François Bonnardel, PhD

Summary

Results-driven Senior Bioinformatics and Pipeline Engineer with a PhD in Bioinformatics and extensive experience in computational biology, data science, and cloud-based solutions. Proven expertise in designing and optimizing bioinformatics pipelines, developing scalable software solutions, and leveraging AWS for high-performance computing. Adept at working in Agile environments and collaborating with cross-functional teams. Seeking to contribute to the pharmaceutical sector by applying advanced computational techniques to accelerate drug discovery, personalized medicine, and genomic research. Skilled in Python, R, Java, and database design, with a strong track record of delivering innovative tools and platforms for data annotation, visualization, and analysis.

Core Competencies

• Programming Languages: Python, R, Java, Perl, C, PHP, Bash, JavaScript (D3.js), HTML
• Cloud Computing & DevOps: AWS (EC2, Batch, S3), Ansible, CircleCI, Docker
• Development Tools: Slurm, SGE, MySQL, Git, Jira, Bitbucket
• Development Practices: AI agent assisted development, Agile methodologies, CI/CD, Unit Testing, Integration Testing, Production Validation
• Computational Biology: NGS, Transcriptomics, Metagenomics, Proteomics, Structural Biology, Phylogenetics
• Data Science & Analytics: Machine Learning, Data Mining, Clustering, High-Dimensional Data Visualization

Professional Experience

• Senior Bioinformatic Pipeline Developer and Solution Architect, Line Manager
  NeoGenomics Laboratories | Cambridge, UK | 01/2024 – Present
  Lead the design and optimization of bioinformatics pipelines to maximize resource efficiency and scalability on AWS. Implement and maintain Unittest and integration tests to ensure pipeline reliability and compliance with regulatory standards. Manage a team of developers, oversee code reviews, project timelines, and deployment strategies. Utilize Ansible for server deployments and collaborate with cross-functional teams to deliver production-ready solutions.
• Bioinformatic Pipeline Developer
  NeoGenomics Laboratories | Cambridge, UK | 10/2021 – 01/2024
  Redesigned and scaled Python and R-based pipelines on AWS, improving computational efficiency and reducing processing times. Maintained pipeline dependencies and ensured compliance with design control regulations. Collaborated with team members on development, code reviews, and troubleshooting using BitBucket, Jira, and CircleCI.
• Bioinformatics Consultant
  IVIDATA & Sanofi Pasteur | Lyon, France | 05/2021 – 10/2021
  Provided expert bioinformatics consulting services for genomics projects.
• Bioinformatician
  SIB Swiss Institute of Bioinformatics | Genève, Switzerland | 02/2021 – 05/2021
  Continued research and development of the UniLectin platform, enhancing its functionality and user experience. Published additional research findings and contributed to collaborative projects in glycobiology and structural bioinformatics. Mentored junior researchers and supported ongoing bioinformatics projects.
• Doctorant, PhD at PIG-SIB
  SIB Swiss Institute of Bioinformatics | Genève, Switzerland | 04/2019 – 02/2021
  Conducted a bioinformatic study of lectins (glycan binding proteins), 3D protein structure and sequence-based classification and prediction in genomes across all living kingdoms. Advanced research on 3D protein structure classification and lectin prediction, resulting in high-impact publications. Developed Python pipelines for automated classification and prediction, integrating machine learning techniques. Designed and implemented the UniLectin web platform (unilectin.unige.ch) for lectin exploration and visualization. Presented research at international conferences, including SIB, JOBIM, and Glyco@Alps.
• Doctorant, PhD at CERMAV
  CNRS - Centre National de la Recherche Scientifique | Grenoble, France | 10/2017 – 03/2019
  Conducted foundational research on lectin classification and prediction, leveraging sequence and structural data. Developed Python pipelines for 3D-based and sequence-based classification of lectins. Created HMM profiles for lectin family prediction across genomes. Designed and implemented databases for storing curated lectin structures and predicted lectins.

