Jay Shendure

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 92

Top Venues

Nature

bioRxiv : the preprint server for biology

Science (New York, N.Y.)

Nature communications

University of Washington

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Washington Oct 01 2007

United States

Professor :: Genome Sciences

Publications

David F Read, Gregory T Booth, Riza M Daza, Dana L Jackson, Rula Green Gladden, Sanjay R Srivatsan, Brent Ewing, Jennifer M Franks, Cailyn H Spurrell, Anne Roshella Gomes, Diana O'Day, Aishwarya A Gogate, Beth K Martin, Haleigh Larson, Christian Pfleger, Joshua T Schiffer, Yiing Lin, Jay Shendure, Shin Lin, Cole Trapnell
Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart. Communications biology 7 (1) (2024)
Jean-Beno Æt Lalanne, Samuel G Regalado, Silvia Domcke, Diego Calderon, Beth K Martin, Xiaoyi Li, Tony Li, Chase C Suiter, Choli Lee, Cole Trapnell, Jay Shendure
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nature methods 21 (6) (2024)
David F Read, Gregory T Booth, Riza M Daza, Dana L Jackson, Rula Green Gladden, Sanjay R Srivatsan, Brent Ewing, Jennifer M Franks, Cailyn H Spurrell, Anne Roshella Gomes, Diana O'Day, Aishwarya A Gogate, Beth K Martin, Haleigh Larson, Christian Pfleger, Joshua T Schiffer, Yiing Lin, Jay Shendure, Shin Lin, Cole Trapnell
Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart. Communications biology 7 (1) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth K Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature (2024)
Florence M Chardon, Troy A McDiarmid, Nicholas F Page, Riza M Daza, Beth K Martin, Silvia Domcke, Samuel G Regalado, Jean-Benoît Lalanne, Diego Calderon, Xiaoyi Li, Joshua T Schiffer, Stephan J Sanders, Nadav Ahituv, Jay Shendure
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. Nature communications 15 (1) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Amanda C Perofsky, Chelsea L Hansen, Roy Burstein, Shanda Boyle, Robin Prentice, Cooper Marshall, David Reinhart, Ben Capodanno, Melissa Truong, Kristen Schwabe-Fry, Kayla Kuchta, Brian Pfau, Zack Acker, Jover Lee, Thomas R Sibley, Evan McDermot, Leslie Rodriguez-Salas, Jeremy Stone, Luis Gamboa, Peter D Han, Amanda Adler, Alpana Waghmare, Michael L Jackson, Michael Famulare, Jay Shendure, Trevor Bedford, Helen Y Chu, Janet A Englund, Joshua T Schiffer, Cecile Viboud
Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. Nature communications 15 (1) (2024)
Ran Zhang, Chengxiang Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine M Disteche, William Stafford Noble
Multi-condition and multi-modal temporal profile inference during mouse embryonic development. bioRxiv : the preprint server for biology (2024)
Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth K Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature 632 (8027) (2024)
Hanna Liao, Junhong Choi, Jay Shendure
Molecular recording using DNA Typewriter. Nature protocols (2024)
Sudarshan Pinglay, Jean-Beno Æt Lalanne, Riza M Daza, Jonas Koeppel, Xiaoyi Li, David S Lee, Jay Shendure
Multiplex generation and single cell analysis of structural variants in a mammalian genome. bioRxiv : the preprint server for biology (2024)
Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth K Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature 632 (8027) (2024)
