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https://www.readbyqxmd.com/read/28200071/adaptive-mcmc-in-bayesian-phylogenetics-an-application-to-analyzing-partitioned-data-in-beast
#1
Guy Baele, Philippe Lemey, Andrew Rambaut, Marc A Suchard
No abstract text is available yet for this article.
February 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28193551/a-gibbs-sampling-method-to-determine-biomarkers-for-asthma
#2
Zhi-Jian Huang, Qin-Hai Shen, Yan-Sheng Wu, Ya-Li Huang
PURPOSE: To identify potential biomarkers and to uncover the mechanisms underlying asthma based on Gibbs sampling. METHODS: The molecular functions (MFs) with genes greater than 5 were determined using AnnotationMFGO of BAGS package, and the obtained MFs were then transformed to Markov chain (MC). Gibbs sampling was conducted to obtain a new MC. Meanwhile, the average probabilities of MFs were computed via MC Monte Carlo (MCMC) algorithm, followed by identification of differentially expressed MFs based on the probabilities of MF more than 0...
January 22, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28187712/vmcmc-a-graphical-and-statistical-analysis-tool-for-markov-chain-monte-carlo-traces
#3
Raja H Ali, Mikael Bark, Jorge Miró, Sayyed A Muhammad, Joel Sjöstrand, Syed M Zubair, Raja M Abbas, Lars Arvestad
BACKGROUND: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e...
February 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28185583/probabilistic-inference-of-lateral-gene-transfer-events
#4
Mehmood Alam Khan, Owais Mahmudi, Ikram Ullah, Lars Arvestad, Jens Lagergren
BACKGROUND: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. RESULTS: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities...
November 11, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28182726/spatial-patterns-of-multidrug-resistant-tuberculosis-and-relationships-to-socio-economic-demographic-and-household-factors-in-northwest-ethiopia
#5
Kefyalew Addis Alene, Kerri Viney, Emma S McBryde, Archie C A Clements
BACKGROUND: Understanding the geographical distribution of multidrug-resistant tuberculosis (MDR-TB) in high TB burden countries such as Ethiopia is crucial for effective control of TB epidemics in these countries, and thus globally. We present the first spatial analysis of multidrug resistant tuberculosis, and its relationship to socio-economic, demographic and household factors in northwest Ethiopia. METHODS: An ecological study was conducted using data on patients diagnosed with MDR-TB at the University of Gondar Hospital MDR-TB treatment centre, for the period 2010 to 2015...
2017: PloS One
https://www.readbyqxmd.com/read/28170425/phylogeny-and-biogeography-of-the-amphi-pacific-genus-aphananthe
#6
Mei-Qing Yang, De-Zhu Li, Jun Wen, Ting-Shuang Yi
Aphananthe is a small genus of five species showing an intriguing amphi-Pacific distribution in eastern, southern and southeastern Asia, Australia, and Mexico, also with one species in Madagascar. The phylogenetic relationships of Aphananthe were reconstructed with two nuclear (ITS & ETS) and two plastid (psbA-trnH & trnL-trnF) regions. Clade divergence times were estimated with a Bayesian approach, and the ancestral areas were inferred using the dispersal-extinction-cladogenesis and Bayesian Binary MCMC analyses...
2017: PloS One
https://www.readbyqxmd.com/read/28166715/bmodeltest-bayesian-phylogenetic-site-model-averaging-and-model-comparison
#7
Remco R Bouckaert, Alexei J Drummond
BACKGROUND: Reconstructing phylogenies through Bayesian methods has many benefits, which include providing a mathematically sound framework, providing realistic estimates of uncertainty and being able to incorporate different sources of information based on formal principles. Bayesian phylogenetic analyses are popular for interpreting nucleotide sequence data, however for such studies one needs to specify a site model and associated substitution model. Often, the parameters of the site model is of no interest and an ad-hoc or additional likelihood based analysis is used to select a single site model...
