long-read sequencing

EZ-DMS provides a simple, cost-effective protocol and software for deep mutational scanning of HIV-1 Env protein variants, enabling analysis of amino acid fitness without bioinformatics expertise.

The paper introduces CycSim, a context-aware simulator for long-read mapping that improves parameter optimization, achieving faster mapping and better accuracy across different sequencing platforms.

FEDRANN improves long-read overlap detection using dimensionality reduction and approximate nearest neighbors, outperforming existing methods on real data.

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

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.

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.

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.

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.

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

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

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

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.

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

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

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.

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

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

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

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

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.

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.

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

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 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.

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

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