Richard A. Bonneau, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
protein structure prediction

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.44
2019 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, ... ... Bonneau R, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/s13059-019-1835-8  0.4
2019 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, et al. High-definition spatial transcriptomics for in situ tissue profiling. Nature Methods. PMID 31501547 DOI: 10.1038/s41592-019-0548-y  0.52
2019 Hill LK, Meleties M, Katyal P, Xie X, Delgado-Fukushima EG, Jihad T, Liu CF, O'Neill SC, Tu RS, Renfrew PD, Bonneau R, Wadghiri YZ, Montclare JK. Thermoresponsive Protein-Engineered Coiled-coil Hydrogel for Sustained Small Molecule Release. Biomacromolecules. PMID 31356057 DOI: 10.1021/acs.biomac.9b00107  0.44
2019 Xu M, Pokrovskii M, Ding Y, Yi R, Au C, Harrison OJ, Galan C, Belkaid Y, Bonneau R, Littman DR. Author Correction: c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont. Nature. PMID 30723268 DOI: 10.1038/s41586-019-0922-z  0.32
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  0.64
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  0.44
2018 Koo DCE, Bonneau R. Towards region-specific propagation of protein functions. Bioinformatics (Oxford, England). PMID 30304483 DOI: 10.1093/bioinformatics/bty834  0.4
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, ... ... Bonneau R, 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  0.44
2017 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, ... ... Bonneau RA, et al. Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2. Cell Reports. 21: 1267-1280. PMID 29091765 DOI: 10.1016/j.celrep.2017.10.009  0.36
2017 Drew K, Müller CL, Bonneau R, Marcotte EM. Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. Plos Computational Biology. 13: e1005625. PMID 29023445 DOI: 10.1371/journal.pcbi.1005625  0.72
2017 Äijö T, Müller CL, Bonneau R. Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing. Bioinformatics (Oxford, England). PMID 28968799 DOI: 10.1093/bioinformatics/btx549  0.52
2017 Olsen AJ, Halvorsen LA, Yang CY, Barak Ventura R, Yin L, Renfrew PD, Bonneau R, Montclare JK. Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function. Molecular Biosystems. PMID 28817149 DOI: 10.1039/c7mb00196g  0.44
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  0.64
2016 Lam KY, Westrick ZM, Müller CL, Christiaen L, Bonneau R. Fused Regression for Multi-source Gene Regulatory Network Inference. Plos Computational Biology. 12: e1005157. PMID 27923054 DOI: 10.1371/journal.pcbi.1005157  0.52
2016 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, ... ... Bonneau R, et al. Accurate de novo design of hyperstable constrained peptides. Nature. PMID 27626386 DOI: 10.1038/nature19791  0.8
2016 Craven TW, Bonneau R, Kirshenbaum K. PPII Helical Peptidomimetics Templated by Cation-π Interactions. Chembiochem : a European Journal of Chemical Biology. PMID 27539882 DOI: 10.1002/cbic.201600248  0.6
2016 Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Medicine. 8: 48. PMID 27124954  0.52
2016 Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ. Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. Genome Medicine. 8: 48. PMID 27121712 DOI: 10.1186/s13073-016-0297-9  0.8
2016 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. Helminth infection promotes colonization resistance via type 2 immunity. Science (New York, N.Y.). PMID 27080105 DOI: 10.1126/science.aaf3229  0.8
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  0.8
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, ... ... Bonneau R, et al. Corrigendum: DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. PMID 26789242 DOI: 10.1038/nature16968  0.8
2016 Youngs N, Shasha D, Bonneau R. Positive-Unlabeled Learning in the Face of Labeling Bias Proceedings - 15th Ieee International Conference On Data Mining Workshop, Icdmw 2015. 639-645. DOI: 10.1109/ICDMW.2015.207  0.8
2016 MacDuffee Metzger M, Bonneau R, Nagler J, Tucker JA. Tweeting identity? Ukrainian, Russian, and #Euromaidan Journal of Comparative Economics. 44: 16-40. DOI: 10.1016/j.jce.2015.12.004  0.8
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  0.8
2015 Hafemeister C, Romero R, Bilal E, Meyer P, Norel R, Rhrissorrakrai K, Bonneau R, Tarca AL. Inter-species pathway perturbation prediction via data-driven detection of functional homology. Bioinformatics (Oxford, England). 31: 501-8. PMID 25150249 DOI: 10.1093/bioinformatics/btu570  0.64
