Richard A. Bonneau, Ph.D. - Publications

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

176 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
2021 Zhang XS, Yin YS, Wang J, Battaglia T, Krautkramer K, Li WV, Li J, Brown M, Zhang M, Badri MH, Armstrong AJS, Strauch CM, Wang Z, Nemet I, Altomare N, ... ... Bonneau RA, et al. Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice. Cell Host & Microbe. PMID 34289377 DOI: 10.1016/j.chom.2021.06.014  0.44
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  0.52
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  0.72
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  0.84
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  0.84
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  0.52
2020 Zhang L, Forst CV, Gordon A, Gussin G, Geber AB, Fernandez PJ, Ding T, Lashua L, Wang M, Balmaseda A, Bonneau R, Zhang B, Ghedin E. Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection. Microbiome. 8: 39. PMID 32178738 DOI: 10.1186/S40168-020-00803-2  0.48
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  0.52
2020 Johnson JS, De Veaux N, Rives AW, Lahaye X, Lucas SY, Perot BP, Luka M, Garcia-Paredes V, Amon LM, Watters A, Abdessalem G, Aderem A, Manel N, Littman DR, Bonneau R, et al. A Comprehensive Map of the Monocyte-Derived Dendritic Cell Transcriptional Network Engaged upon Innate Sensing of HIV. Cell Reports. 30: 914-931.e9. PMID 31968263 DOI: 10.1016/J.Celrep.2019.12.054  0.32
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2019 Zhang H, Christensen CL, Dries R, Oser MG, Deng J, Diskin B, Li F, Pan Y, Zhang X, Yin Y, Papadopoulos E, Pyon V, Thakurdin C, Kwiatkowski N, Jani K, ... ... Bonneau R, et al. CDK7 Inhibition Potentiates Genome Instability Triggering Anti-tumor Immunity in Small Cell Lung Cancer. Cancer Cell. PMID 31883968 DOI: 10.1016/J.Ccell.2019.11.003  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 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. Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates. Cell Host & Microbe. 26: 680-690.e5. PMID 31726030 DOI: 10.1016/J.Chom.2019.10.013  0.32
2019 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, et al. Learning representations of microbe-metabolite interactions. Nature Methods. PMID 31686038 DOI: 10.1038/S41592-019-0616-3  0.44
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  0.44
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  0.76
2019 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, et al. The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host & Microbe. PMID 31607556 DOI: 10.1016/J.Chom.2019.08.018  0.32
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  0.68
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  0.84
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  0.72
2019 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. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. Science (New York, N.Y.). 364: 89-93. PMID 30948552 DOI: 10.1126/Science.Aav9776  0.52
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  0.72
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  0.72
2019 Jackson CA, Castro DM, Saldi G, Bonneau R, Gresham D. Author response: Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments Elife. DOI: 10.7554/Elife.51254.Sa2  0.52
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  0.44
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  0.76
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  0.84
2018 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. Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer. Nature Communications. 9: 4396. PMID 30352998 DOI: 10.1038/S41467-018-06845-3  0.68
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 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, ... ... Bonneau R, et al. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. Elife. 7. PMID 30039798 DOI: 10.7554/Elife.37816  0.44
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  0.52
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  0.72
2018 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, ... ... Bonneau R, et al. Airway Microbiota Is Associated with Up-Regulation of the PI3K Pathway in Lung Cancer. American Journal of Respiratory and Critical Care Medicine. PMID 29864375 DOI: 10.1164/Rccm.201710-2118Oc  0.44
2018 Leman JK, Bonneau R, Ulmschneider MB. Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins. Scientific Reports. 8: 4446. PMID 29535329 DOI: 10.1038/S41598-018-22476-6  0.68
2018 Xu M, Pokrovskii M, Ding Y, Yi R, Au C, Harrison OJ, Galan C, Belkaid Y, Bonneau R, Littman DR. c-MAF-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont. Nature. PMID 29414937 DOI: 10.1038/Nature25500  0.32
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  0.52
2018 Zhang X, 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, ... ... Bonneau R, et al. Author response: Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity Elife. DOI: 10.7554/Elife.37816.059  0.44
2017 Leman JK, Bonneau R. A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures. Biochemistry. 57: 1939-1944. PMID 29185719 DOI: 10.1021/Acs.Biochem.7B00995  0.68
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  0.44
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  0.76
2017 Watkins AM, Craven TW, Renfrew PD, Arora PS, Bonneau R. Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers. Structure (London, England : 1993). PMID 29033287 DOI: 10.1016/J.Str.2017.09.005  0.84
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  0.84
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 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  0.52
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  0.84
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  0.44
2017 Liu CF, Chen R, Frezzo JA, Katyal P, Hill LK, Yin L, Srivastava N, More HT, Renfrew PD, Bonneau R, Montclare JK. Efficient dual siRNA and drug delivery using engineered lipoproteoplexes. Biomacromolecules. PMID 28686014 DOI: 10.1021/Acs.Biomac.7B00203  0.84
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  0.84
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  0.64
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  0.68
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  0.72
2017 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. Disrupting Hepatocyte Cyp51 from Cholesterol Synthesis Leads to Progressive Liver Injury in the Developing Mouse and Decreases RORC Signalling. Scientific Reports. 7: 40775. PMID 28098217 DOI: 10.1038/Srep40775  0.32
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  0.72
2016 Shi J, Hua X, Goedert JJ, Landi MT, Äijö T, Bonneau R, Zhou W, Sherwood B, Ji H, Zappala Z, Montgomery SB, Wang X, Xiao R, Zhu X, Li M, et al. SAGES 2015. Symposium of Advances in Genomics, Epidemiology and Statistics 2015: Abstracts Human Heredity. 81: 51-61. PMID 28076868 DOI: 10.1159/000447110  0.52
