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Items: 16

1.

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells.

Miraldi ER, Pokrovskii M, Watters A, Castro DM, De Veaux N, Hall JA, Lee JY, Ciofani M, Madar A, Carriero N, Littman DR, Bonneau R.

Genome Res. 2019 Mar;29(3):449-463. doi: 10.1101/gr.238253.118. Epub 2019 Jan 29.

2.

Multi-study inference of regulatory networks for more accurate models of gene regulation.

Castro DM, de Veaux NR, Miraldi ER, Bonneau R.

PLoS Comput Biol. 2019 Jan 24;15(1):e1006591. doi: 10.1371/journal.pcbi.1006591. eCollection 2019 Jan.

3.

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate.

Raviram R, Rocha PP, Luo VM, Swanzey E, Miraldi ER, Chuong EB, Feschotte C, Bonneau R, Skok JA.

Genome Biol. 2018 Dec 13;19(1):216. doi: 10.1186/s13059-018-1598-7.

4.

Retraction Note: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions.

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, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR.

Nature. 2018 Oct;562(7725):150. doi: 10.1038/s41586-018-0311-z.

5.

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

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.

Nat Immunol. 2017 Apr;18(4):412-421. doi: 10.1038/ni.3683. Epub 2017 Feb 6.

6.

A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination.

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.

Cell Rep. 2016 Jun 28;16(1):48-55. doi: 10.1016/j.celrep.2016.05.073. Epub 2016 Jun 16.

7.

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.

Raviram R, Rocha PP, Müller CL, Miraldi ER, Badri S, Fu Y, Swanzey E, Proudhon C, Snetkova V, Bonneau R, Skok JA.

PLoS Comput Biol. 2016 Mar 3;12(3):e1004780. doi: 10.1371/journal.pcbi.1004780. eCollection 2016 Mar.

8.

Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions.

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, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR.

Nature. 2016 May 5;533(7601):130. doi: 10.1038/nature16968. Epub 2016 Jan 20. No abstract available.

PMID:
26789242
9.

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses.

Sano T, Huang W, Hall JA, Yang Y, Chen A, Gavzy SJ, Lee JY, Ziel JW, Miraldi ER, Domingos AI, Bonneau R, Littman DR.

Cell. 2016 Jan 14;164(1-2):324. doi: 10.1016/j.cell.2015.12.047. Epub 2016 Jan 14. No abstract available.

10.

DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions.

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, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR.

Nature. 2015 Dec 24;528(7583):517-22. doi: 10.1038/nature16193. Epub 2015 Dec 16. Erratum in: Nature. 2016 May 5;533(7601):130. Rigo, Frank W [Corrected to Rigo, Frank].. Retraction in: Nature. 2018 Oct;562(7725):150.

11.

An IL-23R/IL-22 Circuit Regulates Epithelial Serum Amyloid A to Promote Local Effector Th17 Responses.

Sano T, Huang W, Hall JA, Yang Y, Chen A, Gavzy SJ, Lee JY, Ziel JW, Miraldi ER, Domingos AI, Bonneau R, Littman DR.

Cell. 2015 Oct 8;163(2):381-93. doi: 10.1016/j.cell.2015.08.061. Epub 2015 Sep 24. Erratum in: Cell. 2016 Jan 14;164(1-2):324. Dosage error in article text.

12.

Sparse and compositionally robust inference of microbial ecological networks.

Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA.

PLoS Comput Biol. 2015 May 7;11(5):e1004226. doi: 10.1371/journal.pcbi.1004226. eCollection 2015 May.

13.

CX₃CR1⁺ mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22.

Longman RS, Diehl GE, Victorio DA, Huh JR, Galan C, Miraldi ER, Swaminath A, Bonneau R, Scherl EJ, Littman DR.

J Exp Med. 2014 Jul 28;211(8):1571-83. doi: 10.1084/jem.20140678. Epub 2014 Jul 14.

14.

Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice.

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, Saghatelian A, White FM.

Integr Biol (Camb). 2013 Jul 24;5(7):940-63. doi: 10.1039/c3ib40013a. Epub 2013 May 20.

15.

Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth.

Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM, Flynn RA, Cavenee WK, Furnari FB, White FM.

Mol Biosyst. 2010 Jul;6(7):1227-37. doi: 10.1039/c001196g. Epub 2010 May 11.

16.

Allosteric models for cooperative polymerization of linear polymers.

Miraldi ER, Thomas PJ, Romberg L.

Biophys J. 2008 Sep;95(5):2470-86. doi: 10.1529/biophysj.107.126219. Epub 2008 May 23.

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