Ali Mortazavi

ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 49

Top Venues

bioRxiv : the preprint server for biology

Genome research

Nature communications

Nature methods

University of California Irvine

California Institute of Technology (PHD)

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

Affiliation History

University of California Irvine Jul 01 2011

United States

Professor :: Developmental and Cell Biology

Education History

California Institute of Technology Sep 30 2004 - Jun 08 2008

United States

PHD :: Biology

Publications

Narges Rezaie, Elisabeth Rebboah, Brian A Williams, Heidi Yahan Liang, Fairlie Reese, Gabriela Balderrama-Gutierrez, Louise A Dionne, Laura G Reinholdt, Diane Trout, Barbara J Wold, Ali Mortazavi
Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD. bioRxiv : the preprint server for 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)
Elisabeth Rebboah, Narges Rezaie, Brian A Williams, Annika K Weimer, Minyi Shi, Xinqiong Yang, Heidi Yahan Liang, Louise A Dionne, Fairlie Reese, Diane Trout, Jennifer Jou, Ingrid Youngworth, Laura G Reinholdt, Samuel J Morabito, Michael Paul Snyder, Barbara J Wold, Ali Mortazavi
The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. bioRxiv : the preprint server for biology (2024)
Rebekah Loving, Delaney K Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Yahan Liang, Ghassan Filimban, Shimako Kawauchi, Conrad G Oakes, Diane Trout, Brian A Williams, Grant R MacGregor, Barbara J Wold, Ali Mortazavi, Lior Pachter
Long-read sequencing transcriptome quantification with lr-kallisto. bioRxiv : the preprint server for biology (2024)
Lujia Chen, Xiangduo Kong, Kevin G Johnston, Ali Mortazavi, Todd C Holmes, Zhiqun Tan, Kyoko Yokomori, Xiangmin Xu
Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome research 34 (5) (2024)
Nicole D Schartz, Heidi Y Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea J Tenner
C5aR1 antagonism suppresses inflammatory glial responses and alters cellular signaling in an Alzheimer's disease mouse model. Nature communications 15 (1) (2024)
Lujia Chen, Xiangduo Kong, Kevin G Johnston, Ali Mortazavi, Todd C Holmes, Zhiqun Tan, Kyoko Yokomori, Xiangmin Xu
Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome research 34 (5) (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)
Elisabeth Rebboah, Narges Rezaie, Brian A Williams, Annika K Weimer, Minyi Shi, Xinqiong Yang, Heidi Yahan Liang, Louise A Dionne, Fairlie Reese, Diane Trout, Jennifer Jou, Ingrid Youngworth, Laura G Reinholdt, Samuel J Morabito, Michael Paul Snyder, Barbara J Wold, Ali Mortazavi
The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. bioRxiv : the preprint server for 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)
Nicole D Schartz, Heidi Y Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea J Tenner
C5aR1 antagonism suppresses inflammatory glial responses and alters cellular signaling in an Alzheimer's disease mouse model. Nature communications 15 (1) (2024)
Nicole D Schartz, Heidi Y Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea J Tenner
C5aR1 antagonism suppresses inflammatory glial responses and alters cellular signaling in an Alzheimer's disease mouse model. Nature communications 15 (1) (2024)
