| Year |
Citation |
Score |
| 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 |
0.707 |
|
| 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 |
0.45 |
|
| 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 |
0.748 |
|
| 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 |
0.541 |
|
| 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 |
0.688 |
|
| 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 |
0.453 |
|
| 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 |
0.775 |
|
| 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 |
0.757 |
|
| 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 |
0.59 |
|
| 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 |
0.318 |
|
| 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 |
0.345 |
|
| 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 |
0.747 |
|
| 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 |
0.621 |
|
| 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 |
0.508 |
|
| 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 |
0.728 |
|
| 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 |
0.802 |
|
| 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 |
0.734 |
|
| 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 |
0.358 |
|
| 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 |
0.709 |
|
| 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 |
0.787 |
|
| 2018 |
Koo DCE, Bonneau R. Towards region-specific propagation of protein functions. Bioinformatics (Oxford, England). PMID 30304483 DOI: 10.1093/Bioinformatics/Bty834 |
0.313 |
|
| 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 |
0.302 |
|
| 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 |
0.676 |
|
| 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 |
0.373 |
|
| 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 |
0.727 |
|
| 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 |
0.772 |
|
| 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 |
0.697 |
|
| 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 |
0.758 |
|
| 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 |
0.768 |
|
| 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 |
0.384 |
|
| 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 |
0.326 |
|
| 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 |
0.708 |
|
| 2017 |
Äijö T, Bonneau R. Biophysically Motivated Regulatory Network Inference: Progress and Prospects. Human Heredity. 81: 62-77. PMID 28076866 DOI: 10.1159/000446614 |
0.384 |
|
| 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 |
0.666 |
|
| 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 |
0.79 |
|
| 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 |
0.794 |
|
| 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 |
0.768 |
|
| 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 |
0.31 |
|
| 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 |
0.789 |
|
| 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 |
0.766 |
|
| 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 |
0.775 |
|
| 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 |
0.753 |
|
| 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 |
0.775 |
|
| 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 |
0.679 |
|
| 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 |
0.766 |
|
| 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 |
0.7 |
|
| 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 |
0.796 |
|
| 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 |
0.607 |
|
| 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 |
0.78 |
|
| 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 |
0.68 |
|
| 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 |
0.784 |
|
| 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 |
0.749 |
|
| 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 |
0.524 |
|
| 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 |
0.804 |
|
| 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 |
0.335 |
|
| 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 |
0.787 |
|
| 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 |
0.677 |
|
| 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 |
0.749 |
|
| 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 |
0.701 |
|
| 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 |
0.69 |
|
| 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 |
0.329 |
|
| 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 |
0.386 |
|
| 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 |
0.798 |
|
| 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 |
0.694 |
|
| 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 |
0.795 |
|
| 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 |
0.759 |
|
| 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 |
0.696 |
|
| 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 |
0.772 |
|
| 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 |
0.371 |
|
| 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 |
0.771 |
|
| 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 |
0.795 |
|
| 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 |
0.534 |
|
| 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 |
0.679 |
|
| 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 |
0.717 |
|
| 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 |
0.778 |
|
| 2008 |
Bonneau R. Learning biological networks: from modules to dynamics. Nature Chemical Biology. 4: 658-664. PMID 18936750 DOI: 10.1038/Nchembio.122 |
0.347 |
|
| 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 |
0.716 |
|
| 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 |
0.805 |
|
| 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 |
0.346 |
|
| 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 |
0.705 |
|
| 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 |
0.321 |
|
| 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 |
0.32 |
|
| 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 |
0.689 |
|
| 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 |
0.315 |
|
| 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 |
0.327 |
|
| 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 |
0.328 |
|
| 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 |
0.313 |
|
| 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 |
0.785 |
|
| 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 |
0.72 |
|
| 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 |
0.789 |
|
| 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 |
0.568 |
|
| 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 |
0.789 |
|
| 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 |
0.591 |
|
| 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 |
0.396 |
|
| 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 |
0.408 |
|
| 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 |
0.311 |
|
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