Miraldi Lab

Pokrovskii, M; Hall, JA; Ochayon, DE; Yi, R; Chaimowitz, NS; Seelamneni, H; Carriero, N; Watters, A; Waggoner, SN; Littman, DR; et al. 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. Genome Research. 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.

Skok Gibbs, C; Jackson, CA; Saldi, GA; Tjärnberg, A; Shah, A; Watters, A; De Veaux, N; Tchourine, K; Yi, R; Hamamsy, T; et al. High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0. Computer Applications in the Biosciences. 2022.

Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; et al. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; et al. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; et al. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

Ho, JS Y; Mok, BW Y; Campisi, L; Jordan, T; Yildiz, S; Parameswaran, S; Wayman, JA; Gaudreault, NN; Meekins, DA; Indran, SV; et al. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell. 2021; 184:2618-2632.e17.

Miraldi, ER; Chen, X; Weirauch, MT. Deciphering cis-regulatory grammar with deep learning. Nature Genetics. 2021; 53:266-268.

Moreno-Fernandez, ME; Miraldi, ER; Divanovic, S. Not Chopped Liver-A Careful, Fate-Mapping Study of Macrophages in NASH. Cell Metabolism. 2020; 32:328-330.

Tang, MS; Miraldi, ER; Girgis, NM; Bonneau, RA; Loke, P. Alternative Activation of Macrophages Is Accompanied by Chromatin Remodeling Associated with Lineage-Dependent DNA Shape Features Flanking PU.1 Motifs. Journal of Immunology. 2020; 205:1070-1083.

Almanan, M; Raynor, J; Ogunsulire, I; Malyshkina, A; Mukherjee, S; Hummel, SA; Ingram, JT; Saini, A; Xie, MM; Alenghat, T; et al. IL-10-producing Tfh cells accumulate with age and link inflammation with age-related immune suppression. Science advances. 2020; 6.

Ho, JS Y; Angel, M; Ma, Y; Sloan, E; Wang, G; Martinez-Romero, C; Alenquer, M; Roudko, V; Chung, L; Zheng, S; et al. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell. 2020; 181:1502-1517.e23.

Pokrovskii, M; Hall, JA; Ochayon, DE; Yi, R; Chaimowitz, NS; Seelamneni, H; Carriero, N; Watters, A; Waggoner, SN; Littman, DR; et al. 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. Genome Research. 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.

Raviram, R; Rocha, PP; Luo, VM; Swanzey, E; Miraldi, ER; Chuong, EB; Feschotte, C; Bonneau, R; Skok, JA. Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate. Genome Biology. 2018; 19.