Rebekah Loving, Delaney K Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Yahan Liang, Ghassan Filimban, Shimako Kawauchi, Conrad G Oakes, Diane Trout, Brian A Williams, Grant R MacGregor, Barbara J Wold, Ali Mortazavi, Lior Pachter
Long-read sequencing transcriptome quantification with lr-kallisto. bioRxiv : the preprint server for biology (2024)
Lujia Chen, Xiangduo Kong, Kevin G Johnston, Ali Mortazavi, Todd C Holmes, Zhiqun Tan, Kyoko Yokomori, Xiangmin Xu
Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome research (2024)
Lujia Chen, Xiangduo Kong, Kevin G Johnston, Ali Mortazavi, Todd C Holmes, Zhiqun Tan, Kyoko Yokomori, Xiangmin Xu
Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome research (2024)
Lujia Chen, Xiangduo Kong, Kevin G Johnston, Ali Mortazavi, Todd C Holmes, Zhiqun Tan, Kyoko Yokomori, Xiangmin Xu
Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome research 34 (5) (2024)
Nicole D Schartz, Heidi Y Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea J Tenner
C5aR1 antagonism suppresses inflammatory glial responses and alters cellular signaling in an Alzheimer's disease mouse model. Nature communications 15 (1) (2024)
Lujia Chen, Xiangduo Kong, Kevin G Johnston, Ali Mortazavi, Todd C Holmes, Zhiqun Tan, Kyoko Yokomori, Xiangmin Xu
Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy. Genome research 34 (5) (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)
Rebekah Loving, Delaney K Sullivan, Fairlie Reese, Elisabeth Rebboah, Jasmine Sakr, Narges Rezaie, Heidi Yahan Liang, Ghassan Filimban, Shimako Kawauchi, Conrad G Oakes, Diane Trout, Brian A Williams, Grant R MacGregor, Barbara J Wold, Ali Mortazavi, Lior Pachter
Long-read sequencing transcriptome quantification with lr-kallisto. bioRxiv : the preprint server for biology (2024)
Elisabeth Rebboah, Narges Rezaie, Brian A Williams, Annika K Weimer, Minyi Shi, Xinqiong Yang, Heidi Yahan Liang, Louise A Dionne, Fairlie Reese, Diane Trout, Jennifer Jou, Ingrid Youngworth, Laura G Reinholdt, Samuel J Morabito, Michael Paul Snyder, Barbara J Wold, Ali Mortazavi
The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. bioRxiv : the preprint server for 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)
Narges Rezaie, Elisabeth Rebboah, Brian A Williams, Heidi Yahan Liang, Fairlie Reese, Gabriela Balderrama-Gutierrez, Louise A Dionne, Laura G Reinholdt, Diane Trout, Barbara J Wold, Ali Mortazavi
Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD. bioRxiv : the preprint server for 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 (2024)
Francisco J Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E Loveland, Maite De María, Matthew S Adams, Gabriela Balderrama-Gutierrez, Amit K Behera, Jose M 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 Berry, Salvador Capella, Angela N Brooks, Jose M Fernandez-Gonzalez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Goetz, Carles Hernández-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M Mudge, Nedka G Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Eric C Rouchka, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid Ashley Youngworth, Piero Carnici, Nancy D Denslow, Roderic Guigó, Margaret E Hunter, Hagen U Tilgner, Barbara J Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M Sheynkman, Ali Mortazavi, Ana Conesa
