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Bioinformatics (Oxford, England)|August 28, 2014
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic treesChristina Kratsch, Alice C McHardyMethods in Molecular Biology (Clifton, N.J.)|August 29, 2018
Software for Characterizing the Antigenic and Genetic Evolution of Human Influenza VirusesSusanne Reimering, Alice C McHardyBriefings in Bioinformatics|August 2, 2012
Taxonomic binning of metagenome samples generated by next-generation sequencing technologiesJohannes Dröge, Alice C McHardyCurrent Opinion in Microbiology|October 16, 2007
What's in the mix: phylogenetic classification of metagenome sequence samplesAlice C McHardy, Isidore RigoutsosBriefings in Bioinformatics|May 22, 2021
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA virusesZhi-Luo Deng, Akshay Dhingra, Adrian Fritz, et al.Genome Biology and Evolution|July 12, 2013
Alignment-free genome tree inference by learning group-specific distance metricsKaustubh R Patil, Alice C McHardyBMC Bioinformatics|May 4, 2010
Fine-tuning structural RNA alignments in the twilight zoneAndreas Bremges, Stefanie Schirmer, Robert GiegerichPeerj|July 5, 2013
PTree: pattern-based, stochastic search for maximum parsimony phylogeniesIvan Gregor, Lars Steinbrück, Alice C McHardyPlos Computational Biology|February 8, 2020
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemicSusanne Reimering, Sebastian Muñoz, Alice C McHardyScientific Reports|November 20, 2018
A Fréchet tree distance measure to compare phylogeographic spread paths across treesSusanne Reimering, Sebastian Muñoz, Alice C McHardyPageof 13