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1.

Chromatin context-dependent regulation and epigenetic manipulation of prime editing.

Li, Xiaoyi; Chen, Wei; Martin, Beth K; Calderon, Diego; Lee, Choli; Choi, Junhong; Chardon, Florence M; McDiarmid, Troy A; Daza, Riza M; Kim, Haedong; Lalanne, Jean-Benoît; Nathans, Jenny F; Lee, David S; Shendure, Jay.

Cell ; 187(10): 2411-2427.e25, 2024 May 09.

Article in English | MEDLINE | ID: mdl-38608704

2.

A reference cell tree will serve science better than a reference cell atlas.

Domcke, Silvia; Shendure, Jay.

Cell ; 186(6): 1103-1114, 2023 03 16.

Article in English | MEDLINE | ID: mdl-36931241

3.

Proteostasis governs differential temperature sensitivity across embryonic cell types.

Dorrity, Michael W; Saunders, Lauren M; Duran, Madeleine; Srivatsan, Sanjay R; Barkan, Eliza; Jackson, Dana L; Sattler, Sydney M; Ewing, Brent; Queitsch, Christine; Shendure, Jay; Raible, David W; Kimelman, David; Trapnell, Cole.

Cell ; 186(23): 5015-5027.e12, 2023 11 09.

Article in English | MEDLINE | ID: mdl-37949057

4.

Genomic Medicine-Progress, Pitfalls, and Promise.

Shendure, Jay; Findlay, Gregory M; Snyder, Matthew W.

Cell ; 177(1): 45-57, 2019 03 21.

Article in English | MEDLINE | ID: mdl-30901547

5.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Gasperini, Molly; Hill, Andrew J; McFaline-Figueroa, José L; Martin, Beth; Kim, Seungsoo; Zhang, Melissa D; Jackson, Dana; Leith, Anh; Schreiber, Jacob; Noble, William S; Trapnell, Cole; Ahituv, Nadav; Shendure, Jay.

Cell ; 176(1-2): 377-390.e19, 2019 01 10.

Article in English | MEDLINE | ID: mdl-30612741

6.

Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision.

Abadie, Kathleen; Clark, Elisa C; Valanparambil, Rajesh M; Ukogu, Obinna; Yang, Wei; Daza, Riza M; Ng, Kenneth K H; Fathima, Jumana; Wang, Allan L; Lee, Judong; Nasti, Tahseen H; Bhandoola, Avinash; Nourmohammad, Armita; Ahmed, Rafi; Shendure, Jay; Cao, Junyue; Kueh, Hao Yuan.

Immunity ; 57(2): 271-286.e13, 2024 Feb 13.

Article in English | MEDLINE | ID: mdl-38301652

7.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Cusanovich, Darren A; Hill, Andrew J; Aghamirzaie, Delasa; Daza, Riza M; Pliner, Hannah A; Berletch, Joel B; Filippova, Galina N; Huang, Xingfan; Christiansen, Lena; DeWitt, William S; Lee, Choli; Regalado, Samuel G; Read, David F; Steemers, Frank J; Disteche, Christine M; Trapnell, Cole; Shendure, Jay.

Cell ; 174(5): 1309-1324.e18, 2018 08 23.

Article in English | MEDLINE | ID: mdl-30078704

8.

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.

Liu, Siyang; Huang, Shujia; Chen, Fang; Zhao, Lijian; Yuan, Yuying; Francis, Stephen Starko; Fang, Lin; Li, Zilong; Lin, Long; Liu, Rong; Zhang, Yong; Xu, Huixin; Li, Shengkang; Zhou, Yuwen; Davies, Robert W; Liu, Qiang; Walters, Robin G; Lin, Kuang; Ju, Jia; Korneliussen, Thorfinn; Yang, Melinda A; Fu, Qiaomei; Wang, Jun; Zhou, Lijun; Krogh, Anders; Zhang, Hongyun; Wang, Wei; Chen, Zhengming; Cai, Zhiming; Yin, Ye; Yang, Huanming; Mao, Mao; Shendure, Jay; Wang, Jian; Albrechtsen, Anders; Jin, Xin; Nielsen, Rasmus; Xu, Xun.

Cell ; 175(2): 347-359.e14, 2018 10 04.

Article in English | MEDLINE | ID: mdl-30290141

9.

