long-read sequencing

Performance Test of the QNome Nanopore Sequencer

The paper tests the performance of Qitan Technology's nanopore sequencer, finding it generates accurate DNA barcodes at a lower cost than Oxford Nanopore Technologies' sequencer.

Graph-based learning and read-out of nanopore translocation event signals

This paper develops a graph-based framework for label-free detection of nanopore translocation events, showing it can predict event morphology across a range of voltages.

A class of deep intronic IGHMBP2 variants activate a shared cryptic splice donor, enabling correction of select variants with a single antisense oligonucleotide

This study identifies deep intronic IGHMBP2 variants causing SMARD1 and CMT2S, showing they activate a shared cryptic splice donor, enabling correction with a single antisense oligonucleotide in patient-derived motor neurons.

Transposable Elements Facilitate the De Novo Origin of Antifreeze Protein and the Diversification of Its Gene Family in Snailfishes

This paper shows how transposable elements facilitated the de novo origin and diversification of antifreeze protein genes in snailfishes through regulatory sequence recruitment and locus expansion.

Suppression rather than activation of the integrated-stress-response (GCN2-ATF4) pathway extends lifespan in the fly

This study shows that suppressing the GCN2-ATF4 pathway extends lifespan in flies, while its activation reduces lifespan, revealing a dual role in aging.

Genomic basis of rapid urban evolution revealed by the subgenome-resolved genome of octoploid Oxalis corniculata

This study reveals the genomic basis of urban adaptation in Oxalis corniculata by analyzing leaf color variation linked to heat tolerance using subgenome-resolved genome assemblies.

New high accuracy diagnostics for avian Aspergillus fumigatus infection using Nanopore methylation sequencing of host cell-free DNA and machine learning prediction

The paper develops three diagnostic tests for Aspergillus fumigatus infection in chickens using methylation markers from serum cell-free DNA and machine learning, achieving high accuracy.

RNA2PS: A sequence-specific coarse-grained RNA model linking structure, thermodynamics and phase separation

RNA2PS predicts RNA structure and phase separation behavior from sequence, showing sequence-dependent duplex stability and condensation differences in trinucleotide repeat RNAs.

Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters

This study identifies a phage-resistant sub-population of Eggerthella lenta in mice, linked to reversible genomic inversions and altered capsule production.

Mapping the Peptide Interaction Fingerprint of the Behcet's disease associated HLA-B*51

This study maps the peptide interaction fingerprint of HLA-B*51:01 using MD simulations to understand its role in Behcet's disease and guide therapeutic peptide design.

Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems

The paper presents a framework for real-time genomic characterization of pathogens, resistance, and host range in wetlands using passive sampling and nanopore sequencing, finding higher pathogen and AMR gene abundance in anthropogenically impacted sites.

Profiling and Targeting of Regulatory RNAs to Upregulate Gene Expression

This study develops regRNA Capture-seq to profile regulatory RNAs and demonstrates that targeting these RNAs with ASOs can upregulate gene expression in hepatocytes.

Chromosome-arm-specific telomere length governs dual modes of structural genome evolution in IDH-mutant astrocytoma

This study uses long-read sequencing to show that telomere length differences between chromosome arms influence structural genome changes in IDH-mutant astrocytomas.

A comprehensive DNA methylation atlas for the Chinese population through nanopore long-read sequencing of 106 individuals

The paper constructs a DNA methylation atlas for 106 Chinese individuals using nanopore long-read sequencing, identifying CpG sites and environmental influences on methylation.

Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal

The paper investigates how different high-fat diets affect host and microbiome multi-omic states over time and shows that some changes persist even after returning to a control diet.

BioAutoML-FAST: an automated machine-learning platform for reusable and benchmarked biological sequence models

BioAutoML-FAST provides an automated ML platform for biological sequence analysis, offering reusable models and benchmarking across genomic, transcriptomic, and proteomic tasks.

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium

This study identifies ISL3 elements as drivers of rapid genomic evolution in E. faecium, enabling metabolic adaptation in clinical settings through structural variation and gene regulation.

Dibenzocyclooctyne-modified PCR primers enable direct enzyme-free click chemistry ligation for custom nanopore amplicon sequencing

The paper introduces DBCO-modified PCR primers for enzyme-free click chemistry ligation in nanopore amplicon sequencing, achieving higher pore occupation and reads than commercial solutions.

A long-read RNA sequencing and polysome profiling framework reveals transposable element-driven transcript diversity and translational rewiring in glioblastoma

This study combines long-read RNA sequencing and polysome profiling to show that transposable elements drive transcript diversity and alter translation in glioblastoma stem cells.

The Long Non-coding RNA Landscape of Endurance Exercise Training

This study identifies tissue-specific lncRNA responses to endurance exercise in rats, revealing sex differences and potential therapeutic implications.

Dynamic regulation of long non-coding RNAs across asexual andgametocyte development in Plasmodium falciparum

This study identifies and characterizes long non-coding RNAs in Plasmodium falciparum across asexual and gametocyte stages using long-read sequencing and single-cell transcriptomics.

Modular Deep Learning for Direct RNA Sequence Design via Self-Contained RNA Units

The paper introduces SCRU-DB, a database of RNA units, and two models, SCRU-Seq and SCRU-Diff, to design RNA sequences with high structural accuracy.

Benchmarking Tools for Identification of rRNA Modifications in Escherichia coli using Oxford Nanopore Direct RNA Sequencing

This paper benchmarks RNA modification detection tools on bacterial rRNA using Oxford Nanopore DRS, finding that no single tool recovers all sites and that combining tools improves performance.

Orthrus: Towards Evolutionary and Functional RNA Foundation Models

Orthrus is a Mamba-based RNA foundation model pre-trained with biological augmentations and contrastive learning, achieving better mRNA property prediction than existing models with less fine-tuning data.

GANGE: Achieving Sequencing Without Sequencing With Diffusion Guided Generative Genomic Transformer

GANGE is a deep-learning system that generates accurate genomic sequences from low-coverage, error-prone reads, reducing sequencing costs and enabling regulomics research without genome data.

MSIanalyzer: Targeted Nanopore Sequencing Enables Single Nucleotide Resolution Analysis of Microsatellite Instability Diversity

MSIanalyzer uses targeted nanopore sequencing to analyze microsatellite instability at single-nucleotide resolution, revealing distinct repeat profiles and allelic diversity in cancer cell lines.

Fast and accurate resolution of ecDNA sequence using Cycle-Extractor

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

mdBIRCH for Fast, Scalable, Online Clustering of Molecular Dynamics Trajectories

mdBIRCH clusters molecular dynamics trajectories efficiently using an online method with a RMSD-calibrated merge test, enabling scalable and interpretable analysis.

MitoScope: a comprehensive mitochondrial genome analysis workflow for long-read sequencing data

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

Contemporaneity of the past in stochastic intergenerational homeostasis

The paper identifies an intergenerational scaling law governing stochastic cell size homeostasis in bacteria, revealing two adaptation mechanisms and tradeoffs across species and conditions.