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Items: 1 to 50 of 254

1.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol. 2019 Nov 19;20(1):244. doi: 10.1186/s13059-019-1835-8.

2.

IL-17 Inhibition in Spondyloarthritis Associates with Subclinical Gut Microbiome Perturbations and a Distinctive IL-25-Driven Intestinal Inflammation.

Manasson J, Wallach DS, Guggino G, Stapylton M, Badri MH, Solomon G, Reddy SM, Coras R, Aksenov AA, Jones DR, Girija PV, Neimann AL, Heguy A, Segal LN, Dorrestein PC, Bonneau R, Guma M, Ciccia F, Ubeda C, Clemente JC, Scher JU.

Arthritis Rheumatol. 2019 Nov 14. doi: 10.1002/art.41169. [Epub ahead of print]

PMID:
31729183
3.

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.

Fehlner-Peach H, Magnabosco C, Raghavan V, Scher JU, Tett A, Cox LM, Gottsegen C, Watters A, Wiltshire-Gordon JD, Segata N, Bonneau R, Littman DR.

Cell Host Microbe. 2019 Nov 13;26(5):680-690.e5. doi: 10.1016/j.chom.2019.10.013.

PMID:
31726030
4.

Learning representations of microbe-metabolite interactions.

Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R.

Nat Methods. 2019 Dec;16(12):1306-1314. doi: 10.1038/s41592-019-0616-3. Epub 2019 Nov 4.

PMID:
31686038
5.

Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa.

Brown TS, Challagundla L, Baugh EH, Omar SV, Mustaev A, Auld SC, Shah NS, Kreiswirth BN, Brust JCM, Nelson KN, Narechania A, Kurepina N, Mlisana K, Bonneau R, Eldholm V, Ismail N, Kolokotronis SO, Robinson DA, Gandhi NR, Mathema B.

Proc Natl Acad Sci U S A. 2019 Nov 12;116(46):23284-23291. doi: 10.1073/pnas.1906636116. Epub 2019 Oct 28.

6.

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains.

Lhoumaud P, Badri S, Rodriguez-Hernaez J, Sakellaropoulos T, Sethia G, Kloetgen A, Cornwell M, Bhattacharyya S, Ay F, Bonneau R, Tsirigos A, Skok JA.

Nat Commun. 2019 Oct 24;10(1):4843. doi: 10.1038/s41467-019-12811-4.

7.

Divergent immune responses in behaviorally-inhibited vs. non-inhibited male rats.

Michael KC, Bonneau RH, Bourne RA, Godbolt L, Caruso MJ, Hohmann C, Cavigelli SA.

Physiol Behav. 2020 Jan 1;213:112693. doi: 10.1016/j.physbeh.2019.112693. Epub 2019 Oct 17.

PMID:
31629765
8.

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.

Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, De Filippis F, Magnabosco C, Bonneau R, Lusingu J, Amuasi J, Reinhard K, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N.

Cell Host Microbe. 2019 Nov 13;26(5):666-679.e7. doi: 10.1016/j.chom.2019.08.018. Epub 2019 Oct 10.

9.

Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.

Kuenze G, Bonneau R, Leman JK, Meiler J.

Structure. 2019 Nov 5;27(11):1721-1734.e5. doi: 10.1016/j.str.2019.08.012. Epub 2019 Sep 12.

PMID:
31522945
10.

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL.

Nat Methods. 2019 Oct;16(10):987-990. doi: 10.1038/s41592-019-0548-y. Epub 2019 Sep 9.

PMID:
31501547
11.

Thermoresponsive Protein-Engineered Coiled-Coil Hydrogel for Sustained Small Molecule Release.

Hill LK, Meleties M, Katyal P, Xie X, Delgado-Fukushima E, Jihad T, Liu CF, O'Neill S, Tu RS, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK.

Biomacromolecules. 2019 Sep 9;20(9):3340-3351. doi: 10.1021/acs.biomac.9b00107. Epub 2019 Aug 19.

PMID:
31356057
12.

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells.

Pokrovskii M, Hall JA, Ochayon DE, Yi R, Chaimowitz NS, Seelamneni H, Carriero N, Watters A, Waggoner SN, Littman DR, Bonneau R, Miraldi ER.

Immunity. 2019 Jul 16;51(1):185-197.e6. doi: 10.1016/j.immuni.2019.06.001. Epub 2019 Jul 2.

PMID:
31278058
13.

Computational-guided determination of the functional role of 447-52D long CDRH3.

Kamau E, Bonneau R, Kong XP.

Protein Eng Des Sel. 2018 Dec 1;31(12):479-487. doi: 10.1093/protein/gzz007.

14.

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.

Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivová Ž, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H.

Science. 2019 Apr 5;364(6435):89-93. doi: 10.1126/science.aav9776.

PMID:
30948552
15.

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
16.

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.

17.

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.

18.

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.

19.

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
20.

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.

21.

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.

22.

Towards region-specific propagation of protein functions.

Koo DCE, Bonneau R.

Bioinformatics. 2019 May 15;35(10):1737-1744. doi: 10.1093/bioinformatics/bty834.

23.

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.

24.

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.

25.

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
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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
35.

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
36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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
44.

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.

45.

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.

46.

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
47.

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.

48.

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.

49.

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.

50.

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

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