long-read sequencing

Sequencing and assembling complete plasmids on Oxford Nanopore Technology Sequencers using R2C2 and Chopper

The paper adapts R2C2 sequencing for low-cost, rapid plasmid sequencing and introduces Chopper, a pipeline that generates full-length plasmid sequences from Oxford Nanopore data.

Long-Read Sequencing of the MUC1 VNTR: Genomic Variation, Mutational Landscape, and Its Impact on ADTKD Diagnosis and Progression

This study uses long-read sequencing to characterize MUC1 VNTR variation in ADTKD-MUC1, identifying frameshift mutations and their association with disease progression.

Long-read analysis of tetrameric microsatellites with vmwhere supports GGAA repeat length-dependent chromatin state association in Ewing sarcoma

The paper introduces vmwhere, a tool for analyzing tetrameric microsatellites from long-read sequencing data, and shows its application in linking GGAA repeat structure to chromatin state in Ewing sarcoma.

Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer

The paper uses long-read sequencing to analyze cfDNA fragmentation patterns in cancer patients, identifying hypofragmentation and hyperfragmentation linked to elevated cfDNA levels.

Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries

This study demonstrates nanopore sequencing of 10x Genomics multiome libraries to capture full-length transcripts and identify TSS, showing concordance with short-read methods despite higher error rates.

Epigenomics identifies three sources of DNA methylation in Streptococcus mutans UA159

This study identifies three DNA methylation sources in Streptococcus mutans UA159 using Oxford Nanopore sequencing, revealing a novel methyltransferase and its functional roles in biofilm formation and microbial interactions.

Machine Learning-Enhanced Nanopore ITS Analysis: Evaluating CPU-GPU Pipelines for High-Accuracy Fungal Taxonomic Resolution

This paper evaluates CPU and GPU-based workflows for high-accuracy fungal ITS metabarcoding using machine learning, showing GPU processing improves species-level accuracy while CPU workflows achieve genus-level concordance.

DNA replication errors drive genome-wide small inverted triplication dynamics

The paper identifies DNA replication errors as a source of small inverted triplication (SIT) structural variants in yeast, showing their formation mechanism and characteristics.

Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1

The paper defines the RNA modification landscape in multiple myeloma, identifying m6A modifications on lncRNAs and showing METTL3-dependent regulation of NEAT1 affecting MM cell survival.

Systematic benchmarking of basecalling models for RNA modification detection with highly multiplexed nanopore sequencing

This study benchmarks RNA modification detection models using synthetic and biological data, finding high reliability but issues with false positives and cross-reactivity.

The genome of an enigmatic sea urchin parasite Echinomermella matsi Jones & Hagen, 1987 resolves its place among other invertebrate parasitic nematodes

The paper presents the genome of Echinomermella matsi, a sea urchin parasite, and places it within the nematode order Plectida, highlighting its evolutionary significance for studying aquatic parasitism.

Omitted familial extrinsic risk inflates inferred intrinsic lifespan heritability

The paper shows that omitting familial extrinsic risk in twin lifespan models inflates inferred intrinsic heritability estimates.

OpenAc4C: A gateway to decode the landscape, regulation and pathogenesis of N4-acetylcytidine (ac4C) epitranscriptome

OpenAc4C compiles and analyzes ac4C epitranscriptome data from 33 species, identifying 536,745 ac4C sites and 4,766 pathogenic variants, and provides a web-based platform for exploration.

Lipidomic and metabolomic profiling on low count human spermatozoa: A robust and reproducible method for untargeted HPLC-ESI-MS/MS-based approach

This paper develops a sensitive untargeted HPLC-ESI-MS/MS workflow for lipidomic and metabolomic profiling of human spermatozoa using only 1.25 million cells, revealing interconnected lipid and metabolic pathways.

Comprehensive characterization of V(D)J recombination from long-read transcriptomic data with VDJcraft

VDJcraft is a pipeline for analyzing V(D)J recombination from long-read transcriptome data, showing improved accuracy and novel gene subclass discovery.

LoRTIA Plus: a chemistry-agnostic, feature-first software package for long-read transcriptome annotation

LoRTIA Plus improves transcriptome annotation from long-read RNA-seq data by achieving high F1 scores for TSSs, TESs, and transcripts across multiple chemistries and organisms.

Benchmarking long-read RNA-seq across modalities, methods, and sequencing depth in iNeurons

This study benchmarks long-read RNA-seq across bulk and single-cell platforms, technologies, and sequencing depths, identifying optimal methods for transcript discovery and quantification.

Isoform-Resolved Genetic Architecture of Epilepsy and SUDEP Reveals Divergent Brain and Heart Channelopathy Signatures

The paper identifies tissue- and isoform-level genetic regulation differences between epilepsy and SUDEP, revealing distinct cardiac and neuronal gene expression patterns.

Long-read transcriptome assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function

The paper uses long-read RNA-seq to create a comprehensive placental transcriptome reference, revealing high transcriptional complexity and identifying novel isoforms associated with metabolic and endocrine functions in gestational diabetes.

A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker)

The paper introduces RiboMarker, a method for comprehensive sRNA sequencing that detects all RNA fragment types, improving sensitivity for low-abundance biomarkers.

mRNA-GPT: A Generative Model for Full-Length mRNA Design and Optimization

mRNA-GPT is a generative model that optimizes full-length mRNA sequences by jointly optimizing all three regions, achieving Pareto-optimal designs and outperforming existing methods.

Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read Nanopore sequencing

This study introduces NanoRibolyzer, a long-read nanopore sequencing method to map pre-rRNA processing and modification at single-nucleotide resolution, revealing cleavage sites and modification patterns.

Haplotype-resolved centromeric chromatin organization from a complete diploid human genome

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression

The paper presents an isoform-level lung cell atlas using single-cell long-read RNA-sequencing, revealing genetic effects on isoform regulation that improve cell-type classification and identify novel variants associated with lung cancer risk.

Epigenomic methylome landscape of promoters in vertebrate genomes

The paper characterizes promoter methylation patterns across 82 vertebrate species using long-read sequencing data, revealing conserved and lineage-specific epigenetic features.

methbiome: reference-based DNA methylation profiling of long-read metagenomic data

The paper introduces methbiome, a tool for reference-based DNA methylation profiling of long-read metagenomic data, enabling cross-platform and between-sample comparison of methylation signals in microbiomes.

deluxpore: a Nextflow pipeline for demultiplexing Illumina dual-indexed Nanopore libraries

deluxpore is a Nextflow pipeline that demultiplexes Illumina dual-indexed Nanopore libraries using BLAST and Levenshtein distance, achieving high accuracy in hybrid capture-long-read sequencing.

Barcode Crosstalk in ONT Multiplex Sequencing: Quantification and Mitigation Strategies

The paper quantifies barcode crosstalk in ONT multiplex sequencing and evaluates mitigation strategies across three protocols, finding that protocol C eliminates crosstalk completely.

LORA: a polymorphic multi-sample LOng Read Assembly pipeline.

LORA is a long-read genome assembly pipeline that integrates multiple assemblers and provides quality assessment tools, demonstrating its use on bacterial and eukaryotic genomes.