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31 results for Miraldi,+Emily+R.

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ArticlesPeer ReviewedFull Text
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
Author / Creator:Kurtz, Zachary D. ; Müller, Christian L. ; Miraldi, Emily R. ; Littman, Dan R. ; Blaser, Martin J. ; Bonneau, Richard A.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2015-05, Vol.11 (5), p.e1004226
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Multi-study inference of regulatory networks for more accurate models of gene regulation
Author / Creator:Castro, Dayanne M. ; de Veaux, Nicholas R. ; Miraldi, Emily R. ; Bonneau, Richard
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2019-01, Vol.15 (1), p.e1006591-e1006591
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ArticlesPeer ReviewedFull Text
Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation
Author / Creator:Karwacz, Katarzyna ; Miraldi, Emily R ; Pokrovskii, Maria ; Madi, Asaf ; Yosef, Nir ; Wortman, Ivo ; Chen, Xi ; Watters, Aaron ; Carriero, Nicholas ; Awasthi, Amit ; Regev, Aviv ; Bonneau, Richard ; Littman, Dan ; Kuchroo, Vijay K
Publisher:New York: Nature Publishing Group US
Journal title:Nature immunology, 2017-04, Vol.18 (4), p.412-421
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Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration
Author / Creator:Toth, Andrea ; Kannan, Paranthaman ; Snowball, John ; Kofron, Matthew ; Wayman, Joseph A. ; Bridges, James P. ; Miraldi, Emily R. ; Swarr, Daniel ; Zacharias, William J.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2023-12, Vol.14 (1), p.8452-8452, Article 8452
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DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
Author / Creator:Huang, Wendy ; Thomas, Benjamin ; Flynn, Ryan A. ; Gavzy, Samuel J. ; Wu, Lin ; Kim, Sangwon V. ; Hall, Jason A. ; Miraldi, Emily R. ; Ng, Charles P. ; Rigo, Frank ; Meadows, Sarah ; Montoya, Nina R. ; Herrera, Natalia G. ; Domingos, Ana I. ; Rastinejad, Fraydoon ; Myers, Richard M. ; Fuller-Pace, Frances V. ; Bonneau, Richard ; Chang, Howard Y. ; Acuto, Oreste ; Littman, Dan R.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2015-12, Vol.528 (7583), p.517-522
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ArticlesPeer ReviewedFull Text
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
Author / Creator:Raviram, Ramya ; Rocha, Pedro P. ; Müller, Christian L. ; Miraldi, Emily R. ; Badri, Sana ; Fu, Yi ; Swanzey, Emily ; Proudhon, Charlotte ; Snetkova, Valentina ; Bonneau, Richard ; Skok, Jane A.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2016-03, Vol.12 (3), p.e1004780-e1004780
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ArticlesPeer ReviewedFull Text
Global discovery of lupus genetic risk variant allelic enhancer activity
Author / Creator:Lu, Xiaoming ; Chen, Xiaoting ; Forney, Carmy ; Donmez, Omer ; Miller, Daniel ; Parameswaran, Sreeja ; Hong, Ted ; Huang, Yongbo ; Pujato, Mario ; Cazares, Tareian ; Miraldi, Emily R. ; Ray, John P. ; de Boer, Carl G. ; Harley, John B. ; Weirauch, Matthew T. ; Kottyan, Leah C.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-03, Vol.12 (1), p.1611-1611, Article 1611
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Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
Author / Creator:Raviram, Ramya ; Rocha, Pedro P. ; Luo, Vincent M. ; Swanzey, Emily ; Miraldi, Emily R. ; Chuong, Edward B. ; Feschotte, Cédric ; Bonneau, Richard ; Skok, Jane A.
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2018-12, Vol.19 (1), p.216-216, Article 216
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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Author / Creator:Cazares, Tareian A. ; Rizvi, Faiz W. ; Iyer, Balaji ; Chen, Xiaoting ; Kotliar, Michael ; Bejjani, Anthony T. ; Wayman, Joseph A. ; Donmez, Omer ; Wronowski, Benjamin ; Parameswaran, Sreeja ; Kottyan, Leah C. ; Barski, Artem ; Weirauch, Matthew T. ; Prasath, V. B. Surya ; Miraldi, Emily R.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2023-01, Vol.19 (1), p.e1010863
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ArticlesPeer ReviewedFull Text
Allosteric Models for Cooperative Polymerization of Linear Polymers
Author / Creator:Miraldi, Emily R. ; Thomas, Peter J. ; Romberg, Laura
Publisher:United States: Elsevier Inc
Journal title:Biophysical journal, 2008-09, Vol.95 (5), p.2470-2486
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Deciphering cis-regulatory grammar with deep learning
Author / Creator:Miraldi, Emily R. ; Chen, Xiaoting ; Weirauch, Matthew T.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2021-03, Vol.53 (3), p.266-268
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Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
Author / Creator:Huang, Wendy ; Thomas, Benjamin ; Flynn, Ryan A. ; Gavzy, Samuel J. ; Wu, Lin ; Kim, Sangwon V. ; Hall, Jason A. ; Miraldi, Emily R. ; Ng, Charles P. ; Rigo, Frank ; Meadows, Sarah ; Montoya, Nina R. ; Herrera, Natalia G. ; Domingos, Ana I. ; Rastinejad, Fraydoon ; Myers, Richard M. ; Fuller-Pace, Frances V. ; Bonneau, Richard ; Chang, Howard Y. ; Acuto, Oreste ; Littman, Dan R.
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2018-10, Vol.562 (7725), p.150-150
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ArticlesPeer ReviewedFull Text
Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
Author / Creator:Huang, Wendy ; Thomas, Benjamin ; Flynn, Ryan A ; Gavzy, Samuel J ; Wu, Lin ; Kim, Sangwon V ; Hall, Jason A ; Miraldi, Emily R ; Ng, Charles P ; Rigo, Frank ; Meadows, Sarah ; Montoya, Nina R ; Herrera, Natalia G ; Domingos, Ana I ; Rastinejad, Fraydoon ; Myers, Richard M ; Fuller-Pace, Frances V ; Bonneau, Richard ; Chang, Howard Y ; Acuto, Oreste ; Littman, Dan R
Publisher:England: Nature Publishing Group
