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Items: 1 to 50 of 239

1.

Author Correction: c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont.

Xu M, Pokrovskii M, Ding Y, Yi R, Au C, Harrison OJ, Galan C, Belkaid Y, Bonneau R, Littman DR.

Nature. 2019 Feb;566(7744):E7. doi: 10.1038/s41586-019-0922-z.

PMID:
30723268
2.

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.

3.

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.

4.

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.

5.

Translating microbiome futures.

Taroncher-Oldenburg G, Jones S, Blaser M, Bonneau R, Christey P, Clemente JC, Elinav E, Ghedin E, Huttenhower C, Kelly D, Kyle D, Littman D, Maiti A, Maue A, Olle B, Segal L, van Hylckama Vlieg JET, Wang J.

Nat Biotechnol. 2018 Nov 9;36(11):1037-1042. doi: 10.1038/nbt.4287. No abstract available.

PMID:
30412201
6.

An adaptive geometric search algorithm for macromolecular scaffold selection.

Jiang T, Renfrew PD, Drew K, Youngs N, Butterfoss GL, Bonneau R, Shasha DN.

Protein Eng Des Sel. 2018 Sep 1;31(9):345-354. doi: 10.1093/protein/gzy028.

7.

Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer.

Schneider JA, Craven TW, Kasper AC, Yun C, Haugbro M, Briggs EM, Svetlov V, Nudler E, Knaut H, Bonneau R, Garabedian MJ, Kirshenbaum K, Logan SK.

Nat Commun. 2018 Oct 23;9(1):4396. doi: 10.1038/s41467-018-06845-3.

8.

Towards region-specific propagation of protein functions.

Koo DCE, Bonneau R.

Bioinformatics. 2018 Oct 9. doi: 10.1093/bioinformatics/bty834. [Epub ahead of print]

PMID:
30304483
9.

Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression.

Caulfield JI, Caruso MJ, Bourne RA, Chirichella NR, Klein LC, Craig T, Bonneau RH, August A, Cavigelli SA.

Front Behav Neurosci. 2018 Aug 30;12:188. doi: 10.3389/fnbeh.2018.00188. eCollection 2018.

10.

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity.

Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ.

Elife. 2018 Jul 25;7. pii: e37816. doi: 10.7554/eLife.37816.

11.

Generative Models for Quantification of DNA Modifications.

Äijö T, Bonneau R, Lähdesmäki H.

Methods Mol Biol. 2018;1807:37-50. doi: 10.1007/978-1-4939-8561-6_4.

PMID:
30030802
12.

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.

13.

deepNF: deep network fusion for protein function prediction.

Gligorijevic V, Barot M, Bonneau R.

Bioinformatics. 2018 Nov 15;34(22):3873-3881. doi: 10.1093/bioinformatics/bty440.

14.

Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer.

Tsay JJ, Wu BG, Badri MH, Clemente JC, Shen N, Meyn P, Li Y, Yie TA, Lhakhang T, Olsen E, Murthy V, Michaud G, Sulaiman I, Tsirigos A, Heguy A, Pass H, Weiden MD, Rom WN, Sterman DH, Bonneau R, Blaser MJ, Segal LN.

Am J Respir Crit Care Med. 2018 Nov 1;198(9):1188-1198. doi: 10.1164/rccm.201710-2118OC.

PMID:
29864375
15.

Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks.

Tchourine K, Vogel C, Bonneau R.

Cell Rep. 2018 Apr 10;23(2):376-388. doi: 10.1016/j.celrep.2018.03.048.

16.

Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.

Koehler Leman J, Bonneau R, Ulmschneider MB.

Sci Rep. 2018 Mar 13;8(1):4446. doi: 10.1038/s41598-018-22476-6.

17.

c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont.

Xu M, Pokrovskii M, Ding Y, Yi R, Au C, Harrison OJ, Galan C, Belkaid Y, Bonneau R, Littman DR.

Nature. 2018 Feb 15;554(7692):373-377. doi: 10.1038/nature25500. Epub 2018 Feb 7. Erratum in: Nature. 2019 Feb;566(7744):E7.

18.

Fungi stabilize connectivity in the lung and skin microbial ecosystems.

Tipton L, Müller CL, Kurtz ZD, Huang L, Kleerup E, Morris A, Bonneau R, Ghedin E.

