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Richard A. Bonneau, Ph.D. - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
protein structure prediction
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146 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
2024 Kronenberg J, Britton D, Halvorsen L, Chu S, Kulapurathazhe MJ, Chen J, Lakshmi A, Renfrew PD, Bonneau R, Montclare JK. Supercharged Phosphotriesterase for improved Paraoxon activity. Protein Engineering, Design & Selection : Peds. PMID 39292622 DOI: 10.1093/protein/gzae015  0.769
2024 Ahdritz G, Bouatta N, Floristean C, Kadyan S, Xia Q, Gerecke W, O'Donnell TJ, Berenberg D, Fisk I, Zanichelli N, Zhang B, Nowaczynski A, Wang B, Stepniewska-Dziubinska MM, Zhang S, ... ... Bonneau R, et al. OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization. Nature Methods. PMID 38744917 DOI: 10.1038/s41592-024-02272-z  0.787
2024 Kronenberg J, Chu S, Olsen A, Britton D, Halvorsen L, Guo S, Lakshmi A, Chen J, Kulapurathazhe MJ, Baker CA, Wadsworth BC, Van Acker CJ, Lehman JG, Otto TC, Renfrew PD, ... Bonneau R, et al. Computational Design of Phosphotriesterase Improves V-Agent Degradation Efficiency. Chemistryopen. e202300263. PMID 38426687 DOI: 10.1002/open.202300263  0.77
2022 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, et al. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500  0.765
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, ... Bonneau R, 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  0.696
2021 Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Bonneau R, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7  0.781
2021 Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, et al. SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. The Science of the Total Environment. 805: 150121. PMID 34534872 DOI: 10.1016/j.scitotenv.2021.150121  0.447
2021 Lee SC, Tang MS, Lim YAL, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P. Correction: Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota. Plos Neglected Tropical Diseases. 15: e0009325. PMID 33826625 DOI: 10.1371/journal.pntd.0009325  0.725
2020 Badri M, Kurtz ZD, Bonneau R, Müller CL. Shrinkage improves estimation of microbial associations under different normalization methods. Nar Genomics and Bioinformatics. 2: lqaa100. PMID 33575644 DOI: 10.1093/nargab/lqaa100  0.747
2020 Cirrone J, Brooks MD, Bonneau R, Coruzzi GM, Shasha DE. Author Correction: OutPredict: multiple datasets can improve prediction of expression and inference of causality. Scientific Reports. 10: 14141. PMID 32811842 DOI: 10.1038/S41598-020-69883-2  0.539
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  0.678
2020 Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, et al. SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. Medrxiv : the Preprint Server For Health Sciences. PMID 32607521 DOI: 10.1101/2020.06.15.20117747  0.45
2020 Arrieta-Ortiz ML, Hafemeister C, Shuster B, Baliga NS, Bonneau R, Eichenberger P. Inference of Bacterial Small RNA Regulatory Networks and Integration with Transcription Factor-Driven Regulatory Networks. Msystems. 5. PMID 32487739 DOI: 10.1128/mSystems.00057-20  0.774
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Bonneau R, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.758
2020 Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... ... Bonneau R, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507  0.773
2020 Cirrone J, Brooks MD, Bonneau R, Coruzzi GM, Shasha DE. OutPredict: multiple datasets can improve prediction of expression and inference of causality. Scientific Reports. 10: 6804. PMID 32321967 DOI: 10.1038/S41598-020-63347-3  0.587
2020 Gabitto MI, Rasmussen A, Wapinski O, Allaway K, Carriero N, Fishell GJ, Bonneau R. Characterizing chromatin landscape from aggregate and single-cell genomic assays using flexible duration modeling. Nature Communications. 11: 747. PMID 32029740 DOI: 10.1038/S41467-020-14497-5  0.317
2020 Jackson CA, Castro DM, Saldi GA, Bonneau R, Gresham D. Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. Elife. 9. PMID 31985403 DOI: 10.7554/Elife.51254  0.342
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009  0.748
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008  0.767
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007  0.748
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005  0.739
