MP Cummings

Latest

• BEAGLE 3: Improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics
• Comparative morphology and evolution of the cnidosac in Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)
• Rerooting Trees Increases Opportunities for Concurrent Computation and Results in Markedly Improved Performance for Phylogenetic Inference
• Prey preference follows phylogeny: evolutionary dietary patterns within the marine gastropod group Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia)
• Further progress on the phylogeny of Noctuoidea (Insecta: Lepidoptera) using an expanded gene sample
• Association of a novel mutation in the *Plasmodium falciparum* chloroquine resistance transporter with decreased piperaquine sensitivity
• Configuring concurrent computation of phylogenetic partial likelihoods: accelerating analyses using the BEAGLE library
• Heterogeneous hardware support in BEAGLE, a high-performance computing library for statistical phylogenetics
• Phylotranscriptomics resolves ancient divergences in the Lepidoptera
• Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads
• Phylogeny and Evolution of Lepidoptera
• Phylogeny and feeding trait evolution of the mega-diverse Gelechioidea (Lepidoptera: Obtectomera): new insight from 19 nuclear genes
• Subdividing long-running, variable-length analyses into short, fixed-length BOINC workunits
• A molecular phylogeny and revised classification for the oldest ditrysian moth lineages (Lepidoptera: Tineoidea), with implications for ancestral feeding habits of the mega-diverse Ditrysia
• Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation
• Phylogeny of Cladobranchia (Gastropoda: Nudibranchia): a total evidence analysis using DNA sequence data from public databases
• A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution
• *Plasmodium falciparum* field isolates from areas of repeated emergence of drug resistant malaria show no evidence of hypermutator phenotype
• Independent emergence of artemisinin resistance mutations among *Plasmodium falciparum* in Southeast Asia
• A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0
• AWTY, BAMBE, BEAGLE, BEAST, BEAUti, Bio++, DataMonkey, DendroPy, DnaSP, ENCprime/SeqCount, FigTree, GARLI, genealogical sorting index (gsi), HyPhy, IMa2, jModelTest, JELLYFISH, LAMARC, MacClade, MEGA, Mesquite, MIGRATE-N, Modeltest, Mr- Bayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, Structure, Structurama, Tracer, TreeStat, TreeView X
• Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study
• A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies)
• A molecular phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and its implications for classification, biogeography and the evolution of host plant use
• Genetic loci associated with delayed clearance of *Plasmodium falciparum* following artemisinin treatment in Southeast Asia
• A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification
• A comparative evaluation of sequence classification programs
• A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution
• BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics
• Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?
• Increased gene sampling yields robust support for higher-level clades within Bombycoidea (Lepidoptera)
• Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)
• Computing the Tree of Life: leveraging the Power of Desktop and Service Grids
• Broader incorporation of bioinformatics in education: opportunities and challenges
• Evolutionary framework for Lepidoptera model systems
• Validating the systematic position of *Plationus* Segers, Murugan & Dumont, 1993 (Rotifera: Brachionidae) using sequences of the large subunit of the nuclear ribosomal DNA and of cytochrome C oxidase
• Toward reconstructing the evolution of advanced moths and butterflies (Lepidoptera: Ditrysia): an initial molecular study
• Extreme polymorphism in a vaccine antigen and risk of clinical malaria: implications for vaccine development
• A molecular footprint of limb loss: sequence variation of the autopodial identity gene *Hoxa-13*
• Resolving arthropod phylogeny: exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence
• A genealogical approach to quantifying lineage divergence
• The Lattice Project: a Grid research and production environment combining multiple Grid computing models
• Biased data reduce efficiency and effectiveness of conservation reserve networks
• Expanding the reach of Grid computing: combining Globus-and BOINC-based systems
• Bio-STEER: A Semantic Web workflow tool for Grid computing in the life sciences
• Grid Services Base Library: A high-level, procedural application programming interface for writing Globus-based Grid services
• Grid computing
• Data sharing in ecology and evolution
• Abstracting workflows: unifying bioinformatics task conceptualization and specification through semantic web services
• Few amino acid positions in *rpo*B are associated with most of the rifampin resistance in *Mycobacterium tuberculosis*
• Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA
• A book like its cover
• BAMBE, DnaSP, ENCprime/SeqCount, LAMARC, MacClade, MEGA, Modeltest, MrBayes, PAML, PAUP*, PHYLIP, r8s, readseq, Seq-Gen, Sites, TreeView
• Section-level relationships of North American *Agalinis* (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions
• Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families
• Applying permutation tests to tree-based statistical models: extending the R package rpart
• Comparing bootstrap and posterior probability values in the four-taxon case
• Genetic consequences of ecological reserve design guidelines: an empirical investigation
• Necessity is the mother of invention: a simple grid computing system using commodity tools
• Phylogenetic analysis reveals five independent transfers of the chloroplast gene *rbc*L to the mitochondrial genome in angiosperms
• Effectiveness of conservation targets in capturing genetic diversity
• Phylogenetic analysis based on 18S ribosomal RNA gene sequences supports the existence of class Polyacanthocephala (Acanthocephala)
• Relating Amino Acid Sequence to Phenotype: analysis of Peptide-Binding Data
• A case for evolutionary genomics and the comprehensive examination of sequence biodiversity
• Phylogenetic relationships of *Phytophthora* species based on ribosomal ITS I DNA sequence analysis with emphasis on Waterhouse groups V and VI
• Phylogenetic relationships of Acanthocephala based on analysis of 18S ribosomal RNA gene sequences
• Genes and other samples of DNA sequence data for phylogenetic inference
• Phylogenetic relationships of Platyhelminthes based on 18S ribosomal gene sequences
• Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (*Hordeum vulgare* ssp. *spontaneum*): an evaluation of the background selection hypothesis
• Pigment composition of putatively achlorophyllous angiosperms
• Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus *Nicrophorus* (Coleoptera: Silphidae)
• The evolution of plant nuclear genes
• DNA sequence variation in the ribosomal internal transcribed spacer region of freshwater CIadophora species (Chlorophyta)
• Evolutionary biology of parasitic platyhelminths: the role of molecular phylogenetics
• Inferring phylogenies from DNA sequence data: the effects of sampling
• Sampling properties of DNA sequence data in phylogenetic analysis
• Transmission patterns of eukaryotic transposable elements: arguments for and against horizontal transfer
• Slipped-strand mispairing in a plastid gene: *rpo*C2 in grasses (Poaceae)
• *copia*-like retrotransposons are ubiquitous among plants
• Patterns and processes of sequence evolution: Plant organelle genomes and copia-like retrotransposons
• Copia-like retrotransposons in plants: a brief introduction
• Fundamentals of Molecular Evolution---Wen-Hsiung Li and Dan Graur
• A superfamily of *Arabidopsis thaliana* retrotransposons
• The structure, distribution and evolution of the Ta*1* retrotransposable element family of *Arabidopsis thaliana*
• Evolution of the avocados as revealed by DNA restriction fragment variation