Bruno Fant
Resume
  • Jan 2019 - Now
    myNEO Therapeutics
    Chief Scientific Officer 2025 - Now
    Chief Technology Officer 2020 - 2024
    Senior Bioinformatician 2019 - 2019

    myNEO Therapeutics is a data-driven biotech company pioneering breakthrough immunotherapies in the fight against cancer. Present from the inception of the company, I led its team of scientists in developing solutions for the optimized detection and prioritization of clinically actionable antigens. Our approach delivered several product formulations, both off-the-shelf and personalized, that are now being taken to the clinic.

    Key achievements:

    • Built ML algorithms enabling the optimized discovery and prioritization of tumor-derived antigens. In controlled, unbiased benchmarks, our models outperformed current state-of-the-art clinical options, and in one case, even broke new ground into better immunogenicity prediction

    • Developed a cloud-based neoantigen discovery and prioritization pipeline from the ground up. Established good practices for development and deployment, optimized cloud infrastructure according to a cost-based approach, and ensured compliance to GDPR and ISO norms

    • Led discovery efforts to identify actionable off-the-shelf antigen combinations in various cancer indications, leveraging both the canonical and dark genome of the tumour. One of these solutions is currently being tested in a phase I, while one other is currently undergoing pre-clinical validation before the clinic.

    • Secured multiple collaborations with academics, industrials, and hospitals, both in Europe and the US

  • Jan 2017 - Dec 2019
    Data science and bioIT consultant
    Self-employed

    Supported academics and industrials in data analysis or in the development of analysis toolsuites.

    Key achievements:

    • Led the large-scale data analysis for several high-profile papers (RNAseq, WGS, ChIPseq, exosome sequencing)
    • Built differential expression analysis tools to be used by wet lab scientists
  • Jan 2015 - Dec 2017
    University of Pennsylvania, Pierce lab
    Post-doctoral position

    Explored the importance and clinical actionability of epigenetics in cocaine addiction.

    Key achievements:

    • Led a small team in building histone post-translational modification, DNA methylation, and ATAC-seq analysis pipelines from the ground up
    • Built CRISPR-Cas construct design pipeline for handover to wet lab team
Education
  • University of Nice Sophia Antipolis - PhD - Molecular genetics (2011 - 2015)

    Doctoral research in molecular genetics.

  • University Name - B.S. in Biology (2010 - 2014)

    Undergraduate studies in biological sciences with a focus on molecular biology and genetics.

    • Dean’s List all semesters
    • Undergraduate research in molecular genetics lab
    • President of Biology Students Association
    • Completed honors thesis on genetic regulation
  • Ecole Normale Superieure de Lyon - Master's degree - Biosciences (2008 - 2010)

    Master’s studies in biosciences at one of France’s top research institutions.

  • Ecole Normale Superieure de Lyon - Master's degree - Complex systems (2008 - 2010)

    Master’s studies in complex systems at one of France’s top research institutions.

