Emily R Miraldi (Emily Miraldi)

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 25

Top Topics

Genome Wide Association Study

Top Venues

PLoS computational biology

Nature communications

bioRxiv : the preprint server for biology

Science translational medicine

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

Publications

Guangyuan Li, Shweta Mahajan, Siyuan Ma, Erin D Jeffery, Xuan Zhang, Anukana Bhattacharjee, Meenakshi Venkatasubramanian, Matthew T Weirauch, Emily R Miraldi, H Leighton Grimes, Gloria M Sheynkman, Tamara Tilburgs, Nathan Salomonis
Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science translational medicine 16 (730) (2024)
Joseph A Wayman, Zi Yang, Elizabeth Angerman, Erin Bonkowski, Ingrid Jurickova, Xiaoting Chen, Anthony T Bejjani, Lois Parks, Sreeja Parameswaran, Alexander G Miethke, Kelli L VanDussen, Jasbir Dhaliwal, Matthew T Weirauch, Leah C Kottyan, Lee A Denson, Emily R Miraldi
Accessible chromatin maps of inflammatory bowel disease intestine nominate cell-type mediators of genetic disease risk. bioRxiv : the preprint server for biology (2024)
Guangyuan Li, Shweta Mahajan, Siyuan Ma, Erin D Jeffery, Xuan Zhang, Anukana Bhattacharjee, Meenakshi Venkatasubramanian, Matthew T Weirauch, Emily R Miraldi, H Leighton Grimes, Gloria M Sheynkman, Tamara Tilburgs, Nathan Salomonis
Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science translational medicine 16 (730) (2024)
Joseph A Wayman, Zi Yang, Elizabeth Angerman, Erin Bonkowski, Ingrid Jurickova, Xiaoting Chen, Anthony T Bejjani, Lois Parks, Sreeja Parameswaran, Alexander G Miethke, Kelli L VanDussen, Jasbir Dhaliwal, Matthew T Weirauch, Leah C Kottyan, Lee A Denson, Emily R Miraldi
Accessible chromatin maps of inflammatory bowel disease intestine nominate cell-type mediators of genetic disease risk. bioRxiv : the preprint server for biology (2024)
Joseph A Wayman, Zi Yang, Elizabeth Angerman, Erin Bonkowski, Ingrid Jurickova, Xiaoting Chen, Anthony T Bejjani, Lois Parks, Sreeja Parameswaran, Alexander G Miethke, Kelli L VanDussen, Jasbir Dhaliwal, Matthew T Weirauch, Leah C Kottyan, Lee A Denson, Emily R Miraldi
Accessible chromatin maps of inflammatory bowel disease intestine nominate cell-type mediators of genetic disease risk. bioRxiv : the preprint server for biology (2024)
Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel T Swarr, William J Zacharias
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications 14 (1) (2023)
Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel T Swarr, William J Zacharias
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications 14 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Joseph A Wayman, Alyssa Thomas, Anthony Bejjani, Alexander Katko, Maha Almanan, Alzbeta Godarova, Svetlana Korinfskaya, Tareian A Cazares, Masashi Yukawa, Leah C Kottyan, Artem Barski, Claire A Chougnet, David A Hildeman, Emily R Miraldi
An atlas of gene regulatory networks for T memory cells in youth and old age. bioRxiv : the preprint server for biology (2023)
Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel T Swarr, William J Zacharias
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications 14 (1) (2023)
Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel T Swarr, William J Zacharias
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications 14 (1) (2023)
Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel T Swarr, William J Zacharias
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications 14 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Tareian A Cazares, Faiz W Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T Bejjani, Joseph A Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C Kottyan, Artem Barski, Matthew T Weirauch, V B Surya Prasath, Emily R Miraldi
maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS computational biology 19 (1) (2023)
Andrea Toth, Paranthaman Kannan, John Snowball, Matthew Kofron, Joseph A Wayman, James P Bridges, Emily R Miraldi, Daniel T Swarr, William J Zacharias
Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature communications 14 (1) (2023)
Andrea Toth, Shelby Steinmeyer, Paranthaman Kannan, Jerilyn Gray, Courtney M Jackson, Shibabrata Mukherjee, Martin Demmert, Joshua R Sheak, Daniel Benson, Joseph Kitzmiller, Joseph A Wayman, Pietro Presicce, Christopher Cates, Rhea Rubin, Kashish Chetal, Yina Du, Yifei Miao, Mingxia Gu, Minzhe Guo, Vladimir V Kalinichenko, Suhas G Kallapur, Emily R Miraldi, Yan Xu, Daniel T Swarr, Ian P Lewkowich, Nathan Salomonis, Lisa A Miller, Jennifer M S Sucre, Jeffrey A Whitsett, Claire A Chougnet, Alan H Jobe, Hitesh Deshmukh, William J Zacharias
Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science translational medicine 14 (638) (2022)
Xiaoming Lu, Xiaoting Chen, Carmy Forney, Omer Donmez, Daniel Miller, Sreeja Parameswaran, Ted Hong, Yongbo Huang, Mario Pujato, Tareian Cazares, Emily R Miraldi, John P Ray, Carl G de Boer, John B Harley, Matthew T Weirauch, Leah C Kottyan
Global discovery of lupus genetic risk variant allelic enhancer activity. Nature communications 12 (1) (2021)
Emily R Miraldi, Xiaoting Chen, Matthew T Weirauch
Deciphering cis-regulatory grammar with deep learning. Nature genetics 53 (3) (2021)
Mei San Tang, Emily R Miraldi, Natasha M Girgis, Richard A Bonneau, P'ng Loke
Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs. Journal of immunology (Baltimore, Md. : 1950) 205 (4) (2020)
Maha Almanan, Jana Raynor, Ireti Ogunsulire, Anna Malyshkina, Shibabrata Mukherjee, Sarah A Hummel, Jennifer T Ingram, Ankur Singh Saini, Markus M Xie, Theresa Alenghat, Sing Sing Way, George S Deepe, Senad Divanovic, Harinder Singh, Emily R Miraldi, Allan J Zajac, Alexander L Dent, Christoph Hölscher, Claire Chougnet, David A Hildeman
IL-10-producing Tfh cells accumulate with age and link inflammation with age-related immune suppression. Science advances 6 (31) (2020)