long-read sequencing

A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing

This paper introduces s5PSeq, a streamlined protocol for rapid antimicrobial sensitivity testing using 5P mRNA degradation intermediates, demonstrating its clinical utility in identifying resistant Clostridioides difficile isolates.

LRSomatic: a highly scalable and robust pipeline for somatic variant calling in long-read sequencing data

LRSomatic is a pipeline for somatic variant calling in long-read sequencing data, achieving state-of-the-art performance on cancer samples and resolving complex variants.

Dogme: A nextflow pipeline for reprocessing nanopore RNA and DNA modifications

Dogme is a Nextflow pipeline that automates reprocessing of ONT data for modification detection and transcript quantification, showing reproducible results across biological replicates.

Pioneer factor IRF1 unlocks latent enhancers to rewire chromatin and immunometabolism in inflammatory macrophages

This study identifies IRF1 as a pioneer factor that remodels chromatin and drives metabolic reprogramming in inflammatory macrophages through enhancer activation and transcriptional control.

ITSxRust: ITS region extraction with partial-chain recovery and structured diagnostics for long-read amplicon sequencing

ITSxRust improves ITS region extraction from long-read amplicon sequencing by increasing accuracy and speed, with additional recovery of partial sequences.

Analysis and control of untemplated DNA polymerase activity for guided synthesis of kilobase-scale DNA sequences

This study investigates untemplated DNA synthesis by polymerases, showing that environmental conditions influence sequence composition and providing data for guided DNA synthesis.

Stalled translation on transcripts cleaved by RNase L activates signaling important for innate immunity

The paper shows that RNase L cleavage of mRNAs leads to ribosome stalling, which activates innate immunity via the ribotoxic stress response.

A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification

This study benchmarks PacBio Kinnex long-read RNA sequencing against Illumina short-read RNA-seq, finding Kinnex provides more accurate transcript discovery and quantification with comparable gene-level performance.

KuPID: Kmer-based Upstream Preprocessing of Long Reads forIsoform Discovery

KuPID preprocesses long RNA-seq reads using kmer sketching to improve isoform discovery accuracy and reduce runtime.

A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta

The paper presents a chromosome-level genome assembly and functional genomic resources for Capitella teleta, improving upon an outdated reference and enabling better analysis of multi-omic data.

EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcriptional regulation and controls nucleolar biology

This study identifies EPB41L4A-AS1 as a lncRNA that regulates transcription both cis- and trans-acting, impacting nucleolar biology and gene expression in breast cancer cells.

Resolving eukaryotic river biofilm communities using long-read sequencing for biomonitoring

This study compares short-read and long-read sequencing of 18S rRNA gene amplicons in river biofilms, showing that long-read sequencing improves taxonomic resolution while trimming can introduce mismatches.

An Enhancement of Extrachromosomal Circular DNA Enrichment and Amplification to Address the Extreme Low Overlap Between Replicates

This paper improves eccDNA enrichment and amplification methods, achieving >50% overlap in technical replicates compared to <1% previously observed.

NanoHIVSeq: A Long-Read Bioinformatics Pipeline for High-Throughput Processing of HIV Env Sequences

NanoHIVSeq is a UMI-free pipeline for processing HIV Env sequences from ONT data, achieving high accuracy and efficiency in variant recovery.

Distinct mycorrhizal communities in sympatric Lepanthes orchids revealed by long-read sequencing

This study uses long-read sequencing to show distinct mycorrhizal communities in four sympatric Lepanthes orchid species, suggesting fungal shifts may drive speciation.

Juggling offsets unlocks RNA-seq tools for fast and Scalable differential usage, Aberrant Splicing and Expression Retrieval.

The paper introduces a method to enhance RNA-seq tools for differential usage, aberrant splicing, and expression retrieval by modifying normalization offsets and presents a faster tool for outlier detection.

Fully T2T pedigree assemblies reveal genetic stability and epigenetic plasticity of human centromeres across inheritance and cell-fate transitions

The paper uses fully phased telomere-to-telomere assemblies and long-read epigenomes to study centromere genetic and epigenetic dynamics across inheritance and cell-fate transitions, finding positional stability of CDRs and dynamic epigenetic changes.

Cost-effective hybrid long- and short-read sequencing enables accurate somatic structural variant detection

This paper introduces SomaSV, a hybrid sequencing framework that improves somatic structural variant detection accuracy while reducing costs by combining long- and short-read data.

Expression of nano-engineered RNA organelles in bacteria

This paper designs and expresses non-natural membrane-less RNA organelles in E. coli, enabling algorithmic control over interactions and condensate structure.

PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies

PAQman evaluates long-read eukaryotic genome assemblies using seven reference-free metrics without requiring a reference genome.

Decoding the avian missing gene mystery: dot chromosomes unmask extensive gene loss and novel genetic instability

The paper identifies extensive gene loss and a novel genetic instability called sequence stuttering on avian dot microchromosomes using long-read sequencing.

PathoResist AI: A One-Click Web Platform for Rapid Pathogen Resistance Analysis Based on the all_ratio Algorithm

PathoResistAI is a web platform that uses nanopore sequencing and the all-ratio algorithm to rapidly analyze pathogen resistance, providing automated reports within 30 minutes.

NanoLoop: A deep learning framework leveraging Nanopore sequencing for chromatin loop prediction

NanoLoop predicts genome-wide chromatin loops using Nanopore sequencing data, identifying methylation patterns that influence loop types and reveal new long-range interactions.

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

The paper introduces LRAA, a framework for accurate isoform discovery and quantification in long-read RNA-seq data, outperforming existing methods across multiple benchmarks.

Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing

This study uses long-read nanopore sequencing to analyze carbapenem resistance dynamics in a hospital setting, revealing plasmid spread and environmental reservoirs.

Critical assessment of intratumor and low-biomass microbiome using long-read sequencing

The paper assesses low-biomass microbiome detection in tissues using long-read sequencing, finding that genuine microbiome signals are limited to tissues with natural microbial exposure.

Bayesian analysis of longitudinal RB-TnSeq resolves the fitness seascape in fluctuating environments

The paper develops a Bayesian framework for longitudinal RB-TnSeq to analyze fitness dynamics in fluctuating environments and identifies a 'fitness seascape' model that predicts mutational targets.

Allelic Variation at 9p21.3 Orchestrates Widespread RNA Splicing Shifts Governing Vascular Smooth Muscle Cell Plasticity

This study shows that allelic variation at the 9p21.3 locus affects RNA splicing in vascular smooth muscle cells, leading to phenotypic changes linked to coronary artery disease.

Viral haplotype reconstruction from long reads with virCHap

virCHap reconstructs viral haplotypes from long-read sequencing data, outperforming existing methods in recall, abundance estimation, and read clustering.

LoReMINE: Long Read-based Microbial genome mining pipeline

LoReMINE is an automated pipeline for microbial genome mining that integrates assembly, classification, and biosynthetic gene cluster prediction from long-read data.