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Emily R Miraldi
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Sparse and compositionally robust inference of microbial ecological networks
ZD Kurtz, CL Müller, ER Miraldi, DR Littman, MJ Blaser, RA Bonneau
PLoS computational biology 11 (5), e1004226, 2015
12312015
An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses
DR Sano, T, Huang, W, Hall, JA, Chen, A, Gravzy, SJ, Lee, J, Ziel, J ...
Cell 163 (2), 381-393, 2015
5642015
CX3CR1+ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22
RS Longman, GE Diehl, DA Victorio, JR Huh, C Galan, ER Miraldi, ...
Journal of Experimental Medicine 211 (8), 1571-1583, 2014
3752014
DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
W Huang, B Thomas, RA Flynn, SJ Gavzy, L Wu, SV Kim, JA Hall, ...
Nature 528 (7583), 517-522, 2015
1782015
Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation
K Karwacz, ER Miraldi, M Pokrovskii, A Madi, N Yosef, I Wortman, X Chen, ...
Nature immunology 18 (4), 412-421, 2017
1332017
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells
ER Miraldi, M Pokrovskii, A Watters, DM Castro, N De Veaux, JA Hall, ...
Genome research 29 (3), 449-463, 2019
1042019
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments
R Raviram, PP Rocha, CL Muller, R Miraldi, Emily, S Badri, Y Fu, ...
PLoS Computational Biology 12 (3), 2016
932016
Allosteric models for cooperative polymerization of linear polymers
ER Miraldi, PJ Thomas, L Romberg
Biophysical journal 95 (5), 2470-2486, 2008
912008
IL-10–producing Tfh cells accumulate with age and link inflammation with age-related immune suppression
M Almanan, J Raynor, I Ogunsulire, A Malyshkina, S Mukherjee, ...
Science advances 6 (31), eabb0806, 2020
832020
TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation
JSY Ho, BWY Mok, L Campisi, T Jordan, S Yildiz, S Parameswaran, ...
Cell 184 (10), 2618-2632. e17, 2021
802021
Characterization of transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells
M Pokrovskii, JA Hall, DE Ochayon, R Yi, NS Chaimowitz, H Seelamneni, ...
Immunity 51 (1), 185-197. e6, 2019
762019
Multi-study inference of regulatory networks for more accurate models of gene regulation
DM Castro, NR De Veaux, ER Miraldi, R Bonneau
PLoS computational biology 15 (1), e1006591, 2019
672019
Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth
PH Huang, ER Miraldi, AM Xu, VA Kundukulam, AM Del Rosario, ...
Molecular BioSystems 6 (7), 1227-1237, 2010
562010
Global discovery of lupus genetic risk variant allelic enhancer activity
X Lu, X Chen, C Forney, O Donmez, D Miller, S Parameswaran, T Hong, ...
Nature communications 12 (1), 1611, 2021
412021
Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
R Raviram, PP Rocha, VM Luo, E Swanzey, ER Miraldi, EB Chuong, ...
Genome biology 19, 1-19, 2018
402018
Hybrid gene origination creates human-virus chimeric proteins during infection
JSY Ho, M Angel, Y Ma, E Sloan, G Wang, C Martinez-Romero, ...
Cell 181 (7), 1502-1517. e23, 2020
392020
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0
C Skok Gibbs, CA Jackson, GA Saldi, A Tjärnberg, A Shah, A Watters, ...
Bioinformatics 38 (9), 2519-2528, 2022
382022
A damage-independent role for 53BP1 that impacts break order and Igh architecture during class switch recombination
PP Rocha, R Raviram, Y Fu, JH Kim, VM Luo, A Aljoufi, E Swanzey, ...
Cell reports 16 (1), 48-55, 2016
352016
Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice
ER Miraldi, H Sharfi, RH Friedline, H Johnson, T Zhang, KS Lau, HJ Ko, ...
Integrative biology 5 (7), 940-963, 2013
262013
Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions
W Huang, B Thomas, RA Flynn, SJ Gavzy, L Wu, SV Kim, JA Hall, ...
Nature 562 (7725), 150-150, 2018
182018
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