long-read sequencing

Beyond the gene: contextualizing novel isoforms through pathway analysis in long-read single-cell RNA sequencing

The paper develops a computational framework to contextualize novel isoforms identified through long-read single-cell RNA sequencing by integrating pathway analysis with expression-based neighborhoods.

DUMMEST: A simpler and faster model for frameshift-aware alignment of a DNA sequence to a protein family

DUMMEST improves frameshift-aware alignment of DNA sequences to protein families by combining simplicity and speed, outperforming existing methods in sensitivity and specificity.

Systematic evaluation of transcript normalization methods and quantification pipelines across long-read sequencing platforms

The paper evaluates normalization methods and quantification pipelines for long-read RNA sequencing across PacBio and ONT platforms, showing platform-specific impacts on accuracy.

Multidimensional telomere diversity and inheritance at individual and population scales

This paper introduces TeloXplorer, a framework for analyzing telomere features in long-read data, showing how telomere diversity is inherited across species and populations.

NanoPlasmiQC: Full plasmid sequencing with ONT long-reads and automatic data analysis

NanoPlasmiQC provides a cost-effective workflow for full plasmid sequencing using ONT long-reads and automated data analysis.

Biobank-scale genotyping of Robertsonian translocations reveals hidden structural variation on the human acrocentric chromosomes

Short-read genomes can flag Robertsonian translocation carriers by counting rDNA distal junction (DJ) copies (8 rather than 10); UK Biobank screening found 583 candidates, 1 in 841.

tRNAZAP: Deep learning toolkit for nanopore tRNA signal analysis

tRNAZAP is a deep learning toolkit for analyzing nanopore tRNA sequencing data, achieving high accuracy in segmentation and classification tasks.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

Common centromeric variation associates with molecular and complex traits in humans

This study identifies centromeric structural variants linked to molecular traits and complex diseases in humans using long-read sequencing and haplotype-resolved analysis.

Structural variants from donor-specific assemblies affect recurrent chromatin contact divergence in humans

The paper shows that structural variants from donor-specific assemblies influence chromatin contact divergence in humans, with many SVs linked to regulatory contexts and expression variation.

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

WarpDemuX-custom - Multiplexed sequence-specific direct RNA sequencing

The paper introduces an improved protocol and software for sequence-specific direct RNA sequencing of non-polyadenylated RNAs, validated on human rRNA and other RNA species.

The Genetic Landscape of Structural Variants in Aspergillus flavus using ONT and PacBio Sequencing

This study uses long-read sequencing to analyze structural variants in Aspergillus flavus, identifying homopolymer tracts and deletions that arise spontaneously.

Multilayer analysis reveals extensive hidden population complexity in a dairy starter microbiome comprising few species

The paper analyzes a dairy starter microbiome with low species richness using genomic and metagenomic data to reveal hidden population complexity and phage resilience.

Multi-omic long-read sequencing reveals nucleosome control of transcriptional fidelity at the isoform level

The paper uses long-read sequencing to study how nucleosome positioning affects isoform expression by analyzing chromatin and RNA in yeast.

Interaction-specific early wheat responses to Zymoseptoria tritici share enhanced defense-related transcription during incompatibility

The paper compares early transcriptomic responses in wheat cultivars to Zymoseptoria tritici, finding that defense-related genes show higher expression in incompatible interactions.

High-fidelity long-read metagenomics reveals the metabolic functions of dominant termite gut bacteria

This study uses high-fidelity long-read metagenomics to reconstruct genomes of dominant termite gut bacteria and reveals their lineage-specific metabolic functions.

A novel analysis pipeline and experimental design for measuring expanded repeat instability

Delta plots from targeted long-read data separate repeat instability frequency, expansion bias and change size; a single-clone assay (SCIA) shows FAN1 knockout raises expansion frequency but shrinks expansions.

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

Long-read sequencing reveals genomic landscape of structural variants in a major disease vector

The paper uses long-read sequencing to identify structural variants in Culex quinquefasciatus, revealing their potential role in insecticide resistance and adaptation.

KSHV upregulates the long non-coding RNA PURPL via p73 to suppress p53

This study shows KSHV upregulates the oncogenic lncRNA PURPL through p73 to suppress p53, promoting PEL cell proliferation.

Long-read sequencing with targeted assembly of the opsin locus accurately evaluates genes in expressed positions

This paper evaluates long-read sequencing with targeted assembly for accurately analyzing the opsin gene cluster, showing high concordance and improved detection of color vision deficiencies and carrier status.

High Quality, Long-Read Genome Assemblies of Two Virulent Field Isolates of Pyricularia oryzae from Portugal

Two Portuguese rice-blast fungus isolates were assembled from PacBio HiFi reads into near-complete genomes; one isolate lacks Avr-Pii, Avr-Pia and Avr-Pik yet remains virulent on two rice cultivars.

A novel mitogenome for Euterpe precatoria (Arecaceae)

The paper presents the complete mitochondrial genome of Euterpe precatoria, assembled using PacBio HiFi sequencing and manual curation, revealing structural complexity and gene features characteristic of palm mitochondrial genomes.

Increased burden of endogenous viral elements in Alzheimer's Disease compared to cognitively healthy centenarians

This study compares endogenous viral elements in Alzheimer's Disease patients and cognitively healthy centenarians using long-read sequencing, finding higher EVE burden in AD patients.

3D confinement reshapes RNA folding and enhances circularisation in the Zika virus

This study models how 3D confinement affects RNA folding and circularization in the Zika virus genome, showing increased circularization under confinement.

Rank-based integration identifies convergent disease mechanisms across omics

ORBIT integrates omics data across studies and layers to identify convergent disease mechanisms by prioritizing concordant signals using rank-based methods.

Avian germline-restricted chromosomes are reservoirs for active long-terminal-repeat retroviruses

This study identifies germline-restricted chromosomes in birds as reservoirs for active retroviruses, showing their role in promoting transposition and speciation.

RNA splicing factor mutations drive myeloid neoplasm oncogenesis through protein complex poisoning

This study identifies how RNA splicing factor mutations drive myeloid neoplasm by disrupting proteomic networks through mis-splicing, validated via single-cell transcriptomics and proteomics.

A reference genome without a virus: cDNA reconstruction reveals the provenance and function of the MS2 phage sequence

The paper reconstructs the MS2 phage genome using cDNA and shows that the current NCBI reference genome does not produce infectious phage, highlighting the need to verify reference genome infectivity.