long-read sequencing

Yeast rDNA as a benchmark for rDNAmine repeat analysis pipeline

The paper introduces rDNAmine, a toolkit for analyzing long repetitive genomic sequences, validated using yeast rDNA data showing species-specific polymorphism.

A framework for identifying transcript orthologs: the evolution of sex bias in alternative transcript structure in Drosophila

The paper develops a framework to identify transcript orthologs across Drosophila species, revealing conserved sex-biased alternative transcripts and their potential role in sexual conflict resolution.

Mapping the genomic and transcriptomic features associated with telomere maintenance mechanisms in complex karyotype sarcomas

The paper identifies genomic and transcriptomic features of telomere maintenance mechanisms in complex karyotype sarcomas, linking ALT status to therapeutic vulnerabilities.

Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection

The paper uses long-read sequencing to study HIV transmission and population dynamics in acute infection, finding high multilineage transmission rates and rapid viral evolution.

EMITS: expectation-maximization abundance estimation for fungal ITS communities from long-read sequencing

EMITS improves fungal ITS abundance estimation using expectation-maximization, outperforming naive counting and EMU in resolving closely related species and reducing errors.

Early-life canine gut microbiome maturation follows a shared age-diet trajectory within persistent host-specific structure

This study tracks the maturation of the canine gut microbiome through early life, showing it follows an age-diet trajectory but remains constrained by host-specific factors.

L3R-seq: A long-read 3'RACE approach for deep quantitative analysis of RNA processing

L3R-seq is a long-read sequencing method that improves quantification of RNA processing events by correcting sequencing errors and PCR biases through UMI-based consensus generation.

Portable, multilocus DNA barcoding across the diversity of meiofauna

The paper introduces OrCa-seq, a low-cost protocol for DNA barcoding meiofauna using long-range PCR and nanopore sequencing, demonstrating its broad applicability and utility in biodiversity studies.

Genomic Evidence for a Novel Introduction and Intra-host Diversity of DENV-2 in Dar es Salaam, Tanzania

The paper uses Nanopore sequencing to analyze DENV-2 in Tanzanian mosquitoes, finding a distinct clade related to Asian strains and identifying intra-host variants, suggesting a silent introduction of genotype II.

NanoCortex: A Unified Agentic System for Nanopore Sequencing Analysis

NanoCortex provides a unified agentic framework for nanopore sequencing analysis, improving usability over general-purpose models by integrating data processing and biological interpretation.

A framework for peptide identification on commercial nanopore sequencing platforms

This paper presents a framework for peptide identification using commercial nanopore sequencing platforms, achieving single-amino-acid resolution and reliable performance across sequencing runs.

BioRAG-DRAG: A Multimodal Biological Retrieval Layer for Local-First Biomedical Agents

The paper introduces BioRAG-DRAG, a local-first multimodal retrieval system for biomedical agents, combining neural retrieval, BLAST verification, and graph-based evidence packaging.

SNooPy: a statistical framework for long-read metagenomic variant calling

SNooPy is a statistical framework for long-read metagenomic variant calling that outperforms existing methods and is available on GitHub.

Small RNA-mediated genomic silencing promotes telomere stability in the absence of telomerase in C. elegans

The paper shows that small RNA-mediated genomic silencing maintains telomere stability in C. elegans without telomerase by promoting heterochromatin formation and subtelomeric small RNA biogenesis.

Direct RNA Sequencing reveals epitranscriptomic regulation of brain cells and Alzheimer's Disease pathology

This study uses direct RNA sequencing to analyze epitranscriptomic changes in brain cells, revealing m6A modification patterns linked to Alzheimer's disease progression.

Sequence alignment of the primate lineage reveals evolutionary divergence and conserved secondary structural motifs in noncoding RNAs

The paper develops a computational pipeline to align noncoding RNAs across primate genomes, revealing conserved secondary structural motifs despite rapid evolutionary divergence.

Rapid centromere turnover and the adaptive radiation of lemurs

The paper analyzes centromere evolution in lemurs using long-read sequencing, finding rapid sequence turnover and distinct centromeric repeats across species.

CDK12 and CDK13 suppress distinct intronic polyadenylation sites

This study shows CDK12 and CDK13 suppress distinct intronic polyadenylation sites, leading to premature termination and novel peptides in cancer.

Transcript architecture predetermines m6A remodeling and sensory neuron vulnerability in chemotherapy-induced peripheral neuropathy

The paper shows transcript architecture determines m6A loss and sensory neuron vulnerability in chemotherapy-induced neuropathy using nanopore RNA sequencing and machine learning.

DamageFormer: a damage-aware multimodal deep learning framework for DNA lesion identification from nanopore sequencing

DamageFormer detects and localizes DNA lesions from nanopore sequencing with high accuracy and generalization to unseen damage types.

Multiplexed direct RNA sequencing using RB-dRNAseq with RNA barcodes

This paper introduces RB-dRNAseq, a multiplexed direct RNA sequencing method that improves demultiplexing accuracy and read recovery compared to conventional DNA barcoding methods.

Decoding chromosome organization using CheC-PLS: chromosome conformation by proximity labeling and long-read sequencing

The paper introduces CheC-PLS, a proximity-labeling technique that uses Nanopore sequencing to decode chromosome organization by identifying methylated bases along long reads, demonstrating its application in budding yeast.

OpenBase: a universal framework for high-accuracy single-molecule detection of diverse non-canonical DNA bases using nanopore sequencing

OpenBase provides a framework for high-accuracy detection of diverse non-canonical DNA bases using nanopore sequencing through standardized training data and deep learning models.

Genome sequence of the medicinal plant Urtica dioica reveals the genetic basis of the flavonoid metabolism

The paper presents the genome sequence of Urtica dioica and identifies genes involved in flavonoid biosynthesis, particularly anthocyanin synthesis, linked to stress responses.

LVV SMRTcap reveals extensive proviral variation in lentiviral vector-transduced CAR T cells

The paper uses long-read sequencing to analyze proviral variation in lentiviral vector-transduced CAR T cells, finding deletions and mutations affecting transgene function.

The impact of long-read sequencing on fungal genome assemblies: progress and disparity

This paper reviews the impact of long-read sequencing on fungal genome assemblies, highlighting progress, disparities, and remaining taxonomic gaps.

Modular RNA:DNA nanostructures enable nanopore profiling of ribosomal RNA processing and rRNA variants

This paper introduces modular RNA:DNA nanostructures for direct, amplification-free rRNA profiling, enabling detection of rRNA variants and processing states.

Detecting and quantifying overparametrization in RNA language models with REDIAL

This paper introduces REDIAL, an unsupervised framework to detect overparametrization in RNA language models, revealing inefficiencies and design flaws in current models.

The gene-like promoter and transcription of LTR retrotransposons.

The paper identifies LTR retrotransposons in maize as having promoter-like features and regulatory roles through long-read transcriptomics and coexpression analysis.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.