long-read sequencing

Hierarchical genomic feature annotation with variable-length queries

The paper introduces HKS, a method for exact hierarchical k-mer annotation with variable-length queries, achieving high concordance in human genome assemblies.

RNAElectra: An ELECTRA-Style RNA Foundation Model for RNA Regulatory Inference

RNAElectra is an RNA foundation model pretrained using replaced-token detection, showing strong performance across RNA regulatory tasks and supporting interpretability.

Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas

The paper identifies novel oncogenic gene fusions in fusion-negative gliomas using long-read sequencing and functional validation in Drosophila.

Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression

The paper uses long-read RNA sequencing to analyze isoform diversity in ovarian cancer, identifying key isoform-level changes associated with disease progression and clinical outcomes.

A bioluminescence resonance energy transfer (BRET) assay to detect telomere length in S. cerevisiae

The paper develops a BRET assay to measure telomere length in S. cerevisiae by correlating BRET ratios with telomere length data from long-read sequencing.

ChromSMF: integrated profiling of histone modifications, protein-DNA interactions and DNA methylation on multi-kilobase DNA molecules

ChromSMF integrates histone modifications, protein-DNA interactions, and DNA methylation on multi-kilobase DNA molecules to study epigenetic regulation.

Single Cell Transcriptomics of Refractory Epilepsy patients in Colombia

This study analyzes single-cell transcriptomics data from five pediatric refractory epilepsy patients in Colombia, identifying glia-driven dysregulation and neuroinflammatory processes.

Residue-Specific Modulation of Aggregation-Associated Interactions bySpermine in Tau, α-Synuclein, and Aβ40

This study shows how spermine modulates aggregation of Tau, α-synuclein, and Aβ40 by residue-specific interactions, revealing that net charge alone cannot predict its effects.

Lessons learned from manual curation of thousands of gene models in the nematode Pristionchus pacificus

The paper curates gene models in Pristionchus pacificus, identifying and correcting over 7,500 gene annotations through manual curation and new transcriptome data.

BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing

BenchDrop-seq provides a microfluidics-free, benchtop platform for single-cell long-read RNA sequencing, enabling isoform-resolved transcript analysis from thousands of cells using standard equipment.

HAETAE: A highly accurate and efficient epigenome transformer for tissue-specific histone modification prediction

HAETAE predicts tissue-specific histone modifications with high accuracy using a 5-base framework and long-read sequencing data.

Nanopore-Based Glycan Sequencing via Fragmentation-Reassembly Strategy

This study introduces a nanopore-based method for glycan sequencing that reconstructs full glycan structures from fragments, overcoming limitations of existing approaches.

NanoVI: a Bayesian variational inference Nextflow pipelinefor species-level taxonomic classification from full-length16S rRNA Nanopore reads

NanoVI provides a Bayesian variational inference pipeline for species-level taxonomic classification of full-length 16S rRNA Nanopore reads, achieving comparable accuracy to Emu with faster execution and fewer false positives.

Extensive splicing deficiency in a degenerating mating-type chromosome

The paper identifies splicing deficiency in non-recombining mating-type chromosomes across phytoplankton species, showing how recombination suppression leads to transcript-level dysfunction.

Multi-omics characterization of breast cancer metabolism identifies new metabolic targets

This study identifies metabolic targets in breast cancer by analyzing multi-omics data from cell lines, revealing subtype-specific dependencies and potential drug targets.

Single-cell level characterization of B cell depletion and repopulation following rituximab in systemic lupus erythematosus

This study uses single-cell profiling to track B cell depletion and repopulation in SLE patients after rituximab treatment, revealing changes in B cell subsets and immune cell dynamics.

Application of long-read sequencing for genotyping, epigenetic profiling and surveillance of Yersinia pestis isolates from natural foci and disease outbreaks in Central Asia

This study uses long-read sequencing to genotype and epigenetically profile Yersinia pestis isolates, revealing genetic diversity and host adaptation mechanisms.

Nanopore direct RNA sequencing (DRS) of MS2 bacteriophages in E.coli throughout its life cycle reveals a complex transcriptional activity to control and maintain its growth

This study uses Nanopore DRS to analyze MS2 phage transcriptional dynamics in E. coli, revealing complex transcriptional activity and RNA modifications throughout the life cycle.

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

The paper identifies conserved microproteins from upstream ORFs in yeast using Ribo-Seq and Nanopore data, showing they are subject to purifying selection.

The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures

This study annotates UTRs in Leishmania donovani and finds they vary in length and are enriched in G-quadruplex structures, suggesting a key role in post-transcriptional regulation.

An autonomous system for multi-objective continuous evolution at scale

TurboPRANCE enables large-scale, multi-objective continuous evolution by integrating robotic systems with phage-assisted evolution, generating high-resolution evolutionary data across diverse selection regimes.

High-quality metagenome assembly from nanopore reads with nanoMDBG

nanoMDBG improves metagenome assembly from ONT reads, producing more high-quality MAGs with less computational resources than existing assemblers.

ggDNAvis: a ggplot2-based R package for creating high-quality DNA sequence and modification visualisations

ggDNAvis provides an R package for high-quality DNA sequence and methylation visualizations with customizable features and support for various data formats.

FA-NIVA: A Nextflow framework for automated analysis of Nanopore based long-read sequencing data for genetic analysis in Fanconi anemia

FA-NIVA provides an automated analysis framework for Nanopore long-read sequencing data to detect SNVs and SVs in Fanconi anemia genes with improved genotyping accuracy.

p53 restoration suppresses retrotransposon-driven chromosomal instability through nonlinear let-7 feedback and stochastic burst control

This study shows p53 restoration reduces retrotransposon-driven chromosomal instability by modulating let-7 feedback and burst control of L1 retrotransposition.

Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data

This paper introduces SegPore, a method for improving raw signal segmentation in Nanopore direct RNA sequencing, leading to better RNA modification detection.

Mapping and quantifying nascent transcript start sites using TT-TSS-seq

The paper introduces TT-TSS-seq, a method to map and quantify transcription start sites from nascent transcripts, revealing multiple initiation sites per gene and detecting unstable transcripts.

Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains

The paper analyzes telomere length distributions in 100 Saccharomyces cerevisiae strains, revealing diversity influenced by ploidy, subtelomere structure, and Y element content.

Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles

The paper shows that MALAT1 long noncoding RNA forms condensates with splicing factors to regulate hypoxia-induced alternative splicing near nuclear speckles.

Identification of de novo variants from parent-proband duos via long-read sequencing

duoNovo identifies de novo variants from parent-proband duos using long-read sequencing, achieving high precision and low error rates in diagnostic evaluations.