long-read sequencing

In virio secondary RNA structure analysis of influenza A virus

This study identifies RNA secondary structures in influenza A virus gene segments and shows that mutations in packaging signal structures reduce viral replication.

H19 is a PERK-regulated long non-coding RNA that fine-tunes UPR signalling and inhibits endoplasmic reticulum stress-induced cell death

This study identifies H19 as a PERK-regulated lncRNA that modulates UPR signaling and protects cells from ER stress-induced apoptosis in breast cancer.

Single-cell sequencing of trophoblasts in preeclampsia and chemical hypoxia in BeWo b30 cells reveals EBI3, COL17A1, miR-27a-5p, and miR-193b-5p as hypoxia-response markers

The paper identifies hypoxia-response markers in trophoblasts from preeclampsia and chemical hypoxia models using single-cell and small RNA sequencing.

Functional Annotation Workflow for Fungal Transcriptomes

This study develops a fungal-specific functional annotation workflow for RNA-seq data, achieving high annotation accuracy and applicability to Iso-Seq data without requiring reference genomes.

Integrating SHAPE Probing with Direct RNA Nanopore Sequencing Reveals Dynamic RNA Structural Landscapes

The paper introduces Dashing Turtle (DT), an algorithm for high-resolution detection of RNA structural modifications using direct RNA nanopore sequencing, showing improved accuracy over existing methods.

New insights into the evolution of spider silk proteins illuminated by long-read transcriptomes

This study uses long-read transcriptomes to identify ancestral spider silk proteins and their evolutionary trajectories, revealing how they diversified into modern silk types.

TARPON - a Telomere Analysis and Research Pipeline Optimized for Nanopore

TARPON is a Nextflow pipeline for analyzing telomeres sequenced on Nanopore, providing a user-friendly interface and customizable analysis for various applications.

LncRNA-BERT: An RNA Language Model for classifying Coding and Long Non-Coding RNA

This paper introduces lncRNA-BERT, an RNA language model that classifies coding and long non-coding RNAs, outperforming existing methods on benchmark datasets.

Alternative promoters used during myeloid differentiation and upon activation change the gene products available for innate immune programs.

The paper identifies new gene products and transcript isoforms in macrophage differentiation and activation, revealing how alternative promoters influence innate immune functions.

High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq

This paper introduces sci-L3-Strand-seq, a method for high-throughput mapping of mitotic crossover and genome instability events in single cells, and demonstrates its ability to distinguish crossover types and explore genomic features.

Ultra-fast sample-to-sequencing workflow for clinical diagnostics using micropillars

This paper introduces an integrated microfluidic workflow for Oxford Nanopore sequencing that reduces hands-on time and sample loss while enabling high-quality library preparation from small sample volumes.

Accurate haplotype-resolved de novo assembly of human genomes with RFhap

RFhap improves haplotype-resolved de novo assembly of human genomes by enhancing phasing accuracy and reducing errors compared to existing methods.

Light-inducible proximity labelling in vivo captures sex-specific RNA at excitatory synapses

PSD-95-Halo-seq combined with long-read sequencing reveals sex-specific RNA isoform remodeling in excitatory synapses following fear learning.

Campolina: A Deep Neural Framework for Accurate Segmentation of Nanopore Signals

Campolina improves nanopore signal segmentation accuracy using deep learning, outperforming traditional methods on real datasets.

Large scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

The paper uses nanopore sequencing to analyze capsid-packaged DNA in gut microbiomes, finding bacterial DNA encapsidation is widespread and associated with specific bacterial families.

A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection

The paper introduces AIR-SPACE, a method combining spatial transcriptomics and immune receptor sequencing to map adaptive immune responses in lymph nodes post-viral infection, revealing spatial dynamics of immune cell activation and differentiation.

Expression Levels of the Attachment Protein G Differ Between Strains of a Murine Pneumovirus and Determine the Virulence

The paper identifies differences in G protein expression levels between PVM strains, linking these differences to virulence through genetic variations in the G gene.

Hypatia: Comparative Isoform Profiling Across Cell Populations from Long-Read Single-Cell Transcriptomes

Hypatia compares isoform complexities across cell populations using long-read single-cell transcriptomes, improving detection of isoform usage shifts and diversity.

In vitro model reveals structural and metabolic insights to the porcine caecal microbiota in response to β-mannan exposure

The paper develops an in vitro model to study porcine caecal microbiota response to β-mannan and finds similar microbial responses to in vivo trials with some taxa showing greater changes in vitro.

NanoSimFormer: An end-to-end Transformer-based simulator for nanopore sequencing signal data

NanoSimFormer generates high-fidelity nanopore sequencing signals optimized for accurate basecalling, outperforming existing simulators across multiple datasets and tasks.

Long-Read Sequencing Reveals Increased Isoform Diversity in Key Transcription Factor Effectors of Intercellular Signalling at the Invertebrate-Vertebrate Transition

The paper uses long-read sequencing to compare isoform diversity of key transcription factors in invertebrate and vertebrate species, finding increased diversity in vertebrates.

FASTR: Reimagining FASTQ via Compact Image-inspired Representation

FASTR is a new format for storing sequencing data that reduces file size and improves processing speed compared to FASTQ.

Mapping NMD-coupled alternative splicing in iPSC-derived brain cells: a resource for therapeutic discovery

The paper maps NMD-coupled alternative splicing events in iPSC-derived brain cells and identifies therapeutic targets for neurodevelopmental disorders.

dirCLIP profiles variant-specific RNA-protein interactions via nanopore long-read sequencing

dirCLIP uses nanopore sequencing to profile variant-specific RNA-protein interactions, revealing isoform-selective binding and co-occurring sites with high concordance to short-read data.

Unlocking the Full Potential of Nanopore Sequencing: Tips, Tricks, and Advanced Data Analysis Techniques

This paper provides an overview and analysis of nanopore sequencing, offering guidelines to address challenges and maximize information gain from the technology.

LoFi drafts to map to: 4 haplotype-resolved Cannabis genomes enable characterization of large structural variants

The paper presents four haplotype-resolved Cannabis genomes using Oxford Nanopore reads and Hi-C scaffolding, showing comparable contiguity to HiFi assemblies and enabling phylogenetic and pan-NLRome analysis.

Autolab HBH: A Rapid Hyperbaric Heating Device for Streamlined, PCR-Ready Sample Preparation Across Diverse Biological Matrices and Organisms

The paper introduces a rapid hyperbaric heating device for nucleic acid extraction, demonstrating its effectiveness across diverse biological samples and organisms.

Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets

This study optimizes single-cell long-read sequencing protocols for improved isoform detection in pancreatic islets, showing better transcript identification and longer reads through library preparation and transcript depletion strategies.

Molecular QTL are enriched for structural variants in a cattle long-read cohort

The paper identifies molecular QTL enriched for structural variants in a cattle long-read sequencing cohort, showing SVs have a significant impact on gene expression and splicing.

Programmed Double-stranded RNA Formation Enables Meiotic Stage Transitions

The paper identifies dsRNA formation and NATs as a mechanism for selective mRNA clearance during meiosis, driven by transcription factors like Ndt80p.