long-read sequencing

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

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.

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.

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

The paper introduces TUSCO, a framework for evaluating transcriptome reconstruction quality using long-read sequencing by assessing precision and sensitivity with a curated set of single-isoform genes.

The paper introduces ProteomeGenerator3, an end-to-end proteogenomics method that detects non-canonical proteoforms in cancer using long-read transcriptomics and multi-dimensional proteomics.

The paper characterizes the structural variation and diversification of the NPIP gene family in humans using long-read sequencing and identifies evidence of positive selection and novel gene models.

This paper develops a machine learning framework for classifying peptides using nanopore translocation events, showing that engineered features and tree-based models achieve high accuracy.

SpliceCoord identifies coordinated exon splicing events from long-read transcriptome data using a count matrix and GTF file.

This paper introduces a method to simultaneously measure tRNA sequence, modification, and aminoacylation using nanopore sequencing and machine learning.

WarpDemuX-tRNA improves barcode multiplexing for nanopore tRNA sequencing with higher precision and efficiency.

This study compares long-read sequencing and optical genome mapping in detecting structural variants in Parkinson's disease, finding OGM better detects large variants while ONT provides high-resolution refinement.

The paper identifies intron retention in STAT2 as a regulator of immune signaling and a predictor of immunotherapy response in lung cancer.

This study examines TE expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages, revealing lineage-specific TE expression patterns and chromatin associations.

The paper investigates genome evolution in pelagophyte algae, identifying lateral gene transfers contributing to pangenome diversity and ecological success.

This study compares EV transcriptomics, proteomics, and cfDNA methylation for detecting colorectal neoplasia, finding EV transcriptomics most sensitive for advanced adenomas and CRC.

The paper uses Hi-C and Pore-C sequencing to compare chromosomal conformation in pneumococcal variants, finding that episomal elements drive differential contact patterns through stochastic replication and excision.

The paper identifies replication pause sites in a eukaryotic genome using long-read nanopore sequencing and finds they are enriched near transcribed regions and correlate with transcription and R-loop levels.

The paper identifies RNAs with CAG repeats, including circRNAs with mutant tracts, in polyglutamine disease patients.

The paper compares three methods for long-read sequencing of 10x Genomics single-cell cDNA libraries to evaluate their performance in full-length transcript capture, barcode identification, and isoform detection.

This paper presents a T cell gene correction pipeline using CRISPR/Cas9 and HDR to correct monogenic mutations in IEI models, achieving up to 80% bi-allelic editing with no detectable off-target effects.

This study analyzes organellar genome dynamics in Arabidopsis thaliana using high-quality long-read assemblies, revealing rapid mitochondrial rearrangements and shared structural variants with plastids.

The paper identifies LIPTER, a cardiomyocyte-specific long noncoding RNA, and shows it regulates cytoskeletal maturation and is controlled by a cardiomyocyte-specific enhancer.

deepNGS Navigator uses deep contrastive learning to visualize and analyze antibody sequence datasets, revealing clonal relationships and evolutionary patterns.

RESM improves RNA sequence-structure-function prediction by transferring knowledge from protein language models, outperforming existing models in multiple tasks.

The paper uses Oxford Nanopore DRS to profile m6A modifications at the isoform level in human brain regions, identifying thousands of m6A sites and region-specific patterns.

NOVOLoci improves genome assembly using Oxford Nanopore reads, achieving high-quality phased assemblies for complex and non-model organisms.

This study investigates G-quadruplex (G4) formation in three lncRNAs dysregulated in colorectal cancer and shows their stable G4 structures using in silico and in vitro methods.

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

The paper uses atomistic simulations to study sequence-dependent conformational landscapes of IDPs, identifying a new metric that captures directional structural differences.