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004  0.748
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003  0.759
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002  0.751
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Bonneau R, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001  0.74
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  0.323
2019 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, et al. Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. Proceedings of the National Academy of Sciences of the United States of America. PMID 31659018 DOI: 10.1073/Pnas.1906636116  0.716
2019 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. NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. Nature Communications. 10: 4843. PMID 31649247 DOI: 10.1038/S41467-019-12811-4  0.615
2019 Kuenze G, Bonneau R, Leman JK, Meiler J. Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints. Structure (London, England : 1993). PMID 31522945 DOI: 10.1016/J.Str.2019.08.012  0.507
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  0.717
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  0.801
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  0.725
2019 Gligorijevic V, Barot M, Bonneau R. deepNF: deep network fusion for protein function prediction. Bioinformatics (Oxford, England). 34: 3873-3881. PMID 29868758 DOI: 10.1093/Bioinformatics/Bty440  0.355
2018 Baugh EH, Ke H, Levine AJ, Bonneau RA, Chan CS. Why are there hotspot mutations in the TP53 gene in human cancers? Cell Death and Differentiation. 25: 154-160. PMID 31745308 DOI: 10.1038/cdd.2017.180  0.71
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  0.78
2018 Jiang T, Renfrew PD, Drew K, Youngs N, Butterfoss GL, Bonneau R, Shasha DN. An adaptive geometric search algorithm for macromolecular scaffold selection. Protein Engineering, Design & Selection : Peds. PMID 30407584 DOI: 10.1093/Protein/Gzy028  0.788
2018 Koo DCE, Bonneau R. Towards region-specific propagation of protein functions. Bioinformatics (Oxford, England). PMID 30304483 DOI: 10.1093/Bioinformatics/Bty834  0.312
2018 Äijö T, Bonneau R, Lähdesmäki H. Generative Models for Quantification of DNA Modifications. Methods of Molecular Biology. 1807: 37-50. PMID 30030802 DOI: 10.1007/978-1-4939-8561-6_4  0.301
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  0.665
2018 Tchourine K, Vogel C, Bonneau R. Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks Cell Reports. 23: 376-388. PMID 29641998 DOI: 10.1016/J.Celrep.2018.03.048  0.37
2018 Tipton L, Müller CL, Kurtz ZD, Huang L, Kleerup E, Morris A, Bonneau R, Ghedin E. Fungi stabilize connectivity in the lung and skin microbial ecosystems. Microbiome. 6: 12. PMID 29335027 DOI: 10.1186/S40168-017-0393-0  0.766
2017 Baugh EH, Ke H, Levine AJ, Bonneau RA, Chan CS. Why are there hotspot mutations in the TP53 gene in human cancers? Cell Death and Differentiation. PMID 29099487 DOI: 10.1038/Cdd.2017.180  0.728
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  0.767
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  0.683
2017 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. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. Nature Communications. 8: 518. PMID 28894149 DOI: 10.1038/S41467-017-00531-6  0.757
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  0.773
2017 Wang J, Lesko M, Badri MH, Kapoor BC, Wu BG, Li Y, Smaldone GC, Bonneau R, Kurtz ZD, Condos R, Segal LN. Lung microbiome and host immune tone in subjects with idiopathic pulmonary fibrosis treated with inhaled interferon-γ. Erj Open Research. 3. PMID 28717640 DOI: 10.1183/23120541.00008-2017  0.743
2017 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, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.78
2017 Chen X, Yu B, Carriero N, Silva C, Bonneau R. Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility. Nucleic Acids Research. PMID 28334916 DOI: 10.1093/Nar/Gkx174  0.378
2017 Watkins AM, Bonneau R, Arora PS. Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions. Methods in Molecular Biology (Clifton, N.J.). 1561: 291-307. PMID 28236245 DOI: 10.1007/978-1-4939-6798-8_17  0.328
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  0.698
2017 Äijö T, Bonneau R. Biophysically Motivated Regulatory Network Inference: Progress and Prospects. Human Heredity. 81: 62-77. PMID 28076866 DOI: 10.1159/000446614  0.382
