long-read sequencing

Pooled long-read sequencing for structural variant characterization in schistosome populations

This study uses pooled long-read sequencing to identify and genotype 17,446 structural variants in five Schistosoma mansoni populations, revealing population-specific variants and associations with biomedically relevant traits.

Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types

The paper develops a high-resolution spatial long-read sequencing method and software to analyze isoform variability in brain cell types, revealing both region-specific and cell-type-specific patterns.

The mitochondrial methylation potential gates mitoribosome assembly

The paper shows that mitochondrial SAM is essential for processing mitochondrial ribosomal RNA precursors and ribosome assembly.

Resolving a neonatal intensive care unit outbreak of methicillin-resistant Staphylococcus aureus to the SNV level using Oxford Nanopore simplex reads and HERRO error correction

This paper applies HERRO error correction to Oxford Nanopore sequencing data to resolve a neonatal ICU MRSA outbreak at the SNV level, achieving results comparable to Illumina sequencing.

Rapid and Cost-Effective Digital Quantification of RNA Editing and Maturation in Organelle Transcripts

The paper introduces a cost-effective long-read sequencing method for quantifying RNA editing and intron retention in plant chloroplast transcripts, showing MORF2's role in RNA maturation.

CellSpliceNet: Interpretable Multimodal Modeling ofAlternative Splicing Across Neurons in C. elegans

CellSpliceNet predicts alternative splicing outcomes in C. elegans neurons by integrating multiple data modalities and achieving high predictive accuracy.

Dysregulated MEG3 in Myotonic Dystrophy 1: nuclear retention, pathological role, and therapeutic correction by antisense conjugates.

This study shows MEG3 is upregulated in DM1 and exhibits nuclear retention, with antisense conjugates correcting MEG3 levels in mice.

COmapper: High-resolution mapping of meiotic crossovers by long-read sequencing in Arabidopsis

COmapper uses long-read sequencing to map meiotic crossovers in Arabidopsis with high resolution, showing comparable accuracy to short-read methods and revealing crossover enrichment at gene promoters.

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations

Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health

The paper analyzes how genetics and environmental factors influence metabolic profiles over two years in 101 healthy individuals, identifying 22 genetically determined metabolites and 87 causal metabolite-protein associations.

NSD1 governs H3K36me2-mediated DNA methylation and drives differentiation of human iPSCs by regulating HIDEN lncRNA expression

This study shows NSD1 regulates DNA methylation and endodermal differentiation of human iPSCs through HIDEN lncRNA, revealing a novel mechanism linked to Sotos syndrome.

Characterization of bacterial intrinsic transcription terminators identified with TERMITe - a novel method for comprehensive analysis of Term-seq data

The paper introduces TERMITe, a method for analyzing Term-seq data to identify bacterial transcription terminators and provides an atlas of validated termination sites across 13 species.

Regenotyping structural variants through an accurate force-calling method

The paper introduces cuteSV2, a long-read-based method for accurate structural variant regenotyping, outperforming existing methods in benchmarking.

Direct RNA nanopore sequencing reveals rapid RNA modification changes following glucose stimulation of human pancreatic beta-cell lines

The paper uses direct RNA nanopore sequencing to identify RNA modification changes in human pancreatic beta-cells after glucose stimulation, finding 1,697 differentially modified sites linked to type 2 diabetes genes.

Analysis of 3'-seq data from multiple E. coli studies identifies diverging results sets and raw data characteristics despite similar collection conditions

The paper analyzes 3'-seq data from multiple E. coli studies and identifies large disparities in raw data characteristics and strand-specific inconsistencies despite similar experimental conditions.

APALORD: An R-based tool for differential alternative polyadenylation analysis of long-read RNA-seq data

APALORD is an R-based tool for analyzing differential alternative polyadenylation in long-read RNA-seq data, identifying polyadenylation sites and quantifying their usage across biological conditions.

De novo clustering of long-read amplicons improves phylogenetic insight into microbiome data

The paper introduces LACA, a de novo clustering workflow for long-read amplicons that improves phylogenetic analysis and phenotype characterization in microbiome data.

Breaking Through Biology's Data Wall: Expanding the Known Tree of Life by Over 10x using a Global Biodiscovery Pipeline

The paper introduces BaseData, a new biological sequence database that expands known protein diversity by over 10x using a global biodiscovery pipeline.

G-quadruplex Structures in Dysregulated Long Non-Coding RNA of Ovarian Cancer and their Binding Interactions with Human Serum Albumin

This study identifies G-quadruplex structures in dysregulated lncRNAs of ovarian cancer and their interactions with human serum albumin, suggesting potential diagnostic value.

Resolving RH and GYP hybrid alleles while accessing the entire blood group genome with Nanopore adaptive sampling

This study evaluates adaptive sampling for resolving complex blood group variants using long-read sequencing, identifying novel alleles and hybrid haplotypes in RH and MNS systems.

Transposon-directed insertion-site sequencing (TraDIS) analysis of Enterococcus faecium using nanopore sequencing and a WebAssembly analysis platform

The paper develops a TraDIS platform for Enterococcus faecium using nanopore sequencing and a WebAssembly tool to study vancomycin resistance and persistence.

Deacon: fast sequence filtering and contaminant depletion

Deacon efficiently filters and depletes contaminant sequences from large genomic datasets using a human pangenome index, achieving high accuracy and speed with minimal computational resources.

Spatial characterization of microbiota profiles along the gut in a widely used mouse model: effects of high-fat diet and fructooligosaccharides

This study characterizes gut microbiota composition along the gastrointestinal tract in mice under high-fat diet and prebiotic conditions, revealing species-specific responses and challenges the translational relevance of rodent models.

Regulatory elements of pancreas development license the initiation of pancreatic ductal adenocarcinoma

This study identifies LINC00673, a long noncoding RNA from a Sox9-associated super-enhancer, as critical for pancreatic regeneration and PDAC initiation by regulating cell-autonomous and non-cell-autonomous processes.

Direct detection of 8-oxo-dG using nanopore sequencing

The paper develops a method to directly detect 8-oxo-dG using nanopore sequencing by creating synthetic DNA with context variability and training deep learning models.

Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress

This study introduces DMS-TRAM-seq to map RNA structure across the transcriptome, identifying structured elements and showing structural changes under stress.

Cell-specific RNA isoform remodeling in the aging mouse brain

This study identifies cell-type-specific RNA isoform changes in aging mouse brain using single-cell and long-read sequencing, revealing altered coding potential and senescence markers in immune cells.

Long Read Sequencing reveals transgene concatemerization and backbone integration following AAV-driven electroporation of CRISPR RNP complexes in mouse zygotes

The paper uses long-read sequencing to analyze unintended on-target mutations in mouse zygotes edited with AAV-delivered CRISPR RNP complexes.

NeuID, a novel neuron-specific lncRNA, resolved a key epigenetic mechanisms linking gene silencing to Alzheimer's disease

The paper identifies NeuID, a novel neuron-specific lncRNA downregulated in Alzheimer's disease, as a key regulator of neuronal identity and a therapeutic target.

Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs

This study shows that gammaherpesvirus infection leads to tRNA cleavage, producing tRNA fragments that are regulated by tRNA splicing factors and essential for viral replication.