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For: Ochoa D, Juan D, Valencia A, Pazos F. Detection of significant protein coevolution. ACTA ACUST UNITED AC 2015;31:2166-73. [PMID: 25717190 DOI: 10.1093/bioinformatics/btv102] [Citation(s) in RCA: 24] [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] [Received: 06/18/2014] [Accepted: 02/11/2015] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Lupo U, Sgarbossa D, Milighetti M, Bitbol AF. DiffPaSS-high-performance differentiable pairing of protein sequences using soft scores. Bioinformatics 2024;41:btae738. [PMID: 39672677 PMCID: PMC11676329 DOI: 10.1093/bioinformatics/btae738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 12/05/2024] [Accepted: 12/11/2024] [Indexed: 12/15/2024]  Open
2
Lupo U, Sgarbossa D, Bitbol AF. Pairing interacting protein sequences using masked language modeling. Proc Natl Acad Sci U S A 2024;121:e2311887121. [PMID: 38913900 PMCID: PMC11228504 DOI: 10.1073/pnas.2311887121] [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: 08/12/2023] [Accepted: 12/18/2023] [Indexed: 06/26/2024]  Open
3
Lee YHG, Cerf NT, Shalaby N, Montes MR, Clarke RJ. Bioinformatic Study of Possible Acute Regulation of Acid Secretion in the Stomach. J Membr Biol 2024;257:79-89. [PMID: 38436710 PMCID: PMC11006737 DOI: 10.1007/s00232-024-00310-7] [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: 12/24/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
4
Bernett J, Blumenthal DB, List M. Cracking the black box of deep sequence-based protein-protein interaction prediction. Brief Bioinform 2024;25:bbae076. [PMID: 38446741 PMCID: PMC10939362 DOI: 10.1093/bib/bbae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/09/2024] [Indexed: 03/08/2024]  Open
5
Mishra SK, Priya P, Rai GP, Haque R, Shanker A. Coevolution based immunoinformatics approach considering variability of epitopes to combat different strains: A case study using spike protein of SARS-CoV-2. Comput Biol Med 2023;163:107233. [PMID: 37422941 DOI: 10.1016/j.compbiomed.2023.107233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 06/03/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
6
Gandarilla-Pérez CA, Pinilla S, Bitbol AF, Weigt M. Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins. PLoS Comput Biol 2023;19:e1011010. [PMID: 36996234 PMCID: PMC10089317 DOI: 10.1371/journal.pcbi.1011010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 04/11/2023] [Accepted: 03/08/2023] [Indexed: 04/01/2023]  Open
7
Wangwiwatsin A, Kulwong S, Phetcharaburanin J, Namwat N, Klanrit P, Loilome W, Maleewong W, Reid AJ. Toward novel treatment against filariasis: Insight into genome-wide co-evolutionary analysis of filarial nematodes and Wolbachia. Front Microbiol 2023;14:1052352. [PMID: 37032902 PMCID: PMC10073474 DOI: 10.3389/fmicb.2023.1052352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/16/2023] [Indexed: 04/11/2023]  Open
8
Wei Q, Liu J, Guo F, Wang Z, Zhang X, Yuan L, Ali K, Qiang F, Wen Y, Li W, Zheng B, Bai Q, Li G, Ren H, Wu G. Kinase regulators evolved into two families by gain and loss of ability to bind plant steroid receptors. PLANT PHYSIOLOGY 2023;191:1167-1185. [PMID: 36494097 PMCID: PMC9922406 DOI: 10.1093/plphys/kiac568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
9
Bioinformatic Analysis of Na+, K+-ATPase Regulation through Phosphorylation of the Alpha-Subunit N-Terminus. Int J Mol Sci 2022;24:ijms24010067. [PMID: 36613508 PMCID: PMC9820343 DOI: 10.3390/ijms24010067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/01/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]  Open
10
Xie P, Liu J, Lu R, Zhang Y, Sun X. Molecular evolution of the Pi-d2 gene conferring resistance to rice blast in Oryza. Front Genet 2022;13:991900. [PMID: 36147495 PMCID: PMC9486079 DOI: 10.3389/fgene.2022.991900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/10/2022] [Indexed: 11/15/2022]  Open
11
Gerardos A, Dietler N, Bitbol AF. Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences. PLoS Comput Biol 2022;18:e1010147. [PMID: 35576238 PMCID: PMC9135348 DOI: 10.1371/journal.pcbi.1010147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/26/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]  Open
