Protein evolution depends on multiple distinct population size parameters

Autor: Alexander Platt, Claudia C. Weber, David A. Liberles

Publikováno v: BMC Evolutionary Biology, Vol 18, Iss 1, Pp 1-9 (2018)

Abstract That population size affects the fate of new mutations arising in genomes, modulating both how frequently they arise and how efficiently natural selection is able to filter them, is well established. It is therefore clear that these distinct

Externí odkaz: https://doaj.org/article/97c6ac384c1743ae8b884f7447ff6a83

A new parameter‐rich structure‐aware mechanistic model for amino acid substitution during evolution

Autor: Jason K. Lai, Peter B. Chi, Jan Kubelka, Dohyup Kim, Claudia C. Weber, David A. Liberles, Nadia Bykova

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 86:218-228

Improvements in the description of amino acid substitution are required to develop better pseudo-energy-based protein structure-aware models for use in phylogenetic studies. These models are used to characterize the probabilities of amino acid substi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37c6764812af0d160bdbcee93286ee9c
https://doi.org/10.1002/prot.25429

Whole-genome analyses resolve early branches in the tree of life of modern birds

Autor: Bhanu Rekepalli, Jaime Huerta-Cepas, David Haussler, Beth Shapiro, Frank E. Rheindt, Bo Li, Per Alström, Oliver A. Ryder, Salvador Capella-Gutierrez, Jianwen Li, José Alfredo Samaniego, Binghang Liu, Paula F. Campos, David P. Mindell, Xiangjiang Zhan, An Pas, Yinhua Huang, Liang Liu, Scott V. Edwards, Dave Burt, David A. Ray, Andrew Dixon, Hui Li, Toni Gabaldón, Bastien Boussau, Cai Li, Hans Ellegren, Carsten Rahbek, Shengbin Li, Michael J. Braun, Peter Houde, Peter V. Lovell, Alexandros Stamatakis, Claudia C. Weber, Yong Zhang, Jian Wang, Thomas Sicheritz-Pontén, Volodymyr Zavidovych, Alexander Suh, Xiong Yinqi, Maria Paula Cruz Schneider, Stephen J. O'Brien, Ganesh Ganapathy, Shamsuzzoha Bayzid, Huanming Yang, Guojie Zhang, Alonzo Alfaro-Núñez, Claudio V. Mello, Michael Bunce, Amy C. Driskell, Francisco Prosdocimi, Zijun Xiong, Joel Cracraft, Long Zhou, Mikkel H. Schierup, Brant C. Faircloth, Gary R. Graves, F. Keith Barker, Jon Fjeldså, Benoit Nabholz, Bent E. K. Lindow, Frederick H. Sheldon, Robb T. Brumfield, Nitish Narula, Bent O. Petersen, Kasper Munch, Klaus-Peter Koepfli, Rute R. da Fonseca, Thomas L. Bailey, Kui Wu, Quiemei Zheng, Tandy Warnow, John E. McCormack, Elizabeth P. Derryberry, Linnéa Smeds, Simon Y. W. Ho, Polina L. Perelman, Siavash Mirarab, Qi Zhou, Michael William Bruford, Knud A. Jønsson, M. Thomas P. Gilbert, Ning Li, Richard E. Green, Edward L. Braun, R. Paul Scofield, Wesley C. Warren, Zhenyu Li, Fang Zhang Zhang, Warren E. Johnson, Morgan Wirthlin, Jason T. Howard, Travis C. Glenn, Ludovic Orlando, Mads F. Bertelsen, David M. Lambert, Andre J. Aberer, Erich D. Jarvis, Sankar Subramanian, Amhed Missael Vargas Velazquez, Yongli Zeng, Eske Willerslev, Jin Xiao, Shiping Liu, Wang Jun

Publikováno v: Sicheritz-Pontén, T, Li, C, Li, B, Munch, K, Schierup, M H, Bertelsen, M F, Fjeldsa, J, Jønsson, K A, Wang, J, Willerslev, E & Petersen, B 2014, ' Whole-genome analyses resolve early branches in the tree of life of modern birds ', Science, vol. 346, no. 6215, pp. 1320-1331 . https://doi.org/10.1126/science.1253451
Science
Science, American Association for the Advancement of Science, 2014, 346 (6215), pp.1320-31. ⟨10.1126/science.1253451⟩
Science, 2014, 346 (6215), pp.1320-31. ⟨10.1126/science.1253451⟩
Jarvis, E D, Mirarab, S, Aberer, A J, Li, B, Houde, P, Li, C, Ho, S Y W, Faircloth, B C, Nabholz, B, Howard, J T, Suh, A, Weber, C C, da Fonseca, R R, Li, J, Zhang, F, Li, H, Zhou, L, Narula, N, Liu, L, Ganapathy, G, Boussau, B, Bayzid, M S, Zavidovych, V, Subramanian, S, Gabaldón, T, Capella-Gutiérrez, S, Huerta-Cepas, J, Rekepalli, B, Munch, K, Schierup, M, Lindow, B, Warren, W C, Ray, D, Green, R E, Bruford, M W, Zhan, X, Dixon, A, Li, S, Li, N, Huang, Y, Derryberry, E P, Bertelsen, M F, Sheldon, F H, Brumfield, R T, Mello, C V, Lovell, P V, Wirthlin, M, Schneider, M P C, Prosdocimi, F, Samaniego, J A, Vargas Velazquez, A M, Alfaro-Núñez, A, Campos, P F, Petersen, B, Sicheritz-Ponten, T, Pas, A, Bailey, T, Scofield, P, Bunce, M, Lambert, D M, Zhou, Q, Perelman, P, Driskell, A C, Shapiro, B, Xiong, Z, Zeng, Y, Liu, S, Li, Z, Liu, B, Wu, K, Xiao, J, Yinqi, X, Zheng, Q, Zhang, Y, Yang, H, Wang, J, Smeds, L, Rheindt, F E, Braun, M, Fjeldsa, J, Orlando, L, Barker, F K, Jønsson, K A, Johnson, W, Koepfli, K-P, O'Brien, S, Haussler, D, Ryder, O A, Rahbek, C, Willerslev, E, Graves, G R, Glenn, T C, McCormack, J, Burt, D, Ellegren, H, Alström, P, Edwards, S V, Stamatakis, A, Mindell, D P, Cracraft, J, Braun, E L, Warnow, T, Jun, W, Gilbert, M T P & Zhang, G 2014, ' Whole-genome analyses resolve early branches in the tree of life of modern birds ', Science, vol. 346, no. 6215, pp. 1320-31 . https://doi.org/10.1126/science.1253451

International audience; To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dccb1b8bc34e5e4d44d26964386c4e02
https://doi.org/10.1126/science.1253451

ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability

Autor: Ugo Bastolla, Miguel Arenas, Claudia C. Weber, David A. Liberles

Publikováno v: Systematic biology. 66(6)

The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often ba

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::28781b1087bc720c502da61a63d249c1
https://pubmed.ncbi.nlm.nih.gov/28057858

Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence

Autor: Tobias Warnecke, Laurence D. Hurst, Claudia C. Weber

Publikováno v: Biochemical Society Transactions. 37:756-761

There is considerable variation in the rate at which different proteins evolve. Why is this? Classically, it has been considered that the density of functionally important sites must predict rates of protein evolution. Likewise, amino acid choice is

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::81b659b7d6fc15c50ebb0a450903ea39
https://doi.org/10.1042/bst0370756