| Project name | Role |
| JPIAMR MEGAISurv 2024-2027. MEtaGenome-informed Antimicrobial resistance Surveillance: Harnessing long-read sequencing for an analytical, indicator and risk assessment framework |
Applicant, WP leader |
| ZonMW PINNACLE 2024-2027. PredictINg environmental Niche Adaptation by CampyLobactEr using information stored in CRISPR-Cas spacers and their targets | WP leader, co-applicant |
| NIOZ-UU 2024-2026. Portable DNA Sequencing Lending Service | Applicant |
| TKI 2023-2027 Predict and Prevent. The integration of pan-genomics, population dynamics and clinical outcomes to elucidate emerging pathogen threats using machine learning | Co-applicant |
| JPIAMR COINCIDE 2022-2025 Impact of reducing colistin use on colistin resistance in humans and poultry in Indonesia | WP leader, co-applicant |
| NIOZ KNAW - It takes guts to boost your resilience against climate change | Co-applicant |
| LWV21.217 De integrale aanpak van Escherichia coli in de pluimveeketen, de essentiële stap voorwaarts | Workpackage leader, co-applicant |
| UKRI BBSRC Europe Partnering Award - "One Health Genomic and Metagenomic Approaches to Campylobacter and Food Safety" |
Co-applicant |
| Janssen Pharma 2012-2024 Molecular epidemiology of bacterial pathogens to support bacterial vaccine development | Applicant & project lead |
| OHEJP 2020-2023 FULLFORCE | Co-applicant |
| OHEJP 2020-2023 Discover | Co-applicant |
| JPIAMR 2020-2022 TRIuMPH | Work package leader & co-applicant |
| Topsector Agri&Food 2020-2022: InsectNGS | Project lead & co-applicant. |
| H2020-MSCA-ITN-2019 2020-2023 - BEEP: Bio-inspired and bionic materials for enhanced photosynthesis | advisor PhD student |
| ZonMW 2020-2024 Quantifying the complex drivers of antibiotic resistance transfer by reusing (meta-) genomic databases | Co-applicant, advisory role PhD student |
| UU Exposome Hub | Scientific Coordination Board |
| MSD 2019-2020 The use of cephapirin containing intramammary injectors for mastitis treatment in dairy cattle and selection of ESBL producing Enterobacteriaceae | Project lead & co-applicant. |
| Peer Zwart fonds 2020 Bepaling bacterieel darmmicrobioom voor behoud van de Antilliaanse leguaan | Co-applicant |
| Peer Zwart fonds 2020 Microbioom van de bruinvis | Co-applicant |
| Janssen Pharma 2019 Molecular epidemiology of E. coli ST131 from animal sources | Project lead & co-applicant. |
| NCOH 2019-2023: Antimicrobial resistance in relation to the persistence of antimicrobial residues after treatment of farm animal: Input for risk management. Project lead & co-applicant. | Project lead & co-applicant. |
| COST action 2019-2023 Machine learning for microbiome analysis | Co-applicant and vice workgroup leader |
| Anicura Research Fund 2018: Fecal microbiome signatures of dogs with chronic inflammatory enteropathies. - Co-applicant | Co-applicant |
| Morris Animal Foundation 2018: D18EQ-828: Changes in gut microbiome cause or effect of developing equine metabolic syndrome in Shetland ponies | Co-applicant |
| ZonMW Enabling Technologies Hotels 2018: 43500984102 Living Colour understanding the ecology and evolution of bacterial iridescence | Work package leader & co-applicant |
| ZonMW AMR 2018-2022: BEWARE : Blueprint for Early Warning of Antimicrobial Resistance Emergence in animals– | Work package leader |
| ZonMW AMR 2018-2022: MRSA-PREVENT: Control of MRSA in the pig nasal microbiome to prevent transmission to humans | Work package leader & co-applicant |
| JPIAMR 5th Joint Call: Transmission Dynamics 2018-2022. ExcludeMRSA: Preventing transmission of MRSA from livestock to humans through competitive exclusion. | Project lead & applicant |
| JPIAMR 3rd Joint Call: Transmission Dynamics 2016-2020. STARCS: Selection and Transmission of Antimicrobial Resistance in Complex Systems | Workpackage leader |
| ZonMw Non-alimentary Zoonotic diseases 2016-2020: Discerning Environmental Pathways of Campylobacter Transmission (DEPiCT): An interdisciplinary framework for understanding the origins and spread of non-foodborne campylobacteriosis | Workpackage leader |
| FP7-PEOPLE-2010-IEF 2010-2012: Tn-Seq: Identification of genetic determinants involved in Streptococcus pneumoniae pathogenesis | Applicant & Project lead |
| IRCSET-EMBARK 2007-2009: Identification and characterization of genes of Bifidobacterium breve that are essential for host interaction and survival in the gastrointestinal tract. | Applicant & project lead |