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Author Details

David A Liberles
Temple University
1996
92
30
PMIDPaper TitleJournal TitlePublished Year
36562800The Memory Problem for Neutral Mutational Models of Evolution.J Mol Evol2023
375922192023 BMC Ecology and Evolution image competition: the winning images.BMC Ecol Evol2023
359824022022 BMC Ecology and Evolution image competition: the winning images.BMC Ecol Evol2022
36434497WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events.BMC Bioinformatics2022
33691618Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC Ecol Evol2021
33486547Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.J Mol Evol2021
32046633Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.BMC Evol Biol2020
30298391Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates.Methods Mol Biol2019
29178386A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.Proteins2018
30104502Using the Mutation-Selection Framework to Characterize Selection on Protein Sequences.Genes (Basel)2018
30487453Evolution and Structure of Proteins and Proteomes.Genes (Basel)2018
29422024Protein evolution depends on multiple distinct population size parameters.BMC Evol Biol2018
28057858ProtASR: An Evolutionary Framework for Ancestral Protein Reconstruction with Selection on Folding Stability.Syst Biol2017
28143390Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization.BMC Evol Biol2017
28795237The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates.J Mol Evol2017
28545395Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.BMC Evol Biol2017
26920685Flux Control in Glycolysis Varies Across the Tree of Life.J Mol Evol2016
27393343Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable.Biol Direct2016
27168732Extracting functional trends from whole genome duplication events using comparative genomics.Biol Proced Online2016
27088604The Atlantic salmon genome provides insights into rediploidization.Nature2016
26897341Models for gene duplication when dosage balance works as a transition state to subsequent neo-or sub-functionalization.BMC Evol Biol2016
25371374Genetic simulation tools for post-genome wide association studies of complex diseases.Genet Epidemiol2015
26511837Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.BMC Evol Biol2015
26643106A generalized birth and death process for modeling the fates of gene duplication.BMC Evol Biol2015
26220936What Fraction of Duplicates Observed in Recently Sequenced Genomes Is Segregating and Destined to Fail to Fix?Genome Biol Evol2015
24500774The phylogenetic distribution and evolution of enzymes within the thymidine kinase 2-like gene family in metazoa.J Mol Evol2014
24845553Molecular traces of alternative social organization in a termite genome.Nat Commun2014
24371277A phylogenetic model for understanding the effect of gene duplication on cancer progression.Nucleic Acids Res2014
23914788State-of the art methodologies dictate new standards for phylogenetic analysis.BMC Evol Biol2013
24115604On the need for mechanistic models in computational genomics and metagenomics.Genome Biol Evol2013
22057012The global distribution and evolution of deoxyribonucleoside kinases in bacteria.Gene2012
23221607Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle.Genome Biol Evol2012
22967797The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1.Gene2012
23043301The salmonid myostatin gene family: a novel model for investigating mechanisms that influence duplicate gene fate.BMC Evol Biol2012
22528593The interface of protein structure, protein biophysics, and molecular evolution.Protein Sci2012
22462611Deoxyribonucleoside kinases in two aquatic bacteria with high specificity for thymidine and deoxyadenosine.FEMS Microbiol Lett2012
22651983A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.J Mol Biol2012
21490020Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy.Proc Biol Sci2011
24710290The evolution of protein structures and structural ensembles under functional constraint.Genes (Basel)2011
22171550Biophysical and structural considerations for protein sequence evolution.BMC Evol Biol2011
21800121Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolution.J Mol Evol2011
21920903Toward a general model for the evolutionary dynamics of gene duplicates.Genome Biol Evol2011
20004669Lineage-specific differences in the amino acid substitution process.J Mol Biol2010
21048002Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method.Genome Biol Evol2010
21097902Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate.Science2010
18791694Keeping the blood flowing-plasminogen activator genes and feeding behavior in vampire bats.Naturwissenschaften2009
19760447Phylogenetic analysis of the NEEP21/calcyon/P19 family of endocytic proteins: evidence for functional evolution in the vertebrate CNS.J Mol Evol2009
19497865Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ.Proc Natl Acad Sci U S A2009
18378100The power-law distribution of gene family size is driven by the pseudogenisation rate's heterogeneity between gene families.Gene2008
19461954Characterizing gene family evolution.Biol Proced Online2008
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Collaborators

Russell A Hermansen
University of Wyoming
Co-authored papers 7
Steven A Benner
Foundation for Applied Molecular Evolution
Co-authored papers 6
Stephen G Chamberlin
Southampton General Hospital
Co-authored papers 4
David Schreiber
Weizmann Institute of Science
Co-authored papers 3
Erich Bornberg-Bauer
Institute for Evolution and Biodiversity, University of Munster
Co-authored papers 2
Julie A Mustard
Arizona State University
Co-authored papers 1
Winston Hide
Harvard Medical School
Co-authored papers 1
Zhensheng Chen
Co-authored papers 1
Monica C Munoz-Torres
University of Colorado Anschutz Medical Campus
Co-authored papers 1
Michael A D Goodisman
Georgia Institute of Technology
Co-authored papers 1
Lucy J Colwell
Google Research
Co-authored papers 1
Jean Weissenbach
Institut Francois Jacob, CNRS, Universite Paris-Saclay
Co-authored papers 1
Judith Korb
University of Freiburg
Co-authored papers 1
Shamil R Sunyaev
Harvard Medical School
Co-authored papers 1
Fengming Sun
Oil Crops Research Institute, Chinese Academy of Agricultural Sciences
Co-authored papers 1
Jin Xiao
Beijing Genomics Institute (BGI)-Shenzhen
Co-authored papers 1
Marcin Adamski
Co-authored papers 1
Kimmen Sj??lander
University of California berkeley
Co-authored papers 1
Ying Xu
The China-Japan Union Hospital, Jilin University
Co-authored papers 1
Hailin Pan
Chinese Academy of Sciences
Co-authored papers 1
Zuoquan Yang
Horticultural Research Institute, Shanghai Academy of Agricultural Sciences
Co-authored papers 1
Richard Michael Roe
College of Agriculture and Life Sciences, NC State University
Co-authored papers 1
Kaustubh Gokhale
Arizona State University
Co-authored papers 1
Leah E Mechanic
National Cancer Institute, National Institutes of Health
Co-authored papers 1
Vineet Bafna
University of California San Diego
Co-authored papers 1
Steven J M Jones
University of British Columbia
Co-authored papers 1
Jun Wang
Zhongnan Hospital of Wuhan University
Co-authored papers 1
Justin T Reese
Lawrence Berkeley National Laboratory
Co-authored papers 1
Dietlind L Gerloff
Foundation for Applied Molecular Evolution (FfAME)
Co-authored papers 1
Colin S Brent
USDA ARS, U.S. Arid Land Agricultural Research Center
Co-authored papers 1
Release 1.2