Microbial communities

Data integration and ontologies for microbial cell factories

Ontology-based data integration for synthetic biology and metabolic engineering. Hoehndorf led the data-integration work package. Period: 2016–2018 Funding KAUST Center Competitive Funding — Grant ID: FCC/1/1976-08-01 (WP-lead) — USD 115,691 Team Vladimir Bajic — PI (Former KAUST CBRC director (retired)) Robert Hoehndorf — CoI (KAUST (Professor of Computer Science)) Miguel Angel Rodriguez Garcia — Postdoc (King Juan Carlos University (Research Scientist)) Software AberOWL — Ontology repository providing OWL EL reasoning services and SPARQL query expansion; integrates with PubMed/PMC for

Sequencing and computational analysis of MRSA samples

Microbial genomics and bioinformatics of methicillin-resistant Staphylococcus aureus (MRSA) isolates in Saudi Arabia. Period: 2018–2021 Funding King Abdulaziz City for Science and Technology — Grant ID: RGC/3/3689-01-01 (PI) — USD 362,159 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Mohammed Al Fageeh — PI (KACST) Takashi Gojobori — CoI (KAUST (CBRC)) Vladimir Bajic — CoI (Former KAUST CBRC director (retired)) Topics: Genomics, Microbial communities

Computational methods for functional metagenomics: from protein functions to multi-scale interactions

Multi-scale systems methods for characterising microbial community functions via protein function prediction; downstream produced DeepGOPlus and successor models. Period: 2022–2024 Funding KAUST Competitive Research Grant — Grant ID: URF/1/4675-01-01 (PI) — USD 247,500 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Takashi Gojobori — CoI (KAUST (CBRC)) Maxat Kulmanov — PhD (alumnus), Postdoc (KAUST (Research Scientist)) Rund Tawfiq — PhD (alumnus) (Sano Centre Krakow (Postdoctoral researcher)) Daulet Toibazar — MSc (alumnus) Amal Alhelal — MSc (alumnus) Md Nurul Muttakin —

Metagenomics-based surface prospecting

Metagenomics analysis of surface samples for bioprospecting in support of oil and gas upstream applications. Period: 2022–2024 Funding Saudi Aramco (industry contract) — Grant ID: RGC/3/4267-01-01 (PI) — USD 177,812 Team Robert Hoehndorf — PI (KAUST (Professor of Computer Science)) Takashi Gojobori — CoI (KAUST (CBRC)) Topics: Microbial communities

Enabling mangrove restoration by AI-tailored microbiome fortification

Microbiome-based intervention for mangrove ecosystem restoration in coastal Saudi Arabia. Period: 2023–2023 Funding KAUST Climate and Livability Initiative (CoI) — USD 25,000 Team Heribert Hirt — PI (KAUST (Center for Desert Agriculture)) Robert Hoehndorf — CoI (KAUST (Professor of Computer Science)) Topics: Genomics, Microbial communities, Neuro-symbolic AI

Enabling desert revegetation by AI-tailored soil microbiome fortification

AI-driven design of soil microbiomes for desert plant restoration; functional metagenomics analysis of arid-zone soil microbiomes. Period: 2023–2025 Funding KAUST Near Term Grand Challenge — Grant ID: REI/1/5235-01-01 (CoI) — USD 150,000 Team Heribert Hirt — PI (KAUST (Center for Desert Agriculture)) Robert Hoehndorf — CoI (KAUST (Professor of Computer Science)) Gabriel Wittum — CoI (Goethe University Frankfurt / KAUST) Arne Nägel — CoI (Goethe University Frankfurt) Rund Tawfiq — PhD (alumnus) (Sano Centre Krakow (Postdoctoral researcher)) Publications acknowledging this project (6) (2024)