long-read sequencing

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.

lncOriL, a novel polyadenylated mitochondrial lncRNA common to zebrafish and human

The paper characterizes the zebrafish mitochondrial transcriptome using long-read sequencing, identifying three unusual transcripts including a novel long noncoding RNA lncOriL that is conserved across vertebrates.

Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming During 50S Biogenesis

The paper uses direct RNA sequencing to analyze rRNA modifications in E. coli ribosome assembly intermediates and mature subunits, showing stress-dependent reprogramming of specific modifications.

Highly heterozygous Citrus changshan-huyou Y. B. Chang originated from ancient hybridization between mandarin and pummelo and displayed distinct tissue-specific allelic imbalance

This paper reports the genome sequencing and analysis of Citrus changshan-huyou, revealing its origin from ancient hybridization between mandarin and pummelo and identifying tissue-specific allelic imbalance.

MEIsensor: a deep-learning method for mobile element insertion discovery

MEIsensor detects and classifies mobile element insertions from long-read sequencing data, outperforming existing tools in accuracy and efficiency, especially for complex insertions.

High-resolution metagenome assembly for modern long reads with myloasm

Myloasm improves metagenome assembly using long reads, recovering more complete contigs and resolving antibiotic resistance genes.

The Circadian Isoform Landscape of Mouse Livers

This study identifies circadian oscillating isoforms in mouse livers using full-length cDNA reads and provides accessible resources for further research.

Mobilome of Enterococcus faecalis from healthy nursery pigs exposed to antibiotic pressure

The paper examines the mobilome of multidrug-resistant Enterococcus faecalis from healthy piglets, identifying mobile genetic elements and their roles in antibiotic resistance and adaptation.

Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens

This study uses long-read sequencing to analyze plasmidome and resistome in chicken fecal samples, revealing ARGs associated with 26 antibiotic classes and their dynamic spread.

Allos: an integrated Python toolkit for isoform-level single-cell and spatial in-situ transcriptomics

Allos provides a Python framework for isoform-level analysis of single-cell and spatial transcriptomics data, integrating with existing tools and enabling differential isoform usage screening and visualization.

Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies

Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age

The paper shows PFAS affect birth weight and gestational age through distinct transcriptional network architectures, with network position, not fold-change, determining mediator importance.

Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework

This paper benchmarks circRNA detection tools using a simulation framework and finds they vary in performance, with limited overlap in detected circRNAs and significant computational efficiency differences.

Population-scale interpretation of RNA isoform diversity enabled by Isopedia

Isopedia reduces apparent isoform novelty by up to 26-fold in HG002 benchmarks and provides a reference-agnostic framework for population-scale isoform annotation.

Intron Retention Controls Localization of lncRNAs PURPL and MALAT1 to Promote Cell Proliferation and Migration

The paper identifies U2AF2's role in intron retention of lncRNAs PURPL and MALAT1, showing how this process affects their localization and promotes cell proliferation and migration.

The DoGA Consortium Atlas of Canine Enhancers and Promoters Across Tissues and Development

The paper creates a transcription-based atlas of canine regulatory elements across tissues and development, identifying promoters and enhancers and their activity patterns.

A Long-Context Generative Foundation Model Deciphers RNA Design Principles

EVA is a long-context generative RNA model trained on 114 million sequences, achieving state-of-the-art performance in RNA design tasks and structural modeling.

Biological Foundation Models Enable CRISPR Array Detection Without Metagenomic Assembly

This paper introduces a foundation model for CRISPR array detection that works without metagenomic assembly, achieving high accuracy on both short and long sequences.

Evolutionarily Conserved Decline of tRNA Mannosyl-Queuosine Links Translational Regulation to Aging and Is Reversed by Queuine

This study identifies mannosyl-queuosine (manQ) as an age-related tRNA modification that declines across species and is reversed by queuine supplementation, improving healthspan and lifespan.

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads

LongcallD jointly calls and phases small, structural, and mosaic variants from long reads, improving SV discovery and mosaic variant accuracy.

Hidden Diversity in Yeast tRNAs: Comparative Genomics and Modification Mapping in a Eukaryotic Subphylum

The paper identifies lineage-specific tRNA sequence conservation and variation in modifying enzymes across Saccharomycotina using genomic and sequencing data.

Single-Platform Nanopore Sequencing Enables Diploid Telomere-to-Telomere Genome Assembly and Haplotype-Resolved 3D Chromatin Maps

This paper presents a Nanopore-only workflow for diploid T2T genome assembly and haplotype-resolved 3D chromatin maps, achieving high accuracy without hybrid polishing.

Single-cell RNA sequencing uncovers cell-type-specific reprogramming of water-channel and cell-wall genes in PFOA uptake by lettuce root tips

The paper uses single-cell RNA sequencing to identify cell-type-specific gene expression changes in lettuce root tips exposed to PFOA, revealing mechanisms of uptake and deposition.

Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

The paper quantifies transcriptional readthrough in CML cells after imatinib treatment and shows it precedes alternative splicing changes and resistance development.

Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA

Pro2RNA generates species-adapted mRNA coding sequences from protein sequences using a multimodal language model, outperforming existing methods in benchmark tests.

High specificity meets genomic flexibility in the Siphamia-Photobacterium symbiosis

The paper investigates the Siphamia-Photobacterium symbiosis, finding that temperate siphonfish hosts exclusively associate with P. mandapamensis, which exhibits genomic and phenotypic flexibility.

Improved long transcript representation in Oxford Nanopore direct RNA sequencing with UltraMarathonRT

This paper introduces an improved DRS protocol using UltraMarathonRT to generate longer RNA reads and isoform predictions in Oxford Nanopore sequencing.

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.