Skills
  • Programming Languages
    • Python
      • overwhelmingly my favorite language. Unoriginal, I know, but I like the modularity, the accessibility, and most of all the ecosystem
    • R
      • because I don’t think there exists a bioinformatician without R knowledge. It also remains superior to most (if not all) alternatives for the visual display of information. I haven’t tried Julia yet though, it also looks interesting.
    • Bash/Shell scripting
      • because regardless of what people think, awk is a programming language - and because you cannot do devops without it
    • SQL
      • because I needed to store things once
    • Bash/Shell scripting
  • Bioinformatics
    • Next-generation sequencing (NGS) analysis
    • Genomics and transcriptomics
    • Sequence alignment and variant calling
    • Phylogenetic analysis
    • Biological databases (NCBI, Ensembl, UniProt)
  • Data Science and Machine Learning
    • Machine Learning frameworks (TensorFlow, PyTorch, scikit-learn)
    • Statistical analysis and modeling
    • Data visualization (matplotlib, seaborn, ggplot2)
    • Deep learning and neural networks
    • Natural language processing
  • Team Management
    • Project planning and execution
    • Agile/Scrum methodologies
    • Cross-functional team leadership
    • Mentoring and coaching
    • Stakeholder communication
Publications
  • 2025
    Accelerating Neoantigen Discovery: A High-Throughput Approach to Immunogenic Target Identification
    Lena Pfitzer, Gitta Boons, Lien Lybaert, Wim van Criekinge, Cedric Bogaert, Bruno Fant
    Vaccines, 13(8), 865
    DOI: 10.3390/vaccines13080865
  • 2024
    Methods behind neoantigen prediction for personalized anticancer vaccines
    Kiyana Godazandeh, Lies Van Olmen, Lore Van Oudenhove, Steve Lefever, Cedric Bogaert, Bruno Fant
    Methods in Cell Biology, 183, 161-186
    DOI: 10.1016/bs.mcb.2023.05.002
  • 2023
    Challenges in neoantigen-directed therapeutics
    Lien Lybaert, Steve Lefever, Bruno Fant, Evelien Smits, Bruno De Geest, Karine Breckpot, Luc Dirix, Steven A. Feldman, Wim van Criekinge, Kris Thielemans, Sjoerd H. van der Burg, Patrick A. Ott, Cedric Bogaert
    Cancer Cell, 41(1), 15-40
    DOI: 10.1016/j.ccell.2022.10.013
  • 2022
    Cocaine-Induced Changes in Sperm Cdkn1a Methylation Are Associated with Cocaine Resistance in Male Offspring
    Sarah E. Swinford-Jackson, Bruno Fant, Mathieu E. Wimmer, Donovan Chan, Melissa C. Knouse, Mateo Sarmiento, Arthur S. Thomas, Phillip J. Huffman, Sharvari Mankame, Samantha J. Worobey, R. Christopher Pierce
    Journal of Neuroscience, 42(14), 2905-2916
    DOI: 10.1523/JNEUROSCI.3172-20.2022
  • 2022
    Improving T-cell mediated immunogenic epitope identification via machine learning: the neoIM model
    Lena Pfitzer, Lien Lybaert, Cedric Bogaert, Bruno Fant
    bioRxiv
    DOI: 10.1101/2022.06.03.494687
  • 2022
    neoMS: Attention-based prediction of MHC-I epitope presentation
    Nil Adell Mill, Cedric Bogaert, Wim van Criekinge, Bruno Fant
    bioRxiv
    DOI: 10.1101/2022.05.13.491845
  • 2022
    A synthetic DNA template for fast manufacturing of versatile single epitope mRNA
    Wout de Mey, Phaedra De Schrijver, Dorien Autaers, Lena Pfitzer, Bruno Fant, Hanne Locy, Arthur Esprit, Lien Lybaert, Cedric Bogaert, Magali Verdonck, Kris Thielemans, Karine Breckpot, Lorenzo Franceschini
    Molecular Therapy: Nucleic Acids, 29, 943-954
    DOI: 10.1016/j.omtn.2022.08.021
  • 2021
    Novel algorithm discovers up to 35% more epitopes translated from non-coding regions in cold tumours
    Lena Pfitzer, Lore Van Oudenhove, Cedric Bogaert, Bruno Fant
    Molecular Cancer Therapeutics, 20(12 Suppl), CC01-02
  • 2021
    Novel machine-learning tools improve cost-effective development of personalised immunotherapies: Lowering false positive rates in the search for actionable (personalised and largely shared) immunogenic neoantigens
    Cedric Bogaert, Lena Pfitzer, Nil Adell Mill, Bruno Fant