Jean-Beno Æt Lalanne, Samuel G Regalado, Silvia Domcke, Diego Calderon, Beth K Martin, Xiaoyi Li, Tony Li, Chase C Suiter, Choli Lee, Cole Trapnell, Jay Shendure
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nature methods (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Jean-Beno Æt Lalanne, Samuel G Regalado, Silvia Domcke, Diego Calderon, Beth K Martin, Xiaoyi Li, Tony Li, Chase C Suiter, Choli Lee, Cole Trapnell, Jay Shendure
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nature methods 21 (6) (2024)
Ran Zhang, Chengxiang Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine M Disteche, William Stafford Noble
Multi-condition and multi-modal temporal profile inference during mouse embryonic development. bioRxiv : the preprint server for biology (2024)
David F Read, Gregory T Booth, Riza M Daza, Dana L Jackson, Rula Green Gladden, Sanjay R Srivatsan, Brent Ewing, Jennifer M Franks, Cailyn H Spurrell, Anne Roshella Gomes, Diana O'Day, Aishwarya A Gogate, Beth K Martin, Haleigh Larson, Christian Pfleger, Joshua T Schiffer, Yiing Lin, Jay Shendure, Shin Lin, Cole Trapnell
Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart. Communications biology 7 (1) (2024)
Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth K Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Riddhiman K Garge, Valerie Lynch, Rose Fields, Silvia Casadei, Sabrina Best, Jeremy Stone, Matthew Snyder, Chris D McGann, Jay Shendure, Joshua T Schiffer, Nobuhiko Hamazaki, Devin K Schweppe
The proteomic landscape and temporal dynamics of mammalian gastruloid development. bioRxiv : the preprint server for biology (2024)
Jean-Beno Æt Lalanne, Samuel G Regalado, Silvia Domcke, Diego Calderon, Beth K Martin, Xiaoyi Li, Tony Li, Chase C Suiter, Choli Lee, Cole Trapnell, Jay Shendure
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nature methods 21 (6) (2024)
Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth K Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature 632 (8027) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F Nathans, Beth K Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
Symbolic recording of signalling and cis-regulatory element activity to DNA. Nature 632 (8027) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Nobuhiko Hamazaki, Wei Yang, Connor A Kubo, Chengxiang Qiu, Beth K Martin, Riddhiman K Garge, Samuel G Regalado, Eva K Nichols, Sriram Pendyala, Nicholas Bradley, Douglas M Fowler, Choli Lee, Riza M Daza, Sanjay Srivatsan, Jay Shendure
Retinoic acid induces human gastruloids with posterior embryo-like structures. Nature cell biology (2024)
Amanda C Perofsky, Chelsea L Hansen, Roy Burstein, Shanda Boyle, Robin Prentice, Cooper Marshall, David Reinhart, Ben Capodanno, Melissa Truong, Kristen Schwabe-Fry, Kayla Kuchta, Brian Pfau, Zack Acker, Jover Lee, Thomas R Sibley, Evan McDermot, Leslie Rodriguez-Salas, Jeremy Stone, Luis Gamboa, Peter D Han, Amanda Adler, Alpana Waghmare, Michael L Jackson, Michael Famulare, Jay Shendure, Trevor Bedford, Helen Y Chu, Janet A Englund, Joshua T Schiffer, Cecile Viboud
Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. Nature communications 15 (1) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Jean-Beno Æt Lalanne, Samuel G Regalado, Silvia Domcke, Diego Calderon, Beth K Martin, Xiaoyi Li, Tony Li, Chase C Suiter, Choli Lee, Cole Trapnell, Jay Shendure
Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nature methods 21 (6) (2024)
