

Article in English | MEDLINE | ID: mdl-25914168

13.

Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.

Do, Brian T; Hsu, Peggy P; Vermeulen, Sidney Y; Wang, Zhishan; Hirz, Taghreed; Abbott, Keene L; Aziz, Najihah; Replogle, Joseph M; Bjelosevic, Stefan; Paolino, Jonathan; Nelson, Samantha A; Block, Samuel; Darnell, Alicia M; Ferreira, Raphael; Zhang, Hanyu; Milosevic, Jelena; Schmidt, Daniel R; Chidley, Christopher; Harris, Isaac S; Weissman, Jonathan S; Pikman, Yana; Stegmaier, Kimberly; Cheloufi, Sihem; Su, Xiaofeng A; Sykes, David B; Vander Heiden, Matthew G.

Dev Cell ; 2024 May 30.

Article in English | MEDLINE | ID: mdl-38823395

14.

A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens.

Guna, Alina; Page, Katharine R; Replogle, Joseph M; Esantsi, Theodore K; Wang, Maxine L; Weissman, Jonathan S; Voorhees, Rebecca M.

bioRxiv ; 2023 Aug 14.

Article in English | MEDLINE | ID: mdl-36711738

15.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.

Sunshine, Sara; Puschnik, Andreas S; Replogle, Joseph M; Laurie, Matthew T; Liu, Jamin; Zha, Beth Shoshana; Nuñez, James K; Byrum, Janie R; McMorrow, Aidan H; Frieman, Matthew B; Winkler, Juliane; Qiu, Xiaojie; Rosenberg, Oren S; Leonetti, Manuel D; Ye, Chun Jimmie; Weissman, Jonathan S; DeRisi, Joseph L; Hein, Marco Y.

Nat Commun ; 14(1): 6245, 2023 10 06.

Article in English | MEDLINE | ID: mdl-37803001

16.

Microfluidics-free single-cell genomics with templated emulsification.

Clark, Iain C; Fontanez, Kristina M; Meltzer, Robert H; Xue, Yi; Hayford, Corey; May-Zhang, Aaron; D'Amato, Chris; Osman, Ahmad; Zhang, Jesse Q; Hettige, Pabodha; Ishibashi, Jacob S A; Delley, Cyrille L; Weisgerber, Daniel W; Replogle, Joseph M; Jost, Marco; Phong, Kiet T; Kennedy, Vanessa E; Peretz, Cheryl A C; Kim, Esther A; Song, Siyou; Karlon, William; Weissman, Jonathan S; Smith, Catherine C; Gartner, Zev J; Abate, Adam R.

Nat Biotechnol ; 41(11): 1557-1566, 2023 Nov.

Article in English | MEDLINE | ID: mdl-36879006

17.

MTCH2 is a mitochondrial outer membrane protein insertase.

Guna, Alina; Stevens, Taylor A; Inglis, Alison J; Replogle, Joseph M; Esantsi, Theodore K; Muthukumar, Gayathri; Shaffer, Kelly C L; Wang, Maxine L; Pogson, Angela N; Jones, Jeff J; Lomenick, Brett; Chou, Tsui-Fen; Weissman, Jonathan S; Voorhees, Rebecca M.

Science ; 378(6617): 317-322, 2022 10 21.

Article in English | MEDLINE | ID: mdl-36264797

18.

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.

Wu, David; Poddar, Aunoy; Ninou, Elpiniki; Hwang, Elizabeth; Cole, Mitchel A; Liu, S John; Horlbeck, Max A; Chen, Jin; Replogle, Joseph M; Carosso, Giovanni A; Eng, Nicolas W L; Chang, Jonghoon; Shen, Yin; Weissman, Jonathan S; Lim, Daniel A.

Cell Genom ; 2(11)2022 Nov 09.

Article in English | MEDLINE | ID: mdl-36381608

19.

Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors.

Replogle, Joseph M; Bonnar, Jessica L; Pogson, Angela N; Liem, Christina R; Maier, Nolan K; Ding, Yufang; Russell, Baylee J; Wang, Xingren; Leng, Kun; Guna, Alina; Norman, Thomas M; Pak, Ryan A; Ramos, Daniel M; Ward, Michael E; Gilbert, Luke A; Kampmann, Martin; Weissman, Jonathan S; Jost, Marco.

Elife ; 112022 12 28.

Article in English | MEDLINE | ID: mdl-36576240

20.

Reply: To PMID 25545807.

Replogle, Joseph M; De Jager, Philip L.

Ann Neurol ; 78(4): 659-60, 2015 Oct.

Article in English | MEDLINE | ID: mdl-26059823

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Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.

Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution.

Mapping transcriptomic vector fields of single cells.

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.

GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control.

A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens.

Rheumatoid arthritis-associated RBPJ polymorphism alters memory CD4+ T cells.

Interindividual variation in human T regulatory cells.

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility.

Common risk alleles for inflammatory diseases are targets of recent positive selection.

A TREM1 variant alters the accumulation of Alzheimer-related amyloid pathology.

A pharmacogenetic study implicates SLC9a9 in multiple sclerosis disease activity.

Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress.

A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens.

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq.

Microfluidics-free single-cell genomics with templated emulsification.

MTCH2 is a mitochondrial outer membrane protein insertase.

Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.

Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors.

Reply: To PMID 25545807.