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv : the preprint server for biology (2023)
Xiaojie Wang, Raul Ramos, Anne Q Phan, Kosuke Yamaga, Jessica L Flesher, Shan Jiang, Ji Won Oh, Suoqin Jin, Sohail Jahid, Chen-Hsiang Kuan, Truman Kt Nguyen, Heidi Y Liang, Nitish Udupi Shettigar, Renzhi Hou, Kevin H Tran, Andrew Nguyen, Kimberly N Vu, Jennie L Phung, Jonard P Ingal, Katelyn M Levitt, Xiaoling Cao, Yingzi Liu, Zhili Deng, Nobuhiko Taguchi, Vanessa M Scarfone, Guangfang Wang, Kara Nicole Paolilli, Xiaoyang Wang, Christian F Guerrero-Juarez, Ryan T Davis, Elyse Noelani Greenberg, Rolando Ruiz-Vega, Priya Vasudeva, Rabi Murad, Lily Halida Putri Widyastuti, Hye-Lim Lee, Kevin J McElwee, Alain-Pierre Gadeau, Devon A Lawson, Bogi Andersen, Ali Mortazavi, Zhengquan Yu, Qing Nie, Takahiro Kunisada, Michael Karin, Jan P Tuckermann, Jeffrey D Esko, Anand K Ganesan, Ji Li, Maksim V Plikus
Signalling by senescent melanocytes hyperactivates hair growth. Nature 618 (7966) (2023)
Nicole D Schartz, Heidi Yahan Liang, Klebea Carvalho, Shu-Hui Chu, Adrian Mendoza-Arvilla, Tiffany J Petrisko, Angela Gomez-Arboledas, Ali Mortazavi, Andrea J Tenner
C5aR1 antagonism suppresses inflammatory glial gene expression and alters cellular signaling in an aggressive Alzheimer's model. bioRxiv : the preprint server for biology (2023)
Fairlie Reese, Brian A Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang, Beatrice Borsari, Samuel J Morabito, Heidi Yahan Liang, Cassandra J McGill, Sorena Rahmanian, Jasmine Sakr, Shan Jiang, Weihua Zeng, Klebea Carvalho, Annika K Weimer, Louise A Dionne, Ariel McShane, Karan Bedi, Shaimae I Elhajjajy, Sean Upchurch, Jennifer Jou, Ingrid Youngworth, Aditi K Narayanan, Paul Sud, Otto Jolanki, Benjamin C Hitz, Meenakshi S Kagda, Michael Paul Snyder, Benjamin C Hitz, Jill E Moore, Nishigandha Phalke, David A Bennett, Laura G Reinholdt, Mats Ljungman, Michael A Beer, Mark B Gerstein, Lior Pachter, Roderic Guigo, Barbara J Wold, Ali Mortazavi
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv : the preprint server for biology (2023)
Benjamin Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Paul Sud, Idan Gabdank, J Seth Strattan, Cricket Sloan, Timothy Dreszer, Laurence Rowe, Nikhil Podduturi, Venkat Malladi, Esther T Chan, Jean Davidson, Marcus Ho, Stuart Miyasato, Matt Simison, Forrest Tanaka, Yunhai Luo, Ian Wahling, Khine Zin Lin, Jennifer Jou, Eurie Hong, Laurence D Rowe, Richard Sandstrom, Eric Rynes, Jemma Nelson, Andrew Nishida, Alyssa Ingersoll, Michael Buckley, Mark Frerker, Daniel Kim, Nathan Boley, Diane Trout, Alexander Dobin, Sorena Rahmanian, Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Neva C Durand, Olga Dudchenko, David Weisz, Suhas Rao, Alyssa Blackburn, Dimos Gkountaroulis, Mahdi Sadr, Moshe Olshansky, Yossi Eliaz, Dat Nguyen, Ivan Bochkov, Muhammad Saad Shamim, Ragini Mahajan, Erez Aiden, Thomas Gingeras, Simon Heath, Martin Hirst, W James Kent, Anshul Kundaje, Ali Mortazavi, Barbara J Wold, J Michael Cherry
The ENCODE Uniform Analysis Pipelines. Research square (2023)