Sudarshan Pinglay, Jean-Beno Æt Lalanne, Riza M Daza, Jonas Koeppel, Xiaoyi Li, David S Lee, Jay Shendure
Multiplex generation and single cell analysis of structural variants in a mammalian genome. bioRxiv : the preprint server for biology (2024)
Amanda C Perofsky, Chelsea L Hansen, Roy Burstein, Shanda Boyle, Robin Prentice, Cooper Marshall, David Reinhart, Ben Capodanno, Melissa Truong, Kristen Schwabe-Fry, Kayla Kuchta, Brian Pfau, Zack Acker, Jover Lee, Thomas R Sibley, Evan McDermot, Leslie Rodriguez-Salas, Jeremy Stone, Luis Gamboa, Peter D Han, Amanda Adler, Alpana Waghmare, Michael L Jackson, Michael Famulare, Jay Shendure, Trevor Bedford, Helen Y Chu, Janet A Englund, Joshua T Schiffer, Cecile Viboud
Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. Nature communications 15 (1) (2024)
Kenneth L Chiou, Xingfan Huang, Martin O Bohlen, Sébastien Tremblay, Alex R DeCasien, Diana R O'Day, Cailyn H Spurrell, Aishwarya A Gogate, Trisha M Zintel, null null, Madeline G Andrews, Melween I Martinez, Joshua T Schiffer, Michael J Montague, Michael Louis Platt, Jay Shendure, Noah James Snyder-Mackler
A single-cell multi-omic atlas spanning the adult rhesus macaque brain. Science advances 9 (41) (2023)
Sahar Attar, Valentino E Browning, Yuzhen Liu, Eva K Nichols, Ashley F Tsue, David Michael Shechner, Jay Shendure, Joshua A Lieberman, Shreeram Akilesh, Brian J Beliveau
Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens. bioRxiv : the preprint server for biology (2023)
Sahar Attar, Valentino E Browning, Yuzhen Liu, Eva K Nichols, Ashley F Tsue, David Michael Shechner, Jay Shendure, Joshua A Lieberman, Shreeram Akilesh, Brian J Beliveau
Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens. bioRxiv : the preprint server for biology (2023)
Ran Zhang, Mu Yang, Jacob Schreiber, Diana R O'Day, James M A Turner, Jay Shendure, Christine M Disteche, Xinxian Deng, William Stafford Noble
Cross-species imputation and comparison of single-cell transcriptomic profiles. bioRxiv : the preprint server for biology (2023)
Vikram Agarwal, Fumitaka Inoue, Max Schubach, Beth K Martin, Pyaree Mohan Dash, Zicong Zhang, Ajuni Sohota, William Stafford Noble, Galip Gürkan Yardimci, Martin Kircher, Jay Shendure, Nadav Ahituv
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. bioRxiv : the preprint server for biology (2023)
Bailey A T Weatherbee, Carlos W Gantner, Lisa K Iwamoto-Stohl, Riza M Daza, Nobuhiko Hamazaki, Jay Shendure, Magdalena Zernicka Goetz
Publisher Correction: Pluripotent stem cell-derived model of the post-implantation human embryo. Nature (2023)
Sahar Attar, Valentino E Browning, Yuzhen Liu, Eva K Nichols, Ashley F Tsue, David Michael Shechner, Jay Shendure, Joshua A Lieberman, Shreeram Akilesh, Brian J Beliveau
Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens. bioRxiv : the preprint server for biology (2023)
Sahar Attar, Valentino E Browning, Yuzhen Liu, Eva K Nichols, Ashley F Tsue, David Michael Shechner, Jay Shendure, Joshua A Lieberman, Shreeram Akilesh, Brian J Beliveau
Programmable peroxidase-assisted signal amplification enables flexible detection of nucleic acid targets in cellular and histopathological specimens. bioRxiv : the preprint server for biology (2023)
Junhong Choi, Wei Chen, Hanna Liao, Xiaoyi Li, Jay Shendure
A molecular proximity sensor based on an engineered, dual-component guide RNA. bioRxiv : the preprint server for biology (2023)