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 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  0.64
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 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  0.8
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  0.68
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  0.68
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  0.84
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  0.76
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  0.84
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  0.52
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 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  0.8
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  0.76
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  0.8
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 Chatterjee S, Butterfoss GL, Mandal M, Paul B, Gupta S, Bonneau R, Jaisankar P. Racemization barriers of atropisomeric 3,3′-bipyrroles: An experimental study with theoretical verification Rsc Advances. 6: 71245-71249. DOI: 10.1039/C6Ra07585A  0.84
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 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  0.8
2015 Barberá P, Wang N, Bonneau R, Jost JT, Nagler J, Tucker J, González-Bailón S. The Critical Periphery in the Growth of Social Protests. Plos One. 10: e0143611. PMID 26618352 DOI: 10.1371/Journal.Pone.0143611  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
2015 Barberá P, Jost JT, Nagler J, Tucker JA, Bonneau R. Tweeting From Left to Right: Is Online Political Communication More Than an Echo Chamber? Psychological Science. 26: 1531-42. PMID 26297377 DOI: 10.1177/0956797615594620  0.8
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  0.8
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 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  0.64
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 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  0.44
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  0.84
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  0.8
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  0.8
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  0.8
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  0.84
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 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  0.8
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 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  0.84
2014 Razy-Krajka F, Lam K, Wang W, Stolfi A, Joly M, Bonneau R, Christiaen L. Collier/OLF/EBF-dependent transcriptional dynamics control pharyngeal muscle specification from primed cardiopharyngeal progenitors Developmental Cell. 29: 263-276. PMID 24794633 DOI: 10.1016/J.Devcel.2014.04.001  0.44
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  0.8
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 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  0.8
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 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  0.8
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  0.8
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 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  0.8
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 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  0.8
2012 Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA. De novo structure prediction and experimental characterization of folded peptoid oligomers. Proceedings of the National Academy of Sciences of the United States of America. 109: 14320-5. PMID 22908242 DOI: 10.1073/Pnas.1209945109  0.8
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  0.8
2012 Rusu M, Bonneau R, Holbrook MR, Watowich SJ, Birmanns S, Wriggers W, Freiberg AN. An assembly model of rift valley Fever virus. Frontiers in Microbiology. 3: 254. PMID 22837754 DOI: 10.3389/Fmicb.2012.00254  0.8
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  0.8
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
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  0.8
2012 Cozy LM, Phillips AM, Calvo RA, Bate AR, Hsueh YH, Bonneau R, Eichenberger P, Kearns DB. SlrA/SinR/SlrR inhibits motility gene expression upstream of a hypersensitive and hysteretic switch at the level of σ(D) in Bacillus subtilis. Molecular Microbiology. 83: 1210-28. PMID 22329926 DOI: 10.1111/J.1365-2958.2012.08003.X  0.8
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  0.84
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  0.84
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  0.8
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 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  0.8
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 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  0.8
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  0.8
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
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  0.64
2008 Shah NH, Butterfoss GL, Nguyen K, Yoo B, Bonneau R, Rabenstein DL, Kirshenbaum K. Oligo(N-aryl glycines): a new twist on structured peptoids. Journal of the American Chemical Society. 130: 16622-32. PMID 19049458 DOI: 10.1021/Ja804580N  0.84
2008 Bonneau R. Learning biological networks: from modules to dynamics. Nature Chemical Biology. 4: 658-664. PMID 18936750 DOI: 10.1038/Nchembio.122  0.48
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  0.8
2008 Bonneau R. Dissecting the quorum-sensing receptor LuxN. Cell. 134: 390-391. PMID 18692463 DOI: 10.1016/J.Cell.2008.07.028  0.52
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  0.8
2007 Kye MJ, Liu T, Levy SF, Xu NL, Groves BB, Bonneau R, Lao K, Kosik KS. Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR. Rna (New York, N.Y.). 13: 1224-34. PMID 17592044 DOI: 10.1261/Rna.480407  0.8
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  0.8
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 Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A. A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. The Journal of Experimental Medicine. 204: 393-403. PMID 17283206 DOI: 10.1084/Jem.20061400  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  0.84
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  0.8
2006 Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, et al. UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. Genome Biology. 7: R73. PMID 16901351 DOI: 10.1186/Gb-2006-7-8-R73  0.8
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 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  0.8
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 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  0.8
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
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  0.8
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  0.8
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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