32 research outputs found

    Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy

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    Gene regulatory networks give important insights into the mechanisms underlying physiology and pathophysiology. The derivation of gene regulatory networks from high-throughput expression data via machine learning strategies is problematic as the reliability of these models is often compromised by limited and highly variable samples, heterogeneity in transcript isoforms, noise, and other artifacts. Here, we develop a novel algorithm, dubbed Dandelion, in which we construct and train intraspecies Bayesian networks that are translated and assessed on independent test sets from other species in a reiterative procedure. The interspecies disease networks are subjected to multi-layers of analysis and evaluation, leading to the identification of the most consistent relationships within the network structure. In this study, we demonstrate the performance of our algorithms on datasets from animal models of oculopharyngeal muscular dystrophy (OPMD) and patient materials. We show that the interspecies network of genes coding for the proteasome provide highly accurate predictions on gene expression levels and disease phenotype. Moreover, the cross-species translation increases the stability and robustness of these networks. Unlike existing modeling approaches, our algorithms do not require assumptions on notoriously difficult one-to-one mapping of protein orthologues or alternative transcripts and can deal with missing data. We show that the identified key components of the OPMD disease network can be confirmed in an unseen and independent disease model. This study presents a state-of-the-art strategy in constructing interspecies disease networks that provide crucial information on regulatory relationships among genes, leading to better understanding of the disease molecular mechanisms

    Mapping 123 million neonatal, infant and child deaths between 2000 and 2017

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    Since 2000, many countries have achieved considerable success in improving child survival, but localized progress remains unclear. To inform efforts towards United Nations Sustainable Development Goal 3.2—to end preventable child deaths by 2030—we need consistently estimated data at the subnational level regarding child mortality rates and trends. Here we quantified, for the period 2000–2017, the subnational variation in mortality rates and number of deaths of neonates, infants and children under 5 years of age within 99 low- and middle-income countries using a geostatistical survival model. We estimated that 32% of children under 5 in these countries lived in districts that had attained rates of 25 or fewer child deaths per 1,000 live births by 2017, and that 58% of child deaths between 2000 and 2017 in these countries could have been averted in the absence of geographical inequality. This study enables the identification of high-mortality clusters, patterns of progress and geographical inequalities to inform appropriate investments and implementations that will help to improve the health of all populations

    Characterizing IonTorrent PGM Error Profiles using TSSV

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    <p>This dataset contains sequencing reads used to characterize systematic errors of IonTorrent PGM sequencer as well as all of the analysis results in separate files.</p

    Allele-specific Characterization of STR Structures in Pure and Mixed Forensic Samples using TSSV

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    <p>This dataset contains sequencing reads used to characterize allelic STR structures in pure and mixed forensic samples as well as all of the analysis results in separate files.</p

    Identification of SNPs to determine associated Y-chromosome Haplogroup using TSSV

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    <p>This dataset contains sequencing reads used to identify SNPs in order to determine associated Y-chromosomal haplogroups as well as all of the analysis results in separate files.</p

    Characterization of DeNovo Structural Variations Induced by TALENs Targeting hDMD in Mouse ES Cells using TSSV

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    <p>This dataset contains sequencing reads used to characterize de novo variations induced by TALENs targeting intron 52-53 of hDMD gene in mouse ES cells as well as all of the analysis results in separate files.</p
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