Florence M Chardon, Troy A McDiarmid, Nicholas F Page, Beth Martin, Silvia Domcke, Samuel G Regalado, Jean-Beno Æt Lalanne, Diego Calderon, Joshua T Schiffer, Stephan J Sanders, Nadav Ahituv, Jay Shendure
Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements. bioRxiv : the preprint server for biology (2023)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R Oâ Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay R Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. bioRxiv : the preprint server for biology (2023)
Gregory T Booth, Riza M Daza, Sanjay R Srivatsan, José L McFaline-Figueroa, Rula Green Gladden, Scott N Furlan, Jay Shendure, Cole Trapnell
High-Capacity Sample Multiplexing for Single Cell Chromatin Accessibility Profiling. bioRxiv : the preprint server for biology (2023)
Xingfan Huang, Jana Henck, Chengxiang Qiu, Varun K A Sreenivasan, Saranya Balachandran, Oana Veronica Amarie, Martin Hrabě de Angelis, Rose Yinghan Behncke, Wing-Lee Chan, Alexandra Despang, Diane E Dickel, Madeleine Duran, Annette Feuchtinger, Helmut Fuchs, Valérie Gailus-Durner, Natja Haag, Rene Hägerling, Nils Rouven Hansmeier, Friederike Hennig, Cooper Marshall, Sudha Sunil Rajderkar, Alessa Ringel, Michael I Robson, Lauren M Saunders, Patricia da Silva-Buttkus, Nadine Spielmann, Sanjay R Srivatsan, Sascha Ulferts, Lars Wittler, Yiwen Zhu, Vera M Kalscheuer, Daniel M Ibrahim, Ingo Kurth, Uwe Kornak, Axel Visel, Len A Pennacchio, David R Beier, Cole Trapnell, Junyue Cao, Jay Shendure, Malte Spielmann
Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature (2023)
Lauren M Saunders, Sanjay R Srivatsan, Madeleine Duran, Michael W Dorrity, Brent Ewing, Tor H Linbo, Jay Shendure, David W Raible, Cecilia B Moens, David Kimelman, Cole Trapnell
Embryo-scale reverse genetics at single-cell resolution. Nature (2023)
Bailey A T Weatherbee, Carlos W Gantner, Lisa K Iwamoto-Stohl, Riza M Daza, Nobuhiko Hamazaki, Jay Shendure, Magdalena Zernicka Goetz
A model of the post-implantation human embryo derived from pluripotent stem cells. Nature (2023)
Ana A Weil, Kyle G Luiten, Amanda M Casto, Julia Catherine Bennett, Jessica O'Hanlon, Peter D Han, Luis S Gamboa, Evan McDermot, Melissa Truong, Geoffrey S Gottlieb, Zack Acker, Caitlin R Wolf, Ariana Magedson, Eric J Chow, Natalie K Lo, Lincoln C Pothan, Devon McDonald, Tessa C Wright, Kathryn M McCaffrey, Marlin D Figgins, Janet A Englund, Michael Boeckh, Christina M Lockwood, Deborah A Nickerson, Jay Shendure, Trevor Bedford, James P Hughes, Lea M Starita, Helen Y Chu
Genomic surveillance of SARS-CoV-2 Omicron variants on a university campus. Nature communications 13 (1) (2022)
Junhong Choi, Wei Chen, Anna Minkina, Florence M Chardon, Chase C Suiter, Samuel G Regalado, Silvia Domcke, Nobuhiko Hamazaki, Choli Lee, Beth Martin, Riza M Daza, Jay Shendure
A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature 608 (7921) (2022)
Michael Boeckh, Helen Y Chu, Janet A Englund, Christina M Lockwood, Deborah A Nickerson, Jay Shendure, Lea Starita
The Seattle Flu Study: when regulations hinder pandemic surveillance. Nature medicine 28 (1) (2022)
Beth K Martin, Chengxiang Qiu, Eva Nichols, Melissa Phung, Rula Green-Gladden, Sanjay R Srivatsan, Ronnie Blecher-Gonen, Brian J Beliveau, Cole Trapnell, Junyue Cao, Jay Shendure
Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nature protocols (2022)
