School of Pure and Applied Sciences
Mr. Huxley Mae Makonde
Associate Professor
Professional profile
Prof. Huxley Makonde is an Associate Professor of Biotechnology and Dean of the School of Pure and Applied Sciences at the Technical University of Mombasa (TUM), Kenya. He provides strategic academic and administrative leadership, oversees teaching and research standards, manages institutional resources, develops partnerships, and supports resource mobilisation.
His expertise spans biotechnology, biochemistry, molecular biology, microbial ecology, metagenomics, bioinformatics, biosafety, and microbial biotechnology. He has extensive experience in molecular identification and characterisation of microorganisms, bioprospecting for bioactive compounds, and sustainable environmental management.
His teaching experience includes undergraduate and postgraduate instruction in biotechnology, biochemistry, genetics, microbiology, molecular biology, and related disciplines. He supervises PhD, master’s, and undergraduate students and has contributed to developing curricula for undergraduate, master’s, and doctoral programmes.
His research interests include microbial diversity, insect-associated microorganisms, marine and mangrove microbiomes, bioremediation, studies on antimicrobial compounds, food safety, and aflatoxin studies.
His leadership experience includes serving as Departmental Chairperson, Dean, and member of secondary-school Boards of Management. He has also contributed to internationalisation initiatives, Biorisk management and biosafety mentoring, academic governance, and research capacity development.
His major contributions include numerous peer-reviewed publications, successful postgraduate supervision, competitive research grants, curriculum development, multidisciplinary research collaborations, innovation, and international partnerships at TUM.
Academic qualifications
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2013
PhD Biotechnology JKUAT
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2009
MSc Biotechnology JKUAT
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2005
BSc Biochemistry JKUAT
Professional trainings
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2025-2026
DIES Training Course on Management of Internationalization 1 year DAAD/German Rectors' Conference
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2025-2026
DIES International Deans' Course Africa (2025–2026) 1 year DAAD/German Rectors' Conference
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2025
Gene Editing Technologies 1 week UDSM
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2022
National Management Training (NMT) Programme on Enhancing Strategic Leadership and Management of Higher Education Institutions in the Post-COVID-19 Era 8 Months Moi University/DAAD
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2022
Pedagogy training Workshop 1 week Pwani University/ TUM
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2019
Training on competency-based assessment held at Tvet Institution 1 week Tvet Curriculum Development, Assessment and Certification Council (TVET CDACC)
Current position
Associate Professor
Responsibilities
- Teaching undergraduate and postgraduate students in applied sciences fields such as biotechnology, biochemistry, genetics, microbiology, molecular biology, and related disciplines.
- Supervision and mentorship of PhD, master’s, and undergraduate students
- Contribution to curricula development and review.
- External examinations of theses and examination processes.
- Contribution to external local and internation resaerch collaborations.
- Community outreach engagements.
- Resaerch grants acquisiation.
- Research networking and joint publications.
Teaching & research
Research interests
v Metagenomics; Metatranscriptiomics; Bio-prospecting of bioactive compounds from insect microbiome; plants & their symbionts and other microbes from diverse habitats for industrial applications and bioremediation; Impact assessment of transgenic crops; Roles of soil microorganisms in ecological health of soil; Microbial/insects/plants mutualisms; Studies on Marine biodiversity and Mangrove forest ecosystem; Marine cage culture systems and studies on Aflatoxins
Teaching
Teaches undergraduate and postgraduate students in the following areas:
- Biotechnology, biochemistry, bioinformatics, genetics, microbiology, molecular biology, and other related disciplines.
Publications
Selected Publications
1. Mwangi EK, Karanja EN, Nderitu IM, Makonde HM, Maingi JM, Ngugi MP. Antimicrobial Activity and Metabolomic Profiling of Secondary Metabolites From Endophytic Bacteria Associated With Prunus africana. Chemistry & Biodiversity. 2026: 23(3), e03655. https://doi.org/10.1002/cbdv.202503655
2. Keroro K, Kibiti C, Makonde HM. A Review of the Role of Actinobacteria as a Source of Bioactive Compounds Multidisciplinary Journal of TUM. 2025: 4(2), 36-51. https://doi.org/10.48039/mjtum.v4i2.97
3. Panyako BW, Wacira TN, Njeru EM, Gicharu GK, & Makonde HM. Molecular characterization and lead (Pb) tolerance of Penicillium and Aspergillus species from contaminated soils in Owino Uhuru, Mombasa, Kenya. African Journal of Microbiology Research. 2025:19(8), 171–186. https://doi.org/10.5897/AJMR2025.9793
4. Wacira TN, Makonde HM, Kamau JN, Aura CM, & Kibiti CM. Characterization and bioactivity potential of marine sponges (Biemna fistulosa, Callyspongia diffusa, and Haliclona fascigera) from Kenyan coastal waters. PloS one. 2025:20(7), e0325642. https://doi.org/10.1371/journal.pone.0325642
5. Wacira TN, Makonde HM, Kamau JN, & Kibiti CM. Identification and Antimicrobial Potential of Marine Sponges (Carteriospongia foliascens, Callyspongia fallax, and Paratetilla arcifera) from Kenyan Marine Waters. International Journal of Microbiology. 2025: 4208163. https://doi.org/10.1155/ijm/4208163
6. Wacira TN, Makonde HM, Nyingi JK, Aura CM, Kibiti CM. Marine organisms: a hidden treasure trove from the Kenyan waters for antimicrobial resistance (AMR). Kenya Aquatica Journal. 2025:10(1), 82-100. https://www.kmfri.go.ke/index.php/component/sppagebuilder/page/181
7. Wacira TN, Makonde HM, Aura CM, Nyingi JK, Nyamweya CS, Osore M, Kibiti CM. (2025). Genetic research: Global and Kenyan contextual comprehensive review of freshwater fish populations. Kenya Aquatica Journal. 2025:10(1), 101-127. https://www.kmfri.go.ke/index.php/component/sppagebuilder/page/181
8. Okoth BA, Makonde HM, Bosire CM, Kibiti CM. Characterization and Enzymatic Potential of Bacteria and Fungi from Mwakirunge Dumpsite, Kenya. International Journal of Microbiology. (2025):7818433. Published 2025 Apr 21. doi:10.1155/ijm/7818433
9. Ogare J, Kibiti CM, Ngugi MP, Apiri BO, Makonde HM. Anti-Inflammatory and Antinociceptive Potential of Phytochemicals Derived from Urtica massaica: A Comprehensive Review. Multidisciplinary Journal of TUM. (2024): 3(2) 2024 67 – 73 http://doi.org/ 10.48039/mjtum.v3i2.83.
