Charles Plessy

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

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.

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

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.

The paper optimizes biochemical reaction parameters using a nanoliter platform and computer-generated liquid transfers, revealing non-linear responses and parameter interactions.

The paper translates mitochondrial sequences of non-ascidian tunicates using the ascidian mitochondrial genetic code and recommends its systematic use for all tunicates.

This study introduces Convert-seq, a method combining scRNA-seq and ectopic gene expression to identify gene regulatory networks during cell reprogramming.

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

The paper enhances the FANTOM5 expression atlas by associating gene-orphan promoter regions with their transcripts using CAGEscan.

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.

clonotypeR analyzes T cell receptor sequences from high-throughput data to identify and quantify clonotypes, providing tools for downstream analysis.

This paper introduces pseudo-random primers to reduce abundant transcripts in sequencing libraries, improving efficiency without losing transcriptome diversity.