Benjamin C Hitz, Jin-Wook Lee, Otto Jolanki, Meenakshi S Kagda, Keenan Graham, Paul Sud, Aditi K Narayanan, Benjamin C Hitz, Cricket A Sloan, Timothy Dreszer, Laurence D Rowe, Nikhil R Podduturi, Venkat S Malladi, Esther T Chan, Jean M Davidson, Brian T Lee, Stuart Miyasato, Matt Simison, Forrest Tanaka, Yunhai Luo, Ian Whaling, Eurie L Hong, Laurence D Rowe, Richard S Sandstrom, Eric Rynes, Jemma Nelson, Andrew Nishida, Alyssa Ingersoll, Michael Buckley, Mark Frerker, Daniel S Kim, Nathan Boley, Diane Trout, Alexander Dobin, Sorena Rahmanian, Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, Neva C Durand, Olga Dudchenko, David Weisz, Suhas S P Rao, Alyssa Blackburn, Dimos Gkountaroulis, Mahdi Sadr, Moshe Olshansky, Yossi Eliaz, Dat Nguyen, Ivan Bochkov, Muhammad Saad Shamim, Ragini Mahajan, Erez Lieberman Aiden, Thomas R Gingeras, Simon Charles Heath, Martin Hirst, W James Kent, Anshul Kundaje, Ali Mortazavi, Barbara J Wold, J Michael Cherry
The ENCODE Uniform Analysis Pipelines. bioRxiv : the preprint server for biology (2023)
Rabi Murad, Aide Macias-Muñoz, Ashley Wong, Xinyi Ma, Ali Mortazavi
Coordinated Gene Expression and Chromatin Regulation during Hydra Head Regeneration. Genome biology and evolution 13 (12) (2022)
Kyle J McCulloch, Aide Macias-Muñoz, Ali Mortazavi, Adriana D Briscoe
Multiple Mechanisms of Photoreceptor Spectral Tuning in Heliconius Butterflies. Molecular biology and evolution 39 (4) (2022)
Miguel A Arreola, Neelakshi Soni, Joshua D Crapser, Lindsay A Hohsfield, Monica R P Elmore, Dina P Matheos, Marcelo A Wood, Vivek Swarup, Ali Mortazavi, Kim N Green
Microglial dyshomeostasis drives perineuronal net and synaptic loss in a CSF1R+/- mouse model of ALSP, which can be rescued via CSF1R inhibitors. Science advances 7 (35) (2021)
Fairlie Reese, Ali Mortazavi
Swan: a library for the analysis and visualization of long-read transcriptomes. Bioinformatics (Oxford, England) 37 (9) (2021)
Dalen Chan, Chao Feng, Whitney E England, Dana Wyman, Ryan A Flynn, Xiuye Wang, Yongsheng Shi, Ali Mortazavi, Robert C Spitale
Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic acids research 49 (20) (2021)
Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Liang, Barbara J Wold, Ali Mortazavi
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq. Genome biology 22 (1) (2021)
Jonathan Chau, Xiangduo Kong, Nam Viet Nguyen, Katherine Williams, Miya Ball, Rabi Tawil, Tohru Kiyono, Ali Mortazavi, Kyoko Yokomori
Relationship of DUX4 and target gene expression in FSHD myocytes. Human mutation 42 (4) (2021)
Jill E Moore, Xiao-Ou Zhang, Shaimae I Elhajjajy, Kaili Fan, Henry E Pratt, Fairlie Reese, Ali Mortazavi, Nishigandha Phalke
Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome research 32 (2) (2021)
Gabriela Balderrama-Gutierrez, Ana Milovic, Vanessa J Cook, M Nurul Islam, Youwen Zhang, Hippokratis Kiaris, John T Belisle, Ali Mortazavi, Alan G Barbour
An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin. mBio 12 (2) (2021)
David Baglietto-Vargas, Stefania Forner, Lena Cai, Alessandra Cadete Martini, Laura Trujillo-Estrada, Vivek Swarup, Marie Minh Thu Nguyen, Kelly Do Huynh, Dominic I Javonillo, Kristine Minh Tran, Jimmy Phan, Shan Jiang, Enikö A Kramár, Cristina Nuñez-Diaz, Gabriela Balderrama-Gutierrez, Franklin G Garcia, Jessica Childs, Carlos J Rodriguez-Ortiz, Juan Antonio Garcia-Leon, Masashi Kitazawa, Mohammad Shahnawaz, Dina P Matheos, Xinyi Ma, Celia Da Cunha, Ken C Walls, Rahasson R Ager, Claudio Soto, Antonia Gutierrez, Ines Moreno-Gonzalez, Ali Mortazavi, Andrea J Tenner, Grant R MacGregor, Marcelo Wood, Kim N Green, Frank M LaFerla
