long-read sequencing

Genomic characterization and evolutionary path of human satellite 1B in primates highlight a dynamic relationship with transposable elements

This study characterizes HSat1B across primates, showing its evolutionary origin linked to transposable elements and lineage-specific expansion in Homininae.

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.

Somatic Structural Variant Discovery from Tumor Specific Strings Computed Against a Draft Composite Germline Reference

VESPA-SS detects somatic structural variants from long-read sequencing data without requiring read mapping or a high-quality germline reference, achieving high F1 scores on cancer cell lines.

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.

Towards a foundation model for raw nanopore signal through discrete tokenization

This paper introduces Brieno, a self-supervised model for raw nanopore signals that improves read classification and methylation detection without reference genomes.

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.

Long read sequencing reveals changes in measured isoform structure and abundance due to RNA processing

The paper compares RNA sequencing protocols using long-read sequencing, finding significant changes in isoform structure and abundance due to RNA processing steps.

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.

Accumulation of two distinct alleles causes astringency loss in cultivated polyploid persimmon

This study identifies the TAN gene as the causal factor for astringency loss in PCNA persimmon cultivars through haplotype-resolved forward genetics and long-read sequencing.

Divergent NUMT mimicking functional coding region of the mitochondrial genome

The paper identifies a divergent NUMT in a sawfly species that mimics mitochondrial coding regions and suggests it may result from recent mitochondrial introgression.

Cellular context shapes the transcriptomic impact of somatic variants

The paper shows that somatic variants' transcriptomic impact depends on cellular context, not just sequence, using single-cell transcriptomics and new tools.

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.

LIMBER: A Hybrid RNA Foundation Model for Predicting and Understanding RNA Structure and Function

LIMBER is a hybrid RNA foundation model that predicts RNA structure and function, showing strong performance in secondary-structure prediction and classification, along with transferability to related tasks.

ChAI-Net learns a regulatory code for chromatin co-accessibility

The paper introduces ChAI-Net, a deep learning model that predicts chromatin co-accessibility from DNA sequences in mouse embryonic stem cells, revealing sequence motifs that govern coordinated TF binding.

High quality chromosomal genome assemblies of three human Plasmodium species directly from natural infections

The paper generates high-quality chromosome-level genomes for three Plasmodium species from natural infections, improving understanding of their biology and evolution.

SYMBIO-SCAN, a full-length 16S rRNA gene-based workflow optimized for bacterial symbiont detection and discovery from long read sequencing

SYMBIO-SCAN identifies high-quality full-length 16S rRNA gene sequences from long reads to discover bacterial symbionts in beetles, revealing novel genera and species.

Two genomes in one mitochondrion: mitochondrial heteroplasmy and mitogenome dynamics in Chlamydomonas reinhardtii

The paper revises the model of the Chlamydomonas reinhardtii mitochondrial genome by identifying structural heteroplasmy and a recombination-dependent replication mechanism.

Single-molecule nascent RNA profiling reveals multiple layers of co-transcriptional splicing and their reprogramming by cold in Arabidopsis

This study uses pPOINT-seq to analyze co-transcriptional splicing in Arabidopsis, finding that cold exposure globally enhances splicing and alters intron processing patterns.

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.

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.