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Wu S.H.,University of Auckland | Wu S.H.,Duke University | Black M.A.,University of Otago | North R.A.,Kings College London | And 2 more authors.
BMC Bioinformatics | Year: 2012

Background: Two-dimensional polyacrylamide gel electrophoresis (2D PAGE) is commonly used to identify differentially expressed proteins under two or more experimental or observational conditions. Wu et al (2009) developed a univariate probabilistic model which was used to identify differential expression between Case and Control groups, by applying a Likelihood Ratio Test (LRT) to each protein on a 2D PAGE. In contrast to commonly used statistical approaches, this model takes into account the two possible causes of missing values in 2D PAGE: either (1) the non-expression of a protein; or (2) a level of expression that falls below the limit of detection.Results: We develop a global Bayesian model which extends the previously described model. Unlike the univariate approach, the model reported here is able treat all differentially expressed proteins simultaneously. Whereas each protein is modelled by the univariate likelihood function previously described, several global distributions are used to model the underlying relationship between the parameters associated with individual proteins. These global distributions are able to combine information from each protein to give more accurate estimates of the true parameters. In our implementation of the procedure, all parameters are recovered by Markov chain Monte Carlo (MCMC) integration. The 95% highest posterior density (HPD) intervals for the marginal posterior distributions are used to determine whether differences in protein expression are due to differences in mean expression intensities, and/or differences in the probabilities of expression.Conclusions: Simulation analyses showed that the global model is able to accurately recover the underlying global distributions, and identify more differentially expressed proteins than the simple application of a LRT. Additionally, simulations also indicate that the probability of incorrectly identifying a protein as differentially expressed (i.e., the False Discovery Rate) is very low. The source code is available at https://github.com/stevenhwu/BIDE-2D. © 2012 Wu et al.; licensee BioMed Central Ltd.

Nascimento F.F.,Instituto Oswaldo Cruz | Nascimento F.F.,The National Evolutionary Synthesis Center | Lazar A.,Instituto Oswaldo Cruz | Menezes A.N.,Instituto Nacional Of Cancer | And 7 more authors.
PLoS ONE | Year: 2013

The Neotropics harbors a high diversity of species and several hypotheses have been proposed to account for this pattern. However, while species of forested domains are frequently studied, less is known of species from open vegetation formations occupying, altogether, a larger area than the Amazon Forest. Here we evaluate the role of historical barriers and the riverine hypothesis in the speciation patterns of small mammals by analyzing an ancient rodent lineage (Thrichomys, Hystricomorpha). Phylogenetic and biogeographic analyses were carried out with mitochondrial and nuclear DNA markers to analyze the evolutionary relationships between Thrichomys lineages occurring in dry domains along both banks of the Rio São Francisco. This river is one of the longest of South America whose course and water flow have been modified by inland tectonic activities and climate changes. Molecular data showed a higher number of lineages than previously described. The T. inermis species complex with 2n = 26, FN = 48 was observed in both banks of the river showing a paraphyletic arrangement, suggesting that river crossing had occurred, from east to west. A similar pattern was also observed for the T. apereoides complex. Thrichomys speciation occurred in Late Miocene when the river followed a different course. The current geographic distribution of Thrichomys species and their phylogenetic relationships suggested the existence of frequent past connections between both banks in the middle section of the Rio São Francisco. The extensive palaeodune region found in this area has been identified as a centre of endemism of several vertebrate species and is likely to be a center of Thrichomys diversification. © 2013 Nascimento et al.

Adam Smith N.,The National Evolutionary Synthesis Center
Palaeontologia Electronica | Year: 2015

The Charadriiformes (shorebirds and allies) are an ecologically and morphologically diverse clade with a global geographic distribution. The perceived antiquity of this lineage and the cryptic plumage and morphology of some charadriiforms have made them a frequent focus of study by ornithologists. Likewise, with the relatively recent advent of molecular sequence based divergence estimation methods, no less than seven studies have estimated the timing of cladogenetic events in Charadriiformes. Unfortunately, all of those studies have suffered from poor choice and characterization (i.e., age and taxonomic assignment) of fossil calibrations used for divergence time analysis. Given that studies of both real and simulated data have demonstrated the potential for calibration choice to bias node age estimates, the results of previously published analyses of divergence times for Charadriiformes must, accordingly, be viewed with caution. To alleviate introduction of fossil calibration bias with respect to future analyses of divergence times including Charadriiformes, 16 rigorously evaluated charadriiform fossil calibrations are reported herein. © Society for Vertebrate Paleontology February 2015.

Piwowar H.A.,University of Pittsburgh | Piwowar H.A.,The National Evolutionary Synthesis Center
PLoS ONE | Year: 2011

Many initiatives encourage investigators to share their raw datasets in hopes of increasing research efficiency and quality. Despite these investments of time and money, we do not have a firm grasp of who openly shares raw research data, who doesn't, and which initiatives are correlated with high rates of data sharing. In this analysis I use bibliometric methods to identify patterns in the frequency with which investigators openly archive their raw gene expression microarray datasets after study publication. Automated methods identified 11,603 articles published between 2000 and 2009 that describe the creation of gene expression microarray data. Associated datasets in best-practice repositories were found for 25% of these articles, increasing from less than 5% in 2001 to 30%-35% in 2007-2009. Accounting for sensitivity of the automated methods, approximately 45% of recent gene expression studies made their data publicly available. First-order factor analysis on 124 diverse bibliometric attributes of the data creation articles revealed 15 factors describing authorship, funding, institution, publication, and domain environments. In multivariate regression, authors were most likely to share data if they had prior experience sharing or reusing data, if their study was published in an open access journal or a journal with a relatively strong data sharing policy, or if the study was funded by a large number of NIH grants. Authors of studies on cancer and human subjects were least likely to make their datasets available. These results suggest research data sharing levels are still low and increasing only slowly, and data is least available in areas where it could make the biggest impact. Let's learn from those with high rates of sharing to embrace the full potential of our research output. © 2011 Healther A. Piwowar.

Nascimento F.F.,The National Evolutionary Synthesis Center | Nascimento F.F.,Instituto Oswaldo Cruz | Lazar A.,Instituto Oswaldo Cruz | Seuanez H.N.,Instituto Nacional Of Cancer | And 2 more authors.
Journal of Biogeography | Year: 2015

The data used by Lynch Alfaro et al. (2012a, Journal of Biogeography, 39, 272-288) and the biogeographical hypothesis postulated by these authors to explain the current distribution of capuchin monkeys were reanalysed including additional cytochrome b data from Sapajus xanthosternos and Sapajus flavius. Our reconstructed phylogeny placed S. xanthosternos in a monophyletic clade representing the most basal lineage of this genus. All analyses indicated polyphyletic arrangements for several capuchin species, suggesting that incomplete lineage sorting has occurred during their evolution. These results also suggest that available molecular data lack adequate variation for accurately resolving species relationships. These results suggest that the divergence of capuchin monkey genera may have occurred in the Atlantic Forest. However, a more conclusive scenario and better resolution of the species tree requires correct identification of species, data from several unlinked nuclear loci from a higher number of individuals per species, and careful analysis of ancient DNA data from museum specimens. © 2015 John Wiley & Sons Ltd.

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