long-read sequencing

LinearRaccess: linear-time approximation of RNA accessibility without base-pair span limits

LinearRaccess computes RNA accessibility for long windows in linear time without base-pair span limits, achieving high accuracy and efficiency.

spearfish: ultrafast Δ-mapping of long reads to redundant transcriptomes

spearfish improves long-read mapping efficiency by leveraging transcriptome redundancy, achieving faster speeds and lower memory usage than existing tools.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.

Sex-specific gene and isoform expression characterizes hippocampal aging in rhesus macaques

This study identifies sex-specific gene and isoform expression changes in hippocampal aging of rhesus macaques and finds shared transcriptional signatures with Alzheimer's disease.

SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

SQANTI-evidence annotates genomes from long-read RNA-seq without a reference, achieving high precision in gene and isoform prediction across species.

Leveraging short and long-read sequencing to comprehensively characterize alternatively polyadenylated and alternatively spliced transcripts

The paper uses short and long-read sequencing to identify alternatively spliced and polyadenylated transcripts in mantle cell lymphoma, revealing novel splice variants and polyadenylation signals.

An RNA-centric atlas of human cell cycle regulation

The paper defines an RNA-centric landscape of human cell cycle control by profiling various RNA features and identifies key RNA elements involved in cell cycle regulation.

The small ORF (smORF)-encoded polypeptide MIRINE promotes neuronal differentiation in vertebrate brain development

The paper identifies MIRINE, a small ORF-encoded polypeptide that promotes neuronal differentiation in vertebrate brain development by regulating the balance between proliferation and maturation.

Integrating pangenome and imputation framework reveals structural variants affecting stature and milk composition traits in French dairy cattle

The paper integrates long-read, short-read, and SNP data using a pangenome and imputation framework to identify structural variants associated with stature and milk traits in dairy cattle.

Transcript quantification using context-aware MAPQ modeling

CALMeR improves transcript quantification by context-aware MAPQ modeling, recovering more spike-in transcripts and better matching known concentrations.

Targeted proteomics informed by long-read RNA-sequencing reveals protein isoform expression associated with bone mineral density

This study uses genetics-guided targeted mass spectrometry to detect protein isoforms associated with bone mineral density, confirming their expression in clinical samples.

mito-overview: a mitochondrial report software

mito-overview integrates mitochondrial coverage, allele fractions, annotations, and read co-occurrence to identify and analyze candidate variants in mitochondrial genomic reports.

Extensive and heterogeneous viral circular RNA production during Zika virus infection

This study identifies and validates viral circular RNAs produced during Zika virus infection in neural stem cells.

Ground-truth evaluation of sparse autoencoder features on spatial, single-cell and language-model embeddings

The paper evaluates sparse autoencoder features on various embeddings, finding that reproducibility does not guarantee meaningfulness, and proposes reporting features with concept coverage and purity.

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.

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.

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.

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.

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.

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.

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.

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.