Cole Trapnell

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 63

Top Topics

Duchenne Muscular Dystrophy

Gene Expression

Pulmonary Fibrosis

Genome Wide Association Study

Top Venues

bioRxiv : the preprint server for biology

Science (New York, N.Y.)

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

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)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Juyoung Seong, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. bioRxiv : the preprint server for biology (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)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Juyoung Seong, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. 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 (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)
Kerry L Bubb, Morgan O Hamm, Joseph K Min, Bryan Ramirez-Corona, Nicholas A Mueth, Jane Ranchalis, Mitchell R Vollger, Cole Trapnell, Josh T Cuperus, Christine Queitsch, Andrew Ben Stergachis
The regulatory potential of transposable elements in maize. 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)
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)
Cole Trapnell
Revealing gene function with statistical inference at single-cell resolution. Nature reviews. Genetics (2024)
Yoshihiro Hasegawa, Jennifer M Franks, Yusuke Tanaka, Yasuaki Uehara, David F Read, Claire R Williams, Sanjay R Srivatsan, Lori B Pitstick, Nikolaos M Nikolaidis, Ciara M Shaver, Jonathan A Kropski, Lorraine B Ware, Chase J Taylor, Nicholas E Banovich, Huixing Wu, Jason C Gardner, Andrew R Osterburg, Jane J Yu, Elizabeth J Kopras, Steven L Teitelbaum, Kathryn A Wikenheiser-Brokamp, Cole Trapnell, Francis X McCormack
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. Science advances 10 (28) (2024)
Cole Trapnell
Revealing gene function with statistical inference at single-cell resolution. Nature reviews. Genetics 25 (9) (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)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Juyoung Seong, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. bioRxiv : the preprint server for biology (2024)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Juyoung Seong, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. bioRxiv : the preprint server for biology (2024)
Yoshihiro Hasegawa, Jennifer M Franks, Yusuke Tanaka, Yasuaki Uehara, David F Read, Claire R Williams, Sanjay R Srivatsan, Lori B Pitstick, Nikolaos M Nikolaidis, Ciara M Shaver, Jonathan A Kropski, Lorraine B Ware, Chase J Taylor, Nicholas E Banovich, Huixing Wu, Jason C Gardner, Andrew R Osterburg, Jane J Yu, Elizabeth J Kopras, Steven L Teitelbaum, Kathryn A Wikenheiser-Brokamp, Cole Trapnell, Francis X McCormack
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. Science advances 10 (28) (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)
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)
Kerry L Bubb, Morgan O Hamm, Joseph K Min, Bryan Ramirez-Corona, Nicholas A Mueth, Jane Ranchalis, Mitchell R Vollger, Cole Trapnell, Josh T Cuperus, Christine Queitsch, Andrew Ben Stergachis
The regulatory potential of transposable elements in maize. bioRxiv : the preprint server for biology (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)
Yoshihiro Hasegawa, Jennifer M Franks, Yusuke Tanaka, Yasuaki Uehara, David F Read, Claire R Williams, Sanjay R Srivatsan, Lori B Pitstick, Nikolaos M Nikolaidis, Ciara M Shaver, Jonathan A Kropski, Lorraine B Ware, Chase J Taylor, Nicholas E Banovich, Huixing Wu, Jason C Gardner, Andrew R Osterburg, Jane J Yu, Elizabeth J Kopras, Steven L Teitelbaum, Kathryn A Wikenheiser-Brokamp, Cole Trapnell, Francis X McCormack
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. Science advances 10 (28) (2024)
Yoshihiro Hasegawa, Jennifer M Franks, Yusuke Tanaka, Yasuaki Uehara, David F Read, Claire R Williams, Sanjay R Srivatsan, Lori B Pitstick, Nikolaos M Nikolaidis, Ciara M Shaver, Jonathan A Kropski, Lorraine B Ware, Chase J Taylor, Nicholas E Banovich, Huixing Wu, Jason C Gardner, Andrew R Osterburg, Jane J Yu, Elizabeth J Kopras, Steven L Teitelbaum, Kathryn A Wikenheiser-Brokamp, Cole Trapnell, Francis X McCormack
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. Science advances 10 (28) (2024)
Kerry L Bubb, Morgan O Hamm, Joseph K Min, Bryan Ramirez-Corona, Nicholas A Mueth, Jane Ranchalis, Mitchell R Vollger, Cole Trapnell, Josh T Cuperus, Christine Queitsch, Andrew Ben Stergachis
The regulatory potential of transposable elements in maize. bioRxiv : the preprint server for biology (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)
Cole Trapnell