Journal title:Nature (London), 2016-05, Vol.533 (7601), p.130-130
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ArticlesFull Text
maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks
Author / Creator:Cazares, Tareian A ; Rizvi, Faiz W ; Iyer, Balaji ; Chen, Xiaoting ; Kotliar, Michael ; Wayman, Joseph A ; Bejjani, Anthony ; Donmez, Omer ; Wronowski, Benjamin ; Parameswaran, Sreeja ; Kottyan, Leah C ; Barski, Artem ; Weirauch, Matthew T ; Vb Surya Prasath ; Miraldi, Emily R
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2022-01
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ArticlesFull Text
Alternative activation of macrophages is accompanied by chromatin remodeling and short-term dampening of macrophage secondary response
Author / Creator:Mei San Tang ; Miraldi, Emily R ; Girgis, Natasha M ; Bonneau, Richard A ; Loke, P'ng
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2020-03
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ArticlesFull Text
Genome-wide discovery of SLE genetic risk variant allelic enhancer activity
Author / Creator:Lu, Xiaoming ; Chen, Xiaoting ; ney, Carmy ; Donmez, Omer ; Miller, Daniel ; Parameswaran, Sreeja ; Hong, Ted ; Huang, Yongbo ; Pujato, Mario ; Cazares, Tareian ; Miraldi, Emily R ; Ray, John P ; De Boer, Carl G ; Harley, John B ; Weirauch, Matthew T ; Kottyan, Leah C
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2021-01
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Multi-study inference of regulatory networks for more accurate models of gene regulation
Author / Creator:Castro, Dayanne M ; De Veaux, Nick ; Miraldi, Emily R ; Bonneau, Richard
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2019-01
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Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates
Author / Creator:Toth, Andrea ; Steinmeyer, Shelby ; Kannan, Paranthaman Senthamarai ; Gray, Jerilyn ; Jackson, Courtney ; Mukherjee, Shibabrata ; Demmert, Martin ; Sheak, Joshua R ; Benson, Daniel ; Kitzmiller, Joseph ; Wayman, Joseph A ; Presicce, Pietro ; Cates, Christopher ; Rubin, Rhea ; Chetal, Kashish ; Du, Yina ; Miao, Yifei ; Guo, Minzhe ; Gu, Mingxia ; Kalinichenko, Vladimir V ; Kallapur, Suhas G ; Miraldi, Emily R ; Xu, Yan ; Swarr, Daniel T ; Lewkowich, Ian ; Salomonis, Nathan T ; Miller, Lisa ; Sucre, Jennifer ; Whitsett, Jeffrey A ; Chougnet, Claire ; Jobe, Alan H ; Deshmukh, Hitesh ; Zacharias, William J
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2021-06
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ArticlesPeer ReviewedFull Text
Critical role of the transcription factors IRF1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation
Author / Creator:Karwacz, Katarzyna ; Miraldi, Emily R. ; Pokrovskii, Maria ; Madi, Asaf ; Yosef, Nir ; Wortman, Ivo ; Chen, Xi ; Watters, Aaron ; Carriero, Nicholas ; Awashti, Amit ; Regev, Aviv ; Bonneau, Richard ; Littman, Dan ; Kuchroo, Vijay K.
Journal title:Nature immunology, 2017-02, Vol.18 (4), p.412-421
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ArticlesPeer ReviewedFull Text
Sparse and Compositionally Robust Inference of Microbial Ecological Networks: e1004226
Author / Creator:Kurtz, Zachary D ; Müller, Christian L ; Miraldi, Emily R ; Littman, Dan R ; Blaser, Martin J ; Bonneau, Richard A
Publisher:San Francisco: Public Library of Science
Journal title:PLoS computational biology, 2015-05, Vol.11 (5)
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Showing 1 to 20 of 31 results

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Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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Multi-study inference of regulatory networks for more accurate models of gene regulation

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Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation

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Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration

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DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

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4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

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Global discovery of lupus genetic risk variant allelic enhancer activity

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Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

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Allosteric Models for Cooperative Polymerization of Linear Polymers

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Deciphering cis-regulatory grammar with deep learning

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Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

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Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions

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maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

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Alternative activation of macrophages is accompanied by chromatin remodeling and short-term dampening of macrophage secondary response

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Genome-wide discovery of SLE genetic risk variant allelic enhancer activity

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Multi-study inference of regulatory networks for more accurate models of gene regulation

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Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates

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Critical role of the transcription factors IRF1 and BATF in preparing the chromatin landscape during Type 1 regulatory cell differentiation

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Sparse and Compositionally Robust Inference of Microbial Ecological Networks: e1004226

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