long-read sequencing

High-Resolution Characterization of rAAV Genomes for Vector Quality Using Long-Read Sequencing

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

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques

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

Integrated scFv identification and CAR T cell generation for AML targeting in vivo

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

Population-scale Long-read Sequencing in the All of Us Research Program

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.

Human Kidney Alternative Splicing Information Illuminates Cardiovascular-Kidney-Metabolic Syndrome Risk

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.

Parasite-mediated inbreeding depression in wild red deer

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

Comparison of genomic assembly and annotation based on two clones of avian pathogenic Escherichia coli

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

SARS-CoV-2 reshapes mA methylation in long non-coding RNAs of human lung cells

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.

Long-Read epigenetic clocks identify improved brain aging predictions

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

High Precision Quantification of small RNA Slicing Activity - Native Index Ligation-based Targeted Degradome Sequencing (NIL-TDS)

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.

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

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

Systematic comparative benchmarking of computational methods for the detection of transposable elements in long-read sequencing data

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

A conserved long-range RNA interaction in SARS-CoV-2 recruits ADAR1 to enhance virus proliferation

Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication fork progression, origin and termination sites

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.

Cataloging the potential functional diversity of Cacna1e splice variants using long-read sequencing

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

Aphid-derived cross-kingdom RNA dynamics underpin maize resistance

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

A pangenomic approach reveals the sources of genetic variation fueling the rapid radiation of Capuchino Seedeaters

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.

A STAT3-regulated lncRNA integrates microRNA biogenesis and sequestration to safeguard naive pluripotency

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

Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain

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.

Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19

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.

Insect-derived long non-coding RNAs function as epigenetic effectors to reprogram plant immunity

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

Pore-Based RNA Evaluation for Control of Integrity, Sequence, and Errors - Quality Control (PRECISE-QC)

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.

Diploid assembly of the Mexican lime genome reveals extensive heterozygosity

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

Elimination of myotonia improves myopathy in a muscleblind knockout model of myotonic dystrophy

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.

Comprehensive benchmarking of somatic structural variant detection at ultra-low allele fractions

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.

An evaluation of clustering and assembly strategies from Iso-Seq data in the absence of reference genomes in non-model animals

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.

E2-Regulated Transcriptome Complexity Revealed by Long-Read Direct RNA Sequencing: From Isoform Discovery to Truncated Proteins

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.

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

The paper uses long-read metagenomics to analyze pet dog gut microbiomes, generating high-quality MAGs and identifying antimicrobial resistance elements in a Shanghai cohort.

Polyadenylation landscape of in vivo long-term potentiation in the rat brain

This study uses nanopore sequencing to analyze polyadenylation changes in rat hippocampi during long-term potentiation, revealing dynamic shifts in poly(A) tail length and composition.

Droplet-assisted folding of long regulatory RNAs

The paper proposes a mechanism called droplet-assisted RNA folding, where RNA-binding protein condensates guide the folding of long regulatory RNAs by preventing premature interactions and enabling long-range contacts.