Bio / topics

I am a research associate in BONSAI team (Lille, France). My work focuses on methods and data structures in sequence bioinformatics, with applications to RNA in particular.

Je suis chargée de recherche au CNRS dans l’équipe BONSAI (Lille, France). Je travaille sur des méthodes et structures de données dédiées à la bioinformatique des séquences, avec souvent des applications à l’ARN.

Intéressé.e par une formation à la bioinformatique pour les données de séquençage ? Le CNRS propose une formation à Lille (labos/entreprises) : lien.

After an engineer degree in Bioinformatics from INSA de Lyon and a MsC in Ecology and Evolution from Université Claude Bernard Lyon 1, I worked for two years as an engineer in ERABLE team (LBBE, Lyon) with Vincent Lacroix. I obtained a PhD funding in GenScale team (Rennes, France), where I was supervised by Pierre Peterlongo. I defended my PhD in 2018 and joined BONSAI in the CRIStAL lab afterwards as a postdoc. Lately I was recruited by the CNRS to work as a researcher in the same lab (detailed cv). My research is currently supported by the ANR through PRC and JCJC projects.

My postdoc took part in Transipedia ANR, with Rayan Chikhi and Mikaël Salson. Transipedia aims at being a transcriptome-encyclopedia, e.g., facilitating indexing, query and exploitation of the numerous publicly available RNA-seq data. I am mostly working on new data structures to index large collections of NGS datasets. Before and during my PhD I worked on methods for transcriptomics, in particular for de novo variants discovery and RNA long read analysis.

Job offers

Internship: Visualization and queries for biology in de Bruijn graphs

News

Accepted to WABI 2023: Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching
Hashing-based data-structures for querying large k-mer (collections of) sets at CiE 2023
Our suvery on long read mapping was published in Genome Biology: A survey of mapping algorithms in the long-reads era
Accepted to ISMB 2023: Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees

Blog posts / short articles

Data-structures for sets of k-mer sets: what’s new since 2020
Minimal Perfect Hash Functions in the k-mer world
Sketching for bioinformatics: featuring Niqki (Clément Agret et al.’s recent preprint)
Strobemers, a new kind of spaced seeds from K Sahlin’s preprint
Othello hashing in bioinformatics
Sneak peek at the -tigs! a (very) high-level presentation of the population of -tigs sequences we encounter lately in k-mers related-papers (unitigs, simplitigs, monotigs, omnitigs, macrotigs) but that also includes UST and super-k-mers
A short popularization article about coronavirus assembly with long reads (in French)
A short popularization article about my PhD work (in French)

Research projects

Present

2024-.. Find-RNA ANR JCJC project, Data-structures for collections of sets of (meta-)transcriptomics data (coordinator)
2021-.. INSSANE ANR project, Novel methods for studying RNA structures (partner)
2022-.. Full RNA ANR project,Indexing large scale 2nd and 3rd generation RNA datasets (member)
2020-.. ALPACA ITN, Methods for pangenomics (informal member)

Past

2018-22 Transipédia ANR project, Indexing large scale RNA-seq datasets (member)
2017 CNRS MASTODONS project, Correction of 3rd generation sequencing data (member)
2013-16 Colib’read ANR project, De novo methods for the variant calling in short read sequencing (member)

