| Sparse and compositionally robust inference of microbial ecological networks ZD Kurtz, CL Müller, ER Miraldi, DR Littman, MJ Blaser, RA Bonneau PLoS computational biology 11 (5), e1004226, 2015 | 1456 | 2015 |
| An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses DR Sano, T, Huang, W, Hall, JA, Chen, A, Gravzy, SJ, Lee, J, Ziel, J ... Cell 163 (2), 381-393, 2015 | 606 | 2015 |
| CX3CR1+ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22 RS Longman, GE Diehl, DA Victorio, JR Huh, C Galan, ER Miraldi, ... Journal of Experimental Medicine 211 (8), 1571-1583, 2014 | 399 | 2014 |
| DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions W Huang, B Thomas, RA Flynn, SJ Gavzy, L Wu, SV Kim, JA Hall, ... Nature 528 (7583), 517-522, 2015 | 185 | 2015 |
| Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation K Karwacz, ER Miraldi, M Pokrovskii, A Madi, N Yosef, I Wortman, X Chen, ... Nature immunology 18 (4), 412-421, 2017 | 145 | 2017 |
| Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells ER Miraldi, M Pokrovskii, A Watters, DM Castro, N De Veaux, JA Hall, ... Genome research 29 (3), 449-463, 2019 | 120 | 2019 |
| IL-10–producing Tfh cells accumulate with age and link inflammation with age-related immune suppression M Almanan, J Raynor, I Ogunsulire, A Malyshkina, S Mukherjee, ... Science advances 6 (31), eabb0806, 2020 | 102 | 2020 |
| TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation JSY Ho, BWY Mok, L Campisi, T Jordan, S Yildiz, S Parameswaran, ... Cell 184 (10), 2618-2632. e17, 2021 | 100 | 2021 |
| Allosteric models for cooperative polymerization of linear polymers ER Miraldi, PJ Thomas, L Romberg Biophysical journal 95 (5), 2470-2486, 2008 | 98 | 2008 |
| 4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments R Raviram, PP Rocha, CL Muller, R Miraldi, Emily, S Badri, Y Fu, ... PLoS Computational Biology 12 (3), 2016 | 96 | 2016 |
| Characterization of transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells M Pokrovskii, JA Hall, DE Ochayon, R Yi, NS Chaimowitz, H Seelamneni, ... Immunity 51 (1), 185-197. e6, 2019 | 88 | 2019 |
| Multi-study inference of regulatory networks for more accurate models of gene regulation DM Castro, NR De Veaux, ER Miraldi, R Bonneau PLoS computational biology 15 (1), e1006591, 2019 | 77 | 2019 |
| Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth PH Huang, ER Miraldi, AM Xu, VA Kundukulam, AM Del Rosario, ... Molecular BioSystems 6 (7), 1227-1237, 2010 | 59 | 2010 |
| Global discovery of lupus genetic risk variant allelic enhancer activity X Lu, X Chen, C Forney, O Donmez, D Miller, S Parameswaran, T Hong, ... Nature communications 12 (1), 1611, 2021 | 58 | 2021 |
| Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate R Raviram, PP Rocha, VM Luo, E Swanzey, ER Miraldi, EB Chuong, ... Genome biology 19, 1-19, 2018 | 50 | 2018 |
| High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0 CS Gibbs, CA Jackson, GA Saldi, A Tjärnberg, A Shah, A Watters, ... Bioinformatics 38 (9), 2519, 2022 | 45 | 2022 |
| Hybrid gene origination creates human-virus chimeric proteins during infection JSY Ho, M Angel, Y Ma, E Sloan, G Wang, C Martinez-Romero, ... Cell 181 (7), 1502-1517. e23, 2020 | 42 | 2020 |
| High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0 C Skok Gibbs, CA Jackson, GA Saldi, A Tjärnberg, A Shah, A Watters, ... Bioinformatics 38 (9), 2519-2528, 2022 | 39 | 2022 |
| A damage-independent role for 53BP1 that impacts break order and Igh architecture during class switch recombination PP Rocha, R Raviram, Y Fu, JH Kim, VM Luo, A Aljoufi, E Swanzey, ... Cell reports 16 (1), 48-55, 2016 | 38 | 2016 |
| maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks TA Cazares, FW Rizvi, B Iyer, X Chen, M Kotliar, AT Bejjani, JA Wayman, ... PLOS Computational Biology 19 (1), e1010863, 2023 | 27 | 2023 |