Chengxiang Qiu, Junyue Cao, Beth K Martin, Tony Li, Ian C Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M Disteche, Stephen A Murray, Malte Spielmann, Cecilia B Moens, Cole Trapnell, Jay Shendure
Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature genetics 54 (3) (2022)
Jill M Johnsen, Shelley N Fletcher, Angela Dove, Haley McCracken, Beth K Martin, Martin Kircher, Neil C Josephson, Jay Shendure, Sarah E Ruuska, Leonard A Valentino, Glenn F Pierce, Crystal Watson, Dunlei Cheng, Michael Recht, Barbara A Konkle
Results of genetic analysis of 11 341 participants enrolled in the My Life, Our Future hemophilia genotyping initiative in the United States. Journal of thrombosis and haemostasis : JTH 20 (9) (2022)
Kenneth L Chiou, Alex R DeCasien, Katherina P Rees, Camille Testard, Cailyn H Spurrell, Aishwarya A Gogate, Hannah A Pliner, Sébastien Tremblay, Arianne Mercer, Connor J Whalen, Josué E Negrón-Del Valle, Mareike C Janiak, Samuel E Bauman Surratt, Olga González, Nicole R Compo, Michala K Stock, Angelina V Ruiz-Lambides, Melween I Martínez, null null, Melissa A Wilson, Amanda Dawn Melin, Susan C Antón, Christopher S Walker, Jérôme Sallet, Jason M Newbern, Lea M Starita, Jay Shendure, James P Higham, Lauren J N Brent, Michael J Montague, Michael Louis Platt, Noah James Snyder-Mackler
Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment. Nature neuroscience 25 (12) (2022)
Adam K Glaser, Kevin W Bishop, Lindsey A Barner, Etsuo A Susaki, Shimpei I Kubota, Gan Gao, Robert B Serafin, Pooja Balaram, Emily Turschak, Philip R Nicovich, Hoyin Lai, Luciano A G Lucas, Yating Yi, Eva K Nichols, Hongyi Huang, Nicholas P Reder, Jasmine J Wilson, Ramya Sivakumar, Elya Shamskhou, Caleb R Stoltzfus, Xing Wei, Andrew K Hempton, Marko Pende, Prayag Murawala, Hans-Ulrich Dodt, Takato Imaizumi, Jay Shendure, Brian J Beliveau, Michael Y Gerner, Li Xin, Hu Zhao, Lawrence D True, R Clay Reid, Jayaram Chandrashekar, Hiroki R Ueda, Karel Svoboda, Jonathan T C Liu
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues. Nature methods 19 (5) (2022)
Diego Calderon, Ronnie Blecher-Gonen, Xingfan Huang, Stefano Secchia, James Kentro, Riza M Daza, Beth K Martin, Alessandro Dulja, Christoph Schaub, Cole Trapnell, Erica Larschan, Kate M Oâ Connor-Giles, Eileen E M Furlong, Jay Shendure
The continuum of Drosophila embryonic development at single-cell resolution. Science (New York, N.Y.) 377 (6606) (2022)
Gianluca Amadei, Charlotte E Handford, Chengxiang Qiu, Joachim De Jonghe, Hannah Greenfeld, Martin Tran, Beth K Martin, Dong-Yuan Chen, Alejandro Aguilera-Castrejon, Jacob H Hanna, Michael B Elowitz, Florian Hollfelder, Jay Shendure, David M Glover, Magdalena Zernicka Goetz
Embryo model completes gastrulation to neurulation and organogenesis. Nature 610 (7930) (2022)
Siobhan S Pattwell, Sonali Arora, Nicholas Nuechterlein, Michael A Zager, Keith R Loeb, Patrick J Cimino, Nikolas C Holland, Noemi Reche-Ley, Hamid Bolouri, Damian A Almiron Bonnin, Frank Szulzewsky, Vaishnavi V Phadnis, Tatsuya Ozawa, Michael J Wagner, Michael C Haffner, Junyue Cao, Jay Shendure, Eric C Holland
Oncogenic role of a developmentally regulated NTRK2 splice variant. Science advances 8 (40) (2022)
Sanjay R Srivatsan, Mary C Regier, Eliza R Barkan, Jennifer M Franks, Jonathan S Packer, Parker Grosjean, Madeleine Duran, Sarah H Saxton, Jon J Ladd, Malte Spielmann, Carlos Lois, Paul D Lampe, Jay Shendure, Kelly R Stevens, Cole Trapnell
