Bioinformatics Engineer

Welcome to my GitHub profile! I am a bioinformatics engineer with a strong foundation in experimental biology, genomics and computational analysis of biological data. I enjoy designing reproducible tools and workflows that make it easier for teams to explore complex biological data.

This GitHub contains projects I’ve worked on or contributed to, showing my focus on clear, organized, and collaborative bioinformatics. I aim to connect biology and computing through scripting and pipeline development to support meaningful biomedical research.

• 🎓 Graduated with a Master's in Bioinformatics from the University of Rouen Normandie (France).
• 🧪 Strong foundation in omic data analysis, molecular biology, and pre-clinical research.
• 💻 Skilled in programming (R, bash, Python) and pipeline development for high-throughput sequencing data.

• RNA-Seq / Single-cell RNA-Seq analysis
• ChIP-Seq analysis
• Variant calling and annotation
• High-Performance Computing (using SLURM)
• Programming: Python, R, bash, SQL, HTML/CSS and more
• Pipeline development and workflow management (Snakemake, git)

• Cell culture
• Protein and RNA extraction
• Western Blot,
• RT-PCR, qPCR
• Histological and immunohistochemical staining
• Mouse model experimentation

• Organized and detail-oriented
• Curious
• Good listener and Strong collaborative spirit

• French: Native
• English: Professional Working Proficiency
• Dutch: Elementary
• German: Elementary

• Master Degree in Bioinformatics, Modelisation and Statistics
  University of Rouen Normandie (2020 – 2023)
• Bachelor’s Degree in Genomics
  National School of Physical Chemistry and Biology (ENCPB) of Paris (2017 – 2018)
• Associate of biology
  Bobigny Institute of Technology, Paris 13 University (2015 – 2017)
• First common core year for health studies
  University of Versailles-Saint-Quentin-en-Yvelines (2013 – 2015)
• Baccalaureat, major in biology, french-english bilingual section, with honours
  Lycée Paul Langevin of Suresnes (2010 – 2013)

• Bioinformatics Engineer
  Institut Cochin, Cutaneous Biology Team – Paris, France
  November 2023 – Present

  • RNA-seq analysis (bulk and single-cell): from raw data to biological interpretation. Including: quality control, alignment, quantification, differential expression, functional enrichment analysis (signaling pathways, GO Terms, etc.)
  • Development and use of reproducible pipelines on HPC computing clusters (with SLURM)
  • Support for biologists in skin biology research, presentation of results, and contribution to the writing and publication of scientific papers.

• Bioinformatics Intern
  Leiden University Medical Center, Mahfouz Lab – Leiden, The Netherlands
  March 2023 – August 2023

  • Comparative analysis and optimization of single-cell RNA-seq tools developed in Python.

• Bioinformatics Engineer Apprentice
  Sanofi – Vitry-sur-Seine, France
  September 2021 – January 2023

  • Pipeline development and data analysis for therapeutic research.

• Bioinformatics Intern
  Sanofi – Vitry-sur-Seine, France
  March 2021 – July 2021

  • Statistical analysis of molecular production data.
  • Development of molecular models and molecular dynamics simulations.

• Engineering Assistant
  Imagine Institute of Genetic Diseases, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia – Paris, France
  October 2018 – August 2020

  • In vivo studies aimed at testing and identifying molecules capable of correcting growth defects in mouse models of dwarfism.
  • In vitro studies to better understand the signaling pathways involved in FGFR3 gain-of-function mutations using cellular models of bone or cartilage.

• Engineering Assistant Apprentice
  Imagine Institute, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia – Paris, France
  December 2017 – September 2018

  • Study of chondrocyte differentiation and growth plate biology in a mouse model of achondroplasia.

• Laboratory Technician Intern
  Foch Hospital – Suresnes, France
  November 2016 – February 2017

  • Molecular biology: nucleic acid extraction and PCR/RT-qPCR on automaton
  • Serology: preparation of quality controls, immunochemiluminescence, management of serum banks, immunoblots

• Sterilization Agent
  Foch Hospital – Suresnes, France
  July 2016

  • Validated sterilization and washing cycles, managed drying of medical instruments, and maintained traceability records
  • Performed sterile packaging of medical equipment using pouches and sterilization wraps.

• Peripheral serotonin regulates epidermal differentiation and dermal homeostasis
  Contributors: Matar S, Petit A, Mansour N, Flipo J, Gendrot B, Kanaan P, Fouquet G, Gaillard R, Aractingi S, Oulès B.
  Journal of Investigative Dermatology 2026 June
• Low-Dose Infigratinib increases bone growth and corrects growth plate abnormalities in an achondroplasia mouse model
  Contributors: Demuynck B, Flipo J, Kaci N, Dambkowski C, Paull M, Muslimova E, Shah BP, Legeai-Mallet L.
  J Bone Miner Res. 2024 Jul 23;39(6):765-774.
• Theobroma cacao improves bone growth by modulating defective ciliogenesis in a mouse model of achondroplasia
  Contributors: Martin L, Kaci N, Benoist-Lasselin C, Mondoloni M, Decaudaveine S, Estibals V, Cornille M, Loisay L, Flipo J, Demuynck B, de la Luz Cádiz-Gurrea M, Barbault F, Fernández-Arroyo S, Schibler L, Segura-Carretero A, Dambroise E, Legeai-Mallet L.
  Bone Res 10, 8 - 2022.

• GreenBIM: Environmental impact of Bioinformatics
  Asmae Bachr, Alizée Bardon, Sara Bencheikh, Fiona Bottin, Justine Flipo, Coline Gardou, Sidonie Halluin, Bryce Leterrier, Meije Mathé, Louis Ollivier, et al.
  Preprint, 26 January 2023.
  Collaborative student project during Master’s program
• Prediction of the impact of protein interactions on the production yield and analytical characteristics of complex antibodies
  Justine Flipo, Cendrine Lemoine, Alessandro Masiero, Pierrick Rival, Catherine Prades
  Poster presented during apprenticeship in Sanofi Research and Development, Vitry-sur-Seine (France), 2022 (not published)

• Use of the HPC resource iPOP-UP@RPBS with SLURM (2025)
• MOOC NGS & Cancer 2024 - Single Cell (2024)
• Training in experimental procedures on rodents (2019)
• TOIEC : 815/990 (2018)

• Paris 2024 Volunteer Summer 2024
  Assisted with welcoming, guiding, and supporting spectators at Olympic venues, ensuring a positive and safe experience during the Paris 2024 Olympic Games.

• 👤 LinkedIn: linkedin.com/in/justine-flipo
• 🌱 ORCID: https://orcid.org/0000-0002-9261-7002