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Article
Open AccessDisentangling the genetic basis of rhizosphere microbiome assembly in tomato
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as ...
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Article
Open AccessmirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis
We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized m...
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Article
Open AccessSCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In additio...
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Article
Open AccessVaginal microbiome topic modeling of laboring Ugandan women with and without fever
The composition of the maternal vaginal microbiome influences the duration of pregnancy, onset of labor, and even neonatal outcomes. Maternal microbiome research in sub-Saharan Africa has focused on non-pregna...
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Article
Open AccessSensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia
Epstein Barr virus (EBV) is the etiologic agent involved in numerous human cancers. After infecting the host, EBV establishes a latent infection, with low levels of messenger RNA (mRNA) and protein expression,...
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Article
Open AccessSystematic pan-cancer analysis of somatic allele frequency
Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, and can therefore indicate possible driving potential of the underlying genetic variants. To explore the correl...
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Article
Open AccessOverexpressed somatic alleles are enriched in functional elements in Breast Cancer
Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are po...
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Article
Open AccessAnalysis for co-occurring sequence features identifies link between common synonymous variant and an early-terminated NPC1 isoform
Direct assessment of allelic phase for DNA and RNA features of diploid genomes has been challenging for Sanger sequencing, due to its allele-conflating base-calling signal. Massively parallel sequencing techno...
