long-read sequencing

CORAL: Accurate annotation of compact genomes using long-read RNA-seq, demonstrated in Oikopleura dioica

CORAL and GAMBA improve genome annotation for compact genomes using long-read RNA-seq, increasing gene count and reducing chimeric predictions in Oikopleura dioica.

Resolving the CES1 Genomic Locus with Cas9-Directed Targeted Long-Read Sequencing for Precision Pharmacogenomics

This study uses long-read sequencing to resolve the complex CES1 genomic locus, identifying new haplotypes and structural variants, and highlighting issues with short-read sequencing artifacts.

Phylogenetic Study of Long Non-Coding RNA NEAT1 and MALAT1 to Infer Structural-Functional Connection

The paper conducts a phylogenetic analysis of NEAT1 and MALAT1 lncRNAs to explore their structural and functional conservation across mammals.

Emergent simplicities in an individual cell's stochastic response to disruptive change

The paper identifies universal scaling patterns in bacterial cells' stochastic responses to environmental changes across different temperatures.

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

The paper uses long-read RNA-seq from diverse human populations to reveal ancestry bias in gene annotations and shows improved transcript discovery with personal genome assemblies.

circASbase：A Comprehensive Database of Alternative Splicing Events in circRNAs

circASbase is a database cataloging 452,129 alternative splicing events in 884,047 circRNAs from 581 samples across 13 species, revealing unique splicing features and functional impacts of circRNAs.

Long-read sequencing transcriptome quantification with lr-kallisto

The paper develops lr-kallisto, a tool for accurate long-read transcriptome quantification using ONT data, showing improved results with exome capture.

A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex

This study assesses somatic mosaicism in human frontal cortex using multi-platform sequencing, showing improved variant detection with haplotype-resolved assemblies and single-neuron sequencing.

Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples

This study evaluates the effectiveness of Oxford Nanopore adaptive sampling in metagenomic profiling of clinical sputum samples, finding limited enrichment and significant pore loss issues.

Noninvasive reconstruction of complete mitochondrial genomes from aquatic environmental DNA using PCR-free long-read sequencing

This paper develops a long-read sequencing workflow to reconstruct complete mitochondrial genomes from environmental DNA, demonstrating effectiveness through both PCR-free and PCR-based approaches.

Benchmark for simple and complex genome inversions

The paper presents a benchmark for detecting simple and complex genome inversions using Strand-seq and long-read assemblies, revealing method strengths and limitations across sequencing platforms.

Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance

This study uses long-read sequencing and genome graphs to analyze structural variation in Mycobacterium tuberculosis, identifying SVs linked to drug resistance and virulence.

TE-Seq: A Transposable Element Annotation and RNA-Seq Pipeline

TE-Seq is an RNA-Seq pipeline that annotates transposable elements and analyzes their expression, supporting long-read DNA data for TE-complete genome assembly.

Dynamic changes in mRNA isoform usage during human retinal organoid development

The paper uses long-read RNA sequencing to study dynamic mRNA isoform changes during human retinal organoid development, revealing splicing patterns and allelic imbalance.

LCSKPOA: Enabling banded semi-global partial order alignments via efficient and accurate backbone generation through extended lcsk++

The paper introduces an extended LCSk++ algorithm for graph-based alignment, improving memory and runtime efficiency for local and semi-global POA while maintaining alignment quality.

Long-read transcriptomics of purified human cortical cell types exposes glial isoform complexity and disease-relevant transcript architecture

The paper uses long-read transcriptomics to analyze human cortical cell types, revealing extensive isoform diversity in glial cells and identifying novel transcripts with disease-relevant splice variants.

Transcriptome-wide profiling of alternative splicing regulators with CRISPore-seq

CRISPore-seq combines CRISPR perturbations with long-read transcriptomics to detect alternative splicing changes, revealing that exon skipping is common and linked to RNA-binding protein perturbations.

Targeted sequencing and iterative assembly of near-complete genomes

The paper introduces Cornetto, a method using targeted long-read sequencing to improve genome assembly quality and completeness, particularly for challenging regions and sample types.

Integrative spatial multi-omics reveals prognostic tumor niches in female genital tumors

The paper presents an integrative spatial multi-omics atlas of female genital tumors, identifying prognostic tumor niches and developing a model to predict their abundance from histopathology.

RNA-X: Modeling RNA interactions to design binder RNA and simultaneously target multiple molecules of different types

RNA-X is a foundation model for designing RNA sequences that bind to multiple targets, including proteins, RNA, and DNA, and it outperforms existing methods in binding prediction and design.

Cas9-enriched nanopore sequencing enables comprehensive and multiplexed detection of repeat expansions

The paper introduces a nanopore sequencing method with Cas9 targeting and an analysis algorithm to detect STR expansions, identifying pathogenic repeats in cerebellar ataxia patients.

Sex-biased duplicates are rapidly generated during Drosophila tRNA repertoire evolution

The paper studies tRNA gene evolution in Drosophila, finding rapid duplication and loss, sexual dimorphism in expression, and implications for regulatory diversity.

Enhanced Functional Potential of Pseudogene-associated lncRNA Genes in Mammals

This study identifies pseudogene-associated lncRNA genes across eight species, showing they have enhanced functional attributes and contribute to aging-related transcriptome changes.

Accurate Reconstruction of Circular RNAs from Complex Rolling Circular Long Reads with CircPlex

The paper introduces CircPlex, a method to accurately reconstruct circRNAs from complex rolling circular long reads by addressing repeat pattern complexities, improving detection sensitivity and uncovering novel isoforms.

Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics

The paper develops a workflow using long-read RNA-seq and MS data to construct haplotype-resolved proteomes, enabling detection of variant and allele-specific protein isoforms.

How small molecules stabilize oligomers of a phase-separating disordered protein

This study investigates how small molecules stabilize oligomers of the androgen receptor activation domain using molecular dynamics simulations and NMR spectroscopy, revealing mechanisms that inform inhibitor design.

BiRNA-BERT Allows Efficient RNA Language Modeling with Adaptive Tokenization

BiRNA-BERT is a Transformer-based model pretrained on RNA sequences using adaptive tokenization, achieving state-of-the-art results in long-sequence tasks and efficient performance on short sequences.

LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing

LongPhase-S improves somatic variant accuracy by jointly estimating tumor purity and recalibrating variants using somatic haplotyping in long-read sequencing.

Identification, quantification, and elimination of barcode crosstalk in multiplexed Oxford Nanopore sequencing

The paper identifies and quantifies barcode crosstalk in Oxford Nanopore sequencing and introduces post-ligation pooling to prevent it.

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture

This study reconstitutes gene-scale chromatin arrays with controlled histone modifications to show acetylation increases structural fluctuations and reduces nucleosome contact frequency.