Yin Shen

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 43

Top Topics

Genome Wide Association

Transcription Factor

Endothelial Cells

Top Venues

Nature structural & molecular biology

Science advances

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

Publications

David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
David Yao, Josh Tycko, Jin Woo Oh, Lexi R Bounds, Sager J Gosai, Lazaros Lataniotis, Ava Mackay Smith, Benjamin R Doughty, Aditi K Narayanan, Henri Schmidt, Tania Guerrero-Altamirano, Keith Siklenka, Katherine Guo, Alexander D White, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunhai Luo, Galip Gürkan Yardımcı, Ryan Tewhey, Anshul Kundaje, William J Greenleaf, Pardis C Sabeti, Christina S Leslie, Yuri Pritykin, Jill E Moore, Michael A Beer, Charles A Gersbach, Timothy E Reddy, Yin Shen, Jesse M Engreitz, Michael C Bassik, Steven K Reilly
Multicenter integrated analysis of noncoding CRISPRi screens. Nature methods 21 (4) (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
Author Correction: MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
Author Correction: MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
Junjiao Yang, Chan-I Chung, Jessica Koach, Hongjiang Liu, Ambuja Navalkar, Hao He, Zhimin Ma, Qian Zhao, Xiaoyu Yang, Liang He, Tanja Mittag, Yin Shen, William A Weiss, Xiaokun Shu
MYC phase separation selectively modulates the transcriptome. Nature structural & molecular biology (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods 21 (7) (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark E Diekhans, Silvia Carbonell-Sala, Brian A Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose Manuel Gonzalez, Toby Hunt, Julien Lagarde, Cindy E Liang, Haoran Li, Marcus Jerryd Meade, David A Moraga Amador, Andrey D Prjibelski, Inanc Birol, Hamed Bostan, Ashley M Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R M Du, Colette Felton, Jonathan Goke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E Ritchie, Andre D Sim, Alison D Tang, Yuk Kei Wan, Changqing Wang, Brandon Y Wong, Chen Yang, If Barnes, Andrew E Berry, Salvador Capella, Alyssa Cousineau, Namrita Dhillon, José María Fernandez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric C Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigo, Margaret E Hunter, René Maehr, Yin Shen, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa, Angela N Brooks
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature methods (2024)
Xiaoyu Yang, Jia Wen, Han Yang, Ian R Jones, Xiaodong Zhu, Weifang Liu, Bingkun Li, Claire D Clelland, Wenjie Luo, Man Ying Wong, Xingjie Ren, Xiekui Cui, Michael Song, Hongjiang Liu, Cady Chen, Nicolas Eng, Mirunalini Ravichandran, Yang Sun, David S Lee, Eric Van Buren, Min-Zhi Jiang, Candace S Y Chan, Chun Jimmie Ye, Rushika M Perera, Li Gan, Yun Li, Yin Shen
Functional characterization of Alzheimer's disease genetic variants in microglia. Nature genetics (2023)
Bryce Rowland, Ruth Huh, Zoey Hou, Cheynna A Crowley, Jia Wen, Yin Shen, Ming Hu, Paola Giusti-Rodriguez, Patrick F Sullivan, Yun Li
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data. PLoS genetics 18 (3) (2022)
Ian R Jones, Xingjie Ren, Yin Shen
High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases. Human molecular genetics 31 (R1) (2022)
Han Yang, Xia Ting, Yue-Hang Geng, Yuntao Xie, Jovia L Nierenberg, Yan-Fei Huo, Yan-Ting Zhou, Yang Huang, Yu-Qing Yu, Xin-Yao Yu, Xiao-Fei Li, Elad Ziv, Hongquan Zhang, Wei-Gang Fang, Yin Shen, Xin-Xia Tian
The risk variant rs11836367 contributes to breast cancer onset and metastasis by attenuating Wnt signaling via regulating NTN4 expression. Science advances 8 (23) (2022)
Wei Sun, Nanxi Wang, Hongjiang Liu, Bingchen Yu, Ling Jin, Xingjie Ren, Yin Shen, Lei Wang
Genetically encoded chemical crosslinking of RNA in vivo. Nature chemistry (2022)
Mirunalini Ravichandran, Jingjie Hu, Charles Cai, Nathan P Ward, Anthony Venida, Callum Foakes, Miljan Kuljanin, Annan Yang, Connor J Hennessey, Yang Yang, Brandon R Desousa, Gilles Rademaker, Annelot A L Staes, Zeynep Cakir, Isha H Jain, Andrew J Aguirre, Joseph D Mancias, Yin Shen, Gina M DeNicola, Rushika M Perera
Coordinated Transcriptional and Catabolic Programs Support Iron-Dependent Adaptation to RAS-MAPK Pathway Inhibition in Pancreatic Cancer. Cancer discovery 12 (9) (2022)
Xingjie Ren, Mengchi Wang, Bingkun Li, Kirsty Jamieson, Lina Zheng, Ian R Jones, Bin Li, Maya Asami Takagi, Jerry Lee, Lenka Maliskova, Tsz Wai Tam, Miao Yu, Rong Hu, Lindsay Lee, Armen Abnousi, Gang Li, Yun Li, Ming Hu, Bing Ren, Wei Wang, Yin Shen
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath. Science advances 7 (38) (2021)
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