2015 Vaccari C, Valeriani A, Barberá P, Bonneau R, Jost JT, Nagler J, Tucker JA. Political expression and action on social media: Exploring the relationship between lower- and higher-threshold political activities among twitter users in Italy Journal of Computer-Mediated Communication. 20: 221-239. DOI: 10.1111/jcc4.12108  0.8
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  0.64
2014 Raviram R, Rocha PP, Bonneau R, Skok JA. Interpreting 4C-Seq data: how far can we go? Epigenomics. 6: 455-7. PMID 25431936 DOI: 10.2217/epi.14.47  0.8
2014 Tchourine K, Poultney CS, Wang L, Silva GM, Manohar S, Mueller CL, Bonneau R, Vogel C. One third of dynamic protein expression profiles can be predicted by a simple rate equation. Molecular Biosystems. 10: 2850-62. PMID 25111754 DOI: 10.1039/c4mb00358f  0.8
2014 Yang CY, Renfrew PD, Olsen AJ, Zhang M, Yuvienco C, Bonneau R, Montclare JK. Improved stability and half-life of fluorinated phosphotriesterase using Rosetta. Chembiochem : a European Journal of Chemical Biology. 15: 1761-4. PMID 25066940 DOI: 10.1002/cbic.201402062  0.44
2014 Hume J, Sun J, Jacquet R, Renfrew PD, Martin JA, Bonneau R, Gilchrist ML, Montclare JK. Engineered coiled-coil protein microfibers. Biomacromolecules. 15: 3503-10. PMID 24941228 DOI: 10.1021/bm5004948  0.44
2014 Youngs N, Penfold-Brown D, Bonneau R, Shasha D. Negative example selection for protein function prediction: the NoGO database. Plos Computational Biology. 10: e1003644. PMID 24922051 DOI: 10.1371/journal.pcbi.1003644  0.8
2014 Butterfoss GL, Drew K, Renfrew PD, Kirshenbaum K, Bonneau R. Conformational preferences of peptide-peptoid hybrid oligomers. Biopolymers. 102: 369-78. PMID 24919990 DOI: 10.1002/bip.22516  0.8
2014 Levine PM, Craven TW, Bonneau R, Kirshenbaum K. Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine. Chemical Communications (Cambridge, England). 50: 6909-12. PMID 24840103 DOI: 10.1039/c4cc01928h  0.8
2014 Levine PM, Craven TW, Bonneau R, Kirshenbaum K. Semisynthesis of peptoid-protein hybrids by chemical ligation at serine. Organic Letters. 16: 512-5. PMID 24393000 DOI: 10.1021/ol4033978  0.8
2013 Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, ... ... Bonneau R, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/journal.pone.0067051  0.8
2013 Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/journal.pone.0063906  0.8
2013 Levine PM, Craven TW, Bonneau R, Kirshenbaum K. Chemoselective fragment condensation between peptide and peptidomimetic oligomers. Organic & Biomolecular Chemistry. 11: 4142-6. PMID 23715215 DOI: 10.1039/c3ob40606g  0.8
2013 Greenfield A, Hafemeister C, Bonneau R. Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinformatics (Oxford, England). 29: 1060-7. PMID 23525069 DOI: 10.1093/bioinformatics/btt099  0.72
2013 Youngs N, Penfold-Brown D, Drew K, Shasha D, Bonneau R. Parametric Bayesian priors and better choice of negative examples improve protein function prediction. Bioinformatics (Oxford, England). 29: 1190-8. PMID 23511543 DOI: 10.1093/bioinformatics/btt110  0.8
2013 Vaccari C, Valeriani A, Barberá P, Bonneau R, Jost JT, Nagler J, Tucker J. Social media and political communication: A survey of twitter users during the 2013 Italian general election Rivista Italiana Di Scienza Politica. 43: 381-410. DOI: 10.1426/75245  0.8
2012 Poultney CS, Greenfield A, Bonneau R. Integrated inference and analysis of regulatory networks from multi-level measurements. Methods in Cell Biology. 110: 19-56. PMID 22482944 DOI: 10.1016/B978-0-12-388403-9.00002-3  0.8
2012 Renfrew PD, Choi EJ, Bonneau R, Kuhlman B. Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. Plos One. 7: e32637. PMID 22431978 DOI: 10.1371/journal.pone.0032637  0.8
2012 Kirigin FF, Lindstedt K, Sellars M, Ciofani M, Low SL, Jones L, Bell F, Pauli F, Bonneau R, Myers RM, Littman DR, Chong MM. Dynamic microRNA gene transcription and processing during T cell development. Journal of Immunology (Baltimore, Md. : 1950). 188: 3257-67. PMID 22379031 DOI: 10.4049/jimmunol.1103175  0.8
2011 Jordan PA, Paul B, Butterfoss GL, Renfrew PD, Bonneau R, Kirshenbaum K. Oligo(N-alkoxy glycines): trans substantiating peptoid conformations. Biopolymers. 96: 617-26. PMID 22180909 DOI: 10.1002/bip.21675  0.8