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  0.655
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  0.789
2016 Wilkins O, Hafemeister C, Plessis A, Holloway-Phillips MM, Pham GM, Nicotra AB, Gregorio GB, Jagadish K, Septiningsih EM, Bonneau R, Purugganan MD. EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments. The Plant Cell. PMID 27655842 DOI: 10.1105/Tpc.16.00158  0.793
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  0.769
2016 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, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.789
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  0.309
2016 Watkins AM, Bonneau R, Arora PS. Side Chain Conformational Preferences Govern Protein- Protein Interactions. Journal of the American Chemical Society. PMID 27483190 DOI: 10.1021/Jacs.6B04892  0.3
2016 Jiang T, Raviram R, Snetkova V, Rocha PP, Proudhon C, Badri S, Bonneau R, Skok JA, Kluger Y. Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions. Nucleic Acids Research. PMID 27439714 DOI: 10.1093/Nar/Gkw568  0.784
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  0.767
2016 Proudhon C, Snetkova V, Raviram R, Lobry C, Badri S, Jiang T, Hao B, Trimarchi T, Kluger Y, Aifantis I, Bonneau R, Skok JA. Active and Inactive Enhancers Cooperate to Exert Localized and Long-Range Control of Gene Regulation. Cell Reports. PMID 27239026 DOI: 10.1016/J.Celrep.2016.04.087  0.77
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 DOI: 10.1186/S13073-016-0297-9  0.735
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  0.721
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  0.752
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  0.777
2016 Baugh EH, Simmons-Edler R, Müller CL, Alford RF, Volfovsky N, Lash AE, Bonneau R. Robust classification of protein variation using structural modelling and large-scale data integration. Nucleic Acids Research. PMID 26926108 DOI: 10.1093/Nar/Gkw120  0.754
2016 Thomas-Claudepierre AS, Robert I, Rocha PP, Raviram R, Schiavo E, Heyer V, Bonneau R, Luo VM, Reddy JK, Borggrefe T, Skok JA, Reina-San-Martin B. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. The Journal of Experimental Medicine. 213: 303-12. PMID 26903242 DOI: 10.1084/Jem.20141967  0.77
2016 Craven TW, Cho MK, Traaseth NJ, Bonneau R, Kirshenbaum K. A Miniature Protein Stabilized by a Cation-π Interaction Network. Journal of the American Chemical Society. PMID 26812069 DOI: 10.1021/Jacs.5B10285  0.326
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  0.669
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  0.767
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, ... ... Bonneau R, et al. DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions. Nature. PMID 26675721 DOI: 10.1038/Nature16193  0.69
2015 Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Müller C, Septiningsih EM, Bonneau R, Purugganan M. Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions. Elife. 4. PMID 26609814 DOI: 10.7554/Elife.08411  0.781
2015 Arrieta-Ortiz ML, Hafemeister C, Bate AR, Chu T, Greenfield A, Shuster B, Barry SN, Gallitto M, Liu B, Kacmarczyk T, Santoriello F, Chen J, Rodrigues CD, Sato T, Rudner DZ, ... ... Bonneau R, et al. An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network. Molecular Systems Biology. 11: 839. PMID 26577401 DOI: 10.15252/Msb.20156236  0.795
2015 Shirke AN, Basore D, Butterfoss GL, Bonneau R, Bystroff C, Gross RA. Towards rational thermostabilization of Aspergillus oryzae Cutinase: Insights into catalytic and structural stability. Proteins. PMID 26522152 DOI: 10.1002/Prot.24955  0.609
2015 Mullenders J, Aranda-Orgilles B, Lhoumaud P, Keller M, Pae J, Wang K, Kayembe C, Rocha PP, Raviram R, Gong Y, Premsrirut PK, Tsirigos A, Bonneau R, Skok JA, Cimmino L, et al. Cohesin loss alters adult hematopoietic stem cell homeostasis, leading to myeloproliferative neoplasms. The Journal of Experimental Medicine. PMID 26438359 DOI: 10.1084/Jem.20151323  0.774
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  0.67
2015 Rocha PP, Raviram R, Bonneau R, Skok JA. Breaking TADs: insights into hierarchical genome organization. Epigenomics. 7: 523-6. PMID 26111025 DOI: 10.2217/Epi.15.25  0.778
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  0.801
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  0.748
