[Feb 2025]
Some fresh news on thepangenome graphs front: apreprint proposing anedit distance between two pangenome graphs (PhD work by Siegfried Dubois) ;my slides from aninvited talk at theBIGRE days in Grenoble on the benefits and challenges of these objects forSV analyses ; and co-organisation of amini-symposium atJOBIM 2025, Rendez-vous 10 July in Bordeaux!

[Nov. 2024]
We are hosting and organizingSeqBIM 2024 in Rennes on November 28 and 29 ! This is the annual meeting of the frenchSeqBIM working group, where the most recent work and ideas from French teams in sequence algorithms, sequencing data indexing and analysis, etc. are presented and discussed. Don't miss the chance to present your work on sequences ! Submission deadline: October 17 ; Registration deadline: Nov. 14.

[Oct. 2024]
Happy to welcomeMélody Temperville, as a PhD student, whom I will be co-supervising for the next three years withClaire Mérot (EcoBio, Rennes) andFabrice Legeai (Genscale, Rennes). Mélody will develop methods for the detection and analysis of Structural Variants (and in particular large inversions) with linked-read data (short reads associated to barcodes that give long-distance informations, such as haplotagging).

[Oct. 2023]
Happy to welcometwo new PhD students whom I will be co-supervising for the next three years:Siegfried Dubois will explore pangenome graphs to characterize structural variants andNicolas Maurice will work on metagenome assembly of complex microbial communities associated to plants, taking advantage of latest high fidelity long read technologies.

[July 2023]
SVJedi-graph, our new Structural Variant genotyping tool is published in Bioinformatics ! Look at thepaper here and meet Sandra and me atISMB/ECCB 2023 in Lyon (France) for the corresponding talk.

[July 2023]
MTG-Link, our local assembly tool dedicated to linked-reads is finally published in BMC Bioinformatics ! Look at thegithub repository and read thepaper which presents various biological applications, such as the reconstruction of the sequence of a locus of interest and of dark regions, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants.

[Sept 2022]
Release of a novel SV genotyping tool :SVJedi-graph improves over SVJedi to genotype Structural Variants with long reads thanks to the use of a variation graph to represent the SVs, and in particular close or overlapping SVs.

[May 2022]
As co-chair of the PC, I am very proud of this great program atJOBIM 2022 in Rennes (July 5-8) ! Don't delay in registering, the French bioinformatics community is eager to meet again in person ! (Update: JOBIM is full!)

[March 2022]
Very happy to give an invited talk at the annual meeting of theGDR AIEM and Alphy working group (GDR BIM) about methods for Structural Variation detection and analyses, with a focus on large insertion variants (see myslides)

[Dec 2021]
I just defended myHDR ("Habilitation à Diriger des recherches", or accreditation to supervise research, a final french diploma). The title of my manuscript is "Bioinformatics methods for studying Structural Variations with sequencing data" (look atmy manuscript in french andthe slides of my defense in english).

[Oct 2021]
Here we go forJOBIM 2022 in Rennes ! Happy to be co-chair of the Program Committee of this annual event that federates the French bioinformatics community.

[March 2021]
SARS-CoV-2 and bioinformatics: with theGDR BIM, we wrote a science popularization report onhow Bioinformatics is playing a key role in the study of the virus and its origins.

[Dec 2020]
Two PhD defenses to come in December (4th and 11th), that I am proud to have supervised ! Structural Variations are in the spotlight withLolita Lecompte and Wesley Delage !

[Nov 2020]
Towards a better understanding of the low recall of insertionvariants with short-read based variant callers. Our results on large human insertion variant characterization and how their features impact the recall of short-read based SV callers are out inBMC Genomics

[Sept 2020]
WelcomingPierre Morisse for a 2-year postdoctoral fellowship in our team to develop novel methods for Structural Variation detection with linked-reads sequencing data, and applications to the mimetic butterflyHeliconius numata.

[July 2020]
Finding viral DRJ excision sites with sequencing data : a method I developped a long time ago to refine breakpoints is finally published within the analysis of two genomes of parasitic wasps having peculiar endogenous viruses.Paper in BMC Biology. The method,DrjBreakpointFinder, is available on github.

[July 2020]
MinYS is published inNAR Genomics and Bioinformatics ! : MinYS (for Mine Your Symbiont) is a new software developped with a former PhD student,Cervin Guyomar, for targeted genome assembly with metagenomics data. Freely avaiblable ongithub

[June 2020]
SVJedi finally published inBioinformatics ! SVJedi is a new software developped by my PhD student, Lolita Lecompte, to genotype SVs with long read sequencing datasets. Freely avaiblable ongithub

[June 2020]
DiscoSnpRad finally published inPeerJ ! DiscoSnpRAD is a software to discover SNPs and small indels in RAD-like sequencing datasets. Freely avaiblable ongithub

[Nov 2019]
New software :SVJedi is a new software developped by my PhD student Lolita Lecompte to genotype SVs in long read sequencing datasets. See also thepreprint in BioRxiv, where SVJedi is applied on a real human dataset (HG002, GiaB SV callset)