long-read sequencing

This paper introduces structRFM, a structure-guided RNA foundation model that improves RNA function prediction and structural inference through pre-training on sequence-structure pairs.

The paper shows that transcription termination defects in yeast lead to splicing inefficiency and errors, highlighting its importance for splicing fidelity in compact genomes.

GenMPI provides a scalable variant calling workflow for short and long-read sequencing data using MPI, achieving linear scaling and improved performance over existing methods.

The paper identifies cryptic intronic C9orf72 transcripts as endogenous templates for RAN translation, leading to DPR production in ALS/FTD.

MultiNano uses multi-view deep learning to accurately detect and quantify m6A RNA modifications from Nanopore DRS signals, achieving state-of-the-art performance in multiple tasks.

Snappy identifies DNA methylation sites in bacteria using Oxford Nanopore reads without requiring control samples or motif enrichment heuristics.

This study evaluates ONT R10.4.1 long-read sequencing for accurate genotyping of three respiratory pathogens, showing error rates below 1% for cgMLST.

The paper introduces MoDorado, an algorithm that detects tRNA modifications beyond those trained in existing models, identifying seven new modifications in S. pombe.

The paper identifies cancer driver lncRNAs by analyzing their association with cancer driver genes and topologically associated domains, revealing 256 oncogenic, 177 tumor suppressive, and 75 dual-function lncRNAs.

This study uses long-read sequencing to analyze genomic and transcriptomic changes in AAV-CRISPR therapy for DMD, revealing complex editing outcomes and developing new methods for detection.

The paper optimizes Direct RNA Sequencing to obtain full-length copyback viral genomes and introduces a BLAST-based tool for their detection.

The paper identifies and quantifies transposable elements in chromosomal inversion breakpoints in Atlantic cod, showing their role in driving ectopic recombination and chromosomal reorganization.

This paper presents a long-read transcriptome assembly of Stenochlaena palustris leaves and identifies genes involved in anthocyanin biosynthesis.

This study integrates spatial and multi-omic data from bladder cancer patients to show L1 retrotransposition drives genomic instability, ecDNA formation, and a viral mimicry response.

plasmoRUtils streamlines bioinformatics analysis for Apicomplexan parasites by integrating data retrieval, harmonization, and analysis tools within R.

This study uses long-read sequencing to detect somatic transposable element mobilization in hypomethylated Arabidopsis thaliana mutants, revealing new mobile elements and variable activity within TE families.

The paper develops a CRISPR/Cas13d-based method to specifically knockdown RNA isoforms and provides computational tools for experimental design and analysis.

The paper identifies candidate m6A modification sites on HPV18 early transcripts in HeLa cells using RNA sequencing and perturbation experiments.

The paper maps RNA secondary structure ensembles in living E. coli cells, identifying conserved structural elements and cold shock-responsive RNA thermometers.

The paper introduces a tiling algorithm to accurately characterize structural features of AAV genomes, demonstrating its effectiveness across multiple datasets.

Tranquillyzer is a deep learning framework for processing long-read single-cell RNA-seq data, enabling accurate identification of structural elements and demultiplexing despite sequencing errors and library variability.

The paper shows that disease-associated variants in alternative protein isoforms can cause structural mutations, emphasizing the need to consider tissue-specific expression and full-length transcripts in variant interpretation.

This paper introduces rPRO-seq, a rapid PRO-seq method for nascent RNA profiling, and applies it to study Integrator's role in mouse hematopoietic stem cell homeostasis.

cONcat reconstructs concatenated DNA fragments from Oxford Nanopore reads by matching fragments to reads using edit distance, showing accuracy for short fragments but challenges with read start errors.

This paper introduces SubseqHash2, an improved subsequence-based seeding method that achieves faster computation while maintaining high accuracy for error-prone long reads.

Hybrid HiFi/ultra-long ONT assemblies of 65 diverse humans yield 130 haplotypes, 1,246 complete centromeres, and a pangenome panel enabling short-read genome inference at median QV 45.

The paper analyzes genetic diversity of the malaria parasite antigen MSP2 in Sub-Saharan Africa using PCR and long-read sequencing, revealing extensive sequence variation and regional prevalence patterns.

The paper profiles small and long RNA in human oocytes across stages, showing short-piRNAs broadly suppress transposons while long-piRNAs target specific ERVs.

This study uses long-read RNA sequencing to analyze the transcriptomic response to interferon and influenza infection in ferrets, identifying ISGs and novel transcripts.