long-read sequencing

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.

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.

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.

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.

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.

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.

Systematic evaluation of transcript normalization methods and quantification pipelines across long-read sequencing platforms

The paper evaluates normalization methods and quantification pipelines for long-read RNA sequencing across PacBio and ONT platforms, showing platform-specific impacts on accuracy.

Multidimensional telomere diversity and inheritance at individual and population scales

This paper introduces TeloXplorer, a framework for analyzing telomere features in long-read data, showing how telomere diversity is inherited across species and populations.

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

Rank-based integration identifies convergent disease mechanisms across omics

ORBIT integrates omics data across studies and layers to identify convergent disease mechanisms by prioritizing concordant signals using rank-based methods.

Empirical Validation of Composite Fractional Noise Models in Nanopore Signals

This study empirically validates a composite fractional noise model for nanopore signals across diverse experimental conditions, showing it accurately captures noise structure and separates deterministic from stochastic components.

seqsizzle: decoding complex barcode and adapter architectures in long-read sequencing data

seqsizzle is a tool for visualizing and troubleshooting long-read sequencing data, enabling primer sequence identification and quality control through fuzzy matching and k-mer analysis.

Evaluating the reliability of tools for mRNA annotation and IRES studies

A back-splicing circRNA reporter yields linear trans-spliced artifacts; in orthogonal assays three reported cellular IRESes are inactive, and Iso-Seq 5' ends agree with nAnT-iCAGE start sites.

An RNA Language Model trained on sequence alone reveals the structural logic of Internal Ribosome Entry Sites

Continued pretraining of an RNA language model on picornaviral 5′ UTRs alone predicts IRES base pairs with median precision 0.80 versus 0.47 for Infernal, and reveals a Type II subclass.

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

The paper develops crop-specific Nanopore basecalling models for Rosaceae species to improve sequencing quality and enables community use of these models.

Characterization of recombinase-based genetic parts and circuits using nanopore sequencing

The paper develops a workflow combining robotics, nanopore sequencing, and computational tools to characterize recombinase-based genetic circuits efficiently and at high resolution.

Unlocking Sensitive Data with SPHERE in the Age of AI

SPHERE enables the use of sensitive datasets in AI and open science by creating synthetic twins that preserve statistical properties and privacy.

nanorepertoire: an end-to-end Nextflow pipeline for nanobody repertoire analysis

nanorepertoire is an end-to-end Nextflow pipeline for analyzing camelid nanobody repertoires, providing standardized and reproducible analysis of AIRR-seq data.

Evaluating transcriptome-wide information preservation by ensilication using long-read RNA sequencing

This study evaluates how ensilication preserves transcriptome information during storage using long-read RNA sequencing, finding it retains more transcript data than unprotected RNA.

Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics

Systematic benchmarking of small variant calling pipelines for long-read RNA sequencing data

The paper benchmarks small variant calling pipelines for long-read RNA sequencing data, finding that sequencing quality is the main factor affecting performance, followed by variant caller and alignment strategy.

Hidden assumptions in nascent RNA sequencing pipelines define reproducibility states

The paper identifies how hidden assumptions in nascent RNA sequencing pipelines lead to structured divergence in transcriptional profiles across datasets.

Benchmarking long-read RNA sequencing for de novo transcriptome assembly in non-model plant species: insights from Moricandia arvensis

The paper benchmarks long-read RNA sequencing pipelines for de novo transcriptome assembly in non-model plants, finding organ-specific optimal strategies for flower and leaf tissues.

WGCNA+: AI-powered WGCNA for Integration of Multi-Omics Data

WGCNA+ extends WGCNA to multi-omics data, enabling cross-omics module analysis and visualization with AI-powered interpretation.

Pangenome alignment reveals global diversity and evolution of human centromeric regions

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

Systematic benchmarking of commercial workflows for isoform-resolved single-nucleus transcriptomics

This study benchmarks four commercial LR snRNA-seq workflows, finding 10x Genomics 3' and 5' to be the most balanced for isoform-resolved single-nucleus transcriptomics.