Nicholas M. Luscombe

The paper identifies a class of condensation-prone RNAs during early development and reveals their sequence and structural features using deep learning.

This study uses single-cell RNA-sequencing and spatial transcriptomics to characterize keratinocyte states and fibroblast niches in severe HS lesions, revealing spatially distinct interactions that may explain treatment resistance.

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

This paper investigates how gene loss and duplication in Fgf subfamilies influenced chordate evolution, particularly in appendicularians, revealing evolutionary patterns and functional shifts.

The paper identifies widespread isoform switches of transcription factors across human tissues and predicts their functional consequences.

The paper reports the complete mitochondrial genome of an unidentified Oikopleura species, providing a new resource for ecological and mitochondrial studies of appendicularians.

This study analyzes the evolutionary patterns and genomic instability in Wilms tumors, identifying subtype-specific evolutionary sequences and proposing CNA diversity as a prognostic biomarker.

This study reports the first complete mitogenome assembly of Oikopleura dioica, revealing a high proportion of A and T homopolymers.

The paper shows extreme genome scrambling in cryptic Oikopleura dioica species, revealing high rates of gene order rearrangements and insights into synteny conservation mechanisms.

Flow provides a web platform and database for managing and analyzing large-scale bioinformatics data, addressing challenges in data processing, quality, and accessibility.

The paper uses single-cell RNA sequencing to study cell fate decisions at the neural plate border in chick ectoderm, proposing a gradient border model for fate allocation.

The paper extends a hiCLIP atlas of Staufen1-bound duplexes by 10-fold using computational methods and reveals structural features of RNA binding and their impact on RNA metabolism.

clipplotr is a command-line tool for visualizing and comparing CLIP data with annotations and functional genomic data, producing publication-quality figures.

The paper constructs a gene regulatory network for neural induction using transcriptomics and epigenomics data, revealing 175 regulators and 5,614 interactions with temporal dynamics.

This study shows that Integrator subunit INTS11 is essential for RNA polymerase II processivity during elongation, preventing antisense transcription and ensuring efficient gene expression.

The paper shows that temporal shifts in trunk formation underpin larval diversification in annelids and bilaterian life cycles through comparative genomic and transcriptomic analysis.

This paper describes an automated phenol-chloroform DNA extraction protocol using a robot, achieving high molecular weight DNA suitable for long-read sequencing.

The paper introduces Nanocompore, a method to detect RNA modifications using Nanopore direct RNA sequencing, validated on human polyA+ RNAs and non-coding RNAs.

The paper introduces SPACE and SPACEmap to identify chromatin-associated RBPs and their interactions, revealing that many bind chromatin via intrinsically disordered regions.

The paper identifies that most intergenic RNA originates from fuzzy transcription of known genes, with a smaller portion from long non-coding RNA loci, and characterizes their transcriptional features and degradation patterns.

The paper presents a chromosome-scale genome assembly of Oikopleura dioica using Nanopore, Illumina, and Hi-C data, revealing chromosomal structure and genomic features.

ChromWave predicts TF and nucleosome occupancy competition using deep learning, showing accurate predictions in yeast and human promoters.

The paper identifies LIN28A as a key factor in mRNA decay during epiblast morphogenesis, linking cell identity changes to embryonic growth through nucleo-cytoplasmic translocation.

psiCLIP identifies dynamic RNA binding patterns of spliceosomal helicases before and after exon ligation, revealing their interactions with auxiliary factors.

The paper shows that 3UTR cleavage occurs in sympathetic neuron axons, mediated by Ago2 and HuD, and regulates local protein synthesis and generates new 3UTR RNA fragments.

The paper identifies aberrant cytoplasmic intron-retaining transcripts (IRTs) in ALS and shows their association with RBP mislocalization.

The paper examines CD147 and ACE2 expression in vascular endothelial cells using single-cell RNA sequencing data from multiple tissues, finding CD147 detectable while ACE2 is not.

The paper uses single-cell RNA-seq to identify cell-specific gene expression patterns in the 16-cell stage of the Ciona embryo and validates some new patterns.

The paper investigates how nucleosome positioning stability influences germline mutation rates using de novo mutation data and high-resolution nucleosome maps.

RADICL-seq maps genome-wide RNA-chromatin interactions in intact nuclei, revealing general and cell type-specific patterns of transcript occupancy and the role of transcription in chromatin structure.