long-read sequencing

ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing

ModiDeC is a deep-learning classifier that identifies multiple RNA modifications from direct nanopore sequencing, validated on synthetic data and biological samples.

The structure, folding kinetics and dynamics of long poly(UG) RNA

This study investigates the structure, folding kinetics, and dynamics of long poly(UG) RNAs, revealing a dynamic model for segmental register exchange and double pUG fold formation.

Long-read sequencing to detect full-length protein-protein interactions

The paper introduces AVA-Seq, a method using long-read sequencing to detect full-length protein-protein interactions, achieving a 28.6% recovery rate on a gold standard dataset.

The Polycistronic Transcription Landscape of the Populus Nuclear Genome

The paper identifies widespread polycistronic-like transcripts in Populus species using Nanopore DRS, revealing their molecular features and regulatory patterns.

Single-molecule sequencing maps replication dynamics across the fission yeast genome, including centromeres

This paper introduces DNAscent, a nanopore sequencing method to map DNA replication dynamics in fission yeast at single-molecule resolution, revealing replication patterns in centromeres and rDNA.

Base modification analysis in long read sequencing data using Minimod

This paper introduces minimod, a tool for analyzing base modifications in long-read sequencing data, showing significant speed improvements over existing tools.

Direct RNA Oxford Nanopore sequencing distinguishes between modifications in tRNA at the U34 position

The paper develops methods to distinguish tRNA modifications at the U34 position using Oxford Nanopore sequencing, showing its potential for accurate modification detection.

HIGH PRECISION CHARACTERIZATION OF RCCX REARRANGEMENTS IN A 21-HYDROXYLASE DEFICIENCY LATIN AMERICAN COHORT USING OXFORD NANOPORE LONG READ SEQUENCING

This study uses Oxford Nanopore long-read sequencing to characterize RCCX rearrangements in a Latin American 21-hydroxylase deficiency cohort, identifying new genetic variants and reclassifying a previously overlooked case.

Telomere-to-telomere assemblies reveal complex adaptive variation of 3-ketoacyl-CoA-synthases in Populus trichocarpa likely driven by helitrons

The paper uses long-read sequencing to analyze telomere-to-telomere assemblies in Populus trichocarpa, revealing complex KCS gene variation and its association with helitron transposons.

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis

Comparing nine Solanaceae genomes reveals a conserved withanolide gene cluster; three of its P450s, expressed in yeast and N. benthamiana, oxidise 24-methyldesmosterol toward the withanoside V aglycone.

Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution

The paper introduces Nano3P-seq, a nanopore-based method to analyze RNA polyA tail composition and length at single-molecule resolution, along with software PolyTailor for accurate estimation of transcript abundances and tail dynamics.

Single-nucleotide Resolution Epitranscriptomic Profiling Uncovers Dynamic m6A Regulation in Bovine Preimplantation Development

This study uses SAC-seq to map m6A modifications at single-nucleotide resolution in bovine preimplantation embryos, identifying a critical m6A site in RPL12 that regulates translation and development.

Targeted decontamination of sequencing data with CLEAN

The paper introduces CLEAN, a pipeline to remove contaminants from sequencing data, improving reproducibility and analysis quality.

Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance

The paper introduces Context-Seq, a CRISPR-Cas9 targeted nanopore sequencing method to study AMR transmission between humans and animals, identifying shared ARG clusters and potential pathogenic hosts.

A comparison of long-read single-cell transcriptomic approaches

This study compares long-read single-cell sequencing platforms, identifying common limitations and demonstrating their utility for isoform-resolved analyses.

Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing

The paper reconstructs NOD-like receptor alleles in Podospora anserina using long-read sequencing, revealing structural and functional insights into incompatibility genes.

RNA liquid biopsy via nanopore sequencing for novel biomarker discovery and cancer early detection

This study uses long-read nanopore sequencing of cell-free RNA to detect early-stage cancer and discover novel biomarkers, identifying 270,679 intergenic RNAs and potential therapeutic targets.

Exploiting functional regions in the viral RNA genome as druggable entities

The paper applies SHAPE-MaP to identify functional RNA structures in PEDV to guide antiviral drug design.

Profiling Epigenetic Aging at Cell-Type Resolution Through Long-Read Sequencing

This paper introduces LongReadAge, a probabilistic model for predicting epigenetic age at the cell-type level using long-read sequencing data.

Joint processing of long- and short-read sequencing data with deep learning improves variant calling.

This study combines long- and short-read sequencing data using a hybrid DeepVariant model to improve germline variant detection accuracy.

The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with reduced posterior tagma

This paper presents the first near chromosome-level genome of a sea spider, revealing a single Hox cluster without abdominal-A/Hox9, supporting shared evolutionary patterns in arthropods.

Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification

Oarfish improves long read transcriptome quantification by incorporating a novel coverage score into its probabilistic model, leading to more accurate quantification estimates.

Verkko2: Integrating proximity ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Verkko2 improves genome assembly by integrating proximity ligation data with long-read De Bruijn graphs, enabling complete telomere-to-telomere assemblies for diploid human genomes.

A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry

This study compares two RNA modification detection models, Dorado and m6Anet, using RNA004 sequencing data, finding Dorado has higher recall but both have high false discovery rates for m6A and pseudouridine.

Transposon insertion causes ctnnb2 transcript instability that results in the maternal effect zebrafish ichabod (ich) mutation

The paper identifies a transposon insertion in the 3UTR of ctnnb2 as the cause of the maternal-effect ich mutation in zebrafish, leading to transcript instability and ventralized embryos.

Regulation of the lncRNA malat1/Egr1 Axis by Wnt, Notch and TGF-β signaling: A Key Mechanism in Retina Regeneration

This study identifies the malat1/Egr1 axis regulated by Wnt, Notch, and TGF-β signaling as critical for retina regeneration in zebrafish, with species-specific regulation of talam1 observed between zebrafish and mice.

Long-Read RNA-sequencing reveals transcript-specific regulation in human-derived cortical neurons

This study uses long-read RNA sequencing to analyze transcript diversity and regulation in human fibroblasts, induced pluripotent stem cells, and cortical neurons, revealing transcript-specific changes in disease-related genes.

A new compression strategy to reduce the size of nanopore sequencing data

This paper introduces ex-zd, a compression strategy for nanopore sequencing data that reduces file sizes by removing redundant bits without affecting downstream analyses.

The fungal pathogen Rhizoctonia solani AG-8 has two nuclear haplotypes that differ in abundance

This study reveals that Rhizoctonia solani AG-8 has two nuclear haplotypes with differing abundances and gene expression patterns during plant infection.

NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing

NANOME improves DNA methylation detection using nanopore long-read sequencing by integrating multiple tools and enhancing precision and accuracy in human cell lines.