long-read sequencing

Fusion gene discovery in single cells from high throughput long read single cell transcriptomes

This paper introduces LongFUSE, a tool for detecting fusion genes in single-cell long-read RNA sequencing data, showing improved accuracy over existing methods.

Rapid evolution and comparative analysis of piRNA clusters in D.simulans

The paper analyzes piRNA cluster evolution in D. simulans using genome and piRNA data, finding rapid formation and loss of clusters and distinct transposon involvement compared to D. melanogaster.

Systematic fusion transcript discovery in mantle cell lymphoma using long-read sequencing

This study identifies novel fusion transcripts in mantle cell lymphoma using long-read sequencing, revealing their potential as therapeutic targets and biomarkers.

Pangenome analysis reveals the evolutionary dynamics of repeat-based holocentromeres

The paper analyzes Tyba satellite DNA repeats and transposable elements in holocentric species to reveal evolutionary dynamics of repeat-based holocentromeres across a pangenome.

A novel ISG15 transcript restricts influenza A virus infection

The paper identifies a novel ISG15 transcript that restricts influenza A virus infection through a distinct mechanism independent of its cytokine function.

Convergent evolution of psilocybin biosynthesis by psychedelic mushrooms

Comparative mushroom genomics and fly-rearing experiments reveal an alternative psilocybin biosynthetic gene cluster in Inocybe corydalina, horizontal transfer of the canonical cluster, and incomplete defense against dipteran larvae.

Variant-resolved prediction of context-specific isoform variation with a graph-based attention model

Otari predicts tissue-specific isoform abundance changes caused by genetic variants using a graph-based attention model trained on genomic and long-read transcriptome data.

Ultra-high throughput mapping of genetic design space

The paper introduces CLASSIC, a platform that maps sequence-to-function relationships in synthetic biology by combining long- and short-read sequencing to analyze gene circuits.

Long-range PCR amplification and nanopore sequencing of 8-10 kb mitochondrial fragments from environmental DNA

The paper demonstrates the use of long-range PCR and nanopore sequencing to obtain and analyze long mitochondrial fragments from environmental DNA samples, enabling species identification despite sequencing errors.

Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

The paper shows that New1 prevents ribosomal collisions and subsequent mRNA degradation in yeast by no-go decay, protecting essential genes from downregulation.

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

Sarcomeric Remodelling in Human Heart Failure unraveled by single molecule long read sequencing

The paper uses single molecule long-read sequencing to analyze transcriptomes in heart failure patients and controls, identifying novel isoforms and convergent isoform changes across different cardiomyopathy types.

Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes

The paper introduces HIV SMRTcap, a method for characterizing HIV-1 reservoirs by identifying integration sites and proviral integrity using long-read sequencing, and validates its performance across subtypes and tissue samples.

Whole-genome profiling of native 5-hydroxymethylation in human neurons with long-read sequencing

The paper uses long-read sequencing to profile native 5hmC and 5mC in human neurons, showing 5hmC enrichment in transcribed regions and enhancers.

A sensitive and accurate framework for population-scale structural variant discovery and genotyping across sequence types

PSVGT is a framework for population-scale structural variant discovery and genotyping that integrates multiple sequencing data types and outperforms existing tools, especially in complex genomes and low-coverage long-read data.

ADAM-tRNA-seq: An Optimized Approach for Demultiplexing and Enhanced Hierarchal Mapping in Direct tRNA Sequencing

ADAM-tRNA-seq improves demultiplexing and mapping accuracy in direct tRNA sequencing by addressing sequence similarity and multimapping issues.

TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues

This study identifies TDP-43-dependent cryptic gene-TE fusions (crypTEs) in neurons and ALS/FTD tissues, showing their association with altered gene expression and potential pathogenic effects.

Chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping technologies

This study presents a chromosome-scale genome assembly of Malcolmia littorea using long-read sequencing and single-pollen genotyping, revealing a genome twice the size of Arabidopsis thaliana.

Detecting Foldback Artifacts in Long-reads

The paper identifies foldback artifacts in long-read sequencing data and introduces Breakinator, a tool to detect these artifacts and chimeric reads across different sequencing platforms.

Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes

The paper studies regulatory genome evolution in echinoderms, revealing deep conservation of cis-regulatory elements and chromatin organization, suggesting an ancestral regulatory pattern in animal genomes.

Single-cell omics-based characterization of human basophils reveals two transcriptionally distinct populations

The paper uses single-cell RNA-sequencing and immunoprofiling to identify two transcriptionally distinct basophil populations in human peripheral blood.

MoGAAAP: A modular Snakemake workflow for automated genome assembly and annotation with quality assessment

MoGAAAP automates genome assembly and annotation using HiFi and other long-read data, producing quality assessments for comparative genomics.

ANOMALY: A Snakemake pipeline for identifying NuMTs from Long-Read Sequencing Data

ANOMALY identifies NuMTs from long-read sequencing data with high accuracy, demonstrating the advantages of long-read over short-read data for resolving complex NuMTs.

Defining expansions and perturbations to the RNA polymerase III transcriptome and epitranscriptome by modified direct RNA nanopore sequencing

This paper introduces DRAP3R, a method for analyzing Pol III transcribed RNAs and their modifications, revealing new transcripts and epitranscriptomic changes in infected cells.

Heterogeneity of Genetic Sequence within Quasi-species of Influenza Virus Revealed by Single-Molecule Sequencing

This study uses single-molecule sequencing to reveal genetic heterogeneity in influenza virus quasi-species, showing non-random mutation patterns and biological significance.

Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant Calling

The paper introduces DNAscope Hybrid, a pipeline combining short and long-read sequencing for improved variant calling accuracy and efficiency.

diffONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application

diffONT predicts methylation-specific PCR biomarkers from nanopore sequencing data, improving specificity for hypermethylated regions suitable for MSP primer design.

EZ-DMS - A Simple and Accessible Protocol and Software Package for Deep Mutational Scanning of Virus Proteins

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.

Context-aware simulation enables systematic optimization of long-read mapping parameters

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: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

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