Embryo-scale, single-cell spatial transcriptomics. Science (New York, N.Y.) 373 (6550) (2021)
Vikram Agarwal, Sereno Lopez-Darwin, David R Kelley, Jay Shendure
The landscape of alternative polyadenylation in single cells of the developing mouse embryo. Nature communications 12 (1) (2021)
Nicola Felix Müller, Cassia Wagner, Chris D Frazar, Pavitra Roychoudhury, Jover Lee, Louise H Moncla, Benjamin Pelle, Matthew Richardson, Erica Ryke, Hong Xie, Lasata Shrestha, Amin Addetia, Victoria Mallett Rachleff, Nicole A P Lieberman, Meei-Li W Huang, Romesh Gautom, Geoff C Melly, Brian Hiatt, Philip Dykema, Amanda Adler, Elisabeth Brandstetter, Peter D Han, Kairsten Fay, Misja Ilcisin, Kirsten Lacombe, Thomas R Sibley, Melissa Truong, Caitlin R Wolf, Michael J Boeckh, Janet A Englund, Michael Famulare, Barry R Lutz, Mark J Rieder, Matthew Thompson, Jeffrey S Duchin, Joshua T Schiffer, Helen Y Chu, Jay Shendure, Keith R Jerome, Scott Lindquist, Alexander L Greninger, Deborah A Nickerson, Trevor Felix Bedford
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Science translational medicine 13 (595) (2021)
Junhong Choi, Wei Chen, Chase C Suiter, Choli Lee, Florence M Chardon, Wei Yang, Anh Leith, Riza M Daza, Beth K Martin, Jay Shendure
Precise genomic deletions using paired prime editing. Nature biotechnology (2021)
Patrick A Carroll, Brian W Freie, Pei Feng Cheng, Sivakanthan Kasinathan, Haiwei Gu, Theresa Hedrich, James A Dowdle, Vivek Venkataramani, Vijay Ramani, Xiaoying Wu, Daniel Raftery, Jay Shendure, Donald E Ayer, Charles H Muller, Robert N Eisenman
The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. PLoS biology 19 (10) (2021)
Timothy J Durham, Riza M Daza, Louis Gevirtzman, Darren A Cusanovich, Olubusayo Bolonduro, William Stafford Noble, Jay Shendure, Robert H Waterston
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes. Genome research 31 (10) (2021)
Molly Gasperini, Jacob M Tome, Jay Shendure
Towards a comprehensive catalogue of validated and target-linked human enhancers. Nature reviews. Genetics 21 (5) (2020)
Junyue Cao, Wei Zhou, Frank Steemers, Cole Trapnell, Jay Shendure
Sci-fate characterizes the dynamics of gene expression in single cells. Nature biotechnology 38 (8) (2020)
He Fang, Giancarlo Bonora, Jordan P Lewandowski, Jitendra Thakur, Galina N Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L Rinn, Xinxian Deng, William Stafford Noble, Christine M Disteche
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nature communications 11 (1) (2020)
Xianding Deng, Wei Gu, Scot Federman, Louis du Plessis, Oliver George Pybus, Nuno Rodrigues Faria, Candace Wang, Guixia Yu, Brian Bushnell, Chao-Yang Pan, Hugo Guevara, Alicia Sotomayor Gonzalez, Kelsey C Zorn, Allan Gopez, Venice Servellita, Elaine Hsu, Steve Miller, Trevor Felix Bedford, Alexander L Greninger, Pavitra Roychoudhury, Joshua T Schiffer, Michael Famulare, Helen Y Chu, Jay Shendure, Keith R Jerome, Catie Anderson, Karthik Gangavarapu, Mark Zeller, Emily Spencer, Kristian G Andersen, Duncan R MacCannell, Clinton R Paden, Yan Li, Jing Zhang, Suxiang Tong, Gregory Armstrong, Scott Morrow, Matthew Willis, Bela T Matyas, Sundari Mase, Olivia Kasirye, Maggie Park, Godfred Masinde, Curtis Chan, Alexander Tin Han Yu, Shua J Chai, Elsa Villarino, Brandon Bonin, Debra A Wadford, Charles Y Chiu
Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science (New York, N.Y.) 369 (6503) (2020)
