long-read sequencing

Autocycler: long-read consensus assembly for bacterial genomes

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

Transcriptome Universal Single-isoform COntrol: A Framework for Evaluating Transcriptome reconstruction Quality

The paper introduces TUSCO, a framework for evaluating transcriptome reconstruction quality using long-read sequencing by assessing precision and sensitivity with a curated set of single-isoform genes.

End-to-end proteogenomics for discovery of cryptic and non-canonical cancer proteoforms using long-read transcriptomics and multi-dimensional proteomics

The paper introduces ProteomeGenerator3, an end-to-end proteogenomics method that detects non-canonical proteoforms in cancer using long-read transcriptomics and multi-dimensional proteomics.

Structural variation, selection, and diversification of the NPIP gene family from the human pangenome

The paper characterizes the structural variation and diversification of the NPIP gene family in humans using long-read sequencing and identifies evidence of positive selection and novel gene models.

High-performance machine learning for peptide classification from nanopore translocation events, leveraging event kinetics and duration filtering

This paper develops a machine learning framework for classifying peptides using nanopore translocation events, showing that engineered features and tree-based models achieve high accuracy.

SpliceCoord: A computational toolkit to identify coordinated exon splicing events from long-read transcriptome sequencing data

SpliceCoord identifies coordinated exon splicing events from long-read transcriptome data using a count matrix and GTF file.

Nanopore sequencing of intact aminoacylated tRNAs

This paper introduces a method to simultaneously measure tRNA sequence, modification, and aminoacylation using nanopore sequencing and machine learning.

WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing

WarpDemuX-tRNA improves barcode multiplexing for nanopore tRNA sequencing with higher precision and efficiency.

Complementarity of long-read sequencing and optical genome mapping in Parkinson's disease

This study compares long-read sequencing and optical genome mapping in detecting structural variants in Parkinson's disease, finding OGM better detects large variants while ONT provides high-resolution refinement.

Intron retention regulates STAT2 function and predicts immunotherapy response in lung cancer

The paper identifies intron retention in STAT2 as a regulator of immune signaling and a predictor of immunotherapy response in lung cancer.

Transposable Element Expression and Sub-cellular Dynamics During hPSC Differentiation to Endoderm, Mesoderm, and Ectoderm Lineages

This study examines TE expression and sub-cellular dynamics during hPSC differentiation to endoderm, mesoderm, and ectoderm lineages, revealing lineage-specific TE expression patterns and chromatin associations.

Pangenome biology and evolution in harmful algal-bloom-forming pelagophyte algae

The paper investigates genome evolution in pelagophyte algae, identifying lateral gene transfers contributing to pangenome diversity and ecological success.

Extracellular Vesicle Gene Expression Enables Sensitive Detection of Colorectal Neoplasia

This study compares EV transcriptomics, proteomics, and cfDNA methylation for detecting colorectal neoplasia, finding EV transcriptomics most sensitive for advanced adenomas and CRC.

Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants

The paper uses Hi-C and Pore-C sequencing to compare chromosomal conformation in pneumococcal variants, finding that episomal elements drive differential contact patterns through stochastic replication and excision.

Single-molecule landscape of DNA replication pausing

The paper identifies replication pause sites in a eukaryotic genome using long-read nanopore sequencing and finds they are enriched near transcribed regions and correlate with transcription and R-loop levels.

Overview of non-coding RNAs with CAG repeats and the case of mutation-containing circRNA in polyglutamine disease patients

The paper identifies RNAs with CAG repeats, including circRNAs with mutant tracts, in polyglutamine disease patients.

Isoform-Level Analysis of 10x Genomics Single-Cell cDNA Libraries from Cultured K562 Cells Using Long-Read Sequencing

The paper compares three methods for long-read sequencing of 10x Genomics single-cell cDNA libraries to evaluate their performance in full-length transcript capture, barcode identification, and isoform detection.

T cell correction pipeline for Inborn Errors of Immunity

This paper presents a T cell gene correction pipeline using CRISPR/Cas9 and HDR to correct monogenic mutations in IEI models, achieving up to 80% bi-allelic editing with no detectable off-target effects.

The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana

This study analyzes organellar genome dynamics in Arabidopsis thaliana using high-quality long-read assemblies, revealing rapid mitochondrial rearrangements and shared structural variants with plastids.

LIPTER, a cardiomyocyte-enriched long noncoding RNA, controls cardiac cytoskeletal maturation and is regulated by a cardiomyocyte-specific enhancer.

The paper identifies LIPTER, a cardiomyocyte-specific long noncoding RNA, and shows it regulates cytoskeletal maturation and is controlled by a cardiomyocyte-specific enhancer.

deepNGS Navigator: Exploring antibody NGS datasets using deep contrastive learning

deepNGS Navigator uses deep contrastive learning to visualize and analyze antibody sequence datasets, revealing clonal relationships and evolutionary patterns.

RESM: Capturing sequence and structure encoding of RNAs by mapped transfer learning from ESM (evolutionary scale modeling) protein language model

RESM improves RNA sequence-structure-function prediction by transferring knowledge from protein language models, outperforming existing models in multiple tasks.

Isoform-level profiling of m6A epitranscriptomic signatures in human brain

The paper uses Oxford Nanopore DRS to profile m6A modifications at the isoform level in human brain regions, identifying thousands of m6A sites and region-specific patterns.

Unlocking the full potential of Oxford Nanopore reads with NOVOLoci

NOVOLoci improves genome assembly using Oxford Nanopore reads, achieving high-quality phased assemblies for complex and non-model organisms.

G-quadruplex formation in long non-coding RNAs dysregulated in colorectal cancer

This study investigates G-quadruplex (G4) formation in three lncRNAs dysregulated in colorectal cancer and shows their stable G4 structures using in silico and in vitro methods.

Oatk: a de novo assembly tool for complex plant organelle genomes

Oatk combines a sparse syncmer assembler, profile HMM gene databases and graph path search to assemble plastomes and mitogenomes from HiFi reads for 195 plant species.

Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins

The paper uses atomistic simulations to study sequence-dependent conformational landscapes of IDPs, identifying a new metric that captures directional structural differences.

An open structure-guided RNA foundation model for generalizable prediction

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.

Transcription termination promotes splicing efficiency and fidelity in a compact genome

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: Cluster Scalable Variant Calling forShort/Long Reads Sequencing Data

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.