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

Snyder, Matthew W; Kircher, Martin; Hill, Andrew J; Daza, Riza M; Shendure, Jay.

Cell ; 164(1-2): 57-68, 2016 Jan 14.

Article in English | MEDLINE | ID: mdl-26771485

10.

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.

Dekker, Job; Alber, Frank; Aufmkolk, Sarah; Beliveau, Brian J; Bruneau, Benoit G; Belmont, Andrew S; Bintu, Lacramioara; Boettiger, Alistair; Calandrelli, Riccardo; Disteche, Christine M; Gilbert, David M; Gregor, Thomas; Hansen, Anders S; Huang, Bo; Huangfu, Danwei; Kalhor, Reza; Leslie, Christina S; Li, Wenbo; Li, Yun; Ma, Jian; Noble, William S; Park, Peter J; Phillips-Cremins, Jennifer E; Pollard, Katherine S; Rafelski, Susanne M; Ren, Bing; Ruan, Yijun; Shav-Tal, Yaron; Shen, Yin; Shendure, Jay; Shu, Xiaokun; Strambio-De-Castillia, Caterina; Vertii, Anastassiia; Zhang, Huaiying; Zhong, Sheng.

Mol Cell ; 83(15): 2624-2640, 2023 08 03.

Article in English | MEDLINE | ID: mdl-37419111

11.

Learning the sequence determinants of alternative splicing from millions of random sequences.

Rosenberg, Alexander B; Patwardhan, Rupali P; Shendure, Jay; Seelig, Georg.

Cell ; 163(3): 698-711, 2015 Oct 22.

Article in English | MEDLINE | ID: mdl-26496609

12.

A single-cell time-lapse of mouse prenatal development from gastrula to birth.

Qiu, Chengxiang; Martin, Beth K; Welsh, Ian C; Daza, Riza M; Le, Truc-Mai; Huang, Xingfan; Nichols, Eva K; Taylor, Megan L; Fulton, Olivia; O'Day, Diana R; Gomes, Anne Roshella; Ilcisin, Saskia; Srivatsan, Sanjay; Deng, Xinxian; Disteche, Christine M; Noble, William Stafford; Hamazaki, Nobuhiko; Moens, Cecilia B; Kimelman, David; Cao, Junyue; Schier, Alexander F; Spielmann, Malte; Murray, Stephen A; Trapnell, Cole; Shendure, Jay.

Nature ; 626(8001): 1084-1093, 2024 Feb.

Article in English | MEDLINE | ID: mdl-38355799

13.

Genetic variation meets replication origins.

Hause, Ronald J; Shendure, Jay.

Cell ; 159(5): 973-974, 2014 Nov 20.

Article in English | MEDLINE | ID: mdl-25416936

14.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Gasperini, Molly; Hill, Andrew J; McFaline-Figueroa, José L; Martin, Beth; Kim, Seungsoo; Zhang, Melissa D; Jackson, Dana; Leith, Anh; Schreiber, Jacob; Noble, William S; Trapnell, Cole; Ahituv, Nadav; Shendure, Jay.

Cell ; 176(6): 1516, 2019 Mar 07.

Article in English | MEDLINE | ID: mdl-30849375

15.

Disruptive CHD8 mutations define a subtype of autism early in development.

Bernier, Raphael; Golzio, Christelle; Xiong, Bo; Stessman, Holly A; Coe, Bradley P; Penn, Osnat; Witherspoon, Kali; Gerdts, Jennifer; Baker, Carl; Vulto-van Silfhout, Anneke T; Schuurs-Hoeijmakers, Janneke H; Fichera, Marco; Bosco, Paolo; Buono, Serafino; Alberti, Antonino; Failla, Pinella; Peeters, Hilde; Steyaert, Jean; Vissers, Lisenka E L M; Francescatto, Ludmila; Mefford, Heather C; Rosenfeld, Jill A; Bakken, Trygve; O'Roak, Brian J; Pawlus, Matthew; Moon, Randall; Shendure, Jay; Amaral, David G; Lein, Ed; Rankin, Julia; Romano, Corrado; de Vries, Bert B A; Katsanis, Nicholas; Eichler, Evan E.

Cell ; 158(2): 263-276, 2014 Jul 17.

Article in English | MEDLINE | ID: mdl-24998929

16.