Journal Publications

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; Bioinformatics 2023
BLight: Efficient exact associative structure for k-mers, C Marchet, M Kerbiriou, A Limasset; Bioinformatics, 2021
Scalable long read self-correction and assembly polishing with multiple sequence alignment, P Morisse, C Marchet, A Limasset, T Lecroq, A Lefebvre; Scientific Reports, 2021
Data structures based on k-mers for querying large collections of sequencing data sets, C Marchet, C Boucher, S. J. Puglisi, P Medvedev, M Salson, R Chikhi; Genome Research 2020
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, C Marchet, Z Iqbal, D Gautheret, M Salson, R Chikhi; Bioinformatics, 2020
ELECTOR: Evaluator for long reads correction methods, C Marchet, P Morisse, L Lecompte, A Limasset, A Lefebvre, T Lecroq, P Peterlongo; Nucleic acid research Genomics and Bioinformatics, 2019
Comparative assessment of long-read error-correction software applied to RNA-sequencing data, L Ishi Soares de Lima, C Marchet, S Caboche, C Da Silva, B Istace, J-M Aury, H Touzet, R Chikhi; Briefings in Bioinformatics, 2019
Clustering de Novo by Gene of Long Reads from Transcriptomics Data, C Marchet, L Lecompte, C Da Silva, C Cruaud, J-M Aury, J Nicolas, P Peterlongo; Nucleic Acids Research, 2018
A de novo approach to disentangle partner identity and function in holobiont systems A Meng, C Marchet, E Corre, P Peterlongo, A Alberti, C Da Silva, P Wincker, E Pelletier, I Probert, J Decelle, S Le Crom, F Not, L Bittner; Microbiome, 2018
A resource-frugal probabilistic dictionary and applications in bioinformatics, C Marchet, L Lecompte, A Limasset, L Bittner, P Peterlongo; Discrete Applied Mathematics, 2018
Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data C Benoit-Pilven, C Marchet, E Chautard, L Lima, M-P Lambert, G Sacomoto, A Rey, C Bourgeois, D Auboeuf, V Lacroix; Scientific Reports, 2018
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads L Lima, B Sinaimeri, G Sacomoto, H Lopez-Maestre, C Marchet, V Miele, M-F Sagot and V Lacroix; Algorithms for Molecular Biology, 2017
SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence H Lopez Maestre, L Brinza, C Marchet, J Kielbassa, S Bastien, M Boutigny, D Monnin, A El Filali, CM Carareto, C Vieira, F Picard, N Kremer, F Vavre, M-F Sagot, V Lacroix; Nucleic Acids Research, 2016
Colibread on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads E Rivals, A Andrieux, A Z El Aabidine, B Cazaux, C Marchet, C Lemaitre, C Monjeaud, G Sacomoto, L Salmela, O Collin, P Peterlongo, R Uricaru, S Alves-Carvalho, V Lacroix, V Miele, Y LeBras; GigaScience, 2016

Research papers accepted to peer-reviewed conferences

Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching, T Rouzé, I Martayan, C Marchet & A Limasset, WABI 2023
Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees, C Marchet & A Limasset; ISMB 2023
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, C Marchet, Z Iqbal, D Gautheret, M Salson, R Chikhi; ISMB 2020
Indexing De Bruijn graphs with minimizers, C Marchet, A Kerbiriou, A Limasset; RECOMB-SEQ 2019
CONSENT: Scalable self-correction of long reads with multiple sequence alignment , P Morisse, C Marchet, A Limasset, A Lefebvre, T Lecroq; RECOMB-SEQ 2019
A resource-frugal probabilistic dictionary and applications in (meta)genomics, C Marchet, A Limasset, L Bittner, P Peterlongo; PSC 2016
Navigating in a Sea of Repeats in RNA-seq without Drowning, G Sacomoto, B Sinaimeri, C Marchet, V Miele, MF Sagot, V Lacroix; WABI 2014

Preprints

Read correction for non-uniform coverages, C Marchet, Y Dufresne, A Limasset

Communications

Invited talks

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, UK
2022 Scalable sequence database search using Partitioned Aggregated Bloom Comb-Trees, Genome Informatics, Cambridge (UK)
2022 How to improve student/advisor relationships, WABI, ALPACA 2nd Annual Workshop, Potsdam (Germany)
2022 Data-structures for querying large k-mer (collections of) sets, JOBIM mini-symposium, Rennes (France)
2022 Data-structures for querying large k-mer (collections of) sets, KIM Data and Life Sciences seminars, Montpellier (France, online) [slides] [recording (in French)]
2022 Data structures for large k-mer sets, MIAT seminars, Toulouse (France, online) [slides]
2020 From reads to transcripts: de novo methods for the analysis of transcriptome second and third generation sequencing, SIF congress, INSA de Lyon (France)
2020 Scalable data structures for sequencing data, Symposium GDR Madics, Lyon (France) (covid-19 : canceled)
2019 New methodologies for the analysis of transcriptome sequences, MAB team seminar, LIRMM Montpellier (France)
2018 CARNAC-LR and C2C: de novo clustering and detection of alternative isoforms in Third Generation Sequencing transcriptomes, Genotoul Biostats/Bioinfo day, INRA Toulouse (France)
2018 From reads to transcripts: de novo methods to analyze transcriptome 2d and 3d generations sequencing data, Roscoff Biological Station seminar (France)
2018 A de novo approach to disentangle partner identity and function in holobiont systems, Advances techniques to study and exploit the sponge and coral microbiomes Workshop, ULB Brussels (Belgium)
2018 A highly scalable data structure for read similarity computation and its application to marine holobionts, EEB group meeting, ULB Brussels (Belgium)
2018 CARNAC-LR: clustering genes expressed variants from long read RNA sequencing, team TIBS seminar, LITIS Rouen (France)
2017 De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets at workshop RNA-Seq and Nanopore sequencing, Genoscope Evry (France)
2017 Rconnector: a resource-frugal probabilistic dictionary and applications in (meta)genomics and transcriptomics, LBBE NGS group seminar, Lyon (France)

