long-read sequencing

This paper demonstrates real-time transcriptomic analysis using nanopore sequencing for quality control and differential expression in various experimental conditions.

The paper presents a low-cost lab-made spatial transcriptomics chip that enables isoform-resolved analysis using a dual-platform sequencing workflow, identifying novel splicing events in tomato-pepper grafts and mouse embryos.

MosaicTR quantifies somatic instability of tandem repeats from long-read sequencing data, improving accuracy over short-read methods.

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

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

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

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.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

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.

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.

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

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

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.

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

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

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.