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
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
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
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
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
Allosteric models for cooperative polymerization of linear polymers
ER Miraldi, PJ Thomas, L Romberg
Biophysical journal 95 (5), 2470-2486, 2008
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
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
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
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
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
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
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
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
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
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
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
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
Genotet: An interactive web-based visual exploration framework to support validation of gene regulatory networks
B Yu, H Doraiswamy, X Chen, E Miraldi, ML Arrieta-Ortiz, C Hafemeister, ...
IEEE transactions on visualization and computer graphics 20 (12), 1903-1912, 2014
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
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