Internships

• Master 6-month Bioinformatician Internship
  CEA IDMIT | Paris, France | 01/2017 – 07/2017
  Developed a Java-based tool for automated transcriptomics sequence annotation and visualization. Designed a web platform for transcriptomics data analysis, hosted on GitHub.
• Master 3-month Internship in the IDMIT Team
  CEA IDMIT | Paris, France | 04/2016 – 06/2016
  Developed an R package for the visualization of high-dimensional biological objects. Implemented C and optimization of a Multi-Dimensional Scaling (MDS) algorithm.
• Bachelor Internship in the Genoscope LABGEM Team
  CEA Genoscope | Paris, France | 06/2015 – 08/2015
  Created a Python tool for operon prediction in prokaryotic genomes, enabling the discovery of novel metabolic pathways.
• Professional Oriented Bachelor Internship
  Genostar | Grenoble, France | 04/2014 – 07/2014
  Developed a Java module to integrate and benchmark automatic annotation software for prokaryote genomics.

Key Achievements

• Optimized pipeline execution cost and time through algorithm optimization on AWS cloud.
• Mentored 3 junior developers, boosting team productivity and code quality standards.
• Maintained HIPAA and GDPR compliance standards for 3+ years.
• Conducted monthly code reviews, resulting in fewer bugs and improved production output.

Education

• PhD, Bioinformatics, University of Geneva | 04/2019 – 02/2021
• PhD, Bioinformatics and Structural Biology, Université Grenoble Alpes | 10/2017 – 03/2019
• Master in Bioinformatics, Genomics Informatics and Mathematics for Health and Environment, Université Paris-Saclay | 09/2015 – 06/2017
• License, Bioinformatics, Université Paris-Saclay | 09/2014 – 06/2015
• Professional Oriented Bachelor, Bioinformatics, Université Clermont Auvergne | 09/2012 – 06/2014

Certifications & Training

• Master de bio-informatique et mathématiques, Université Paris-Saclay
• TOEIC 915, Université Paris-Saclay
• TD - Introduction à la programmation des algorithmes, Professional Training

Languages

• English – Fluent
• Français – Native

Projects & Portfolio

Selected Publications

• LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification
  Nucleic Acids Research | 2021
  F Bonnardel, J Mariethoz, S Pérez, A Imberty, F Lisacek
  https://doi.org/10.1093/nar/gkaa1019
• UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands
  Nucleic Acids Research | 2019
  F Bonnardel, J Mariethoz, S Salentin, X Robin, M Schroeder, S Perez, F Lisacek, A Imberty
  https://doi.org/10.1093/nar/gky832
• A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom
  J. Fungi, mdpi | 2021
  A Lebreton, F Bonnardel, YC Dai, A Imberty, FM Martin, F Lisacek
• Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome
  Biofilms and Microbiomes, npj | 2021
  F Bonnardel, SM Haslam, A Dell, T Feixl, Y Liu, V Tajadura-Ortega, Y Akune, L Sykes, PR Bennett, D MacIntyre, F Lisacek, A Imberty
• Structural Database for Lectins and the UniLectin Web Platform
  Lectin Purification and Analysis, Springer | 2020
  F Bonnardel, S Perez, F Lisacek, A Imberty
  Springer Protocol
• Structure and engineering of tandem repeat lectins
  Current Opinion in Structural Biology, Elsevier | 2020
  S Notova, F Bonnardel, F Lisacek, A Varrot, A Imberty
  https://doi.org/10.1016/j.sbi.2019.11.006
• A Bioinformatics View of Glycan–Virus Interactions
  Viruses, mdpi | 2019
  P Le Mercier, J Mariethoz, J Lascano-Maillard, F Bonnardel, A Imberty, S Ricard-Blum, F Lisacek
• Architecture and Evolution of Blade Assembly in β-propeller Lectins
  Structure, cell | 2019
  F Bonnardel, A Kumar, M Wimmerova, M Lahmann, S Perez, A Varrot, F Lisacek, A Imberty
  https://doi.org/10.1016/j.str.2019.02.002

References

• Margus Lukk, PhD – Supervisor (Available upon request)
• Anne Imberty, PhD – Supervisor (Available upon request)
• Frédérique Lisacek, PhD – Supervisor (Available upon request)
• Nicolas Tchitchek, Master Internship Supervisor (Available upon request)