Pluripotent stem cell-derived model of the post-implantation human embryo.

Weatherbee, Bailey A T; Gantner, Carlos W; Iwamoto-Stohl, Lisa K; Daza, Riza M; Hamazaki, Nobuhiko; Shendure, Jay; Zernicka-Goetz, Magdalena.

Nature ; 622(7983): 584-593, 2023 Oct.

Article in English | MEDLINE | ID: mdl-37369347

17.

Embryo-scale reverse genetics at single-cell resolution.

Saunders, Lauren M; Srivatsan, Sanjay R; Duran, Madeleine; Dorrity, Michael W; Ewing, Brent; Linbo, Tor H; Shendure, Jay; Raible, David W; Moens, Cecilia B; Kimelman, David; Trapnell, Cole.

Nature ; 623(7988): 782-791, 2023 Nov.

Article in English | MEDLINE | ID: mdl-37968389

18.

Single-cell, whole-embryo phenotyping of mammalian developmental disorders.

Huang, Xingfan; Henck, Jana; Qiu, Chengxiang; Sreenivasan, Varun K A; Balachandran, Saranya; Amarie, Oana V; Hrabe de Angelis, Martin; Behncke, Rose Yinghan; Chan, Wing-Lee; Despang, Alexandra; Dickel, Diane E; Duran, Madeleine; Feuchtinger, Annette; Fuchs, Helmut; Gailus-Durner, Valerie; Haag, Natja; Hägerling, Rene; Hansmeier, Nils; Hennig, Friederike; Marshall, Cooper; Rajderkar, Sudha; Ringel, Alessa; Robson, Michael; Saunders, Lauren M; da Silva-Buttkus, Patricia; Spielmann, Nadine; Srivatsan, Sanjay R; Ulferts, Sascha; Wittler, Lars; Zhu, Yiwen; Kalscheuer, Vera M; Ibrahim, Daniel M; Kurth, Ingo; Kornak, Uwe; Visel, Axel; Pennacchio, Len A; Beier, David R; Trapnell, Cole; Cao, Junyue; Shendure, Jay; Spielmann, Malte.

Nature ; 623(7988): 772-781, 2023 Nov.

Article in English | MEDLINE | ID: mdl-37968388

19.

A time-resolved, multi-symbol molecular recorder via sequential genome editing.

Choi, Junhong; Chen, Wei; Minkina, Anna; Chardon, Florence M; Suiter, Chase C; Regalado, Samuel G; Domcke, Silvia; Hamazaki, Nobuhiko; Lee, Choli; Martin, Beth; Daza, Riza M; Shendure, Jay.

Nature ; 608(7921): 98-107, 2022 08.

Article in English | MEDLINE | ID: mdl-35794474

20.

Embryo model completes gastrulation to neurulation and organogenesis.

Amadei, Gianluca; Handford, Charlotte E; Qiu, Chengxiang; De Jonghe, Joachim; Greenfeld, Hannah; Tran, Martin; Martin, Beth K; Chen, Dong-Yuan; Aguilera-Castrejon, Alejandro; Hanna, Jacob H; Elowitz, Michael B; Hollfelder, Florian; Shendure, Jay; Glover, David M; Zernicka-Goetz, Magdalena.

Nature ; 610(7930): 143-153, 2022 10.

Article in English | MEDLINE | ID: mdl-36007540

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Chromatin context-dependent regulation and epigenetic manipulation of prime editing.

A reference cell tree will serve science better than a reference cell atlas.

Proteostasis governs differential temperature sensitivity across embryonic cell types.

Genomic Medicine-Progress, Pitfalls, and Promise.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Reversible, tunable epigenetic silencing of TCF1 generates flexibility in the T cell memory decision.

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History.

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.

Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.

Learning the sequence determinants of alternative splicing from millions of random sequences.

A single-cell time-lapse of mouse prenatal development from gastrula to birth.

Genetic variation meets replication origins.

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.

Disruptive CHD8 mutations define a subtype of autism early in development.

Pluripotent stem cell-derived model of the post-implantation human embryo.

Embryo-scale reverse genetics at single-cell resolution.

Single-cell, whole-embryo phenotyping of mammalian developmental disorders.

A time-resolved, multi-symbol molecular recorder via sequential genome editing.

Embryo model completes gastrulation to neurulation and organogenesis.