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For: Tal G, Boca SM, Mittenthal J, Caetano-Anollés G. A Dynamic Model for the Evolution of Protein Structure. J Mol Evol 2016;82:230-43. [PMID: 27146880 DOI: 10.1007/s00239-016-9740-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/12/2016] [Indexed: 10/21/2022]
Number Cited by Other Article(s)
1
Caetano-Anollés K, Aziz MF, Mughal F, Caetano-Anollés G. On Protein Loops, Prior Molecular States and Common Ancestors of Life. J Mol Evol 2024;92:624-646. [PMID: 38652291 PMCID: PMC11458777 DOI: 10.1007/s00239-024-10167-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
2
Amangeldina A, Tan ZW, Berezovsky IN. Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation. Curr Res Struct Biol 2024;7:100129. [PMID: 38327713 PMCID: PMC10847869 DOI: 10.1016/j.crstbi.2024.100129] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024]  Open
3
Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021;18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
4
Evolution of networks of protein domain organization. Sci Rep 2021;11:12075. [PMID: 34103558 PMCID: PMC8187734 DOI: 10.1038/s41598-021-90498-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023]  Open
5
Mughal F, Caetano-Anollés G. MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PLoS One 2019;14:e0224201. [PMID: 31648227 PMCID: PMC6812854 DOI: 10.1371/journal.pone.0224201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/08/2019] [Indexed: 11/30/2022]  Open
6
Caetano-Anollés D, Nasir A, Kim KM, Caetano-Anollés G. Testing Empirical Support for Evolutionary Models that Root the Tree of Life. J Mol Evol 2019;87:131-142. [PMID: 30887086 PMCID: PMC6443624 DOI: 10.1007/s00239-019-09891-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
7
Clark DP, Pazdernik NJ, McGehee MR. Molecular Evolution. Mol Biol 2019. [DOI: 10.1016/b978-0-12-813288-3.00029-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
8
Caetano-Anollés G, Nasir A, Kim KM, Caetano-Anollés D. Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. Evol Bioinform Online 2018;14:1176934318805101. [PMID: 30364468 PMCID: PMC6196624 DOI: 10.1177/1176934318805101] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022]  Open
9
Nasir A, Kim KM, Caetano-Anollés G. Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells. Front Microbiol 2017;8:1178. [PMID: 28690608 PMCID: PMC5481351 DOI: 10.3389/fmicb.2017.01178] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/09/2017] [Indexed: 01/05/2023]  Open
10
Danchin A. From chemical metabolism to life: the origin of the genetic coding process. Beilstein J Org Chem 2017;13:1119-1135. [PMID: 28684991 PMCID: PMC5480338 DOI: 10.3762/bjoc.13.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/19/2017] [Indexed: 12/11/2022]  Open
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