James E. Tarver
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View article: NOTUM inhibition increases endocortical bone formation and bone strength
NOTUM inhibition increases endocortical bone formation and bone strength Open
The disability, mortality and costs caused by non-vertebral osteoporotic fractures are enormous. Existing osteoporosis therapies are highly effective at reducing vertebral but not non-vertebral fractures. Cortical bone is a major determina…
View article: Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss
Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss Open
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and …
View article: Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i>
Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i> Open
Our recent study evaluated the performance of parsimony and probabilistic
\nmodels of phylogenetic inference based on categorical data [1]. We found that a
\nBayesian implementation of a probabilistic Markov model produced more accurate
\n…
View article: Rapid Evolution of microRNA Loci in the Brown Algae
Rapid Evolution of microRNA Loci in the Brown Algae Open
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on the analysis of a…
View article: Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data
Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data Open
Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured b…
View article: MicroRNA annotation of plant genomes − Do it right or not at all
MicroRNA annotation of plant genomes − Do it right or not at all Open
MicroRNAs are non‐coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions wh…
View article: Supplementary material from "Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i>"
Supplementary material from "Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i>" Open
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View article: Literature reviewed from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i>.
Literature reviewed from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i>. Open
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View article: Electronic supplementary material from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history. A response to Brown <i>et al.</i>
Electronic supplementary material from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history. A response to Brown <i>et al.</i> Open
Literature reviewed
View article: Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data
Bayesian methods outperform parsimony but at the expense of precision in the estimation of phylogeny from discrete morphological data Open
Different analytical methods can yield competing interpretations of evolutionary history and, currently, there is no definitive method for phylogenetic reconstruction using morphological data. Parsimony has been the primary method for anal…
View article: The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference
The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference Open
Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controv…
View article: Puttick_et_al_R_script from Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data
Puttick_et_al_R_script from Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data Open
The R script used to generate the simulated data on which this analysis was based
View article: Supplementary material from "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data"
Supplementary material from "Uncertain-tree: discriminating among competing approaches to the phylogenetic analysis of phenotype data" Open
Morphological data provide the only means of classifying the majority of life's history, but the choice between competing phylogenetic methods for the analysis of morphology is unclear. Traditionally, parsimony methods have been favoured b…