long-read sequencing

A comprehensive benchmark of transcriptome-wide fusion detection using long-read RNA sequencing

This study benchmarks fusion detection methods using long-read RNA sequencing, finding that ONT PCR-cDNA with CTAT-LR-Fusion offers the best balance of precision and recall.

Molecular co-accessibility identifies coordinated regulation between distant cis-regulatory elements

The paper quantifies co-accessibility between cis-regulatory elements in Drosophila using single-molecule footprinting and long-read sequencing, revealing coordinated regulation across genomic distances.

Integrated sequencing approach to probe rRNA modification landscape during human embryonic stem cell differentiation

The paper identifies dynamic changes in rRNA modifications during human embryonic stem cell differentiation using Nanopore sequencing and snoRNA profiling.

Chromosome assembly for the Black bean aphid Aphis fabae

The paper presents two chromosome-scale assemblies of the Black bean aphid Aphis fabae using HiFi and Hi-C, revealing expanded UDP-glycosyltransferases linked to insecticide tolerance.

Full-length transcriptome atlas of Panax vietnamensis var. fuscidiscus reveals novel genes and alternative splicing in tissue-specific biosynthesis of ocotillol-type saponins

This study constructs the first full-length transcriptome atlas of Panax vietnamensis var. fuscidiscus, identifying novel genes and extensive alternative splicing events related to OCT-type saponin biosynthesis.

A chromosome-scale genome of Colletotrichum cereale reveals a large, dynamic accessory genome within a deeply structured species

This paper presents the first chromosome-scale genome assembly of Colletotrichum cereale, revealing three large accessory chromosomes and a deeply structured genome with significant intraspecific divergence.

A pangenome-graph approach for mapping and imputing barley sequences

Pan20, a Practical Haplotype Graph of 20 barley genomes, assigns sequences MorexV3 coordinates and imputes genotyping-by-sequencing (GBS) reads at 0.06% base-call error versus 0.32% for variant calling.

Nanopore-based sequence deconvolution of diverse glycosaminoglycans

This paper develops a nanopore-based method to deconvolute glycosaminoglycan structures at single-molecule resolution, achieving high precision in detecting sulfate groups and stereochemistry.

The fate of a dynasty: Population genomics uncovers the demographic history of Ardea insignis, one of the rarest bird species in the world

This study uses population genomics to reveal the long-term demographic history of the critically endangered White-bellied Heron, showing persistent small population size rather than recent collapse.

Identifying crossovers in a cattle pangenome containing haplotype-resolved assemblies from half-siblings

The paper identifies crossover events in cattle using haplotype-resolved assemblies and methylation data from long-read sequencing, finding more events in half-siblings than in cousins.

Chloroplast Genome Evolution, Heteroplasmy, and Inverted Repeat Dynamics in the Elymus Complex (Triticeae, Poaceae): Insights from Single-Molecule Sequencing of Elymus ciliaris and Comparative Analysis of St-Genome Lineages

The paper uses single-molecule sequencing to analyze chloroplast genome heteroplasmy and structural dynamics in Elymus species, revealing inversion polymorphisms and lineage-specific IR boundary shifts.

Population-scale disease-associated tandem repeat analysis reveals locus and ancestry-specific insights.

The paper analyzes disease-associated tandem repeat loci across diverse populations using long-read data, revealing ancestry-specific variation and complex genotype-phenotype relationships.

Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne Parasite Babesia divergens

This study reports cryo-EM ribosome structures and rRNA modifications in Babesia divergens, revealing novel modifications with potential therapeutic implications.

Pangenome discovery and characterization of human protein-coding duplicated genes

The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes

This paper benchmarks 7 TR genotyping tools using Nanopore long-read data, finding that no single tool is best across all metrics, and that sequence-level accuracy is crucial for clinical and population studies.

The Fontan EV Score: A Circulating Extracellular Vesicle-Based Risk Stratification Tool for Fontan-Associated Liver Disease

This paper develops the Fontan EV Score, a non-invasive biomarker using circulating extracellular vesicles to predict Fontan-associated liver disease severity, outperforming existing serological indices.

Nucleolar endonuclease MBLAC2 orchestrates co-transcriptional ribosomal RNA processing and global transcriptional output

This study identifies MBLAC2 as a nucleolar nuclease essential for co-transcriptional rRNA processing and global transcriptional output.

Meta-PseU: A Meta-Classifier for Robust Prediction of RNA Pseudouridine Modification Sites from Long Sequences

Meta-PseU is a meta-classifier that improves RNA pseudouridine site prediction using long sequences, outperforming existing methods across species.

SVkhor: a unified framework for structural variant integration across long-read, short-read, and optical genome mapping data

SVkhor normalizes, merges and integrates long-read, short-read and optical-mapping structural variant calls; on HG002 it retained 98.6% of naive concatenation's true positives with 58.2% fewer false positives.

Omega-seq: ultra-low-background RNA sequencing with faithful molecular counting and precise transcript-end capture

USER-excisable uracil TSOs, a uracil-intolerant polymerase and excess primer confine UMI incorporation to reverse transcription, minimizing background and UMI inflation; a separate Omega-shaped dT primer captures stranded transcript ends.

A hyperspherical deep Bayesian model for interpretable clustering and relationship prediction in microbiome multi-omics integration

DBayesCM integrates multi-omics microbiome data using a deep Bayesian model to enable interpretable clustering and relationship prediction across diseases.

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

Genomic alterations enable BRCA1 methylation loss and promoter bypass to drive resistance in high-grade serous ovarian cancer

This study identifies genomic mechanisms enabling BRCA1 methylation loss and promoter bypass in ovarian cancer, leading to PARP inhibitor resistance.

Structural Analysis of Recombinant AAV Vector Genomes at Single-Molecule Resolution

The paper develops a pipeline to classify AAV genome structures at single-molecule resolution using long-read sequencing, revealing structural heterogeneity and its contributing factors.

Scalable single-cell isoform profiling with sequencing-by-expansion

This paper introduces a high-throughput single-cell RNA isoform sequencing method using sequencing-by-expansion (SBX) and the CUDLL algorithm, achieving high accuracy and enabling isoform-level analysis across cell types.

Rich mobilomes and a conserved adaptive core in bacteria from an intensifying Mexican soda lake

The paper studies bacteria from a Mexican soda lake, finding rich mobilomes but a conserved adaptive core for haloalkaliphily.

Cytoplasmic DNA Sensing Links LINE-1 Expression to Neuronal Senescence in Alzheimer's Disease

This study identifies LINE-1 retrotransposons as drivers of neuronal senescence in Alzheimer's disease through cytoplasmic DNA sensing and the cGAS-STING pathway.

Locus-Scale Massively Parallel Reporter Assays

The paper introduces LAMPRAs to measure how cis-regulatory element composition affects gene expression using synthetic loci.

SQUARNA: stem maximization for accurate de novo RNA secondary structure prediction

SQUARNA improves RNA secondary structure prediction by combining stem maximization with free energy minimization, outperforming existing methods including deep learning models.

TCR germline diversity reveals evidence of natural selection on variable and joining alpha chain genes

The paper maps common TCR alleles in 2,668 donors, finds natural selection on TRAJ and TRAV genes, and shows allelic polymorphism affects T cell function.