long-read sequencing

BIRD-Seq: B2 Protein Integrated End-to-End Pipeline for dsRNA Detection and Nanopore Sequencing for Virus Monitoring

This paper introduces BIRD-Seq, a dsRNA detection and sequencing pipeline using engineered B2 protein and nanopore sequencing, achieving sub-ng mL-1 sensitivity and enabling virus identification without RNA extraction.

A chromosome-scale, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei

The paper presents a high-quality, haplotype-resolved genome assembly of the barley stripe rust pathogen Puccinia striiformis f. sp. hordei using long-read and Hi-C sequencing.

Consistent consensus-based annotation of spatial adaptive immune receptor repertoires from long-read sequencing using LongAIRR

The paper develops LongAIRR, a computational framework for spatially resolving adaptive immune receptor repertoires from long-read sequencing, improving consensus accuracy and enabling platform-agnostic analysis.

FoldARE, an RNA secondary structure analysis and prediction tool via generative pseudo-SHAPE modeling

FoldARE improves RNA secondary structure prediction by using pseudo-SHAPE constraints from structural ensembles, achieving high accuracy across benchmark datasets.

kmerRRR: A k-mer based tool for functional genomics in Repeat Rich Regions

kmerRRR improves analysis of repetitive genomic regions by using k-mer frequency analysis to enhance mappability and recover lost biological signals in chromatin and small RNA data.

Bamsnap-LRS: an automated batch visualization tool for long-read sequencing alignments

Bamsnap-LRS automates batch visualization of long-read sequencing alignments, supporting genomic, transcriptomic, and haplotype-aware analyses with publication-ready figure generation.

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

Temporal and Regional Circular RNA profiling in a Tauopathy Mouse Model: Implications for Tau Pathology and Neurodegeneration

The paper profiles circRNA in a tauopathy mouse model across age and brain regions, identifying circRNA-miRNA regulatory networks linked to tau pathology and neurodegeneration.

High rate of mutation and efficient removal by selection of structural variants from natural populations of Caenorhabditis elegans

The paper estimates the mutation rate and removal efficiency of structural variants in C. elegans using long-read sequencing and finds a lower mutation rate compared to SNVs and short indels, with natural selection effectively removing SVs in both exonic and intergenic regions.

Female-specific m6A remodeling in the liver correlates with post-transcriptional metabolic adaptation to high fat diet

The paper identifies female-specific m6A RNA methylation changes in mouse livers under high-fat diet that correlate with post-transcriptional metabolic adaptations and protein remodeling.

segSHAPE: RNA secondary structure prediction from nanopore direct RNA sequencing

segSHAPE improves RNA secondary structure prediction from Nanopore DRS data by enhancing signal alignment and modification rate estimation, achieving higher accuracy than existing methods.

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

Structural variation landscape of Middle Eastern and North African individuals from long-read nanopore sequencing reveals medically relevant variants

The paper identifies structural variants in MENA individuals using long-read sequencing, revealing previously unreported variants and population-specific disease-related variants.

Complete chromosome 21 centromere sequencing of families with Down syndrome reveals centromere size asymmetry

The paper sequences chromosome 21 centromeres in Down syndrome families, finding extreme size asymmetry in some cases and suggesting it may be a genetic risk factor.

ModkitOpt: An optimised workflow for RNA modification stoichiometry estimation and site calling from nanopore sequencing

ModkitOpt optimizes RNA modification site calling by selecting the best parameters and stoichiometry cutoff for nanopore sequencing data, improving precision and recall across modification types.

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

AMaNITA provides an end-to-end workflow for analyzing nanopore native tRNA sequencing data, enabling differential abundance and modification stoichiometry analysis.

Accelerating k-mer-based sequence filtering

The paper introduces K2Rmini, a tool that efficiently filters sequences based on k-mer matches, achieving 2 Gbp/s on a consumer laptop.

High-resolution transcriptome analysis reveals a multilayered and dynamic transcriptional architecture in the archaeal virus SSV1

This study uses high-resolution transcriptomics to reveal complex transcriptional architecture in the archaeal virus SSV1, including new transcription start and termination sites and antisense RNAs.

The long noncoding RNA Dory is required for female but not male spatial learning and memory

This study identifies the lncRNA Dory as essential for female spatial memory and balance, with no effect in males, using CRISPR and RNA sequencing in mice.

Influence of cis-regulatory elements on expression divergence in human segmental duplications

The paper investigates how cis-regulatory elements in human segmental duplications contribute to expression divergence, finding that duplicated CREs show moderate functional divergence and may drive human-specific regulatory patterns.

scIsoAgent enables autonomous isoform-resolved characterization and sequence-informed interpretation of long-read single-cell transcriptomes

scIsoAgent improves long-read single-cell RNA-seq analysis by creating reproducible, isoform-resolved workflows and linking sequence data to functional hypotheses.

Extended poly(A) tails are a shared feature of herpesvirus mRNAs

The paper uses nanopore sequencing to show herpesvirus mRNAs have longer poly(A) tails than cellular or other viral transcripts, suggesting a unique mechanism for enhancing gene expression.

Tandem repeat variation within and between species reveals signatures of selection in humans and chimpanzees

This study analyzes tandem repeat variation in humans and chimpanzees to identify signatures of selection, revealing roles in neural evolution and adaptive expression.

Long-read single-cell genomics: resolving chimeras in multiple displacement amplification

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

Physics-Informed Neural Network Methods for Predicting Plant Height Development

The paper develops a Physics-Informed Neural Network (PINN) for predicting plant height growth, showing improved accuracy over traditional models with limited data.

A global map for introgressed structural variation and selection in humans

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Population-scale detection of methylation outliers from long-read genome sequencing

METAFORA calls depth-aware, covariate-adjusted methylation outlier regions from PacBio and Nanopore long reads; in 551 rare-disease genomes, outliers tracked structural variants, repeat expansions, and imprinting defects.

inquiSTR: a toolkit for accurate and efficient population-scale tandem repeat genotyping and analysis

inqiSTR is a toolkit for efficient and accurate tandem repeat genotyping from long-read sequencing data, enabling population-scale analysis and downstream applications.

Rapid identification of microbial pathogens and antimicrobial resistance from bloodstream infections using long-read sequencing

This paper presents a workflow using long-read sequencing to rapidly identify microbial pathogens and antimicrobial resistance in bloodstream infections, achieving faster results than conventional methods.

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

DModE provides an end-to-end framework for analyzing Nanopore DRS data, enabling integrated differential expression and modification analysis with automated reporting.