Microbiome. 2018 Jan 15;6(1):12. doi: 10.1186/s40168-017-0393-0.

19.

Detecting Bots on Russian Political Twitter.

Stukal D, Sanovich S, Bonneau R, Tucker JA.

Big Data. 2017 Dec;5(4):310-324. doi: 10.1089/big.2017.0038.

PMID:
29235918
20.

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures.

Koehler Leman J, Bonneau R.

Biochemistry. 2018 Apr 3;57(13):1939-1944. doi: 10.1021/acs.biochem.7b00995. Epub 2017 Dec 11.

PMID:
29185719
21.

Why are there hotspot mutations in the TP53 gene in human cancers?

Baugh EH, Ke H, Levine AJ, Bonneau RA, Chan CS.

Cell Death Differ. 2018 Jan;25(1):154-160. doi: 10.1038/cdd.2017.180. Epub 2017 Nov 3. Review.

22.

Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2.

Modrek AS, Golub D, Khan T, Bready D, Prado J, Bowman C, Deng J, Zhang G, Rocha PP, Raviram R, Lazaris C, Stafford JM, LeRoy G, Kader M, Dhaliwal J, Bayin NS, Frenster JD, Serrano J, Chiriboga L, Baitalmal R, Nanjangud G, Chi AS, Golfinos JG, Wang J, Karajannis MA, Bonneau RA, Reinberg D, Tsirigos A, Zagzag D, Snuderl M, Skok JA, Neubert TA, Placantonakis DG.

Cell Rep. 2017 Oct 31;21(5):1267-1280. doi: 10.1016/j.celrep.2017.10.009.

23.

Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers.

Watkins AM, Craven TW, Renfrew PD, Arora PS, Bonneau R.

Structure. 2017 Nov 7;25(11):1771-1780.e3. doi: 10.1016/j.str.2017.09.005. Epub 2017 Oct 12.

24.

Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.

Drew K, Müller CL, Bonneau R, Marcotte EM.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005625. doi: 10.1371/journal.pcbi.1005625. eCollection 2017 Oct.

25.

Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing.

Äijö T, Müller CL, Bonneau R.

Bioinformatics. 2018 Feb 1;34(3):372-380. doi: 10.1093/bioinformatics/btx549.

26.

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity.

Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, Zheng X, Iizumi T, Mullins BJ, Müller CL, Cadwell K, Bonneau R, Perez-Perez GI, Blaser MJ.

Nat Commun. 2017 Sep 11;8(1):518. doi: 10.1038/s41467-017-00531-6.

27.

Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models.

Leffler AE, Kuryatov A, Zebroski HA, Powell SR, Filipenko P, Hussein AK, Gorson J, Heizmann A, Lyskov S, Tsien RW, Poget SF, Nicke A, Lindstrom J, Rudy B, Bonneau R, Holford M.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):E8100-E8109. doi: 10.1073/pnas.1703952114. Epub 2017 Sep 5.

28.

Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function.

Olsen AJ, Halvorsen LA, Yang CY, Barak Ventura R, Yin L, Renfrew PD, Bonneau R, Montclare JK.

Mol Biosyst. 2017 Sep 26;13(10):2092-2106. doi: 10.1039/c7mb00196g.

PMID:
28817149
29.

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells.

Tang MS, Bowcutt R, Leung JM, Wolff MJ, Gundra UM, Hudesman D, Malter LB, Poles MA, Chen LA, Pei Z, Neto AG, Abidi WM, Ullman T, Mayer L, Bonneau RA, Cho I, Loke P.

Inflamm Bowel Dis. 2017 Sep;23(9):1544-1554. doi: 10.1097/MIB.0000000000001208.

30.

Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ.

Wang J, Lesko M, Badri MH, Kapoor BC, Wu BG, Li Y, Smaldone GC, Bonneau R, Kurtz ZD, Condos R, Segal LN.

ERJ Open Res. 2017 Jul 12;3(3). pii: 00008-2017. doi: 10.1183/23120541.00008-2017. eCollection 2017 Jul.

31.

Efficient Dual siRNA and Drug Delivery Using Engineered Lipoproteoplexes.

Liu CF, Chen R, Frezzo JA, Katyal P, Hill LK, Yin L, Srivastava N, More HT, Renfrew PD, Bonneau R, Montclare JK.

