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Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control
BackgroundWe propose a novel variational Bayes network reconstruction algorithm to extract the most relevant disease factors from high-throughput...
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Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait map** and genomic prediction
BackgroundIn quantitative trait map** and genomic prediction, Bayesian variable selection methods have gained popularity in conjunction with the...
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A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum
BackgroundAccording to the World Health organization, half the world's population is at risk of contracting malaria. They estimated that in 2010...
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DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference
BackgroundInferring molecular pathway activity is an important step towards reducing the complexity of genomic data, understanding the heterogeneity...
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puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis
BackgroundMicroarrays have been a popular tool for gene expression profiling at genome-scale for over a decade due to the low cost, short turn-around...
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MixSIH: a mixture model for single individual haploty**
BackgroundHaplotype information is useful for various genetic analyses, including genome-wide association studies. Determining haplotypes...
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Beyond Spandrels: Stephen J. Gould, EvoDevo, and the Extended Synthesis
In evolutionary biology, the term “spandrel” infallibly elicits the memory of Steve Gould. It has become a standard in referring to constructional...
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Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory
BackgroundStochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex...
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The Developmental Basis of Quantitative Craniofacial Variation in Humans and Mice
The human skull is a complex and highly integrated structure that has long held the fascination of anthropologists and evolutionary biologists....
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It was (not) me: Causal Inference of Agency in goal-directed actions
Summary:The perception of one’s own actions depends on both sensory information and predictions derived from internal forward models [1]. The...
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It was (not) me: Causal Inference of Agency in goal-directed actions
Summary:The perception of one's own actions depends on both sensory information and predictions derived from internal forward models [1]. The...
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Critical assessment of automated flow cytometry data analysis techniques
Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational...
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Bayesian semiparametric regression models to characterize molecular evolution
BackgroundStatistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the...
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A LDA-based approach to promoting ranking diversity for genomics information retrieval
BackgroundIn the biomedical domain, there are immense data and tremendous increase of genomics and biomedical relevant publications. The wealth of...
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Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution
The past decade has seen a growing interest in evolutionary models that relax the assumption of site-independent evolution for non-coding sequences....
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Bayesian inference of the number of factors in gene-expression analysis: application to human virus challenge studies
BackgroundNonparametric Bayesian techniques have been developed recently to extend the sophistication of factor models, allowing one to infer the...
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The complete mitochondrial genome of the butterfly Apatura metis (Lepidoptera: Nymphalidae)
As an important pest in the Slender Leaved Willow ( Salix alba ), Apatura metis is called Freyer’s purple emperor, and its mitochondrial genome is...
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Life’s Attractors
We propose an approach to evolutionary systems biology which is based on reverse engineering of gene regulatory networks and in silico evolutionary...
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Global Parameter Identification of Stochastic Reaction Networks from Single Trajectories
We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the...