long-read sequencing

Hyper3D-lite: count-preserving representation auditing for long-read multi-contact genome data

Hyper3D-lite audits long-read multi-contact genome data by preserving counts during all-pair projections to avoid overcounting contact evidence.

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

ANCHOR improves variant calling and allele-specific expression analysis in single-cell long-read RNA-seq by integrating haplotype-aware methods and beta-binomial modeling.

Recovery of an 18th Century Rhinovirus Genome through Ancient RNA Isolation of Human Lungs

This study recovers an 18th-century rhinovirus genome from ancient RNA isolated from human lung specimens, revealing insights into viral evolution.

Long-read cross-platform validation reveals novel repeat features in myotonic dystrophy type 2

The paper validates long-read sequencing methods for analyzing repeat expansions in DM2, identifying new repeat motifs and improving bioinformatic workflows.

tRNA isodecoder analysis using Nanopore ionic current signals and deep learning

The paper introduces tRNAZAP, a deep learning method using nanopore ionic current signals to classify tRNA isodecoders, achieving better alignment results than BWA-MEM in E. coli and S. cerevisiae.

Imputed graph-genotyped structural variants identify regulatory haplotypes associated with gene expression in Atlantic salmon

Long-read cDNA sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS

This paper uses long-read cDNA sequencing to identify novel transcripts and spliceosome-mutant-enriched isoforms in AML and MDS, providing a resource for improving short-read RNA-seq analyses.

An integrated human immunoglobulin germline resource linking allele diversity to expressed repertoire structure

This paper constructs HUSA, a comprehensive germline resource linking allele diversity to expressed antibody repertoires by integrating long-read sequencing and AIRR-seq data.

Transcriptionally Active HIV Reservoirs Enriched for Interferon-Inducible APOBEC3-Related Mutational Signatures Associate with Arterial Inflammation

This study finds that APOBEC3-associated premature stop codon signatures in HIV reservoirs are linked to aortic inflammation in ART-suppressed individuals, suggesting a role in cardiovascular risk.

Nanopore Direct RNA Sequencing Enables Reproducible, Site-Resolved Pseudouridine Quantification in Human Ribosomal RNA

This study benchmarks nanopore direct RNA sequencing for pseudouridine quantification in human ribosomal RNA, showing high accuracy and reproducibility across multiple cell types.

Transcript architecture sets the m6A landscape: CSTF2 and CSTF2T reshape m6A through cleavage-dependent and -independent mechanisms

The paper identifies CSTF2 and CSTF2T as factors that shape the m6A landscape through cleavage-dependent and -independent mechanisms by altering transcript architecture and polyadenylation sites.

Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles

This paper introduces MethylSeqNet, a model that improves sequence-based gene regulation predictions by conditioning on CpG methylation, showing benefits for cell-type-specific regulation and allele-specific phenomena.

Long-read RNA-seq resolves isoform-level and context-specific regulatory architecture of complex traits in cattle

The paper uses long-read RNA-seq to uncover isoform-level and context-specific regulatory effects in cattle, improving the resolution of molecular atlases and GWAS loci.

SWARM resolves nanopore signal interference between RNA modification types and reveals splicing-shaped pseudouridylation

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

De novo mutation of an RNA virus is increased in the presence of engineered synonymous mutations that disrupt RNA structural elements

The paper shows that engineered synonymous mutations disrupting RNA structural elements increase de novo mutations in a virus, suggesting structural perturbations affect genomic stability.

RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis

RAD is a demultiplexer for single-cell long-read sequencing that improves speed and sensitivity over existing methods while supporting complex read structures.

High-accuracy hierarchical rRNA operon profiling resolves genomovar-level taxonomy and microdiversity using Nanopore sequencing.

UltraRes-rrn uses Nanopore sequencing and hierarchical rRNA operon profiling to achieve genomovar-level taxonomy resolution and microdiversity detection in microbial communities.

Bayesian optimisation and graph-based rheology enable sequence-dependent modelling of DNA materials

This paper uses Bayesian optimisation and graph-based rheology to model DNA materials by linking sequence design to material properties.

FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

FIRST-seq uses nanopore cDNA sequencing to profile RNA modifications and structures by analyzing RT errors, achieving single-nucleotide resolution without PCR or second-strand synthesis.

Regulatory Genomics of Preeclampsia-Specific Risk Variants Highlights Immune and Endothelial Mechanisms

This study identifies PE-specific genetic variants and their regulatory effects, highlighting immune and endothelial mechanisms involved in preeclampsia.

HyDRA: a pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly

HyDRA integrates long- and short-read RNAseq data to improve transcriptome assembly, identifying over 50,000 new long noncoding RNAs in ovarian and fallopian tube samples.

Sensitive long-read amplicon sequence variant recovery with savont

Savont improves ASV recovery from long-read amplicon sequencing with high accuracy and lower sequencing depth.

SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser

SQANTI-browser converts SQANTI3 classifications into UCSC Genome Browser Track Hubs for visualizing and curating long-read transcriptomes with metadata and filtering capabilities.

Long-read sequencing reveals transposable element-derived chimeric transcripts at zygotic genome activation in mammalian embryos

This study uses long-read sequencing to identify chimeric transcripts from transposable elements in mouse and bovine embryos during zygotic genome activation, revealing species-specific patterns.

Unimeth: A unified transformer framework for accurate DNA methylation detection from nanopore reads

Unimeth improves DNA methylation detection from nanopore reads across species and modification types by using a transformer framework with multi-phase training.

Draft genome assembly of the Woolly bottlebrush (Greyia radlkoferi) using Pacbio long-read sequencing technology.

This paper generates the first draft genome of Greyia radlkoferi using PacBio long-read sequencing, providing insights into its environmental resilience and medicinal properties.

Decoding the human PBMC isonome: Isoform-level resolution with single-cell long-read transcriptomics

This study uses long-read single-cell sequencing to analyze isoform-level diversity in human PBMCs, identifying novel isoforms and cell-type-specific patterns.

Pervasive bacterial and prophage hybridization during chronic gut inflammation

The paper shows that chronic gut inflammation drives bacterial and prophage hybridization in E. coli, leading to new genetic lineages associated with inflammatory bowel disease.

Ghost in the Machine: Evidence for Non-Random Errors During Direct RNA Nanopore Sequencing Due to Post-Translocated RNA Folding

The paper shows that direct RNA nanopore sequencing has non-random error patterns linked to RNA folding and sequence complexity, not random distribution as previously assumed.

Comparing fine-scale mutation and recombination landscapes in rhesus macaque (Macaca mulatta) populations of Chinese and Indian descent inferred from both short- and long-read sequencing data

This study compares mutation and recombination landscapes in rhesus macaques from Chinese and Indian populations using short- and long-read sequencing data, revealing population-specific recombination hotspots.