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Items: 15


Evolution and Structure of Proteins and Proteomes.

Liberles DA, Teufel AI.

Genes (Basel). 2018 Nov 28;9(12). pii: E583. doi: 10.3390/genes9120583.


Withdrawn as Duplicate: The many nuanced evolutionary consequences of duplicated genes.

Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO.

Mol Biol Evol. 2018 Dec 1;35(12):e1. doi: 10.1093/molbev/msy216. No abstract available.


The many nuanced evolutionary consequences of duplicated genes.

Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO.

Mol Biol Evol. 2018 Nov 14. doi: 10.1093/molbev/msy210. [Epub ahead of print]


Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences.

Teufel AI, Ritchie AM, Wilke CO, Liberles DA.

Genes (Basel). 2018 Aug 13;9(8). pii: E409. doi: 10.3390/genes9080409. Review.


Beyond Thermodynamic Constraints: Evolutionary Sampling Generates Realistic Protein Sequence Variation.

Jiang Q, Teufel AI, Jackson EL, Wilke CO.

Genetics. 2018 Apr;208(4):1387-1395. doi: 10.1534/genetics.118.300699. Epub 2018 Jan 30.


Sicegar: R package for sigmoidal and double-sigmoidal curve fitting.

Caglar MU, Teufel AI, Wilke CO.

PeerJ. 2018 Jan 16;6:e4251. doi: 10.7717/peerj.4251. eCollection 2018.


Accelerated simulation of evolutionary trajectories in origin-fixation models.

Teufel AI, Wilke CO.

J R Soc Interface. 2017 Feb;14(127). pii: 20160906. doi: 10.1098/rsif.2016.0906.


Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization.

Teufel AI, Liu L, Liberles DA.

BMC Evol Biol. 2016 Feb 20;16:45. doi: 10.1186/s12862-016-0616-1.


A generalized birth and death process for modeling the fates of gene duplication.

Zhao J, Teufel AI, Liberles DA, Liu L.

BMC Evol Biol. 2015 Dec 8;15:275. doi: 10.1186/s12862-015-0539-2.


What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?

Teufel AI, Masel J, Liberles DA.

Genome Biol Evol. 2015 Jul 27;7(8):2258-64. doi: 10.1093/gbe/evv139.


Integrating landscape genomics and spatially explicit approaches to detect loci under selection in clinal populations.

Jones MR, Forester BR, Teufel AI, Adams RV, Anstett DN, Goodrich BA, Landguth EL, Joost S, Manel S.

Evolution. 2013 Dec;67(12):3455-68. doi: 10.1111/evo.12237. Epub 2013 Sep 4.


On the need for mechanistic models in computational genomics and metagenomics.

Liberles DA, Teufel AI, Liu L, Stadler T.

Genome Biol Evol. 2013;5(10):2008-18. doi: 10.1093/gbe/evt151.


The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.


Toward a general model for the evolutionary dynamics of gene duplicates.

Konrad A, Teufel AI, Grahnen JA, Liberles DA.

Genome Biol Evol. 2011;3:1197-209. doi: 10.1093/gbe/evr093. Epub 2011 Sep 13.

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