Generation of a humanized Aβ expressing mouse demonstrating aspects of Alzheimer's disease-like pathology. Nature communications 12 (1) (2021)
Stefania Forner, Shimako Kawauchi, Gabriela Balderrama-Gutierrez, Enikö A Kramár, Dina P Matheos, Jimmy Phan, Dominic I Javonillo, Kristine M Tran, Edna Hingco, Celia da Cunha, Narges Rezaie, Joshua A Alcantara, David Baglietto-Vargas, Camden Jansen, Jonathan Neumann, Marcelo A Wood, Grant R MacGregor, Ali Mortazavi, Andrea J Tenner, Frank M LaFerla, Kim N Green
Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer's disease. Scientific data 8 (1) (2021)
Nan W Hultgren, Jennifer S Fang, Mary E Ziegler, Ricardo N Ramirez, Duc T T Phan, Michaela M S Hatch, Katrina M Welch-Reardon, Antonio E Paniagua, Lin S Kim, Nathan N Shon, David S Williams, Ali Mortazavi, Christopher C W Hughes
Slug regulates the Dll4-Notch-VEGFR2 axis to control endothelial cell activation and angiogenesis. Nature communications 11 (1) (2020)
Shan Jiang, Katherine Williams, Xiangduo Kong, Weihua Zeng, Nam Viet Nguyen, Xinyi Ma, Rabi Tawil, Kyoko Yokomori, Ali Mortazavi
Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei. PLoS genetics 16 (5) (2020)
null null, Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L Van Nostrand, Peter Freese, David U Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A Williams, Ali Mortazavi, Cheryl A Keller, Xiao-Ou Zhang, Shaimae I Elhajjajy, Jack Huey, Diane E Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B Chhetri, Jialing Zhang, Alec Victorsen, Kevin P White, Axel Visel, Gene W Yeo, Christopher B Burge, Eric Lécuyer, David M Gilbert, Job Dekker, John L Rinn, Eric M Mendenhall, Joseph R Ecker, Manolis Kellis, Robert J Klein, William S Noble, Anshul Kundaje, Roderic Guigó, Peggy J Farnham, J Michael Cherry, Richard M Myers, Bing Ren, Brenton R Graveley, Mark B Gerstein, Len A Pennacchio, Michael Paul Snyder, Bradley E Bernstein, Barbara Wold, Ross Cameron Hardison, Thomas R Gingeras, John A Stamatoyannopoulos, Nishigandha Phalke
Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583 (7818) (2020)
Anthony D Long, James Baldwin-Brown, Yuan Tao, Vanessa J Cook, Gabriela Balderrama-Gutierrez, Russell B Corbett-Detig, Ali Mortazavi, Alan G Barbour
The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections. Science advances 5 (7) (2019)
Shan Jiang, Noriko Kamei, Jessica L Bolton, Xinyi Ma, Hal S Stern, Tallie Z Baram, Ali Mortazavi
Intra-individual methylomics detects the impact of early-life adversity. Life science alliance 2 (2) (2019)
Lorrayne Serra, Marissa Macchietto, Aide Macias-Muñoz, Cassandra Joan McGill, Isaryhia Maya Rodriguez, Bryan Rodriguez, Rabi Murad, Ali Mortazavi
Hybrid Assembly of the Genome of the Entomopathogenic Nematode Steinernema carpocapsae Identifies the X-Chromosome. G3 (Bethesda, Md.) 9 (8) (2019)
Dennis Z Chang, Lorrayne Serra, Dihong Lu, Ali Mortazavi, Adler R Dillman
A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema. PLoS pathogens 15 (5) (2019)
Camden Jansen, Ricardo N Ramirez, Nicole C El-Ali, David Gomez-Cabrero, Jesper Tegner, Matthias Merkenschlager, Ana Conesa, Ali Mortazavi
Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps. PLoS computational biology 15 (11) (2019)

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Ali Mortazavi