Workshops/conferences/seminars

2020 REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, BIATA, St Petersburg (Russia, virtual conference)
2020 REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, ISMB, Montreal (Canada, virtual conference)
2020 REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, JOBIM, Montpellier (France, virtual conference)
2020 REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets, DSB, Rennes (France)
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, DSB, Dortmund (Germany)
2019 Survey of k-mer set of sets data structures for querying large collections of sequencing datasets, Helsinki Bioinformatics Day (Finland)
2019 Read correction for non-uniform coverages, RCAM Institut Pasteur Paris (France)
2019 Survey of k-mer set of sets data structures for querying large collections of sequencing datasets, at SeqBim, Marne La Vallée (France)
2018 BCOOL-Trans: accurate and variant-preserving correction for RNA-seq, Seqbio, Rouen (France)
2018 ELECTOR: EvaLuator of Error CorrectionTools for lOng Reads, Seqbio, Rouen (France)
2018 CARNAC-LR : Clustering coefficient-based Acquisition of RNA Communities in Long Reads, JOBIM, Marseille (France)
2017 De novo Clustering of Gene Expression in Transcriptomic Long Reads Data Sets, Seqbio, Lille (France)
2017 A highly scalable data structure for read similarity computation and its application to marine holobionts, RCAM, Paris (France)
2017 A scaling transcriptomic approach to study holobiont data sets, 4e colloque Génomique Environnementale, Marseille (France)
2016 Rconnector: a resource-frugal probabilistic dictionary and applications in (meta)genomics and transcriptomics, SeqBio, Nantes (France)
2015 kissDE : a replicate-wise and annotation-free R package for testing the association between differential variants and experimental conditions in high throughput sequencing data, SeqBio 2015, Orsay (France)
2015 kissDE : a package to test for differences in reads counts derived from variants in RNA sequencing data, Quatriemes rencontres R 2015, Lyon (France)

Other talks

2022 A little tour of assembly methods with Antoine Limasset, for Evomics school on genomics in Cesky Krumlov
2021 An introduction to data-structures for k-mer sets indexing for ENS Rennes students

Involvement in scientific events

Program committee and venue organization

2023 PC, OC @SeqBIM (France)
2021 OC @SPIRE (virtual)
2020 PC @SPIRE (virtual)
2020 PC @RECOMB-Seq (virtual)
2019 PC @SeqBIM (France)
2018 Volunteer @RECOMB-seq and RECOMB, Paris
2016 OC “Biological insights from raw high-throughput sequencing data” - Colib’read ANR workshop, Paris

Tutoring for scientists

2020,2022,2023 Evomics, workshop on Genomics, Cesky Krumlov, Czech Republic
2019,2022,2023 Tutor at Bilille training courses (RNA-seq analysis), Lille.
2015 Tutor at CNRS course: “Bioinformatique pour les NGS”, Montpellier
2014 Tutor at BGE & EMBnet tutorials: “RNA-seq analysis”, Lyon
2014 Tutor at PRABI training courses, “Analyse de données RNA-seq sous l’environnement Galaxy”, Lyon

Supervision

2022 Louis-Maël Gueguen (M2 internship, with Laurent Jacob), subject: GWAS for metagenomics
2022 Thomas Baudeau (M2 internship), subject: Mapping of structural long reads
2021-.. Khodor Hannoush (PhD student, with Pierre Peterlongo), subject: Dynamic pangenome graphs
2020 Agathénaïs Adiguna (L3 internship, with Rayan Chikhi), subject: Data-structures for large scale RNA queries
2018 Benjamin Churcheward (M2 internship, with Pierre Peterlongo), subject: Isoform prediction using long reads sequencing
2017 Lolita Lecompte (M2 internship, with Pierre Peterlongo), subject: Conception and evaluation of a pipeline for de novo study of long reads in transcriptomics
2014 Camille Sessegolo (L3 internship, with Vincent Lacroix), subject: Improvements in the kissplice2refgenome software

Teaching

Year	Level	Topic
2021/2022	M1 bioinformatique Université de Lille	responsable de l'UE structures de données
2019/2020	L2 informatique Université de Lille	TP/TP Algorithmique et structures de données
2018/2019	L2 informatique Université de Lille	TP/TP Algorithmique et structures de données
2016/2017	4ème et 5ème année école d'ingenieur (M1/M2) INSA Rennes	Modélisation et ingénierie pour le vivant
2016/2017	2ème année cycle prépa INSA Rennes	TP/TP Bases de Données
2016/2017	M1 ENS Rennes	Biostatistiques, programmation avec R
2015/2016	M1 ENS Rennes	Biostatistiques, programmation avec R
2014/2015	L1 Université Lyon 1	TD Mathématiques pour les Sciences de la Vie

Press review

Camille Marchet, bioinformaticienne des séquences