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For: Fraser JS, Gross JD, Krogan NJ. From systems to structure: bridging networks and mechanism. Mol Cell 2013;49:222-31. [PMID: 23352243 DOI: 10.1016/j.molcel.2013.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Kosoglu K, Aydin Z, Tuncbag N, Gursoy A, Keskin O. Structural coverage of the human interactome. Brief Bioinform 2023;25:bbad496. [PMID: 38180828 PMCID: PMC10768791 DOI: 10.1093/bib/bbad496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/16/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024]  Open
2
Yang M, Harrison BR, Promislow DEL. In search of a Drosophila core cellular network with single-cell transcriptome data. G3 GENES|GENOMES|GENETICS 2022;12:6670625. [PMID: 35976114 PMCID: PMC9526075 DOI: 10.1093/g3journal/jkac212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022]
3
Amacher JF, Brooks L, Hampton TH, Madden DR. Specificity in PDZ-peptide interaction networks: Computational analysis and review. JOURNAL OF STRUCTURAL BIOLOGY-X 2020;4:100022. [PMID: 32289118 PMCID: PMC7138185 DOI: 10.1016/j.yjsbx.2020.100022] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/26/2020] [Accepted: 02/29/2020] [Indexed: 01/03/2023]
4
A Quantitative Genetic Interaction Map of HIV Infection. Mol Cell 2020;78:197-209.e7. [PMID: 32084337 DOI: 10.1016/j.molcel.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/10/2020] [Accepted: 02/02/2020] [Indexed: 12/16/2022]
5
Schneidman-Duhovny D, Wolfson HJ. Modeling of Multimolecular Complexes. Methods Mol Biol 2020;2112:163-174. [PMID: 32006285 DOI: 10.1007/978-1-0716-0270-6_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
6
Tutuncuoglu B, Krogan NJ. Mapping genetic interactions in cancer: a road to rational combination therapies. Genome Med 2019;11:62. [PMID: 31640753 PMCID: PMC6805649 DOI: 10.1186/s13073-019-0680-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023]  Open
7
Fragata I, Blanckaert A, Dias Louro MA, Liberles DA, Bank C. Evolution in the light of fitness landscape theory. Trends Ecol Evol 2019;34:69-82. [DOI: 10.1016/j.tree.2018.10.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 01/28/2023]
8
Rosell M, Fernández-Recio J. Hot-spot analysis for drug discovery targeting protein-protein interactions. Expert Opin Drug Discov 2018;13:327-338. [PMID: 29376444 DOI: 10.1080/17460441.2018.1430763] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
9
Barradas-Bautista D, Rosell M, Pallara C, Fernández-Recio J. Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems. PROTEIN-PROTEIN INTERACTIONS IN HUMAN DISEASE, PART A 2018;110:203-249. [DOI: 10.1016/bs.apcsb.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
10
DEEPN as an Approach for Batch Processing of Yeast 2-Hybrid Interactions. Cell Rep 2017;17:303-315. [PMID: 27681439 DOI: 10.1016/j.celrep.2016.08.095] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/06/2016] [Accepted: 08/29/2016] [Indexed: 01/06/2023]  Open
11
Kazantsev F, Akberdin I, Lashin S, Ree N, Timonov V, Ratushny A, Khlebodarova T, Likhoshvai V. MAMMOTh: A new database for curated mathematical models of biomolecular systems. J Bioinform Comput Biol 2017;16:1740010. [PMID: 29172865 DOI: 10.1142/s0219720017400108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
12
Barradas-Bautista D, Fernández-Recio J. Docking-based modeling of protein-protein interfaces for extensive structural and functional characterization of missense mutations. PLoS One 2017;12:e0183643. [PMID: 28841721 PMCID: PMC5571915 DOI: 10.1371/journal.pone.0183643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/08/2017] [Indexed: 01/23/2023]  Open
13
Kumar A, Pathak RK, Gupta SM, Gaur VS, Pandey D. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016;19:581-601. [PMID: 26484978 DOI: 10.1089/omi.2015.0106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
14
Scott NE, Brown LM, Kristensen AR, Foster LJ. Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments. J Proteomics 2014;118:112-29. [PMID: 25464368 DOI: 10.1016/j.jprot.2014.10.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/18/2014] [Accepted: 10/27/2014] [Indexed: 01/12/2023]
15
Modeling thrombin generation: plasma composition based approach. J Thromb Thrombolysis 2014;37:32-44. [PMID: 24214371 DOI: 10.1007/s11239-013-1006-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
16
Clancy T, Hovig E. From proteomes to complexomes in the era of systems biology. Proteomics 2014;14:24-41. [PMID: 24243660 DOI: 10.1002/pmic.201300230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 10/22/2013] [Accepted: 11/06/2013] [Indexed: 01/16/2023]
17
Petrey D, Honig B. Structural bioinformatics of the interactome. Annu Rev Biophys 2014;43:193-210. [PMID: 24895853 DOI: 10.1146/annurev-biophys-051013-022726] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
18
Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast. J Mol Biol 2014;426:2854-70. [PMID: 24862281 DOI: 10.1016/j.jmb.2014.05.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/13/2014] [Accepted: 05/18/2014] [Indexed: 01/26/2023]
19
Hingorani KS, Gierasch LM. Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge. Curr Opin Struct Biol 2014;24:81-90. [PMID: 24434632 DOI: 10.1016/j.sbi.2013.11.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/21/2013] [Accepted: 11/21/2013] [Indexed: 01/09/2023]
20
Carter H, Hofree M, Ideker T. Genotype to phenotype via network analysis. Curr Opin Genet Dev 2013;23:611-21. [PMID: 24238873 PMCID: PMC3866044 DOI: 10.1016/j.gde.2013.10.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/04/2013] [Accepted: 10/09/2013] [Indexed: 02/06/2023]
21
High-resolution network biology: connecting sequence with function. Nat Rev Genet 2013;14:865-79. [PMID: 24197012 DOI: 10.1038/nrg3574] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
22
Hleap JS, Susko E, Blouin C. Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture. BMC STRUCTURAL BIOLOGY 2013;13:20. [PMID: 24131821 PMCID: PMC4016585 DOI: 10.1186/1472-6807-13-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/11/2013] [Indexed: 12/23/2022]
23
Kurata H, Maeda K, Onaka T, Takata T. BioFNet: biological functional network database for analysis and synthesis of biological systems. Brief Bioinform 2013;15:699-709. [PMID: 23894104 DOI: 10.1093/bib/bbt048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
24
Almo SC, Garforth SJ, Hillerich BS, Love JD, Seidel RD, Burley SK. Protein production from the structural genomics perspective: achievements and future needs. Curr Opin Struct Biol 2013;23:335-44. [PMID: 23642905 PMCID: PMC4163025 DOI: 10.1016/j.sbi.2013.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 01/31/2023]
25
Lim WA, Lee CM, Tang C. Design principles of regulatory networks: searching for the molecular algorithms of the cell. Mol Cell 2013;49:202-12. [PMID: 23352241 DOI: 10.1016/j.molcel.2012.12.020] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/30/2012] [Indexed: 12/28/2022]
26
Gajendrarao P, Krishnamoorthy N, Kassem HS, Moharem-Elgamal S, Cecchi F, Olivotto I, Yacoub MH. Molecular modeling of disease causing mutations in domain C1 of cMyBP-C. PLoS One 2013;8:e59206. [PMID: 23527136 PMCID: PMC3602012 DOI: 10.1371/journal.pone.0059206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/12/2013] [Indexed: 11/20/2022]  Open
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