    Molecular Cancer Therapeutics, 20(12 Suppl), P006
  • 2019
    H3.3 Barcoding of Nucleus Accumbens Transcriptional Activity Identifies Novel Molecular Cascades Associated with Cocaine Self-administration in Mice
    Mathieu E. Wimmer, Bruno Fant, Sarah E. Swinford-Jackson, Alexander Testino, Duncan Van Nest, Ted Abel, R. Christopher Pierce
    Journal of Neuroscience, 39(27), 5247-5254
    DOI: 10.1523/JNEUROSCI.0015-19.2019
  • 2019
    Preconception maternal cocaine self-administration increases the reinforcing efficacy of cocaine in male offspring
    Bruno Fant, Mathieu E Wimmer, Sarah E Swinford-Jackson, John Maurer, Duncan Van Nest, R Christopher Pierce
    Psychopharmacology, 236(12), 3429-3437
    DOI: 10.1007/s00213-019-05307-y
  • 2019
    Novel biomarkers to assess in utero effects of maternal opioid use: First steps toward understanding short- and long-term neurodevelopmental sequelae
    Laura Goetzl, Tara Thompson-Felix, Nune Darbinian, Nana Merabova, Salim Merali, Carmen Merali, Kathryne Sanserino, Tamara Tatevosian, Bruno Fant, Mathieu E Wimmer
    Genes Brain and Behavior, 18(6), e12583
    DOI: 10.1111/gbb.12583
  • 2018
    Environmental, genetic and epigenetic contributions to cocaine addiction
    R Christopher Pierce, Bruno Fant, Sarah E Swinford-Jackson, Elizabeth A Heller, Wade H Berrettini, Mathieu E Wimmer
    Neuropsychopharmacology, 43(7), 1471-1480
    DOI: 10.1038/s41386-018-0008-x
  • 2018
    Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
    Florian Douam, Carly G K Ziegler, Gabriela Hrebikova, Bruno Fant, Robert Leach, Lance Parsons, Wei Wang, Jenna M Gaska, Benjamin Y Winer, Brigitte Heller, Alex K Shalek, Alexander Ploss
    Nature Communications, 9(1), 5031
    DOI: 10.1038/s41467-018-07478-2
  • 2017
    Paternal cocaine taking elicits epigenetic remodeling and memory deficits in male progeny
    M E Wimmer, L A Briand, B Fant, L A Guercio, A C Arreola, H D Schmidt, S Sidoli, Y Han, B A Garcia, R C Pierce
    Molecular Psychiatry, 22(11), 1641-1650
    DOI: 10.1038/mp.2017.8
  • 2015
    Comprehensive interactome of Otx2 in the adult mouse neural retina
    Bruno Fant, Alexander Samuel, Stéphane Audebert, Agnès Couzon, Salsabiel El Nagar, Nathalie Billon, Thomas Lamonerie
    Genesis, 53(11), 685-694
    DOI: 10.1002/dvg.22903
  • 2014
    Otx2 ChIP-seq reveals unique and redundant functions in the mature mouse retina
    Alexander Samuel, Michael Housset, Bruno Fant, Thomas Lamonerie
    PLoS One, 9(2), e89110
    DOI: 10.1371/journal.pone.0089110
Patents
  • filed
    Novel polypeptides for the treatment, prevention, and diagnosis of cancer, particularly colorectal cancer
    EP23195733.3
  • granted
    Multi-epitope construct (COVID-19)
    112116809 (Taiwan)
  • granted
    Method, system and computer program product for determining presentation likelihoods of neoantigens
    EP20185779.4 | US2023/0298692
  • granted
    Method, system and computer program product for determining peptide immunogenicity
    EP21791393.8 | US18/031139
Grants, funding, partnerships secured
  • 2025 - secured
    University of Liverpool
    Partnership deal for identification of epitopes in a personalized trial
    €225k
  • 2023 - secured
    Curevac
    Licensing deal for select epitopes in two cancer indications
    €800k secured, €2.4M pending on milestones
  • 2022 - secured
    Hookipa
    Clinical analysis efforts in a HPV off-the-shelf cancer vaccine
    €550k
  • 2021 - pending
    Odimma
    Partnership deal for identification of epitopes in a personalized trial
    €1.5M
  • 2020 - secured
    eTheRNA
    Discovery and vaccine design for a COVID-19 vaccine
    €150k
  • 2019 - secured
    Immunopepx VLAIO grant
    Exploring the neoantigen landscape of colorectal cancer
    €1.5M
  • 2015 - secured
    NIH R01 renewal
    Transgenerational effects of cocaine self-administration on behavior
    $1.2M
  • 2015 - secured
    NIH R21
    Effect of cocaine intake and incubation on histone modification landscape
    $275k