| Year |
Citation |
Score |
| 2023 |
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. 19: e1010863. PMID 36719906 DOI: 10.1371/journal.pcbi.1010863 |
0.388 |
|
| 2022 |
Gibbs CS, Jackson CA, Saldi GA, Tjärnberg A, Shah A, Watters A, De Veaux N, Tchourine K, Yi R, Hamamsy T, Castro DM, Carriero N, Gorissen BL, Gresham D, Miraldi ER, et al. High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0. Bioinformatics (Oxford, England). PMID 35188184 DOI: 10.1093/bioinformatics/btac117 |
0.633 |
|
| 2020 |
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). PMID 32661179 DOI: 10.4049/Jimmunol.2000258 |
0.504 |
|
| 2019 |
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. PMID 31278058 DOI: 10.1016/J.Immuni.2019.06.001 |
0.636 |
|
| 2019 |
Miraldi ER, Pokrovskii M, Waters A, Castro DM, De Veaux N, Hall J, Lee JY, Ciofani M, Madar A, Carriero N, Littman D, Bonneau R. Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. Genome Research. PMID 30696696 DOI: 10.1101/Gr.238253.118 |
0.76 |
|
| 2019 |
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. 15: e1006591. PMID 30677040 DOI: 10.1371/Journal.Pcbi.1006591 |
0.613 |
|
| 2018 |
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. 19: 216. PMID 30541598 DOI: 10.1186/S13059-018-1598-7 |
0.723 |
|
| 2018 |
Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, et al. Retraction Note: DDX5 and its associated lncRNA Rmrp modulate T17 cell effector functions. Nature. PMID 29973715 DOI: 10.1038/S41586-018-0311-Z |
0.446 |
|
| 2017 |
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. PMID 28166218 DOI: 10.1038/Ni.3683 |
0.572 |
|
| 2016 |
Sano T, Huang W, Hall JA, Yang Y, Chen A, Gavzy SJ, Lee JY, Ziel JW, Miraldi ER, Domingos AI, Bonneau R, Littman DR. An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses. Cell. 164: 324. PMID 28915371 DOI: 10.1016/J.Cell.2015.12.047 |
0.453 |
|
| 2016 |
Rocha PP, Raviram R, Fu Y, Kim J, Luo VM, Aljoufi A, Swanzey E, Pasquarella A, Balestrini A, Miraldi ER, Bonneau R, Petrini J, Schotta G, Skok JA. A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination. Cell Reports. PMID 27320916 DOI: 10.1016/J.Celrep.2016.05.073 |
0.683 |
|
| 2016 |
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. 12: e1004780. PMID 26938081 DOI: 10.1371/Journal.Pcbi.1004780 |
0.699 |
|
| 2016 |
Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo F, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, et al. Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. PMID 26789242 DOI: 10.1038/Nature16968 |
0.467 |
|
| 2015 |
Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo FW, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, et al. DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. PMID 26675721 DOI: 10.1038/Nature16193 |
0.54 |
|
| 2015 |
Sano T, Huang W, Hall JA, Yang Y, Chen A, Gavzy SJ, Lee JY, Ziel JW, Miraldi ER, Domingos AI, Bonneau R, Littman DR. An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses. Cell. PMID 26411290 DOI: 10.1016/J.Cell.2015.08.061 |
0.485 |
|
| 2015 |
Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. Plos Computational Biology. 11: e1004226. PMID 25950956 DOI: 10.1371/Journal.Pcbi.1004226 |
0.726 |
|
| 2014 |
Yu B, Doraiswamy H, Chen X, Miraldi E, Arrieta-Ortiz ML, Hafemeister C, Madar A, Bonneau R, Silva CT. Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks. Ieee Transactions On Visualization and Computer Graphics. 20: 1903-12. PMID 26356904 DOI: 10.1109/Tvcg.2014.2346753 |
0.673 |
|
| 2014 |
Longman RS, Diehl GE, Victorio DA, Huh JR, Galan C, Miraldi ER, Swaminath A, Bonneau R, Scherl EJ, Littman DR. CX₃CR1⁺ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22. The Journal of Experimental Medicine. 211: 1571-83. PMID 25024136 DOI: 10.1084/Jem.20140678 |
0.478 |
|
| 2013 |
Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, et al. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integrative Biology : Quantitative Biosciences From Nano to Macro. 5: 940-63. PMID 23685806 DOI: 10.1039/C3Ib40013A |
0.472 |
|
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