Adebola Enikanolaiye, Julie Ruston, Rong Zeng, Christine Taylor, Marijke Schrock, Christie M Buchovecky, Jay Shendure, Elif F Acar, Monica J Justice
Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology. Genome research 30 (4) (2020)
Jes Alexander, Quincey C LaPlant, Siobhan S Pattwell, Frank Szulzewsky, Patrick J Cimino, Francesca Pia Caruso, Pietro Pugliese, Zhihong Chen, Florence Chardon, Andrew J Hill, Cailyn H Spurrell, Dakota Ahrendsen, Alexander Pietras, Lea M Starita, Dolores Hambardzumyan, Antonio Iavarone, Jay Shendure, Eric C Holland
Multimodal single-cell analysis reveals distinct radioresistant stem-like and progenitor cell populations in murine glioma. Glia 68 (12) (2020)
Jason C Klein, Vikram Agarwal, Fumitaka Inoue, Aidan Keith, Beth Martin, Martin Kircher, Nadav Ahituv, Jay Shendure
A systematic evaluation of the design and context dependencies of massively parallel reporter assays. Nature methods 17 (11) (2020)
Trevor Felix Bedford, Alexander L Greninger, Pavitra Roychoudhury, Joshua T Schiffer, Michael Famulare, Meei-Li W Huang, Arun Nalla, Gregory Pepper, Adam Reinhardt, Hong Xie, Lasata Shrestha, Truong N Nguyen, Amanda Adler, Elisabeth Brandstetter, Shari Cho, Danielle Giroux, Peter D Han, Kairsten Fay, Chris D Frazar, Misja Ilcisin, Kirsten Lacombe, Jover Lee, Anahita Kiavand, Matthew Richardson, Thomas R Sibley, Melissa Truong, Caitlin R Wolf, Deborah A Nickerson, Mark J Rieder, Janet A Englund, null null, James Hadfield, Emma B Hodcroft, John Huddleston, Louise H Moncla, Nicola Felix Müller, Richard A Neher, Xianding Deng, Wei Gu, Scot Federman, Charles Y Chiu, Jeffrey S Duchin, Romesh Gautom, Geoff C Melly, Brian Hiatt, Philip Dykema, Scott Lindquist, Krista Queen, Ying Tao, Anna Uehara, Suxiang Tong, Duncan R MacCannell, Gregory L Armstrong, Geoffrey Stuart Baird, Helen Y Chu, Jay Shendure, Keith R Jerome
Cryptic transmission of SARS-CoV-2 in Washington state. Science (New York, N.Y.) 370 (6516) (2020)
Silvia Domcke, Andrew J Hill, Riza M Daza, Junyue Cao, Diana R O'Day, Hannah A Pliner, Kimberly A Aldinger, Dmitry Pokholok, Fan Zhang, Jennifer H Milbank, Michael A Zager, Ian A Glass, Frank J Steemers, Daniel A Doherty, Cole Trapnell, Darren A Cusanovich, Jay Shendure
A human cell atlas of fetal chromatin accessibility. Science (New York, N.Y.) 370 (6518) (2020)
M Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulos-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S Pollard, Jay Shendure, Martin Kircher, Nadav Ahituv
lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature protocols 15 (8) (2020)
Junyue Cao, Diana R O'Day, Hannah A Pliner, Paul D Kingsley, Mei Deng, Riza M Daza, Michael A Zager, Kimberly A Aldinger, Ronnie Blecher-Gonen, Fan Zhang, Malte Spielmann, James Palis, Daniel A Doherty, Frank J Steemers, Ian A Glass, Cole Trapnell, Jay Shendure
A human cell atlas of fetal gene expression. Science (New York, N.Y.) 370 (6518) (2020)
M Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulos-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S Pollard, Jay Shendure, Martin Kircher, Nadav Ahituv
Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature protocols (2020)
Jason C Klein, Aidan Keith, Sarah J Rice, Colin Shepherd, Vikram Agarwal, John Loughlin, Jay Shendure
Functional testing of thousands of osteoarthritis-associated variants for regulatory activity. Nature communications 10 (1) (2019)