February 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28139001/projecting-the-future-burden-of-cancer-bayesian-age-period-cohort-analysis-with-integrated-nested-laplace-approximations
#8
Andrea Riebler, Leonhard Held
The projection of age-stratified cancer incidence and mortality rates is of great interest due to demographic changes, but also therapeutical and diagnostic developments. Bayesian age-period-cohort (APC) models are well suited for the analysis of such data, but are not yet used in routine practice of epidemiologists. Reasons may include that Bayesian APC models have been criticized to produce too wide prediction intervals. Furthermore, the fitting of Bayesian APC models is usually done using Markov chain Monte Carlo (MCMC), which introduces complex convergence concerns and may be subject to additional technical problems...
January 31, 2017: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/28113852/local-autoencoding-for-parameter-estimation-in-a-hidden-potts-markov-random-field
#9
Sanming Song, Bailu Si, J Michael Herrmann, Xisheng Feng
A local-autoencoding (LAE) method is proposed for the parameter estimation in a Hidden Potts-Markov random field (MRF) model. Due to sampling cost, Markov chain Monte Carlo (MCMC) methods are rarely used in real-time applications. Like other heuristic methods, LAE is based on a conditional independence assumption. It adapts, however, the parameters in a block-by-block style with a simple Hebbian learning rule. Experiments with given label fields show that LAE is able to converge in far less time than required for a scan...
March 22, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#10
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28099991/bayescat-bayesian-co-estimation-of-alignment-and-tree
#11
Heejung Shim, Bret Larget
Traditionally, phylogeny and sequence alignment are estimated separately: first estimate a multiple sequence alignment and then infer a phylogeny based on the sequence alignment estimated in the previous step. However, uncertainty in the alignment is ignored, resulting, possibly, in overstated certainty in phylogeny estimates. We develop a joint model for co-estimating phylogeny and sequence alignment which improves estimates from the traditional approach by accounting for uncertainty in the alignment in phylogenetic inferences...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28081166/comparison-of-criteria-for-choosing-the-number-of-classes-in-bayesian-finite-mixture-models
#12
Kazem Nasserinejad, Joost van Rosmalen, Wim de Kort, Emmanuel Lesaffre
Identifying the number of classes in Bayesian finite mixture models is a challenging problem. Several criteria have been proposed, such as adaptations of the deviance information criterion, marginal likelihoods, Bayes factors, and reversible jump MCMC techniques. It was recently shown that in overfitted mixture models, the overfitted latent classes will asymptotically become empty under specific conditions for the prior of the class proportions. This result may be used to construct a criterion for finding the true number of latent classes, based on the removal of latent classes that have negligible proportions...
2017: PloS One
https://www.readbyqxmd.com/read/28053140/efficient-bayesian-species-tree-inference-under-the-multispecies-coalescent
#13
Bruce Rannala, Ziheng Yang
We develop a Bayesian method for inferring the species phylogeny under the multispecies coalescent (MSC) model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we implement two efficient MCMC proposals: the first is based on the Subtree Pruning and Regrafting (SPR) algorithm and the second is based on a node-slider algorithm. Like the Nearest-Neighbor Interchange (NNI) algorithm we implemented previously, both new algorithms propose changes to the species tree while simultaneously altering the gene trees at multiple genetic loci to automatically avoid conflicts with the newly proposed species tree...
January 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28027885/structural-differences-in-mixing-behavior-informing-the-role-of-asymptomatic-infection-and-testing-symptom-heritability
#14
Eva Santermans, Kim Van Kerckhove, Amin Azmon, W John Edmunds, Philippe Beutels, Christel Faes, Niel Hens
Most infectious disease data is obtained from disease surveillance which is based on observations of symptomatic cases only. However, many infectious diseases are transmitted before the onset of symptoms or without developing symptoms at all throughout the entire disease course, referred to as asymptomatic transmission. Fraser and colleagues [1] showed that this type of transmission plays a key role in assessing the feasibility of intervention measures in controlling an epidemic outbreak. To account for asymptomatic transmission in epidemic models, methods often rely on assumptions that cannot be verified given the data at hand...