Revealing gene function with statistical inference at single-cell resolution. Nature reviews. Genetics 25 (9) (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)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Juyoung Seong, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. bioRxiv : the preprint server for biology (2024)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. bioRxiv : the preprint server for biology (2023)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. bioRxiv : the preprint server for biology (2023)
Elise Mozin, Emmanuelle Massourides, Virginie Mournetas, Clémence Lièvre, Audrey Bourdon, Dana L Jackson, Jonathan S Packer, Cole Trapnell, Caroline Le Guiner, Oumeya Adjali, Christian Pinset, David L Mack, Jean-Baptiste Dupont
Dystrophin deficiency impairs cell junction formation during embryonic myogenesis. 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)
Yoshihiro Hasegawa, Jennifer M Franks, Yusuke Tanaka, Yasuaki Uehara, David F Read, Claire R Williams, Sanjay R Srivatsan, Lori B Pitstick, Nikolaos M Nikolaidis, Ciara M Shaver, Huixing Wu, Jason C Gardner, Andrew R Osterburg, Jane J Yu, Elizabeth J Kopras, Steven L Teitelbaum, Kathryn A Wikenheiser-Brokamp, Cole Trapnell, Francis X McCormack
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. bioRxiv : the preprint server for biology (2023)
Yoshihiro Hasegawa, Jennifer M Franks, Yusuke Tanaka, Yasuaki Uehara, David F Read, Claire R Williams, Sanjay R Srivatsan, Lori B Pitstick, Nikolaos M Nikolaidis, Ciara M Shaver, Huixing Wu, Jason C Gardner, Andrew R Osterburg, Jane J Yu, Elizabeth J Kopras, Steven L Teitelbaum, Kathryn A Wikenheiser-Brokamp, Cole Trapnell, Francis X McCormack
Pulmonary osteoclast-like cells in silica induced pulmonary fibrosis. 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)
Hyeon-Jin Kim, Gregory T Booth, Lauren M Saunders, Sanjay Srivatsan, José L McFaline-Figueroa, Cole Trapnell
Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. Nature communications 13 (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)
Sara A Rubin, Chloé S Baron, Cecilia Pessoa Rodrigues, Madeleine Duran, Alexandra F Corbin, Song P Yang, Cole Trapnell, Leonard I Zon
Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish. The Journal of experimental medicine 219 (9) (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)
Brandon Hadland, Barbara Varnum-Finney, Stacey Dozono, Tessa Dignum, Cynthia Nourigat-McKay, Adam M Heck, Takashi Ishida, Dana L Jackson, Tomer Itkin, Jason M Butler, Shahin Rafii, Cole Trapnell, Irwin D Bernstein
Engineering a niche supporting hematopoietic stem cell development using integrated single-cell transcriptomics. Nature communications 13 (1) (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)
Michael W Dorrity, Lauren M Saunders, Christine Queitsch, Stanley Fields, Cole Trapnell
Dimensionality reduction by UMAP to visualize physical and genetic interactions. Nature communications 11 (1) (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)
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)
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)
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)
Hannah A Pliner, Jay Shendure, Cole Trapnell
Supervised classification enables rapid annotation of cell atlases. Nature methods 16 (10) (2019)
Ken Jean-Baptiste, José L McFaline-Figueroa, Cristina M Alexandre, Michael W Dorrity, Lauren M Saunders, Kerry L Bubb, Cole Trapnell, Stanley Fields, Christine Queitsch, Josh T Cuperus
Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. The Plant cell 31 (5) (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)
John R Sinnamon, Kristof A Torkenczy, Michael W Linhoff, Sarah A Vitak, Ryan M Mulqueen, Hannah A Pliner, Cole Trapnell, Frank J Steemers, Gail Mandel, Andrew C Adey
The accessible chromatin landscape of the murine hippocampus at single-cell resolution. Genome research 29 (5) (2019)
Jonathan S Packer, Qin Zhu, Chau Huynh, Priya Sivaramakrishnan, Elicia Preston, Hannah Dueck, Derek J Stefanik, Kai Tan, Cole Trapnell, Junhyong Kim, Robert H Waterston, John Isaac Murray
A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science (New York, N.Y.) 365 (6459) (2019)
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)
Andrew J Hill, José L McFaline-Figueroa, Lea M Starita, Molly J Gasperini, Kenneth A Matreyek, Jonathan Packer, Dana Jackson, Jay Shendure, Cole Trapnell
On the design of CRISPR-based single-cell molecular screens. Nature methods 15 (4) (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)
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma, Cole Trapnell
Single-cell mRNA quantification and differential analysis with Census. Nature methods 14 (3) (2017)
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell
Reversed graph embedding resolves complex single-cell trajectories. Nature methods 14 (10) (2017)