Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells.
Pokrovskii, M; Hall, JA; Ochayon, DE; Yi, R; Chaimowitz, NS; Seelamneni, H; Carriero, N; Watters, A; Waggoner, SN; Littman, DR; et al.
Immunity.
2019;
51:185-197.e6.
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.
Miraldi, ER; Pokrovskii, M; Watters, A; Castro, DM; De Veaux, N; Hall, JA; Lee, J; Ciofani, M; Madar, A; Carriero, N; et al.
Genome Research.
2019;
29:449-463.
Multi-study inference of regulatory networks for more accurate models of gene regulation.
Castro, DM; de Veaux, NR; Miraldi, ER; Bonneau, R.
PLoS Computational Biology.
2019;
15:e1006591-e1006591.
Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.
Karwacz, K; Miraldi, ER; Pokrovskii, M; Madi, A; Yosef, N; Wortman, I; Chen, X; Watters, A; Carriero, N; Awasthi, A; et al.
Nature Immunology.
2017;
18:412-421.
4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.
Raviram, R; Rocha, PP; Mueller, CL; Miraldi, ER; Badri, S; Fu, Y; Swanzey, E; Proudhon, C; Snetkova, V; Bonneau, R; et al.
PLoS Computational Biology.
2016;
12:e1004780-e1004780.
Sparse and Compositionally Robust Inference of Microbial Ecological Networks.
Kurtz, ZD; Mueller, CL; Miraldi, ER; Littman, DR; Blaser, MJ; Bonneau, RA.
PLoS Computational Biology.
2015;
11:e1004226-e1004226.
Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.
Miraldi, ER; Sharfi, H; Friedline, RH; Johnson, H; Zhang, T; Lau, KS; Ko, HJ; Curran, TG; Haigis, KM; Yaffe, MB; et al.
Integrative Biology: interdisciplinary approaches for molecular and cellular life sciences.
2013;
5:940-963.
Alternative activation of macrophages is accompanied by chromatin remodeling associated with lineage-dependent DNA shape features flanking PU.1 motifs.
Tang, MS; Miraldi, ER; Girgis, NM; Bonneau, RA; Loke, P.
Journal of immunology (Baltimore, Md. : 1950).
2020;
205:1070-1083.
IL-10–producing Tfh cells accumulate with age and link inflammation with age-related immune suppression.
Almanan, M; Raynor, J; Ogunsulire, I; Malyshkina, A; Mukherjee, S; Hummel, SA; Ingram, JT; Saini, A; Xie, MM; Alenghat, T; et al.
Science Advances.
2020;
6:eabb0806-eabb0806.
Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection.
Ho, JS Y; Angel, M; Ma, Y; Sloan, E; Wang, G; Martinez-Romero, C; Alenquer, M; Roudko, V; Chung, L; Zheng, S; et al.
Cell.
2020;
181:1502-1517.e23.