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Pharmacokinetic recall study of Estonian Biobank participants with novel genetic variants in CYP2C19 and CYP2D6
CYP2C19 and CYP2D6 are involved in the hepatic metabolism of approximately 35-40% of clinically used drugs. We conducted an in vivo phenotyping study encompassing 114 Estonian Biobank participants to evaluate the functional impact of rare …
Read PDFTEvarSim: A genome simulator for transposable element (TE) variants
Transposable element (TE) variants, the presence or absence of TE sequences such as LINE-1, Alu, SVA, and endogenous retroviruses, are a major source of genomic diversity and play critical roles in human health, evolution, and …
Read PDFmiRNA regulation in brain tissue space: the 3'UTR perspective
MicroRNAs (miRNAs) are key regulators of gene expression in both health and disease. Their expression and regulatory functions are highly complex and spatiotemporally organized within tissues. In recent years, spatial transcriptomics has made significant progress …
Read PDFRecent advances in the detection technologies for balanced chromosomal rearrangements
Balanced chromosomal rearrangements (BCRs) refer to a type of chromosomal structural variations without chromosomal gains or losses. BCR carriers may experience fertility issues, including a higher risk of infertility, recurrent miscarriages, or having offspring with …
Read PDFLong-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
DNA conformation may deviate from the classical B-form in ∼13% of the human genome. Non-B DNA regulates many cellular processes; however, its effects on DNA polymerization speed and accuracy have not been investigated genome-wide. Such …
Read PDFisoespy: an integrated long-read transcriptome workflow for isoform resolution and visualization
<h4>Summary</h4>Long-read RNA-seq uncovers complex transcriptome diversity, opening new avenues for isoform-level expression analysis. Nevertheless, the functional diversity of individual isoforms is still poorly understood. We introduce isoespy, an analysis pipeline for integrating isoform structures, differential …
Read PDFDark and camouflaged genomic regions remain challenging in CHM13
Comprehensive genomic analysis is essential for advancing our understanding of human genetics and disease. However, short-read sequencing technologies are inherently limited in their ability to resolve highly repetitive, structurally complex, and low-mappability genomic regions, previously …
Read PDFInspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data
<h4>Motivation</h4>The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our understanding of what parts of the transcriptome are translated. Many alternative open reading …
Read PDFImproved reconstruction of transcripts and coding sequences from RNA-seq data
Annotation of genes and transcripts is a key prerequisite for understanding the information that is encoded in newly sequenced genomes. One source of information suited for this purpose is RNA-seq data mapped to the respective …
Read PDFExpanding the landscape of tRNA pathogenic variants in mitochondrial DNA
We present a comprehensive molecular and histopathological characterization of nine patients with mitochondrial myopathy, predominantly manifesting progressive external ophthalmoplegia (PEO), associated with heteroplasmic variants in mitochondrial tRNA genes (mt-tRNA). Among the ten variants identified, four …
Read PDFIntegrated genomic and clinical indicators for predicting foetal chromosomal abnormalities: development and validation of a nomogram model
<h4>Background</h4>Foetal chromosomal abnormalities are identified as one of the leading causes of adverse pregnancy outcome in pregnancies that are referred on suspicion of structural abnormalities in the foetus. While various types of genomic analyses can …
Read PDFHIV-1 virome profiling using HIV-PULSE to guide therapeutic and curative interventions
<h4>Background</h4>The persistent HIV-1 reservoir remains a major barrier to curing HIV-1, underscoring the need for a detailed understanding of its composition to inform targeted interventions.<h4>Methods</h4>Here, we apply the HIV Proviral Unique molecular identifier-mediated Long-read Sequencing …
Read PDFOrthogonal characterization of rAAV reveals vector attributes that drive ITR repair, self-complementary genome formation, and transgene expression
Recombinant adeno-associated virus (rAAVs) vectors are the flagship vehicles for delivering DNA payloads for human gene therapy. However, only a few outstanding therapies have reached the market in the past decade. One reason for the …
Read PDFGenome-wide associations of structural variants with human traits through imputation from long-read assemblies
Structural variants (SVs) are a major type of genetic variation, yet their role in human traits remains largely uncharacterized, primarily due to challenges in genotyping them on a genome-wide scale in large cohorts. Here we …
Read PDFComplete genome sequence of <i>Paenibacillus</i> sp. PK1-4R (DSM 120655) isolated from the rhizosphere of <i>Brassica napus</i> in Rostock, Germany
We report on the complete genome sequence of the rhizobacterium <i>Paenibacillus</i> sp. PK1-4R. This might be a new species within the genus <i>Paenibacillus</i>, as evidenced by the taxonomic classification using the TYGS web server. It …
Read PDFSensitivity of HiFi long-read genome sequencing for difficult-to-detect pathogenic variants when applied to real-world clinical laboratory samples
Leveraging new sequencing and omic technologies to enhance the detection of pathogenic variants in known disease genes is a key step toward increasing the likelihood of a precise genetic diagnosis for affected individuals. Short-read sequencing …
Read PDFMolecular QTL are enriched for structural variants in a cattle long-read cohort
Sequencing cohorts with long-read technology is crucial to understand the impact of structural variants (SVs) on complex traits. Here, we obtain 4.86 terabases of HiFi reads with an average read N50 of 16.3 Kb from …
Read PDFDefining the breakpoints of the v <i>ermilion white</i> ( <i>v <sup>w</sup></i> ) mutation, a deletion that removes <i>vermilion, gustatory receptor candidate 58,</i> and <i>norpA</i>
A key mutation for generating transgenics in <i>Tribolium castaneum</i> is <i>vermilion <sup>white</sup></i> ( <i>v <sup>w</sup></i> ). <i> v <sup>w</sup></i> is a deletion that removes most of the <i>vermilion</i> locus, but the upstream breakpoint has not been …
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