long-read sequencing

LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery

LRP2 is a proteogenomics pipeline that integrates long-read RNA sequencing and mass spectrometry to detect novel protein isoforms and improve their translation inference.

A B1 SINE element within the mouse Malat1 long noncoding RNA acts as an internal ribosome entry site mediating micropeptide translation

Epi-PoreC: a nanopore-based method for simultaneous profiling of chromatin conformation, DNA methylation, and chromatin accessibility

Epi-PoreC profiles chromatin conformation, DNA methylation, and chromatin accessibility simultaneously using nanopore sequencing on single DNA molecules.

Unlocking Sensitive Data with SPHERE in the Age of AI

SPHERE enables the use of sensitive datasets in AI and open science by creating synthetic twins that preserve statistical properties and privacy.

Oncogenic fusions induce an extensive cancer-restricted cryptic proteome in Ewing sarcoma

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

Post-hoc long-read sequencing links leukemic mutation status to single-cell transcriptomes

The paper develops a post-hoc method to link mutation status to single-cell transcriptomes using long-read sequencing, showing it can detect BCR::ABL1-positive cells in chronic myeloid leukemia.

nanorepertoire: an end-to-end Nextflow pipeline for nanobody repertoire analysis

nanorepertoire is an end-to-end Nextflow pipeline for analyzing camelid nanobody repertoires, providing standardized and reproducible analysis of AIRR-seq data.

Nuclear body assembly by a viral repeat RNA promotes Kaposi's sarcoma-associated herpesvirus gene expression

The paper shows that Kaposin, a viral lncRNA, remodels nuclear speckles to enhance KSHV gene expression by interacting with repetitive elements.

Evaluating transcriptome-wide information preservation by ensilication using long-read RNA sequencing

This study evaluates how ensilication preserves transcriptome information during storage using long-read RNA sequencing, finding it retains more transcript data than unprotected RNA.

Identification and characterization of bacterial repeat-in-toxin adhesins using long-read genome analysis

This study identifies and characterizes RTX adhesins in seven bacterial species using long-read sequencing and AlphaFold3 modeling, revealing 35 unique variants with diverse LBD arrangements.

Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations

The paper investigates whether diversity at the HYP1 locus in potato cyst nematodes arises from developmental editing or sequencing errors, concluding it is due to evolutionary forces.

Metagenomic analysis of the effects of European bison Bison bonasus (Linnaeus, 1758) presence on soil community structure and function in West Blean and Thornden Woods, Kent

Nanopore shotgun metagenomics of 56 Kent woodland soils finds stable alpha diversity but significantly shifted KEGG functional composition two years after European bison release.

Single-molecule nanopore sequencing reveals spatial coordination of rRNA modifications in human ribosomes

This study uses single-molecule nanopore sequencing to analyze rRNA modifications in human cells, revealing local coordination of modifications and their response to drug treatment.

NanoDel: Identification of large-scale mitochondrial DNA deletions using long-read sequencing

NanoDel detects large-scale mitochondrial DNA deletions using long-read sequencing, showing improved sensitivity and accuracy over existing methods.

Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence

The paper presents a single-cell long-read isoform atlas across 26 human tissues, revealing novel isoforms and their role in cellular identity and senescence.

Characterization of a maintainable human myeloid model of VEXAS syndrome with enhanced TNF-induced cell death and DAMP release

This study creates a human myeloid cell model of VEXAS syndrome with UBA1 mutations, showing increased TNF-induced cell death and DAMP release.

Isocall enables scalable transcript identification from long-read RNA-sequencing data

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

Markov models of SHAPE data improve secondary structure prediction

This paper improves RNA secondary structure prediction by incorporating Markov models to capture context dependencies in SHAPE data, enhancing prediction accuracy.

40S Ribosome Remodeling Triggers 18S rRNA U-tailing and DIS3L2-dependent Decay

RIOK3 displaces eS26 from ubiquitinated 40S subunits, exposing the 18S rRNA 3' end for U-tailing by TUT4/TUT7 and exonucleolytic decay by DIS3L2, which commits defective subunits to turnover.

Persistent co-infection mediates inter-virus and host-virus gene exchange in marine protists

The paper identifies a new viral order, Skiavirales, in marine protists through long-read sequencing and shows gene exchange between viruses and host genomes.

Long-Read Metagenomic Sequencing Reveals Persistent Gut Microbiome Alterations in Children with Celiac Disease in Remission

Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics

Systematic benchmarking of small variant calling pipelines for long-read RNA sequencing data

The paper benchmarks small variant calling pipelines for long-read RNA sequencing data, finding that sequencing quality is the main factor affecting performance, followed by variant caller and alignment strategy.

SPLISOFORMS: a Structure-Resolved Knowledge Base of Alternative Splicing Isoforms

A web database and REST API of 124,687 AlphaFold 3 structures for human splice isoforms, annotated against canonical proteins for domains, decay, modifications, neoantigens and drug pockets.

Gene conversion facilitates rapid evolution of inversions across avian immunoglobulin loci

The paper shows that avian immunoglobulin loci use gene conversion instead of V(D)J recombination, with rapid evolution of inversions that generate pseudogenes as donors for antibody diversity.

NLR DNA copy-number expansion outpaces accumulation of predicted coding-intact copies

The paper compares NLR DNA copy-number expansion with predicted coding-intact copies in Capsicum and Arabidopsis genomes, finding sublinear scaling and heterogeneous coding recovery.

Hidden assumptions in nascent RNA sequencing pipelines define reproducibility states

The paper identifies how hidden assumptions in nascent RNA sequencing pipelines lead to structured divergence in transcriptional profiles across datasets.

Full-length transcriptomics and proteomics reveal how genome minimization reshapes gene expression in synthetic bacteria

The paper characterizes RNA and protein expression in synthetic bacteria Syn1.0 and Syn3A, showing genome minimization alters gene expression and resource allocation.

RAPID: A Targeted Long-Read RNA Workflow for Functional Resolution of Splicing Variants in Rare Disease

RAPID uses targeted long-read RNA sequencing to resolve splice variants in rare disease cases, providing functional evidence for diagnosis and variant interpretation.

Revisiting bacterial division control with likelihood inference: limited identifiability of simple models

Likelihood comparison on six E. coli mother-machine datasets finds sizer, adder, and log-foldchange division rules only weakly separable, while a neural conditional cycle-duration model fits best.