Clea Siguret

Charbonnières Les Vieilles, Puy-de-Dôme, France · clea.siguret@gmail.com

I am a bioinformatics research engineer with a strong background in data science, comparative genomics, and evolutionary biology. With a Ph.D. in Bioinformatics and several years of professional experience in both academic and industrial settings, I specialize in developing robust pipelines for large-scale genomic analyses and delivering user-friendly tools on platforms such as GALAXY. I enjoy working at the intersection of biology and computer science, contributing to meaningful projects in agriculture, health, and biodiversity. Known for my autonomy, curiosity, and collaborative spirit, I value team dynamics and continuous learning as keys to impactful research.


Professional Experience

Bioinformatics Research Engineer (Fixed-term Contract)

Institut Français de Bioinformatique (CNRS), Plateforme AuBi (UCA), Aubière

  • Pipelines creation on GALAXY servers to identify Antibiotic Resistance in bacterial isolates
  • GALAXY administration and support: implementation of new features, user training, tool and workflow documentations
  • R-Shiny workshop animation: brainstorming and coding on the development of current or future applications between public Clermont laboratories
Supervisor: Nadia GOUÉ

Since April 2024

Bioinformatics Research Engineer (Postdoctoral)

PaleoEVO team, GDEC - UMR 1095 INRAE/UCA, Clermont-Ferrand

  • Method for selecting EMS mutants for translational research
  • Comparative genomics of 271 vertebrate species, study of their evolution
  • Visualizations development of gene flow and orthologous SNPs between populations for the Whealbi Project
  • Evolutionary history study of gymnosperm species
Supervisor: Jérôme SALSE

October 2023 – March 2024

Ph.D. in Bioinformatics - Specialization in Data Science, Genomics, Evolution

PaleoEVO team, GDEC - UMR 1095 INRAE/UCA, Clermont-Ferrand

  • Comparative genomics of 84 flowering plants, study of their evolution and translational research
  • Comparative genomics of gymnosperm species and study of their evolution
  • Identification and analysis of orthologous SNPs in triticeae (Whealbi Project)
Supervisor: Jérôme SALSE

June 2020 – September 2023

Bioinformatician (Fixed-term Contract)

Integration of NGS Analysis Pipelines on a GALAXY Interface

BIOGEMMA/LIMAGRAIN, Centre de Recherche de Chappes

  • Integration of production pipelines on the LIMAGRAIN GALAXY platform
  • Expansion of the tool portfolio and improvement of analysis pipelines' efficiency
  • GALAXY administration and support: implementation of new features, user support (Training, Issue Resolution, Responding to Requests), and documentation
Supervisors: Magalie LEVEUGLE, Frédéric SAPET

October 2018 – March 2020

Bioinformatician (Fixed-term Contract)

NGS Data Analysis (Sequencing Genotyping, RNA-seq, Whole Genome Shotgun, TILLING)

BIOGEMMA, Centre de Recherche de Chappes

  • NGS analysis results production from data of cultivable plants (crops and vegetables) and bacterial samples
  • Preparation of analysis reports and production monitoring at each project stage until deliverables
  • Modification and adaptation of pipelines according to project needs and technological advancements to improve pipeline efficiency (Speed and Quality)
Supervisors: Magalie LEVEUGLE, Frédéric SAPET, Jorge DUARTE

September 2017 – June 2018

Education

Ph.D. in Bioinformatics - Specialization in Data Science, Genomics, Evolution

Understanding the Paleo-evolution of Flowering Plants for Modern Agriculture Challenges

Université Clermont-Auvergne, Clermont-Ferrand, France

Methodology: Comparative genomics of 84 species of flowering plants

  • Understanding the Evolution of Angiosperm Genomes:
    • Identification of gene functions conserved among Angiosperms and within botanical families.
    • Characterization of key drivers of gene sequence evolution in plants.
    • Dating the emergence and polyploidy events within Angiosperms.
    • Analysis of the impact of polyploidy events on genes and associated functions.
    • Study of life history traits in Angiosperms: identification of genes specific to species groups.
  • Translational Research of Knowledge from a Model or Key Plant to an Agronomically Important Plant:
    • Cataloging functionally validated genes in model plants related to agronomic traits of interest.
    • Characterization of potentially transferable and exploitable conserved traits among Angiosperms.
    • Selection and validation strategy for genes potentially involved in desirable traits in common wheat.
    • Identification of genes and agronomic traits impacted by life history traits.

