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BMC Bioinformatics|October 17, 2025
SMILES alignment: a dynamic programming approach for the alignment of metabolites and other small organic moleculesAlexis L Tang, David A LiberlesGenome Biology and Evolution|September 28, 2021
Characterizing Amino Acid Substitution with Complete Linkage of Sites on a LineageTristan L Stark, David A LiberlesJournal of Microbiology & Biology Education|May 27, 2026
Teaching bioinformatics with generative AI: judgment, uncertainty, and responsibilityAshley I Teufel, David A LiberlesBMC Bioinformatics|June 1, 2005
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing dataRoald Rossnes, Ingvar Eidhammer, David A LiberlesGene|September 13, 2012
The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1Anke Konrad, Jure Piškur, David A LiberlesBMC Bioinformatics|May 1, 2004
Visualising very large phylogenetic trees in three dimensional hyperbolic spaceTimothy Hughes, Young Hyun, David A LiberlesBiophysical Chemistry|July 14, 2006
Evaluation of models for the evolution of protein sequences and functions under structural constraintShruti Rastogi, Nathalie Reuter, David A LiberlesJournal of Molecular Evolution|October 14, 2025
Understanding Functional Evolution in Orthologs and ParalogsMaeva Perez, Katherine Hurm, David A LiberlesBMC Evolutionary Biology|February 10, 2018
Protein evolution depends on multiple distinct population size parametersAlexander Platt, Claudia C Weber, David A LiberlesJournal of Molecular Evolution|July 30, 2011
Fast side chain replacement in proteins using a coarse-grained approach for evaluating the effects of mutation during evolutionJohan A Grahnen, Jan Kubelka, David A LiberlesPageof 11