Network Inference for a Whole-Genome Data-Set
Statistical inference and modelling for nosocomial infections and the incorporation of whole genome sequence data
... a set of individual-level patient ...carriage data described in the second ...of whole genome sequence data into a hospital transmission ...sequence data were collected from MRSA ...
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epiG:statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data
... We repeated the genotype validation study on the same ∼74k SNPs using different configurations of the prior. The percentage of correctly called AA and TT genotypes is unaffected by the prior settings (including with and ...
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Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences
... Having established that our algorithm can correctly recover simulated recombination events, we consider how many events we capture as we vary other parame- ters. In Figure 3 we consider the inferred r for a range of ARGs ...
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Models and Algorithms for Whole-Genome Evolution and their Use in Phylogenetic Inference
... from whole-genome data, ...one genome, but absent in the ...high-resolution data, as even just a few such genomes may require days or weeks of ...
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epiG: statistical inference and profiling of DNA methylation from whole genome bisulfite sequencing data
... We repeated the genotype validation study on the same ∼ 74k SNPs using different configurations of the prior. The percentage of correctly called AA and TT genotypes is unaffected by the prior settings (including with and ...
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Using Mendelian inheritance errors as quality control criteria in whole genome sequencing data set
... substantial data cleaning. Indeed, the uncleaned sequence data for chromosome 3 includes 1,607,227 variants passing SVM and INDEL5 ...cleaned data set contained 1,215,399 ...binary data ...
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Demographic and Population Separation History Inference Based on Whole Genome Sequences.
... genetic data of contemporary ca- nines alone since it is possible that dogs are domesticated from a wolf population that later went ...Irish genome suggested a Late Neolithic population replacement and a ...
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Evolution After Whole-genome Duplication: A Network Perspective
... In a recent study by (Qian et al. 2011), the authors experimentally examined 87 potential interactions between Kluyveromyces waltii proteins, whose one-to-one orthologs in the related budding yeast Saccharomyces ...
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Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates
... or annotation artifacts due to heterozygosity for instance. We therefore believe that there is no convincing signal for a shared Pinaceae WGD, as was also originally concluded by Nystedt et al. (2013). A possible ...
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Whole genome analyses accounting for structures in genotype data
... c, set c ∗ to be the WPPA of the current ...for inference at QTL would be valid given the condition that SNPs in a window completely capture the signal from QTL in that window and do not receive any signal ...
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Bioinformatics analysis of whole genome resequencing data in the chicken
... the data set of indels detected using mapping distances between mate- pairs, could be the gaps and duplicated regions in the chicken genome, as such errors are not considered in the algorithm of ...
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Bioinformatic analysis of Mycobacterium tuberculosis whole genome data
... the! genome! sequence! ...start!sites!(TSSs)!(Cortes!et#al.!2013)!and!identification!of!non9coding!RNAs!in!the!Mtb! genome! (Miotto! et# ...the! genome! for! the! first! time! (Galagan! et# ...
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GAMIBHEAR: whole-genome haplotype reconstruction from genome architecture mapping data
... sequencing data. Chromatin conformation data obtained from 3C experiments allows inference of haplotypes because inter-chromosomal contacts are more frequent than homologous intra-chromosomal ...
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Module network inference from a cancer gene expression data set identifies microRNA regulated modules
... module network inference ...module network inferred from both miRNA and mRNA expression data, using our recently developed module network inference algorithm based on ...
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
... and MCL algorithms that are freely available. These standalone applications must be installed separately to OrthoFinder and are not included in the OrthoFinder package. The implementation makes use of sparse matri- ces ...
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Probabilistic Cross-Species Inference of Orthologous Genomic Regions Created by Whole-Genome Duplication in Yeast
... a whole- genome duplication ...a set of genomes with a shared WGD (here five yeast ...another set of genes may be initially preserved in duplicate by natural selection for reasons including ...
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Analysis of homozygosity disequilibrium using whole genome sequencing data
... WGS data were provided by the T2D- GENES Consortium, which is supported by NIH grants U01 DK085524, U01 DK085584, U01 DK085501, U01 DK085526, and U01 ...phenotypic data for GAW18 were provided by the San ...
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Confidence set of putative quantitative trait loci in whole genome scans with application to the Genetic Analysis Workshop 17 simulated data
... the data themselves, usually with high accuracy, depending on the sample ...of data available for the ...particular data used. However, for whole-genome scans involving a large number ...
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The feasibility of genome-scale biological network inference using Graphics Processing Units
... for data-driven identification of network interactions include statisti- cal inference-based approaches and methods to identify dynamical systems models that are capable of fitting multi- variate ...
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Whole-genome data reveal the complex history of a diverse ecological community
... TreeMix (71)]. Parametric bootstrap. Maximizing the CL across blocks and subsamples ignores linkage between blocks but gives an unbiased point estimate of parameters. To measure the uncertainty in demographic parameter ...
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