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; Surya Prasath, VB; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. Editor, Przytycka TM. PLoS Computational Biology. 2023; 19: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; 51:185-197.e6.

Miraldi, ER; Pokrovskii, M; Watters, A; Castro, DM; De Veaux, N; Hall, JA; Lee, J; 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; 29:449-463.

Castro, DM; de Veaux, NR; Miraldi, ER; Bonneau, R. Multi-study inference of regulatory networks for more accurate models of gene regulation. Editor, van Nimwegen E. PLoS Computational Biology. 2019; 15: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; 18:412-421.

Raviram, R; Rocha, PP; Mueller, 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. Editor, Morozov AV. PLoS Computational Biology. 2016; 12:e1004780.

Kurtz, ZD; Mueller, CL; Miraldi, ER; Littman, DR; Blaser, MJ; Bonneau, RA. Sparse and compositionally robust inference of microbial ecological networks. Editor, von Mering C. PLoS Computational Biology. 2015; 11: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: interdisciplinary approaches for molecular and cellular life sciences. 2013; 5:940-963.

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: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; 14:8452.

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; Surya Prasath, VB; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. Editor, Przytycka TM. PLoS Computational Biology. 2023; 19:e1010863.

Skok Gibbs, C; Jackson, CA; Saldi, GA; 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. Editor, Mathelier A. Bioinformatics. 2022; 38:2519-2528.

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:eabl8574.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12:1611.

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

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

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 (Baltimore, Md. : 1950). 2020; 205:1070-1083.

Almanan, M; Raynor, J; Ogunsulire, I; Malyshkina, A; Mukherjee, S; Hummel, SA; Ingram, JT; Saini, A; Xie, MM; Alenghat, T; Dent, AL; Holscher, C; Chougnet, C; Hildeman, DA. IL-10-producing Tfh cells accumulate with age and link inflammation with age-related immune suppression. Science Advances. 2020; 6:eabb0806.

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