12
Gai Z, Wang Y, Tian L, Gong G, Zhao J. Whole Genome Level Analysis of the Wnt and DIX Gene Families in Mice and Their Coordination Relationship in Regulating Cardiac Hypertrophy. Front Genet 2021;12:608936. [PMID: 34168671 PMCID: PMC8217762 DOI: 10.3389/fgene.2021.608936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 05/17/2021] [Indexed: 12/27/2022]  Open
13
Xu C, Chang X, Hou Z, Zhang Z, Zhu Z, Zhong B. The origin of SPA reveals the divergence and convergence of light signaling in Archaeplastida. Mol Phylogenet Evol 2021;161:107175. [PMID: 33862251 DOI: 10.1016/j.ympev.2021.107175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
14
Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors. Int J Mol Sci 2021;22:ijms22052332. [PMID: 33652738 PMCID: PMC7956259 DOI: 10.3390/ijms22052332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/28/2022]  Open
15
Bloch I, Sherill-Rofe D, Stupp D, Unterman I, Beer H, Sharon E, Tabach Y. Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals. Bioinformatics 2021;36:4116-4125. [PMID: 32353123 DOI: 10.1093/bioinformatics/btaa281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 12/11/2022]  Open
16
Salmanian S, Pezeshk H, Sadeghi M. Inter-protein residue covariation information unravels physically interacting protein dimers. BMC Bioinformatics 2020;21:584. [PMID: 33334319 PMCID: PMC7745481 DOI: 10.1186/s12859-020-03930-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/09/2020] [Indexed: 01/04/2023]  Open
17
Phylogenetic correlations can suffice to infer protein partners from sequences. PLoS Comput Biol 2019;15:e1007179. [PMID: 31609984 PMCID: PMC6812855 DOI: 10.1371/journal.pcbi.1007179] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/24/2019] [Accepted: 09/25/2019] [Indexed: 12/30/2022]  Open
18
Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS. Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality. Cell Rep 2019;28:1635-1647.e5. [PMID: 31390575 PMCID: PMC6693557 DOI: 10.1016/j.celrep.2019.07.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/28/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022]  Open
19
Pascual-García A, Arenas M, Bastolla U. The Molecular Clock in the Evolution of Protein Structures. Syst Biol 2019;68:987-1002. [DOI: 10.1093/sysbio/syz022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 03/20/2019] [Accepted: 04/09/2019] [Indexed: 12/11/2022]  Open
20
Garrido-Martín D, Pazos F. Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. BMC Bioinformatics 2018;19:67. [PMID: 29482506 PMCID: PMC5827975 DOI: 10.1186/s12859-018-2084-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022]  Open
21
Rice DW, Sheehan KB, Newton ILG. Large-Scale Identification of Wolbachia pipientis Effectors. Genome Biol Evol 2017;9:1925-1937. [PMID: 28854601 PMCID: PMC5544941 DOI: 10.1093/gbe/evx139] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2017] [Indexed: 12/13/2022]  Open
22
Chapa TJ, Du Y, Sun R, Yu D, French AR. Proteomic and phylogenetic coevolution analyses of pM79 and pM92 identify interactions with RNA polymerase II and delineate the murine cytomegalovirus late transcription complex. J Gen Virol 2017;98:242-250. [PMID: 27926822 DOI: 10.1099/jgv.0.000676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
23
Jiménez-Sánchez A. Coevolution of RAC Small GTPases and their Regulators GEF Proteins. Evol Bioinform Online 2016;12:121-31. [PMID: 27226705 PMCID: PMC4872645 DOI: 10.4137/ebo.s38031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 03/31/2016] [Accepted: 04/03/2016] [Indexed: 01/16/2023]  Open
24
Stimulation of Na(+),K(+)-ATPase Activity as a Possible Driving Force in Cholesterol Evolution. J Membr Biol 2015;249:251-9. [PMID: 26715509 DOI: 10.1007/s00232-015-9864-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022]
25
Grayson P. Izumo1 and Juno: the evolutionary origins and coevolution of essential sperm-egg binding partners. ROYAL SOCIETY OPEN SCIENCE 2015;2:150296. [PMID: 27019721 PMCID: PMC4807442 DOI: 10.1098/rsos.150296] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/17/2015] [Indexed: 05/29/2023]
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