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.

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.

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.

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.

tRNAZAP: Deep learning toolkit for nanopore tRNA signal analysis

tRNAZAP is a deep learning toolkit for analyzing nanopore tRNA sequencing data, achieving high accuracy in segmentation and classification tasks.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

Multilayer analysis reveals extensive hidden population complexity in a dairy starter microbiome comprising few species

The paper analyzes a dairy starter microbiome with low species richness using genomic and metagenomic data to reveal hidden population complexity and phage resilience.

High-fidelity long-read metagenomics reveals the metabolic functions of dominant termite gut bacteria

This study uses high-fidelity long-read metagenomics to reconstruct genomes of dominant termite gut bacteria and reveals their lineage-specific metabolic functions.

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.

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

RNASeek: A Cross-Phyla Generative Foundation Model for Multipurpose RNA Modeling and Reinforcement Learning-Based Design

RNASeek is a generative foundation model for RNA sequence design and functional prediction, using reinforcement learning to optimize RNA properties like stability and cleavage activity.

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.

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

Post-hoc long-read sequencing links leukemic mutation status to single-cell transcriptomes

The paper develops a post-hoc method to link mutation status to single-cell transcriptomes using long-read sequencing, showing it can detect BCR::ABL1-positive cells in chronic myeloid leukemia.

Identification and characterization of bacterial repeat-in-toxin adhesins using long-read genome analysis

This study identifies and characterizes RTX adhesins in seven bacterial species using long-read sequencing and AlphaFold3 modeling, revealing 35 unique variants with diverse LBD arrangements.

Single-molecule nanopore sequencing reveals spatial coordination of rRNA modifications in human ribosomes

This study uses single-molecule nanopore sequencing to analyze rRNA modifications in human cells, revealing local coordination of modifications and their response to drug treatment.

SPLISOFORMS: a Structure-Resolved Knowledge Base of Alternative Splicing Isoforms

A web database and REST API of 124,687 AlphaFold 3 structures for human splice isoforms, annotated against canonical proteins for domains, decay, modifications, neoantigens and drug pockets.

Revisiting bacterial division control with likelihood inference: limited identifiability of simple models

Likelihood comparison on six E. coli mother-machine datasets finds sizer, adder, and log-foldchange division rules only weakly separable, while a neural conditional cycle-duration model fits best.

Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

This study uses single-cell multi-omics to analyze transcript isoform and immune repertoire changes in aging human immune cells, identifying age-related molecular features in T cells and B cells.

Decoding Radiation-Induced Transcriptomic Signatures of Human Leukocytes using Long-Read RNA-Seq: Clinical and Biodosimetric Implications

Nanopore long-read RNA-seq of leukocytes from 4 Gy X-irradiated blood (three donors, 6 h) recovers p53 signaling and reveals isoform-level regulation plus candidate unannotated FBXO22/PHPT1 isoforms.

scLANTERN: High-Throughput Retrospective Lineage Tracing via Full-Length Single-Cell Transcriptomics and Expressed Repeat Variation

This paper introduces scLANTERN, a method using full-length single-cell transcriptomics and expressed repeat variation to enable high-throughput retrospective lineage tracing in cancer.