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Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells.
Immunity.
2019;
51:185-197.e6.
Miraldi, ER; Pokrovskii, M; Watters, A; Castro, DM; De Veaux, N; Hall, JA; Lee, J; Ciofani, M; Madar, A; Carriero, N; et al.
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.
PCR Methods and Applications.
2019;
29:449-463.
Castro, DM; de Veaux, NR; Miraldi, ER; Bonneau, R.
Multi-study inference of regulatory networks for more accurate models of gene regulation.
PLoS Computational Biology.
2019;
15.
Karwacz, K; Miraldi, ER; Pokrovskii, M; Madi, A; Yosef, N; Wortman, I; Chen, X; Watters, A; Carriero, N; Awasthi, A; et al.
Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.
Nature Immunology.
2017;
18:412-421.
Raviram, R; Rocha, PP; Mueller, CL; Miraldi, ER; Badri, S; Fu, Y; Swanzey, E; Proudhon, C; Snetkova, V; Bonneau, R; et al.
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.
PLoS Computational Biology.
2016;
12.
Kurtz, ZD; Mueller, CL; Miraldi, ER; Littman, DR; Blaser, MJ; Bonneau, RA.
Sparse and compositionally robust inference of microbial ecological networks.
PLoS Computational Biology.
2015;
11.
Miraldi, ER; Sharfi, H; Friedline, RH; Johnson, H; Zhang, T; Lau, KS; Ko, HJ; Curran, TG; Haigis, KM; Yaffe, MB; et al.
Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.
Integrative Biology (United Kingdom).
2013;
5:940-963.