Miraldi Lab
Publications

Publications

Selected Publications

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; Kottyan, LC; Barski, A; Weirauch, MT; Prasath, VBS; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Computational Biology. 2023; 19(1):e1010863.

Pokrovskii, M; Hall, JA; Ochayon, DE; Yi, R; Chaimowitz, NS; Seelamneni, H; Carriero, N; Watters, A; Waggoner, SN; Littman, DR; Bonneau, R; Miraldi, ER. Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells. Immunity. 2019; 51(1):185-197.e6.

Miraldi, ER; Pokrovskii, M; Watters, A; Castro, DM; De Veaux, N; Hall, JA; Lee, J-Y; Ciofani, M; Madar, A; Carriero, N; Littman, DR; Bonneau, R. Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. Genome Research. 2019; 29(3):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(1):e1006591.

Karwacz, K; Miraldi, ER; Pokrovskii, M; Madi, A; Yosef, N; Wortman, I; Chen, X; Watters, A; Carriero, N; Awasthi, A; Regev, A; Bonneau, R; Littman, D; Kuchroo, VK. Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation. Nature Immunology. 2017; 18(4):412-421.

Raviram, R; Rocha, PP; Müller, CL; Miraldi, ER; Badri, S; Fu, Y; Swanzey, E; Proudhon, C; Snetkova, V; Bonneau, R; Skok, JA. 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments. PLoS Computational Biology. 2016; 12(3):e1004780.

Kurtz, ZD; Müller, CL; Miraldi, ER; Littman, DR; Blaser, MJ; Bonneau, RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Computational Biology. 2015; 11(5):e1004226.

Miraldi, ER; Sharfi, H; Friedline, RH; Johnson, H; Zhang, T; Lau, KS; Ko, HJ; Curran, TG; Haigis, KM; Yaffe, MB; Kim, JK; Neel, BG; Saghatelian, A; White, FM. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integrative Biology (United Kingdom). 2013; 5(7):940-963.

Kudira, R; Yang, ZF; Osuji, I; Damen, MSMA; Yang Vom Hofe, A; Singh, M; Karns, R; Bariya, P; Pfuhler, L; Mullen, M; Subramanian, S; Salomonis, N; Miraldi, ER; Miethke, AG. Bile acids engage the SIPR-STAT3 signaling axis to modulate regulatory T cell responses in fibrosing cholangiopathies. Journal of Hepatology. 2025; 83(5):1128-1141.

Secchia, S; Beilinson, V; Chen, X; Gucwa, M; Denson, LA; Miraldi, ER; Weirauch, MT; Ikegami, K. Starvation activates ECM-remodeling gene transcription and putative enhancers in fibroblasts despite inducing quiescence. Cell reports. 2025; 44(7):115896.

Li, G; Mahajan, S; Ma, S; Jeffery, ED; Zhang, X; Bhattacharjee, A; Venkatasubramanian, M; Weirauch, MT; Miraldi, ER; Grimes, HL; Sheynkman, GM; Tilburgs, T; Salomonis, N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16(730):eade2886.

Toth, A; Kannan, P; Snowball, J; Kofron, M; Wayman, JA; Bridges, JP; Miraldi, ER; Swarr, D; Zacharias, WJ. Alveolar epithelial progenitor cells require Nkx2-1 to maintain progenitor-specific epigenomic state during lung homeostasis and regeneration. Nature Communications. 2023; 14(1):8452.

Thomas, AL; Godarova, A; Wayman, JA; Miraldi, ER; Hildeman, DA; Chougnet, CA. Accumulation of immune-suppressive CD4 + T cells in aging - tempering inflammaging at the expense of immunity. Seminars in Immunology. 2023; 70:101836.

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; Kottyan, LC; Barski, A; Weirauch, MT; Prasath, VBS; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Computational Biology. 2023; 19(1):e1010863.

Skok Gibbs, C; Jackson, CA; Saldi, G-A; Tjärnberg, A; Shah, A; Watters, A; De Veaux, N; Tchourine, K; Yi, R; Hamamsy, T; Gorissen, BL; Gresham, D; Miraldi, ER; Bonneau, R. High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0. Bioinformatics. 2022; 38(9):2519-2528.

Toth, A; Steinmeyer, S; Kannan, P; Gray, J; Jackson, CM; Mukherjee, S; Demmert, M; Sheak, JR; Benson, D; Kitzmiller, J; Chougnet, CA; Jobe, AH; Deshmukh, H; Zacharias, WJ. Inflammatory blockade prevents injury to the developing pulmonary gas exchange surface in preterm primates. Science Translational Medicine. 2022; 14(638):eabl8574.

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