December 24, 2016: Mathematical Biosciences
https://www.readbyqxmd.com/read/28025203/accelerating-bayesian-inference-for-evolutionary-biology-models
#15
Xavier Meyer, Bastien Chopard, Nicolas Salamin
MOTIVATION: Bayesian inference is widely used nowadays and relies largely on Markov chain Monte Carlo (MCMC) methods. Evolutionary biology has greatly benefited from the developments of MCMC methods, but the design of more complex and realistic models and the ever growing availability of novel data is pushing the limits of the current use of these methods. RESULTS: We present a parallel Metropolis-Hastings (M-H) framework built with a novel combination of enhancements aimed towards parameter-rich and complex models...
December 24, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28018015/bayesian-nonparametric-estimation-for-dynamic-treatment-regimes-with-sequential-transition-times
#16
Yanxun Xu, Peter Müller, Abdus S Wahed, Peter F Thall
We analyze a dataset arising from a clinical trial involving multi-stage chemotherapy regimes for acute leukemia. The trial design was a 2 × 2 factorial for frontline therapies only. Motivated by the idea that subsequent salvage treatments affect survival time, we model therapy as a dynamic treatment regime (DTR), that is, an alternating sequence of adaptive treatments or other actions and transition times between disease states. These sequences may vary substantially between patients, depending on how the regime plays out...
2016: Journal of the American Statistical Association
https://www.readbyqxmd.com/read/28008726/multi-objective-global-optimization-mogo-algorithm-and-case-study-in-gradient-elution-chromatography
#17
Lars Freier, Eric von Lieres
Biotechnological separation processes are routinely designed and optimized using parallel high-throughput experiments and/or serial experiments. Well-characterized processes can further be optimized using mechanistic models. In all these cases - serial/parallel experiments and modeling - iterative strategies are customarily applied for planning novel experiments/simulations based on the previously acquired knowledge. Process optimization is typically complicated by conflicting design targets, such as productivity and yield...
December 23, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/28002465/inference-of-functionally-relevant-n-acetyltransferase-residues-based-on-statistical-correlations
#18
Andrew F Neuwald, Stephen F Altschul
Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27998816/out-of-southern-africa-origin-biogeography-and-age-of-the-aizooideae-aizoaceae
#19
Cornelia Klak, Pavel Hanáček, Peter V Bruyns
The Aizooideae is an early-diverging lineage within the Aizoaceae. It is most diverse in southern Africa, but also has endemic species in Australasia, Eurasia and South America. We derived a phylogenetic hypothesis from Bayesian and Maximum Likelihood analyses of plastid DNA-sequences. We find that one of the seven genera, the fynbos-endemic Acrosanthes, does not belong to the Aizooideae, but is an ancient sister-lineage to the subfamilies Mesembryanthemoideae & Ruschioideae. Galenia and Plinthus are embedded inside Aizoon and Aizoanthemum is polyphyletic...
December 18, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27978814/switchfinder-a-novel-method-and-query-facility-for-discovering-dynamic-gene-expression-patterns
#20
Svetlana Bulashevska, Colin Priest, Daniel Speicher, Jörg Zimmermann, Frank Westermann, Armin B Cremers
BACKGROUND: Biological systems and processes are highly dynamic. To gain insights into their functioning time-resolved measurements are necessary. Time-resolved gene expression data captures temporal behaviour of the genes genome-wide under various biological conditions: in response to stimuli, during cell cycle, differentiation or developmental programs. Dissecting dynamic gene expression patterns from this data may shed light on the functioning of the gene regulatory system. The present approach facilitates this discovery...
December 15, 2016: BMC Bioinformatics
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