long-read sequencing

Glial cells gate small RNA transport from germline to brain during transgenerational epigenetic inheritance of behavior

The paper identifies glial cells as the gatekeepers for small RNA transport from the germline to the nervous system in C. elegans, revealing a mechanism for transgenerational epigenetic inheritance of behavior.

Multiplex-GCN Predicts Clinically Actionable Tumor Microenvironment Subtypes in Pancreatic Cancer

The paper develops a multi-layered GCN to identify TME-guided PDAC subtypes, revealing seven subtypes with distinct molecular and prognostic features.

Isoform-Resolved Temporal Remodeling of Transcriptome Architecture in Monkeypox Virus

The paper reanalyzes sequencing data to reconstruct full-length monkeypox virus transcripts and shows temporal changes in gene regulation and transcript structure.

Long-read sequencing reveals telomere inheritance patterns from human trios

The paper uses long-read sequencing to analyze telomere inheritance patterns in human trios, finding parent-of-origin effects and heritable influences on telomere length.

piRNA loss unleashes episodic transposition bursts

This study shows that loss of the piRNA pathway in Drosophila leads to episodic and stochastic transposition bursts, not just increased transposition rates.

Pervasive short hairpin folding in non-encapsidated RNA viruses

The paper identifies pervasive short hairpin RNA structures in non-encapsidated viruses and shows their association with structural constraints and evolutionary origins.

flodl-bio: First Rust data, transformers and model layer for entire deep learning on biological sequences

flodl-bio introduces a Rust framework for deep learning on biological sequences, achieving state-of-the-art performance on transcription-factor-binding datasets.

RiboCouple links RNA backbone generation to sequence design through a learned interaction topology

The paper introduces RiboCouple, a method that links RNA backbone geometry to sequence design using learned interaction topologies, improving refolding validity in RNA structure prediction.

Evaluating the added value of sequence models in noncoding RNA assays: a baseline-aware framework

The paper evaluates sequence models in noncoding RNA assays by comparing model increments against baselines and highlights the importance of baseline content and regularization.

ONT-LibQC: rapid quality control of chromatin assay libraries using shallow nanopore sequencing

ONT-LibQC uses shallow nanopore sequencing to rapidly assess chromatin assay library quality before deep sequencing, showing consistent results with Illumina sequencing.

Nonsense-mediated decay constrains transposable element-driven evolutionary innovation

This study shows NMD limits TE-driven transcriptomic innovation by degrading TE-derived transcripts, affecting evolutionary novelty and cancer outcomes.

Sexually dimorphic alternative splicing and its erosion following the loss of sex in stick insects

The paper examines sex differences in gene expression and alternative splicing in stick insects, finding that splicing variation declines more rapidly than gene expression after the transition to asexuality.

A prediction-interval framework for identifying outlier control cohorts in lifespan studies

The paper develops a prediction-interval framework to identify outlier control cohorts in lifespan studies using data from the National Institute on Aging Interventions Testing Program.

Panagram reveals pangenome architectures underlying trait variation in plants and animals

Alignment-free pan-k-mer profiles track minimap2 similarity (whole-chromosome r^2 0.959-0.968), profile 605 vertebrate genomes in about a day on 40 cores, and nominate trait-linked loci across plants and animals.

T2G: fast and accurate transcriptome to genome BAM liftover for short and long read RNA sequencing

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

Direct RNA sequencing of beet yellows virus replicative intermediates reveals diverse deletion containing RNAs and break point patterns

The paper uses direct RNA sequencing to analyze defective RNAs in beet yellows virus, identifying deletion patterns and breakpoint features.

Chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana

The paper presents a chromosome-level genome assembly and transcriptome resource for the medicinal leech Hirudo verbana using PacBio and Hi-C data.

Accurate repeat expansion genotyping from whole-genome and real-time targeted nanopore sequencing with Mahi-mahi

Mahi-mahi accurately genotypes repeat expansions from nanopore sequencing data, matching orthogonal methods and identifying pathogenic alleles.

Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line

The paper uses in vitro transcribed RNA from genomic DNA to benchmark RNA modification detection by Nanopore direct RNA sequencing models.

Strain resolution and wide relative abundance quantification of bacterial microbiomes with nanopore sequencing of the ribosomal RNA operon

This paper demonstrates strain-level resolution and quantification of bacterial microbiomes using nanopore sequencing of the ribosomal RNA operon, showing accurate relative abundance quantification over multiple orders of magnitude.

Kinetic decoupling of early transcription reveals Mediator regulates paused RNA polymerase II stability

This study uncouples Mediator's role in RNAPII transcription initiation from its effects on promoter-proximal pausing, showing Mediator regulates paused RNAPII stability rather than P-TEFb recruitment.

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes at gene and isoform resolution

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes, resolving targets at gene and isoform levels and linking genetic risk to disease.

Modulator Resolves Transcript-, Allele-, and Condition-associated RNA Modification Differences from Direct RNA Sequencing

Modulator processes nanopore direct-RNA sequencing data to differentiate transcript-, allele-, and condition-associated RNA modifications, improving the analysis of RNA modifications in single molecules.

A host enzyme pseudouridylates an RNA bacteriophage genome and accelerates virus production

The paper identifies pseudouridylated RNA in bacteriophages and shows host enzymes modify phage genomes to enhance virus production.

Nanopore sequencing reveals the DNA replication timing programme of the malaria parasite Plasmodium falciparum

This study uses nanopore sequencing to determine the replication timing programme of Plasmodium falciparum and links it to DNA breaking and replication fork stalling.

Resolving functional mRNA units clarifies the decay landscape of the bacterial transcriptome

The paper clarifies bacterial mRNA decay kinetics by resolving full-length mRNAs, revealing first-order decay and 5'-dependent decay mechanisms.

SLAFIT: Viral fitness inference and structural variant detection from TGS data

SLAFIT infers viral fitness and detects structural variants from third-generation sequencing data by analyzing linkage disequilibrium and haplotype frequencies.

SF3B1 mutation generates novel peptides from long non-coding RNAs

The paper uses long-read sequencing to identify novel lncRNAs generated by SF3B1 mutation and shows they produce functional peptides linked to cancer prognosis.

Telomere dynamics parameters inferred from mathematical modeling of telomere length distribution

The paper develops a mathematical model to infer telomere dynamics parameters from telomere length distributions in yeast using long-read sequencing data.

DIPLER: rapid k-mer-based locus identification

DIPLER identifies structurally complex loci using k-mer analysis and de novo assembly from low-coverage sequencing data.