long-read sequencing

Retrotransposon-mediated duplication of SSU1 in high SO2 tolerant Brettanomyces bruxellensis winery isolates

The paper identifies retrotransposon-mediated duplication of SSU1 as a mechanism for increased SO2 tolerance in high-tolerant Brettanomyces bruxellensis isolates.

Quantitative Full-length transcriptome analysis by nanopore sequencing with Error-Aware UMI mapping

The paper introduces UMImap, a pipeline for accurate UMI identification and error correction in nanopore sequencing, enabling reliable full-length transcriptome analysis and discovery of novel isoforms.

Morphogenomic description of Cranifera cranifera (Chitwood, 1932) Kloss, 1960 from captive Blaptica dubia Serville, 1838 cockroach

Third nuclear genome for arthropod pinworms (Thelastomatoidea): a PacBio long-read Cranifera cranifera assembly (242 Mb, N50 43 kb, 90.5-94% BUSCO) plus a 24644-base mitogenome and male redescription.

Benchmarking methods for genome annotation using Nanopore direct RNA in a non-model crop plant

This study benchmarks genome annotation tools using Nanopore dRNA data from a non-model crop plant, finding significant variation in performance and identifying novel transcripts.

Multimodal AI for Single cfDNA Profiling and Cancer Screening

The paper develops a Transformer-based model called cfAI to profile and detect cancer-derived cfDNA by integrating methylation, fragmentomics, and histone modifications, achieving high sensitivity and specificity in multi-cancer detection.

Genome-wide analysis of FSHD cell lines using Nanopore sequencing reveals allele-specific differences at DUX4 target genes and complex repeats

RefLA: Efficient reference-guided genome assembly from long reads

RefLA improves genome assembly speed and quality by using a reference genome to guide long-read assembly, outperforming both de novo and fast assemblers.

Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides

Modanovo is a de novo peptide sequencing model that handles post-translational modifications, outperforming existing methods and complementing database searches in phosphoproteomics.

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

The paper maps ecDNA structures in glioblastoma using long-read sequencing and ecLego3, revealing structural variation, evolutionary dynamics, and transcriptional links to tumor adaptation.

Large generative mRNA language foundation model for efficient coding sequence generation and design with mRNA-GPT

The paper introduces mRNA-GPT, a generative mRNA language model trained on sequences from bacteria, eukaryotes, and archaea, showing improved translation efficiency and stability in mRNA design.

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data

Clair3-RNA is a deep learning variant caller for long-read RNA sequencing data that achieves high accuracy in SNP detection across different platforms.

Rapid detection of G6PD deficiency SNPs using a novel amplicon-based MinION Sequencing Assay

This paper develops a cost-effective MinION sequencing assay to detect G6PD deficiency SNPs in malaria-endemic regions, showing high reliability and concordance with Sanger sequencing.

Optical genome mapping identifies a novel PSIP1::TBL1X fusion in metastatic pancreatic neuroendocrine tumors

The paper identifies a novel PSIP1::TBL1X fusion in pancreatic neuroendocrine tumors using optical genome mapping and validates its expression and clinical relevance.

The lncRNA PACER Regulates Lung Adenocarcinoma Phenotypes via COX-2 Signaling and RNA Structural Dynamics

This study identifies PACER as a lncRNA that regulates lung adenocarcinoma progression through COX-2 signaling and structural dynamics.

Influenza A defective viral genomes and non-infectious particles are in-creased by host PI3K inhibition via anti-cancer drug alpelisib

This study shows that alpelisib, a PI3K inhibitor, increases defective viral genomes and particles in A/H3N2 but decreases total particles in A/H1N1, suggesting host metabolism influences viral defectiveness.

A simple method to efficiently generate structural variation in plants

This paper describes a method to generate heritable structural variation in Arabidopsis thaliana using etoposide, leading to altered phenotypes and identified deletions and inversions.

Retrotransposon Activation in the Aged and Alzheimer's Disease Brain Examined by Nanopore Long-read DNA Sequencing

The paper uses Nanopore long-read DNA sequencing to analyze retrotransposon activation in aged and Alzheimer's disease brains, identifying somatic insertions and epigenetic changes.

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

Genome-Wide Identification of Conditionally Essential Genes Supporting Streptococcus suis Growth in Serum and Cerebrospinal Fluid

This study identifies conditionally essential genes for Streptococcus suis growth in serum and cerebrospinal fluid using Tn-Seq and Nanopore sequencing.

Genomic Flexibility Through Extrachromosomal Amplifications: A Leishmania Survival Strategy

This study shows Leishmania parasites use extrachromosomal DNA amplification to adapt to drug pressure, with linear and circular amplicons forming through recombination events.

To join or not to join: handling biological replicates in long-read RNA sequencing data

This study compares two strategies for combining biologically replicated long-read RNA-seq data to identify transcripts, finding that 'Join & Call' is better for novel isoforms while 'Call & Join' is more efficient for large datasets.

Telomere-to-telomere reference genome of the common five-lined skink, Plestiodon fasciatus (Squamata: Scincidae)

The paper presents the first telomere-to-telomere, chromosome-level reference genome for the common five-lined skink, providing a highly complete and annotated genome sequence.

Nanopore sequencing reveals operon-specific ribosome remodeling accompanying naphthyridone resistance in Staphylococcus aureus

This study uses nanopore sequencing to identify operon-specific ribosome remodeling in Staphylococcus aureus resistant to naphthyridone antibiotics.

Unraveling miRNA-Driven DNA Damage Response Networks in Pancreatic Adenocarcinoma: A Multi-Omics and Machine Learning Approach

The paper uses multi-omics data and machine learning to identify miRNA-DDR gene interactions in PAAD, revealing miRNAs correlated with patient outcomes and potential targets for precision oncology.

RNA BaseCode: Long-Read RNA Sequences with Short-Read Accuracy

RNA BaseCode is a synthetic long-read RNA sequencing method that achieves short-read accuracy and improves full-length transcript reconstruction compared to existing long-read methods.

Establishing Conserved Biosynthetic Gene Clusters of the Phylum Myxococcota

The paper identifies five conserved biosynthetic gene clusters in Myxococcota using pan-genome analysis of 195 genomes, revealing ecological roles for their metabolites.

A multi-modal cell-free RNA language model for liquid biopsy applications

Exai-1 is a transformer-based model that integrates RNA sequence and expression data to improve cfRNA analysis for disease detection.

SquiDBase: a community resource of raw nanopore data from microbes

SquiDBase provides a centralized repository for raw nanopore sequencing data from microbes, along with tools to process and expand reference datasets.

Negative resilience trends to more frequent extreme droughts in Mediterranean oak species

This study examines the decline in resilience of Mediterranean oak species to extreme droughts, showing reduced recovery capacity since 1970 in wetter regions.

CiFi: Accurate long-read chromosome conformation capture with low-input requirements

CiFi improves Hi-C analysis by combining 3C with PacBio HiFi sequencing, enabling better coverage in repetitive regions and low-input samples.