long-read sequencing

This paper describes methods for isolating and analyzing nascent RNA using long-read sequencing in budding and fission yeasts to study RNA processing and transcription dynamics.

The paper creates a tandem repeat atlas for 39 inbred mouse strains using long-read sequencing, showing TRs are abundant but differ from human TRs in expansion and transposable element association.

The paper uses long-read sequencing to map Drp1 transcript variants in human and mouse tissues, revealing tissue-specific expression and isoform-dependent mitochondrial fission activity.

This paper uses long-read sequencing to characterize rAAV genomes and impurities, enabling better quality control in gene therapy production.

RawBench benchmarks raw nanopore signal analysis techniques, showing they can achieve competitive quality with reduced resource requirements for real-time and edge deployment.

This study integrates scFv development with CAR T cell generation to target CLL1-positive AML, showing effective tumor killing in vivo.

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

The paper identifies splicing variants in human kidney tissue associated with kidney function and cardiovascular-kidney-metabolic syndrome traits using long-read RNA sequencing and QTL analysis.

This study investigates parasite-mediated inbreeding depression in red deer, finding three pathways linking inbreeding to reduced fitness through parasitism.

The paper compares genomic assembly and annotation methods for two clones of avian pathogenic Escherichia coli using short and long-read sequencing.

This paper uses machine learning on direct RNA-seq data to show SARS-CoV-2 increases mA methylation in antiviral lncRNAs, potentially affecting IFN signaling and viral persistence.

The paper develops epigenetic clocks using long-read DNA methylation data from diverse ancestries, showing improved aging predictions and identifying ancestry-specific aging pathways.

The paper introduces NIL-TDS, a method for quantifying small RNA slicing activity, and demonstrates its application in detecting slicing events in plants and mammals.

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

This study benchmarks TE detection tools on long-read data, showing significant variation in performance and highlighting tool-specific strengths and limitations.

The paper uses nanopore sequencing and DNAscent to measure replication fork progression and origin/termination sites in Drosophila, revealing non-uniform fork speeds and variable origin positions.

The paper uses long-read sequencing to catalog Cacna1e splice variants in rat thalamus and computationally identifies four functionally distinct isoforms.

This study identifies aphid-derived lncRNAs that influence maize resistance by showing their systemic movement and impact on aphid fecundity and colonization.

The paper uses a pangenome of Capuchino Seedeaters to show that small SNPs and indels, not large structural variants, drive species divergence and plumage diversity.

The paper identifies Asgard, a STAT3-regulated lncRNA, which controls microRNA biogenesis and sequestration to maintain naive pluripotency in mouse embryonic stem cells.

The paper uses long-read sequencing to identify novel RNA isoforms in neuropsychiatric risk genes, revealing previously undetected exons and isoforms that may contribute to disease mechanisms.

This study uses long-read single-cell RNA sequencing to identify cell-type specific alternative splicing changes in COVID-19 patients compared to healthy controls.

This study identifies insect-derived lncRNAs that reprogram plant immunity by epigenetically suppressing defense genes.

The paper introduces a quality control method for synthetic RNA using Oxford Nanopore sequencing to assess integrity, sequence accuracy, and modification sites, improving synthesis fidelity and yield.

The paper assembles the diploid genome of Mexican lime, revealing high heterozygosity and structural variants between thorned and thornless lineages.

This study shows that removing a specific splice variant of ClC-1 in a DM1 mouse model eliminates myotonia and improves muscle function and histology.

The paper benchmarks somatic structural variant detection at ultra-low allele fractions using synthetic data and evaluates 12 pipelines, finding long-read sequencing provides higher accuracy than short-read methods.

The paper evaluates clustering and assembly methods for Iso-Seq data in non-model animals without reference genomes, finding CD-HIT at 99% similarity provides the best transcriptome quality.

This study uses long-read RNA sequencing to uncover E2-regulated transcriptome complexity, revealing novel isoforms and truncated proteins with functional implications in ER+ breast cancer.