Biomacromolecules. 2017 Sep 11;18(9):2688-2698. doi: 10.1021/acs.biomac.7b00203. Epub 2017 Aug 4.

PMID:
28686014
32.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ.

J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

33.

Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility.

Chen X, Yu B, Carriero N, Silva C, Bonneau R.

Nucleic Acids Res. 2017 May 5;45(8):4315-4329. doi: 10.1093/nar/gkx174.

34.

Peri-adolescent asthma symptoms cause adult anxiety-related behavior and neurobiological processes in mice.

Caulfield JI, Caruso MJ, Michael KC, Bourne RA, Chirichella NR, Klein LC, Craig T, Bonneau RH, August A, Cavigelli SA.

Behav Brain Res. 2017 May 30;326:244-255. doi: 10.1016/j.bbr.2017.02.046. Epub 2017 Mar 8.

35.

Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions.

Watkins AM, Bonneau R, Arora PS.

Methods Mol Biol. 2017;1561:291-307. doi: 10.1007/978-1-4939-6798-8_17.

PMID:
28236245
36.

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP.

Koehler Leman J, Lyskov S, Bonneau R.

BMC Bioinformatics. 2017 Feb 20;18(1):115. doi: 10.1186/s12859-017-1541-z.

37.

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.

38.

Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling.

Urlep Ž, Lorbek G, Perše M, Jeruc J, Juvan P, Matz-Soja M, Gebhardt R, Björkhem I, Hall JA, Bonneau R, Littman DR, Rozman D.

Sci Rep. 2017 Jan 18;7:40775. doi: 10.1038/srep40775.

39.

Biophysically Motivated Regulatory Network Inference: Progress and Prospects.

Äijö T, Bonneau R.

Hum Hered. 2016;81(2):62-77. doi: 10.1159/000446614. Epub 2017 Jan 12. Review.

40.

Fused Regression for Multi-source Gene Regulatory Network Inference.

Lam KY, Westrick ZM, Müller CL, Christiaen L, Bonneau R.

PLoS Comput Biol. 2016 Dec 6;12(12):e1005157. doi: 10.1371/journal.pcbi.1005157. eCollection 2016 Dec.

41.

Accurate de novo design of hyperstable constrained peptides.

Bhardwaj G, Mulligan VK, Bahl CD, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SV, Kaas Q, Eletsky A, Huang PS, Johnsen WA, Greisen PJ, Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, Baker D.

Nature. 2016 Oct 20;538(7625):329-335. doi: 10.1038/nature19791. Epub 2016 Sep 14.

42.

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments.

Wilkins O, Hafemeister C, Plessis A, Holloway-Phillips MM, Pham GM, Nicotra AB, Gregorio GB, Jagadish SV, Septiningsih EM, Bonneau R, Purugganan M.

Plant Cell. 2016 Oct;28(10):2365-2384. Epub 2016 Sep 21.

43.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

44.

PPII Helical Peptidomimetics Templated by Cation-π Interactions.

Craven TW, Bonneau R, Kirshenbaum K.

Chembiochem. 2016 Oct 4;17(19):1824-1828. doi: 10.1002/cbic.201600248. Epub 2016 Aug 19.

PMID:
27539882
45.

Side-Chain Conformational Preferences Govern Protein-Protein Interactions.

Watkins AM, Bonneau R, Arora PS.

J Am Chem Soc. 2016 Aug 24;138(33):10386-9. doi: 10.1021/jacs.6b04892. Epub 2016 Aug 9.

46.

Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.

Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y.

Nucleic Acids Res. 2016 Oct 14;44(18):8714-8725. Epub 2016 Jul 20.

47.

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.

48.

Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation.

Proudhon C, Snetkova V, Raviram R, Lobry C, Badri S, Jiang T, Hao B, Trimarchi T, Kluger Y, Aifantis I, Bonneau R, Skok JA.

Cell Rep. 2016 Jun 7;15(10):2159-2169. doi: 10.1016/j.celrep.2016.04.087. Epub 2016 May 26.

49.

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet.

Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ.

Genome Med. 2016 Apr 27;8(1):48.

50.

Helminth infection promotes colonization resistance via type 2 immunity.

Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K.

Science. 2016 Apr 29;352(6285):608-12. doi: 10.1126/science.aaf3229. Epub 2016 Apr 14.

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