Biography

I am a temporary research and teaching assistant in MIDI team (Etis,Cergy Pontoise, France). My work focuses on methods and data structures in sequence bioinformatics, with applications to pangenome in particular.

After a bachelor’s degree in computer science and a master’s degree in Science and Digital for Health, Bioinformatics, Knowledge, Data at the University of Montpellier, I did my PhD within of the GAIA doctoral school (584), between Cirad and LIRMM. My thesis focuses on the development of a k-mers indexing data structure intended to support the analysis of hundreds or even thousands of similar genomes.

This general purpose data structure is intended to store information about many close genomes, but can also be adapted to store information on collections genomes derived from sequencing, upstream or downstream of classification into families of related species.

(detailed cv).

Ongoing work

2025: HLX: Implementation and evaluation of the HyperLogLog family of algorithms (HL2, HL3, HL4)
2025: BijectHash: Generation of permutations of kmers and encoding into unique integers
2025: Use and adaptation of kmer-based methods to detect precise fusions in myelomas/lymphomas

GenomeHarvest project:

2019: When RedOak™ draws trees
2019: Poster: Resources to manage Rice Big Genomics Data
2018: Presentation of a tool under development allowing the indexing of a large collection of unassembled genomes
2017: Pangenome Indexing Structure applied to rice

SeqBIM: working group common to the GDR Molecular Bioinformatics (BIM) at the GDR Informatique

CNRS Mathematics (IM):

JOBIM: Biology, Computer Science and Mathematics Open Days, the conference of the French Society of Bioinformatics:

2022: Co-organization of the mini-symposium “Indexing and Querying Large Sequencing Data Collections.” URL: jobim2022.sciencesconf.org
2020: Co-organization of the Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) conference, held from June 30 to July 3, 2020. I assisted with logistics management and supported the evaluation of scientific contributions. URL: jobim2020.scienceconf.org
2017: Poster: Development of indexing compressed structure for analyzing a collection of similar genomes: application to rice.
2015: Poster: Use of Illumina sequencing for accessing viral genomes Cocoa swollen shoot virus (CSSV).

Journal Publications

International publications

2024 Evaluating k-mer Transformations for Cache Coherence and Uniformity Clément Agret, Annie Chateau, Camille Marchet, Alban Mancheron et Antoine Limasset.
2022 RedOak: a reference-free and alignment-free structure for indexing a collection of similar genomes Clément Agret, Annie Chateau, Gaetan Droc, Gautier Sarah, Manuel Ruiz et Alban Mancheron.
2018 Next generation sequencing elucidates cocoa badna virus diversity and reveals the existence of more than ten viral species., E.Muller, S.Ravel, C.Agret, F.Abrokwah, H.Dzahini-Obiatey, I.Galyuon, K.Kouakou, E.C.Jeyaseelan, J.Allainguillaume, A.Wetten.

International conferences with published proceedings

2022 Toward Optimal Fingerprint Indexing for Large Scale Genomics Clément Agret, Bastien Cazaux, Antoine Limasset

Communications

Invited talks

2020 Thesis defense : Thesis
2019 When RedOak™ draws trees : Slides
2018 Presentation of a tool in development for indexing a large collection of genomes unassembled : Slides
2017 Pangenome Indexing Structure applied to rice, Genomeharvest

Conferences

2022 Clement Agret, Annie Chateau,and Alban Mancheron. Comptage massif et distribué de k-mers Proceedings
2018 Development of indexing compressed structure for analyzing a large collection of similar genomes: application to rice : Proceedings
2017 Compressed structure for analyzing a collection of similar genomes: application to rice, Abstracts
2017 Machine learning science popularization of supervised and unsupervised learning, MAB team seminar, LIRMM Montpellier (France)

Other

2020 Co-organization of the Open Days of Biology, Computer Science and Mathematics Congress of 30 June to July 3, 2020. I helped with logistics management and I was a support in the evaluation of productions scientists. Jobim
2018 Co-creator and co-organizer and Agapiades. This is the first symposium organized by the doctoral rants from Agap for the personnel of the various research centers of Cirad, INRA, IRD, CNRS and SupAgro. I took care of the general organization, the communication and proofreading part scientific productions.Agapiades
2016 Co-organizer of Montpellier Omics days 2016 (MOD2016). MODs are a scientific event organized by master’s students for biologists and bioinformatics scientists. The days born are generally divided into two days, a day of colloquium and one or two days of training.
2016 Co-organized the MODs, I actively chose the subject and the participants, with Y.COGNE and A.VERDIER we prepared and gave training on From Linux to Differential Gene Analysis (DESeq2). MOD2016
2014 Co-creator, then president of the AsTICo association of the Master Sciences and Digital for Health. The purpose of this association is to create a directory of alumni to allow inter-generational communication. Nationally, facilitate the organization of scientific events such as MODs, and facilitate the exchange of course support between teachers and students. AsTICo

Supervision

2020-2021 : A.Cuhadar (M2 internship), subject: Maize pangenomics study.
2019-2020 : N.Mijovic (M2 internship),subject: Comparison of a large collection of rice genomes using Formal Concept Analysis (FCA) and Data mining.
2017-2018 : L.Djardin Bretones (M1 internship),subject: Study of succinct structures for the compression of binary vectors.

Teaching

Zhejiang University of Science - ZUST

Semestre 1

Semestre 2

University of Mauritius - UoM

Semestre 1

Semestre 2

University of Cergy Paris - CYU

Semestre 2

Institution	Workload Description	Total
CY Cergy Paris Université / Polytech	Contract Lecturer 4×400	1600h
Lille	ATER 191 + 10	201h
IUT of Montpellier-Sète	ATER 207 + 3	210h
Faculty of Sciences, Montpellier	80 + 58 + 52	190h
Total		2201h

Teaching Activities

Status	Institution	Year(s)	Level	Subject(s)	Teaching hours	Class size	Notes
Contract Lecturer	CYU, ZUST, UoM	2021–2025	M1, L3	Operating Systems, Formal Languages, Cloud Computing, …	30h, 45h, 82.5h, 75h, 37.5h, 45h, 37.5h, 45h	1×60, 1×60, 1×60, 1×20, 1×20, 1×55, 1×20, 1×55	Course management or design, tutorials, practicals, exams depending on the course
ATER	Polytech Lille	2020–2021	M1, L3	Databases, Advanced Programming, Algorithms, OS, etc.	12h, 63h, 20h, 42h, 12h, 20h, 22h, 10h	1×15, 1×15, 1×15, 1×50, 1×16, 2×25, 1×15, 2×1	Management or design depending on the course
	IUT Montpellier	2019–2020	L1 to M2	Networks, UI, Testing, Web client, Projects, Internships, Bioinfo	28h, 96h, 12h, 21h, 10h, 5h, 20h, 15h, 3h	2×30, 6×27, 1×28, 1×28, –, 1×1, 2×25, 4×1, 1×12	Lectures, co-design, supervision, exam creation
Adjunct Lecturer	–	2018–2019	L1, L2, M2	Binary to Web, Imperative C/C++ Programming, Systems Biology & Bioinfo	50h, 28h, 2h	1×45, 1×35, 1×16	Refresher courses, C/C++, exam creation
	FDS Montpellier	2017–2018	L2, M1, M2	Algorithms & Complexity, Research Internship, Systems Biology & Bioinfo	28h, 28h, 2h	2×35, 1×1, 1×16	Refresher courses, co-supervision, exam creation
	–	2016–2017	L1, M2	Binary to Web, Systems Biology & Bioinfo	50h, 2h	1×45, 1×16	Refresher courses, course and exam design