2015 Plessis A, Hafemeister C, Wilkins O, Gonzaga ZJ, Meyer RS, Pires I, Müller C, Septiningsih EM, Bonneau R, Purugganan M. Author response: Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions Elife. DOI: 10.7554/Elife.08411.021  0.522
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  0.803
2014 Bate AR, Bonneau R, Eichenberger P. Bacillus subtilis Systems Biology: Applications of -Omics Techniques to the Study of Endospore Formation. Microbiology Spectrum. 2. PMID 26105826 DOI: 10.1128/Microbiolspec.Tbs-0019-2013  0.333
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  0.781
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  0.778
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  0.666
2014 Guedan S, Chen X, Madar A, Carpenito C, McGettigan SE, Frigault MJ, Lee J, Posey AD, Scholler J, Scholler N, Bonneau R, June CH. ICOS-based chimeric antigen receptors program bipolar TH17/TH1 cells. Blood. 124: 1070-80. PMID 24986688 DOI: 10.1182/Blood-2013-10-535245  0.748
2014 Lao BB, Drew K, Guarracino DA, Brewer TF, Heindel DW, Bonneau R, Arora PS. Rational design of topographical helix mimics as potent inhibitors of protein-protein interactions. Journal of the American Chemical Society. 136: 7877-88. PMID 24972345 DOI: 10.1021/Ja502310R  0.689
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  0.799
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  0.677
2014 Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P. Helminth colonization is associated with increased diversity of the gut microbiota. Plos Neglected Tropical Diseases. 8: e2880. PMID 24851867 DOI: 10.1371/Journal.Pntd.0002880  0.763
2014 Renfrew PD, Craven TW, Butterfoss GL, Kirshenbaum K, Bonneau R. A rotamer library to enable modeling and design of peptoid foldamers. Journal of the American Chemical Society. 136: 8772-82. PMID 24823488 DOI: 10.1021/Ja503776Z  0.33
2014 Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, Xi X, Basilico C, Brown S, Bonneau R, Kluger Y, Dailey L. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nature Methods. 11: 559-65. PMID 24658142 DOI: 10.1038/Nmeth.2885  0.381
2013 Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins. 81: 2201-9. PMID 24123494 DOI: 10.1002/Prot.24425  0.799
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  0.793
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  0.788
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  0.685
2013 Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, et al. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific Reports. 3: 1449. PMID 23618955 DOI: 10.1038/Srep01449  0.778
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  0.802
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  0.787
2013 Imberg-Kazdan K, Ha S, Greenfield A, Poultney CS, Bonneau R, Logan SK, Garabedian MJ. A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells. Genome Research. 23: 581-91. PMID 23403032 DOI: 10.1101/Gr.144774.112  0.764
2012 Ciofani M, Madar A, Galan C, Sellars M, Mace K, Pauli F, Agarwal A, Huang W, Parkurst CN, Muratet M, Newberry KM, Meadows S, Greenfield A, Yang Y, Jain P, ... ... Bonneau R, et al. A validated regulatory network for Th17 cell specification. Cell. 151: 289-303. PMID 23021777 DOI: 10.1016/J.Cell.2012.09.016  0.794
2012 Levine PM, Lee E, Greenfield A, Bonneau R, Logan SK, Garabedian MJ, Kirshenbaum K. Androgen receptor antagonism by divalent ethisterone conjugates in castrate-resistant prostate cancer cells. Acs Chemical Biology. 7: 1693-701. PMID 22871957 DOI: 10.1021/Cb300332W  0.754
2012 Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular Cell. 46: 674-90. PMID 22681889 DOI: 10.1016/J.Molcel.2012.05.021  0.783
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  0.793
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  0.541
2012 Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD. The plant proteome folding project: structure and positive selection in plant protein families. Genome Biology and Evolution. 4: 360-71. PMID 22345424 DOI: 10.1093/Gbe/Evs015  0.751
2012 Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, Lichtervelde LD, Mul JD, Peut DVD, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, Smet ASD, ... ... Bonneau R, et al. Erratum: A protein domain-based interactome network for C. elegans early embryogenesis (Cell (2008) 134 (534-545)) Cell. 151. DOI: 10.1016/J.Cell.2012.11.042  0.681