2011 Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R. Comparative microbial modules resource: generation and visualization of multi-species biclusters. Plos Computational Biology. 7: e1002228. PMID 22144874 DOI: 10.1371/journal.pcbi.1002228  0.44
2011 Poultney CS, Butterfoss GL, Gutwein MR, Drew K, Gresham D, Gunsalus KC, Shasha DE, Bonneau R. Rational design of temperature-sensitive alleles using computational structure prediction. Plos One. 6: e23947. PMID 21912654 DOI: 10.1371/journal.pone.0023947  0.8
2011 Renfrew PD, Campbell G, Strauss CE, Bonneau R. The 2010 Rosetta developers meeting: macromolecular prediction and design meets reproducible publishing. Plos One. 6: e22431. PMID 21909349 DOI: 10.1371/journal.pone.0022431  0.44
2010 Greenfield A, Madar A, Ostrer H, Bonneau R. DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models. Plos One. 5: e13397. PMID 21049040 DOI: 10.1371/journal.pone.0013397  0.8
2010 Madar A, Greenfield A, Vanden-Eijnden E, Bonneau R. DREAM3: Network inference using dynamic context likelihood of relatedness and the inferelator Plos One. 5. PMID 20339551 DOI: 10.1371/journal.pone.0009803  0.8
2009 Butterfoss GL, Renfrew PD, Kuhlman B, Kirshenbaum K, Bonneau R. A preliminary survey of the peptoid folding landscape. Journal of the American Chemical Society. 131: 16798-807. PMID 19919145 DOI: 10.1021/ja905267k  0.8
2009 Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS. Diurnally entrained anticipatory behavior in archaea. Plos One. 4: e5485. PMID 19424498 DOI: 10.1371/journal.pone.0005485  0.32
2007 Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS. General transcription factor specified global gene regulation in archaea. Proceedings of the National Academy of Sciences of the United States of America. 104: 4630-5. PMID 17360575 DOI: 10.1073/pnas.0611663104  0.8
2007 Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R. BioNetBuilder: automatic integration of biological networks. Bioinformatics (Oxford, England). 23: 392-3. PMID 17138585 DOI: 10.1093/bioinformatics/btl604  0.72
2006 Reiss DJ, Baliga NS, Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. Bmc Bioinformatics. 7: 280. PMID 16749936 DOI: 10.1186/1471-2105-7-280  0.56
2006 Shannon PT, Reiss DJ, Bonneau R, Baliga NS. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. Bmc Bioinformatics. 7: 176. PMID 16569235 DOI: 10.1186/1471-2105-7-176  0.56
2004 Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biology. 5: R52. PMID 15287974 DOI: 10.1186/gb-2004-5-8-r52  0.32
2003 Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53: 524-33. PMID 14579342 DOI: 10.1002/prot.10529  0.8
2003 Tsai J, Bonneau R, Morozov AV, Kuhlman B, Rohl CA, Baker D. An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53: 76-87. PMID 12945051 DOI: 10.1002/prot.10454  0.8
2003 Chivian D, Robertson T, Bonneau R, Baker D. Ab initio methods Methods of Biochemical Analysis. 44: 547-557. PMID 12647404 DOI: 10.1002/0471721204.ch27  0.8
2002 Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. Journal of Molecular Biology. 322: 65-78. PMID 12215415 DOI: 10.1016/S0022-2836(02)00698-8  0.8
2002 Bonneau R, Ruczinski I, Tsai J, Baker D. Contact order and ab initio protein structure prediction. Protein Science : a Publication of the Protein Society. 11: 1937-44. PMID 12142448 DOI: 10.1110/ps.3790102  0.8
2002 Ruczinski I, Kooperberg C, Bonneau R, Baker D. Distributions of beta sheets in proteins with application to structure prediction Proteins: Structure, Function and Genetics. 48: 85-97. PMID 12012340 DOI: 10.1002/prot.10123  0.8
2001 Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss CE, Baker D. Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. 119-26. PMID 11835488 DOI: 10.1002/prot.1170  0.8
2001 Bonneau R, Tsai J, Ruczinski I, Baker D. Functional inferences from blind ab initio protein structure predictions. Journal of Structural Biology. 134: 186-90. PMID 11551178 DOI: 10.1006/jsbi.2000.4370  0.8
2001 Bonneau R, Baker D. Ab initio protein structure prediction: progress and prospects. Annual Review of Biophysics and Biomolecular Structure. 30: 173-89. PMID 11340057 DOI: 10.1146/annurev.biophys.30.1.173  0.36
2001 Bonneau R, Strauss CE, Baker D. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins. 43: 1-11. PMID 11170209 DOI: 10.1002/1097-0134(20010401)43:1<1::AID-PROT1012>3.0.CO;2-A  0.8
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