Sanjay R Srivatsan, José L McFaline-Figueroa, Vijay Ramani, Lauren M Saunders, Junyue Cao, Jonathan S Packer, Hannah A Pliner, Dana L Jackson, Riza M Daza, Lena Christiansen, Fan Zhang, Frank Steemers, Jay Shendure, Cole Trapnell
Massively multiplex chemical transcriptomics at single-cell resolution. Science (New York, N.Y.) 367 (6473) (2019)
Seungsoo Kim, Maitreya J Dunham, Jay Shendure
A combination of transcription factors mediates inducible interchromosomal contacts. eLife 8 (2019)
Hannah A Pliner, Jay Shendure, Cole Trapnell
Supervised classification enables rapid annotation of cell atlases. Nature methods 16 (10) (2019)
José L McFaline-Figueroa, Andrew J Hill, Xiaojie Qiu, Dana Jackson, Jay Shendure, Cole Trapnell
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. Nature genetics 51 (9) (2019)
Anna Minkina, Jay Shendure
Expanding the single-cell genomics toolkit. Nature genetics 51 (6) (2019)
Bushra Raj, Daniel E Wagner, Aaron McKenna, Shristi Pandey, Allon M Klein, Jay Shendure, James A Gagnon, Alexander F Schier
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nature biotechnology 36 (5) (2018)
Ryan M Mulqueen, Dmitry Pokholok, Steven J Norberg, Kristof A Torkenczy, Andrew J Fields, Duanchen Sun, John R Sinnamon, Jay Shendure, Cole Trapnell, Brian J O'Roak, Zheng Xia, Frank J Steemers, Andrew C Adey
Highly scalable generation of DNA methylation profiles in single cells. Nature biotechnology 36 (5) (2018)
Zev N Kronenberg, Ian T Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris, Olivia S Meyerson, Jason G Underwood, Bradley J Nelson, Mark J P Chaisson, Max L Dougherty, Katherine M Munson, Alex R Hastie, Mark E Diekhans, Fereydoun Hormozdiari, Nicola Lorusso, Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, AnneMarie E Welch, Melanie Sorensen, Carl Baker, Robert S Fulton, Joel Armstrong, Tina A Graves-Lindsay, Ahmet M Denli, Emma R Hoppe, PingHsun Hsieh, Christopher M Hill, Andy Wing Chun Pang, Joyce Lee, Ernest T Lam, Susan K Dutcher, Fred H Gage, Wesley C Warren, Jay Shendure, David Haussler, Valerie A Schneider, Han Cao, Mario Ventura, Richard K Wilson, Benedict Paten, Alex Aaron Pollen, Evan E Eichler
High-resolution comparative analysis of great ape genomes. Science (New York, N.Y.) 360 (6393) (2018)
Junyue Cao, Darren A Cusanovich, Vijay Ramani, Delasa Aghamirzaie, Hannah A Pliner, Andrew J Hill, Riza M Daza, José L McFaline-Figueroa, Jonathan S Packer, Lena Christiansen, Frank J Steemers, Andrew C Adey, Cole Trapnell, Jay Shendure
Joint profiling of chromatin accessibility and gene expression in thousands of single cells. Science (New York, N.Y.) 361 (6409) (2018)
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers, Andrew C Adey, Robert H Waterston, Cole Trapnell, Jay Shendure
Comprehensive single-cell transcriptional profiling of a multicellular organism. Science (New York, N.Y.) 357 (6352) (2017)
Jay Shendure, Stanley Fields
Massively Parallel Genetics. Genetics 203 (2) (2017)
Seungsoo Kim, Ivan Liachko, Donna G Brickner, Kate Cook, William S Noble, Jason H Brickner, Jay Shendure, Maitreya J Dunham
The dynamic three-dimensional organization of the diploid yeast genome. eLife 6 (2017)
Fumitaka Inoue, Martin Kircher, Beth K Martin, Gregory M Cooper, Daniela M Witten, Michael T McManus, Nadav Ahituv, Jay Shendure
A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity. Genome research 27 (1) (2016)

Jay Shendure.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Jay Shendure