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  0.777
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  0.774
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  0.373
2011 Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Research. 21: 1981-94. PMID 21824995 DOI: 10.1101/Gr.121475.111  0.763
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  0.79
2010 Waltman P, Kacmarczyk T, Bate AR, Kearns DB, Reiss DJ, Eichenberger P, Bonneau R. Multi-species integrative biclustering. Genome Biology. 11: R96. PMID 20920250 DOI: 10.1186/Gb-2010-11-9-R96  0.761
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  0.791
2009 Madar A, Greenfield A, Ostrer H, Vanden-Eijnden E, Bonneau R. The Inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 5448-51. PMID 19964678 DOI: 10.1109/IEMBS.2009.5334018  0.794
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  0.533
2009 Wang KH, Isidro AL, Domingues L, Eskandarian HA, McKenney PT, Drew K, Grabowski P, Chua MH, Barry SN, Guan M, Bonneau R, Henriques AO, Eichenberger P. The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis. Molecular Microbiology. 74: 634-49. PMID 19775244 DOI: 10.1111/J.1365-2958.2009.06886.X  0.665
2009 Konieczka JH, Drew K, Pine A, Belasco K, Davey S, Yatskievych TA, Bonneau R, Antin PB. BioNetBuilder2.0: bringing systems biology to chicken and other model organisms. Bmc Genomics. 10: S6. PMID 19607657 DOI: 10.1186/1471-2164-10-S2-S6  0.703
2009 Madar A, Bonneau R. Learning global models of transcriptional regulatory networks from data. Methods in Molecular Biology (Clifton, N.J.). 541: 181. PMID 19381524 DOI: 10.1007/978-1-59745-243-4_9  0.777
2008 Bonneau R. Learning biological networks: from modules to dynamics. Nature Chemical Biology. 4: 658-664. PMID 18936750 DOI: 10.1038/Nchembio.122  0.345
2008 Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, ... ... Bonneau R, et al. A protein domain-based interactome network for C. elegans early embryogenesis. Cell. 134: 534-45. PMID 18692475 DOI: 10.1016/J.Cell.2008.07.009  0.703
2007 Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, et al. A predictive model for transcriptional control of physiology in a free living cell. Cell. 131: 1354-65. PMID 18160043 DOI: 10.1016/J.Cell.2007.10.053  0.804
2007 Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology Plos Biology. 5. PMID 17373854 DOI: 10.1371/Journal.Pbio.0050076  0.738
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  0.343
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  0.69
2006 Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 6: 6146-57. PMID 17133367 DOI: 10.1002/Pmic.200600159  0.319
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  0.318
2006 Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology. 7: R36. PMID 16686963 DOI: 10.1186/Gb-2006-7-5-R36  0.687
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  0.313
2004 Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Research. 14: 2221-34. PMID 15520287 DOI: 10.1101/Gr.2700304  0.326
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  0.328
2004 Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Research. 14: 1025-35. PMID 15140832 DOI: 10.1101/Gr.1993504  0.327
2004 Facciotti MT, Bonneau R, Hood L, Baliga NS. Systems biology experimental design - Considerations for building predictive gene regulatory network models for prokaryotic systems Current Genomics. 5: 527-544. DOI: 10.2174/1389202043348850  0.312
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  0.784
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  0.786
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  0.719
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  0.79
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  0.569
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  0.41
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  0.79
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  0.59
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  0.394
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  0.406
1999 Simons KT, Bonneau R, Ruczinski I, Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA Proteins: Structure, Function, and Genetics. 37: 171-176. DOI: 10.1002/(Sici)1097-0134(1999)37:3+<171::Aid-Prot21>3.0.Co;2-Z  0.31
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