Barbara J Wold (Barbara Wold)

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 20

Top Topics

Circulating Tumor Cells

Quality Control

Top Venues

bioRxiv : the preprint server for biology

Research square

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

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)
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)
Michal Polonsky, Louisa M S Gerhardt, Jina Yun, Kari Koppitch, Katsuya Lex Colón, Henry Amrhein, Barbara J Wold, Shiwei Zheng, Guo-Cheng Yuan, Matt Thomson, Long Cai, Andrew P McMahon
Spatial transcriptomics defines injury specific microenvironments and cellular interactions in kidney regeneration and disease. 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)
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)
Bao Zhang, Peng He, John E G Lawrence, Shuaiyu Wang, Elizabeth Tuck, Brian A Williams, Kenny Roberts, Vitalii Kleshchevnikov, Lira Mamanova, Liam Bolt, Krzysztof Polański, Tong Li, Rasa Elmentaite, Eirini S Fasouli, Martin Prete, Xiaoling He, Nadav Yayon, Yixi Fu, Hao Yang, Chen Liang, Hui Zhang, Raphael Blain, Alain Chédotal, David R FitzPatrick, Helen Firth, Andrew Dean, Omer Ali Bayraktar, John C Marioni, Roger A Barker, Mekayla A Storer, Barbara J Wold, Hongbo Zhang, Sarah A Teichmann
A human embryonic limb cell atlas resolved in space and time. Nature (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)
Peng He, Brian A Williams, Diane Trout, Georgi K Marinov, Henry Amrhein, Libera Berghella, Say-Tar Goh, Ingrid Plajzer-Frick, Veena Afzal, Len A Pennacchio, Diane E Dickel, Axel Visel, Bing Ren, Ross Cameron Hardison, Yu Zhang, Barbara J Wold
The changing mouse embryo transcriptome at whole tissue and single-cell resolution. Nature 583 (7818) (2020)