long-read sequencing

Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing

The paper uses long-read RNA-seq and isoLASER to distinguish cis- and trans-directed splicing events in human and mouse data, identifying thousands of cis-regulated events in disease-relevant genes.

Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7

The paper develops Nano-Mod-Amp, a Nanopore sequencing tool, to analyze PUS7-dependent pseudouridylation, revealing structural and cell-type specific regulatory mechanisms.

Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes

The paper develops tools to analyze phased genomes of polar fishes, revealing haplotype diversity in antifreeze protein copy numbers while mitigating assembly errors.

Complete post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species

The paper provides a comprehensive analysis of tRNA modifications in Staphylococcus aureus, revealing species-specific features and decoding dynamics.

Epstein-Barr Virus Encoded lncRNAs Control the Viral Lytic Switch

This study identifies viral lncRNAs that regulate EBV reactivation by interacting with CTCF and modulating enhancer-promoter looping.

Long-read RNA-seq delineates temporal transcriptional dynamics in multiplexed and sexed single medfly embryos

The paper uses long-read RNA-seq to analyze temporal transcriptional dynamics in single medfly embryos, identifying novel genes and developmental transitions.

The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations

The paper identifies structural variants and coding polymorphisms in the human IGHC locus, revealing population-specific diversity and potential functional impacts.

Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia

The paper uses Cappable-Seq to analyze transcriptional start sites in Wolbachia under stress conditions, revealing differential regulation and insights into gene operon organization.

Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires

The paper analyzes the genome of Phytophthora theobromicola using long-read sequencing and comparative genomics to reveal dynamic structure and variable effector repertoires.

Direct identification of de novo mobile element insertions from single molecule sequencing of human sperm

The paper directly identifies de novo mobile element insertions in human sperm using long-read sequencing and finds age-related increases in retrotransposition rates.

High-Resolution Variant Profiling of CAH-Associated Genes Using a Long-Read Sequencing Assay

NanoCAH, a long-read sequencing assay, accurately detects all known variants and resolves haplotypes in CAH-associated genes, outperforming conventional methods.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

Integrated multi-omic and functional evidence uncover substantial strain-specific divergence in zebrafish

The paper compares two zebrafish strains using multi-omic data to identify genetic and regulatory differences affecting circadian rhythms and immune response.

REFLEX, a Novel Immune Profiling Assay, Combining TCR Repertoire and Multiome at Massively Scalable Single-cell Resolution to Catapult Exploration of T-cell Derived Immunity

REFLEX enables scalable, multiomic T cell profiling with TCR sequencing, identifying novel CMV-reactive clonotypes in over 1.4 million T cells.

Unraveling the Transcriptional Landscape within a Minimized Bacterium via Comparative Analysis

This study compares transcriptomes of two minimized bacteria to understand gene expression patterns and highlights limitations of bioinformatics alone.

Comparative analysis of CRISPR/Cas9-targeted nanopore sequencing approaches in repeat expansion disorders

This study compares CRISPR/Cas9-targeted nanopore sequencing approaches for characterizing repeat expansions in DM1 and OPDM, showing the impact of basecalling strategies and identifying somatic mosaicism and hypermethylation.

Barbell Resolves Demultiplexing and Trimming Issues in Nanopore Data

Barbell improves demultiplexing of Nanopore sequencing data by addressing barcode artifacts, reducing trimming errors and barcode bleeding.

Analyzing long-read CRISPR experiments with CRISPRLungo

CRISPRLungo is a computational pipeline for analyzing long-read CRISPR experiments, improving accuracy in detecting structural variants and small indels through UMI-based error correction and benchmarking.

Fine Mapping Regulatory Variants by Characterizing Native CpG Methylation with Nanopore Long Read Sequencing

This paper uses nanopore long-read sequencing to characterize native CpG methylation and identify allele-specific methylation regions in the prostate genome.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

Single cell transcriptomics reveals enrichment of aggregation-prone alpha-synuclein isoforms across synucleinopathies

The paper uses long-read and single nucleus RNA-seq to identify novel SNCA transcript isoforms and their association with Parkinson's and Lewy body dementia.

Flamenco plasticity tunes somatic piRNAs, rewiring host isoforms and opening a route to heritable transposon spread

The paper shows how the transposon Springer rewires gene expression and how Flamenco piRNA clusters remodel to allow transposon spread to the germline.

Comprehensive benchmarking of somatic mutation detection by the SMaHT Network

The paper benchmarks somatic mutation detection methods using short-read and long-read sequencing across multiple samples, showing improved accuracy with donor-specific assemblies and highlighting the complementary value of bulk, single-cell, and duplex analyses.

From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding

This paper introduces BaNaNA, a pipeline for generating high-quality OTUs from Nanopore long-read sequencing data, showing its effectiveness for protist biodiversity studies and its advantages over short-read methods.

Multi-platform framework for mapping somatic retrotransposition in human tissues

The paper develops a framework to detect and trace somatic retrotransposition events in human tissues, identifying rare L1 insertions and improving detection accuracy.

Scalable long-read Nanopore HPV16 Amplicon-based Whole-Genome Sequencing

This paper develops a scalable long-read sequencing method for HPV16 genome analysis, showing high accuracy and capturing full genetic diversity across multiple lineages.

High-resolution HIV-1 m6A epitranscriptome reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications

The paper identifies 18 m6A sites in HIV-1 using Nanopore sequencing and reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications.

Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts

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.

A Tandem Repeat Atlas for the Genome of Inbred Mouse Strains: A Genetic Variation Resource

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.

Long-read sequencing-based atlas of tissue-specific expression of Drp1 transcript variants

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.