long-read sequencing

Human-specific tandem repeat in CACNA1C modulates responses to neuronal stimulation

The paper investigates a human-specific VNTR in CACNA1C and shows it modulates neuronal calcium responses and transcription programs.

A ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seq

This paper develops a ratio-based framework using Quartet reference materials to integrate long- and short-read RNA-seq data, showing hybrid-seq achieves the highest quantification accuracy.

Genome assembly of five Tephritid species for the enhancement of the Sterile Insect Technique

The paper presents chromosome-level genome assemblies for five Tephritid species using long-read sequencing, short-read polishing, and Hi-C scaffolding.

Latent endogenous viral elements drive active infection and inheritance in a multicellular host

The paper shows that endogenous viral elements in brown algae can reactivate, replicate, and transmit viruses, challenging the view of EVEs as inert.

Integrative genotyping and analysis of canine structural variation using long-read and short-read data

The paper integrates long-read and short-read data to analyze structural variation in canines, identifying new variants and selection signatures.

Generative design of novel bacteriophages with genome language models

Fine-tuned Evo 1 and Evo 2 genome language models designed complete ΦX174-like phage genomes; 16 of 285 assembled designs were viable, and some outperformed ΦX174 in competition.

Single-cell long-read sequencing of the experience-induced transcriptome

This study uses single-cell long-read sequencing to profile experience-induced gene and isoform expression in mouse hippocampal cells, identifying 1,266 experience-variable isoforms.

Quantifying HLA transcripts by genotype in chimeric mixtures at single-cell resolution

This paper introduces scrHLA-typing, a method to quantify HLA transcripts in single cells using long-read sequencing, showing its ability to detect allele-specific expression in post-transplant relapse samples.

Genomic plasticity of the mating-type loci underlies reproductive strategy transitions in Rhodotorula yeasts

This study examines genomic changes in mating-type loci across Rhodotorula yeast species, revealing structural divergence and inheritance patterns associated with shifts in reproductive strategies.

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches

LongBench benchmarks long-read RNA-sequencing technologies using a cross-platform dataset of cancer cell lines, showing high gene-level concordance but reduced transcript-level consistency across platforms.

Early life adversity shapes life history trade-offs between growth and reproduction in free-ranging rhesus macaques

This study shows that early life adversity in rhesus macaques affects growth, reproductive timing, and lifetime reproductive success, with adversity intensifying trade-offs between growth and reproduction.

Deep Learning-Based Classification of Peptide Analytes from Single-Channel Nanopore Translocation Events

This paper develops a deep learning pipeline for classifying peptides from nanopore translocation events using simulated data, achieving high accuracy for pure samples and reasonable accuracy for mixtures.

Plasmids from a complex biome exist as communities

This study sequenced plasmids from wastewater treatment plant effluent and found they exist in communities rather than as isolated entities, with implications for antimicrobial resistance gene spread.

RNA-tailor: accurate gene-level identification of transcript isoform diversity from long reads

RNA-tailor identifies transcript isoform diversity at the gene level with high accuracy using long-read sequencing data.

A modular pipeline for evidence-integrated genome annotation across species: a case study on Schmidtea mediterranea

The paper develops a modular genome annotation pipeline for non-model organisms, demonstrating its effectiveness in improving gene annotation in Schmidtea mediterranea.

Taf1 expression in mouse: novel transcripts and protein distribution

The paper identifies novel Taf1 transcripts and protein distribution in mouse, revealing transcriptional diversity and elevated expression in cerebellum.

Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads

This study uses long-read sequencing to analyze CRISPR-Cas9 editing outcomes and mosaicism in zebrafish, revealing genetic mosaicism in founder fish and its inheritance to offspring.

Long-read single-cell genome, transcriptome and open chromatin profiling links genotype to phenotypes.

SPLONGGET enables comprehensive genotype-phenotype analysis by integrating long-read single-cell genome, transcriptome, and open chromatin profiling in thousands of cells.

Phasing single-molecule nano-NOMe-seq reveals chromatin state heterogeneity in the context of transcription and long-range interactions

The paper uses nano-NOMe-seq to phase single-molecule chromatin states and link them to transcriptional activity, revealing heterogeneity in enhancer-promoter interactions.

PhyloAug: An Evolutionary and Structure-Aware Data Augmentation Tool

PhyloAug improves GLM performance by generating biologically plausible RNA sequence augmentations using evolutionary signals and RNA structure.

Neighbour Typing Using Long Read Sequencing Provides Rapid Prediction of Sequence Type and Antimicrobial Susceptibility of Klebsiella pneumoniae

This paper evaluates RASE, a neighbor typing method using long-read sequencing, for predicting sequence types and antimicrobial susceptibility of Klebsiella pneumoniae in real time.

NucleicBERT: Deciphering the language of nucleic acids

NucleicBERT is a self-supervised masked-language model for RNA that learns contextual representations without alignments or evolutionary data, outperforming existing models in structural and functional tasks.

Enhanced Detection of RNA Modifications in Escherichia coli Utilizing Nanopore RNA004 Technology

The paper evaluates RNA modification detection in E. coli using nanopore RNA004 technology, introduces nanoSundial for improved detection, and identifies 190 modified CDS regions.

scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing

The paper introduces a Nextflow-based pipeline for analyzing Oxford Nanopore single-cell RNA sequencing data, enabling gene and transcript-level quantification with portability and reproducibility.

Inferring Phylogenetic Trees of Cancer Evolution from Longitudinal Single-Cell Copy Number Profiles

This paper introduces NestedBD-Long, a method for inferring cancer evolution phylogenetic trees from longitudinal single-cell copy number data, showing improved accuracy with more temporal samples.

Tech Note - Adaptive Sampling: targeted Oxford Nanopore long-read sequencing

This paper evaluates adaptive sampling in Oxford Nanopore long-read sequencing, finding it increases ROI coverage but shows positional effects.

A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types.

The paper introduces a spatial long-read sequencing method to study developmental splicing and polyadenylation changes in cortical layers and cell types, finding layer-specific and age-related regulatory patterns.

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner

TranSigner improves transcript abundance estimation by accurately assigning long reads to transcripts, outperforming existing tools in simulated and experimental data.

A direct RNA-seq-based EBV Latency Transcriptome Offers Insights into the Biogenesis of EBV Gene Products.

This paper uses long-read RNA-seq to analyze EBV transcriptomes in LCLs, identifying new splicing variants, polyA sites, and transcript structures, and provides tools and annotations for future studies.

High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions

The paper uses long-read sequencing to analyze intrapopulation diversity in tandem repeat regions of Mareks disease virus strains, revealing phenotypic links to virulence and attenuation.