2020–2023

Master in Genetics and Physiology, Bioinformatics - Specialization in Data Analysis and Modeling

Université Clermont-Auvergne, Clermont-Ferrand, France

Data Analysis, Bioinformatics, Evolutionary Biology, Biostatistics, Comparative Genomics

2015–2017

License in Organismal Biology

Université de Pau et des Pays de l'Adour, Pau/Anglet, France

Evolutionary Biology, Animal/Plant Physiology, Biostatistics, Population Genetics, Microbiology

2012–2015

Skills

Programming Languages & Tools
Bioinformatics
  • Genome annotation, sequence alignment
  • Comparative genomics, phylogeny, clustering
  • Statistical analysis, data manipulation
  • Environment & workflow managers
Platforms
  • GNU/Linux, Windows
  • Cluster computing (PBS, Slurm)
Soft Skills
  • Teamwork, Planning, Troubleshooting
  • Decision-making, Persuasion, Conflict resolution
Languages
  • French (Native)
  • English (Proficient)

Interests

Sewing

  • Accessories: buttons, patches, bags
  • Garment creation from scratch
Relaxing and expressive hobby

Sports

  • Former rugby player
  • Now exploring:
    • Gym & Pilates
    • Yoga
    • 🏸Badminton
Focus on fun & wellbeing

Reading

  • Manga, comics, and novels
  • Genres:
    • Fantasy
    • Romance
    • Science Fiction
    • Adventure
Imagination & storytelling

Cooking

  • Sweet and savory dishes
  • Creative cooking & baking
Sharing food and joy

Publications

  • Siguret C., Olivier M., Huneau C., Sow M. D., Klopp C., Martin M-L., Tamby J-P., Civan P., Pont C., Mathieu O., Salse J. Plant Ancestral Genomes for Translational Research of key Traits and Processes in Modern Crops.
    Submission ongoing (Nature Communications)
  • Sow M. D., Forestan C., Pont C., Civan P., Seidel M., Siguret C., Luca Curci P., Tondelli A., Bustos Korts D., Mazzucotelli E., Leroy T., Huneau C., Delayhe M., ... Salse J. Striking convergent selection history of wheat and barley and its potential for breeding.
    Submission ongoing (Nature Plants)
  • Nasr E., Amato P., Bhardwaj A., Blankenberg D., Brites D., Cumbo F., Do K., Ferrari E., Griffin T., Grüning B., Hiltemann S., Jagtap P., Mehta S., Métris K., Momin S., Oba A., Pavloudi C., Pechlivanis N., Péguilhan R., Psomopoulos F., Rosic N., Schatz M., Schiml V., Siguret C., Soranzo N., Stubbs A., van Heusden P., Vohra M., microGalaxy Community, Zierep P., Batut B. The Microbiology Galaxy Lab: A community-driven gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data
    BioRxiv (2025) – doi:10.1101/2024.12.23.629682
  • Debroas D., Siguret C. Viruses as key reservoirs of antibiotic resistance genes in the environment.
    The ISME Journal, 13(11), 2019 – doi:10.1038/s41396-019-0478-9

Talks & Posters

  • Siguret C., Batut B., Goué N. ATELIER - Dépôt et curation de données - Communauté Biologie et Santé (plateforme de bioanalyses Galaxy)
    Printemps de la donnée 2025 de l'Université Clermont-Auvergne, Clermont-Ferrand, France ⟨hal-05095680⟩
  • Siguret C. ABRomics : Une plateforme basée sur Galaxy pour la recherche sur la résistance aux antibiotiques et la santé publique.
    Journée d’animation annuelle de la plateforme AuBi 2024, Clermont-Ferrand, France ⟨hal-05084079⟩
  • Lao J., Tackx R., Marin P., Dieuaide A., Mignon T., Batut B., Siguret C. , Dallet R., Hillion K.-H., Goué N., Ruppé E., Corguillé G. L., Glaser P., Mareuil F., Médigue C. The ABRomics platform — a One Health Antimicrobial resistance analysis service.
    JOBIM 2024, Toulouse, France ⟨hal-04618645⟩
  • Siguret C., Huneau C., Sow M. D., Salse J. Consequences of polyploidy events on angiosperm genome evolution.
    Journées Jeunes Chercheurs 2023 du département de Biologie et Amélioration des Plantes de l'INRAE, Clermont-Ferrand, France ⟨hal-04620735⟩
  • Siguret C., Salse J. Recurrences and consequences of polyploidy events on gene evolution in angiosperms: Comparative analysis of 80 genomes.
    Journées scientifiques de l'École Doctorale des Sciences de la Vie, de la Santé, de l’Agronomie, et de l’Environnement 2022, Clermont-Ferrand, France ⟨hal-04622228⟩
  • Siguret C., Huneau C., Salse J. L’origine des plantes à fleurs.
    Journées Portes Ouvertes du Centre Clermont-Auvergne-Rhône-Alpes 2022, Clermont-Ferrand, France
  • Siguret C. Les réseaux pour analyser les flux de gènes au sein des écosystèmes : application à l’étude des gènes de résistance aux antibiotiques.
    Journées Scientifiques 2017 – Colloque 14 : Journée Réseaux du GDR Génomique Environnementale, Nantes, France