long-read sequencing

The paper analyzes telomere length distributions in 100 Saccharomyces cerevisiae strains, revealing diversity influenced by ploidy, subtelomere structure, and Y element content.

The paper shows that MALAT1 long noncoding RNA forms condensates with splicing factors to regulate hypoxia-induced alternative splicing near nuclear speckles.

duoNovo identifies de novo variants from parent-proband duos using long-read sequencing, achieving high precision and low error rates in diagnostic evaluations.

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

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

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

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

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

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presents a chromosome-level genome assembly and functional genomic resources for Capitella teleta, improving upon an outdated reference and enabling better analysis of multi-omic data.

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.

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.

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

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

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

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.

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.

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.

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

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

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

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

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

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

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.

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.