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For: Foy SG, Wilson BA, Bertram J, Cordes MHJ, Masel J. A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution. Genetics 2019;211:1345-1355. [PMID: 30692195 PMCID: PMC6456324 DOI: 10.1534/genetics.118.301719] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/25/2019] [Indexed: 01/06/2023]  Open
Number Cited by Other Article(s)
1
Weibel CA, Wheeler AL, James JE, Willis SM, McShea H, Masel J. The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.02.530449. [PMID: 38712167 PMCID: PMC11071303 DOI: 10.1101/2023.03.02.530449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
2
Acheson K, Kirrander A. Automatic Clustering of Excited-State Trajectories: Application to Photoexcited Dynamics. J Chem Theory Comput 2023;19:6126-6138. [PMID: 37703098 PMCID: PMC10536988 DOI: 10.1021/acs.jctc.3c00776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 09/14/2023]
3
Tang QY, Ren W, Wang J, Kaneko K. The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database. Mol Biol Evol 2022;39:6701686. [PMID: 36108094 PMCID: PMC9550990 DOI: 10.1093/molbev/msac197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
4
Kosinski LJ, Aviles NR, Gomez K, Masel J. Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful. Genome Biol Evol 2022;14:evac085. [PMID: 35668555 PMCID: PMC9210321 DOI: 10.1093/gbe/evac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/01/2022] [Accepted: 05/27/2022] [Indexed: 11/15/2022]  Open
5
Weisman CM, Murray AW, Eddy SR. Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes. Curr Biol 2022;32:2632-2639.e2. [PMID: 35588743 DOI: 10.1016/j.cub.2022.04.085] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
6
Parakkunnel R, Bhojaraja Naik K, Susmita C, Girimalla V, Bhaskar KU, Sripathy KV, Shantharaja CS, Aravindan S, Kumar S, Lakhanpaul S, Bhat KV. Evolution and co-evolution: insights into the divergence of plant heat shock factor genes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022;28:1029-1047. [PMID: 35722513 PMCID: PMC9203654 DOI: 10.1007/s12298-022-01183-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 05/03/2023]
7
Papadopoulos C, Callebaut I, Gelly JC, Hatin I, Namy O, Renard M, Lespinet O, Lopes A. Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution. Genome Res 2021;31:2303-2315. [PMID: 34810219 PMCID: PMC8647833 DOI: 10.1101/gr.275638.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/23/2021] [Indexed: 01/08/2023]
8
Dubreuil B, Levy ED. Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins. Front Mol Biosci 2021;8:626729. [PMID: 33996892 PMCID: PMC8119896 DOI: 10.3389/fmolb.2021.626729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/29/2021] [Indexed: 12/02/2022]  Open
9
James JE, Willis SM, Nelson PG, Weibel C, Kosinski LJ, Masel J. Universal and taxon-specific trends in protein sequences as a function of age. eLife 2021;10:e57347. [PMID: 33416492 PMCID: PMC7819706 DOI: 10.7554/elife.57347] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 01/05/2021] [Indexed: 01/12/2023]  Open
10
Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes. Genetics 2020;214:1047-1057. [PMID: 32107278 DOI: 10.1534/genetics.120.302815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/18/2020] [Indexed: 11/18/2022]  Open
11
Dubreuil B, Matalon O, Levy ED. Protein Abundance Biases the Amino Acid Composition of Disordered Regions to Minimize Non-functional Interactions. J Mol Biol 2019;431:4978-4992. [PMID: 31442477 PMCID: PMC6941228 DOI: 10.1016/j.jmb.2019.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/07/2019] [Accepted: 08/10/2019] [Indexed: 02/07/2023]
12
Van Oss SB, Carvunis AR. De novo gene birth. PLoS Genet 2019;15:e1008160. [PMID: 31120894 PMCID: PMC6542195 DOI: 10.1371/journal.pgen.1008160] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
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