Camille Marchet

I am a CNRS researcher in sequence bioinformatics. My topics are data structures for indexing sequencing data at scale, and algorithms to work with sequences, in particular de novo and RNA-seq long and short reads.

Education

2015-2018 PhD in Computer Science, University of Rennes (France). Direction: Pierre Peterlongo (IRISA/INRIA): From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing.
2013 MS in Ecology Evolution Biometry**, Claude Bernad University of Lyon (France)
2013 Engineer degree in Bioinformatics and modeling, INSA Lyon (France)
2007 Baccalauréat, Lycée Romain Rolland (Clamecy, France)

Professional career

2021-present, Chargée de recherche CNRS (junior researcher) in BONSAI team, CRIStAL lab, Lille, France
2022-2023 and 2020-2021 Career breaks (parental leave)
2018 visiting in Zamin Iqbal’s group, Cambridge
2018-2020 Postdoc in BONSAI team, CRIStAL lab, Lille, France (supervisors: Rayan Chikhi, Mikaël Salson)
2015-2018 PhD student in GenScale team, IRISA lab, Rennes, France (director: Pierre Peterlongo)
2013-2015 Research engineer in ERABLE team, LBBE lab, Lyon, France (supervisor: Vincent Lacroix)

Teaching, training and dissemination of science

PhD students (as a co-supervisor)
- 2021-present Khodor Hannoush, subject: Dynamic pangenome graphs, with Pierre Peterlongo (IRISA Rennes, France)
- 2022-present Thomas Baudeau, subject: Mapping methods for new long reads viral data, with Mikaël Salson (CRIStAL Lille, France)
- 2023-present Igor Martayan, subject: Data structures for efficient operations on sequence sets, with Jean-Stéphane Varré (CRIStAL Lille, France)
Teaching
- 2019, 2021, 2023: Data structures (MISO Masters, Bioinformatics, University of Lille)
- 2019, 2020: Algorithmics and data structures (Licence 2, Computer Science, University of Lille)
- 2017: Modeling and engineering for the living (Masters, Computer Science, INSA Rennes)
- 2016: Data bases (Licence 2, INSA Rennes)
- 2015, 2016: Biostatistics, R programming (Licence 3, Mathematics/Comp Sci, ENS Rennes)
- 2014: Mathematics for biology (Licence 1, Biology, Lyon University Claude Bernard)
Training
- 2020, 2022, 2023, 2024: Teacher at Evomics Workshop on Genomics (Czech Republic)
- 2021: Teacher at (JC)2BIM, GDR BIM’s school on algorithmics and statistics for bioinformatics (France)
- 2019, 2021-23: courses on RNA-seq analysis for Bilille and CNRS (France)
Popularization
- 2020: Two press articles for Binaire of Le Monde journal
- 2015: Genome Assembly workshop, IRISA Lab open day (France)
Organization of scientific events
- SPIRE (2021), JOBIM (2022), SeqBIM (2023)

Research administration and management

PhD defense jurys
- 2023: Victor Epain, Assemblage de fragments ADN : structures de graphes et échafaudage de génomes de chloroplastes (directed by Rumen Andonov), IRISA Rennes (France)
- 2021: Claudio Lorenzi, Design and implementation of bioinformatic tools for RNA sequencing data analysis (directed by William RITCHIE & Alban MANCHERON), IGH Montpellier (France)

Editorial/program committees

Reviewing for journals, conferences
- Regular reviews for Nature Methods, Bioinformatics, Nature Communication, NAR, RECOMB, ISMB/ECCB, RECOMB-seq
Program committee for conferences/workshops
- ISBM (2022), WABI (2022), ECCB (2022), SPIRE (2020), RECOMB-seq (2020, 2018)

Research

Selected Publications since 2015
- A survey of mapping algorithms in the long-reads era, K Sahlin, T Baudeau, B Cazaux & C Marchet; Genome Biology 2023
- Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees, C Marchet & A Limasset; ISMB 2023
- Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching, T Rouzé, I Martayan, C Marchet & A Limasset, WABI 2023
- BLight: Efficient exact associative structure for k-mers, C Marchet, M Kerbiriou, A Limasset; Bioinformatics, 2021
- REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, C Marchet, Z Iqbal, D Gautheret, M Salson, R Chikhi; Bioinformatics, 2020
- Data structures based on k-mers for querying large collections of sequencing data sets, C Marchet, C Boucher, SJ Puglisi, P Medvedev, M Salson, R Chikhi; Genome Research, 2020
Software
- https://transipedia.fr and github.com/kamimrcht/
Involvement in research projects since 2018
- 2024-.. Find-RNA ANR,Data-structures for collections of sets of (meta-)transcriptomics data(coordinator)
- 2023-.. Full-RNA ANR, Indexing large scale 2nd and 3rd generation RNA datasets(member)
- 2022-.. INSSANE ANR, Novel methods for studying RNA structures(responsible for Univ Lille)
- 2021-.. ALPACA ITN, Methods for pangenomics(member)
- 2019-.. Seqdigger ANR, Indexing large scale genomic samples” (member)
- 2018-2022 Transipédia ANR, _Indexing large scale RNA-seq datasets__(member)
Communication
Selection of invited talks since 2017
- 2023: Hashing-based data-structures for querying large k-mer (collections of) sets, CiE, Batumi (Georgia)
- 2023: Hashing-based data-structures for querying large k-mer (collections of) sets, Sequences in London (United Kingddom)
- 2022: Scalable sequence database search using approximate membership data structures, Genome Informatics, Cambridge (United Kingdom)
- 2022: How to improve student/advisor relationships, WABI, ALPACA 2nd Annual Workshop, Potsdam (Germany)
- 2020: From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing, SIF congress, INSA de Lyon (France)
Selection of talks in workshops/conferences since 2015
- 2020: REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, ISMB, Montreal (Canada, virtual conference)
- 2019: Indexing De Bruijn graphs with minimizers, RECOMB-seq, Washington DC (US)
- 2019: Indexing De Bruijn graphs with minimizers, BiATA, St Petersburg (Russia)
- 2019: Survey of k-mer set of sets data structures for querying large collections of sequencing datasets, Helsinki Bioinformatics Day (Finland)
- 2018: CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads, JOBIM, Marseille (France)

Research contracts

2024-2028, as a coordinator: ANR project Find-RNA, ~190k euros, collaboration with CRIL, University of Lens and SciLife lab, University of Stockholm
2022-2026, as a partner: ANR project INSSANE, ~330k euros, collaboration with LIX Polytechnique, CiTCoM Université de Paris and LCBPT Université de Paris

Prizes, awards, fellowships

2019: Honorable mention for the Gilles Kahn prize of the Société Informatique de France for PhDs in Computer Science