10. Apiri BO, Makonde HM, Ngugi MP, Ogare J, Kibiti CM. Medicinal Potential of Tragia involucrata Linn for Management of Diabetes Mellitus in Kenya, A Review. Multidisciplinary Journal of TUM. (2024): 3(2) 2024 67 – 73 http://doi.org/ 10.48039/mjtum.v3i2.83.
11. Wacira TN, Makonde HM, Bosire CM, Kibiti CM. Molecular Characterization and Antibacterial Potential of Endophytic Fungal isolates from selected Mangroves along the Coastline of Kenya. International Journal of Microbiology. (2024):15. https://doi.org/10.1155/2024/1261721.
12. Ronoh P, Toroitich FJ, Makonde HM, Lelmen EK, Obonyo MA. Reliability of the chemical, metabolic, and molecular methods in discriminating aflatoxigenic from non-aflatoxigenic Aspergillus isolates, The Microbe. Vol.4 (2024):100115. https://doi.org/10.1016/j.microb.2024.100115.
13. Muwawa EM, Makonde HM, Obieze CC, de Oliveira IG, Jefwa JM, Kahindi JH, Khasa DP. Diversity and assembly patterns of mangrove rhizosphere mycobiome along the Coast of Gazi Bay and Mida Creek in Kenya. PloS one. (2024):19(4):e0298237.
14. Okioga FM, Ngugi MP, Makonde HM, ‘’Phytochemical Characterization of Dichloromethane Stem Bark Extract of Piliostigma thonningii (Schum.).’’ International Journal of Innovative Science and Research Technology. Vol. 8, No. 9 (2023):8(9): DOI: https://doi.org/10.5281/zenodo.8337945.
15. Okoth BA, Makonde HM, Bosire CM, Mwajuma JJ, Kibiti CW, ''A Review on the Role of Microbes in Polyethene Degradation'' Multidisciplinary Journal of Technical University of Mombasa. Vol. 2, No. 1(2023): Pp. 1-18.
16. Wafula EN, Muhonja CN, Kuja JO, Owaga EE, Makonde HM, Mathara JM, Virginia W. Kimani VW, ''Lactic Acid Bacteria from African Fermented Cereal-Based Products: Potential Biological Control Agents for Mycotoxins in Kenya'' Hindawi Journal of Toxicology. Vol. 2022 (2022): Pp 17. doi.org/10.1155/2022/2397767.
17. Muwawa EM, Obieze CC, Makonde HM, Jefwa JM, Kahindi JHP, Khasa DP, ‘’16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya.’’ PLoS ONE. Vol. 16, No. 3 (2021): e0248485. doi.org/10.1371/journal.pone.0248485.
18. Chagona P, Kwamboka N, Gaya H, Makonde H, Adem A, Osano K, Kawaka F. Phytochemical Analysis and Antibacterial Activity of the Kenyan Wild Orchids. Micro Environer. Vol. 1, No. 2 (2021): Pp. 93-100. doi.org/10.54458/mev.v1i02.6677
19. Mwabonje R, Makonde H, Kanga AJ, Adem A, Saidi S, Jeza VT, ''Vernoa Hildebranditii, Acacia stuhlmannii and Moringa Oleifera Leaf and Root-bark Extracts Exhibit Antimicrobial Effects on Selected Diarrheagenic Microorganisms'' Multidisciplinary Journal of Technical University of Mombasa. Vol. 1, No.1 (2020): pp. 31-36.
20. Allard SM, Costa MT, Bulseco AN, Helfer V, Wilkins LGE, Hassenrück C, Zengler K, Zimmer M, Erazo N, Rodrigues JLM, Duke N, Melo VMM, Vanwonterghem I, Junca H, Makonde HM, Jiménez DJ, Tavares TCL, Fusi M, Daffonchio D, Duarte CM, Peixoto RS, Rosado AS, Gilbert JA, Bowman J, ''Introducing the Mangrove Microbiome Initiative: Identifying Microbial Research Priorities and Approaches To Better Understand, Protect, and Rehabilitate Mangrove Ecosystems'' Msystems, Vol. 5, No. 5, (2020). Doi.org/10.1128/mSystems.00658-20.
21. Wacira TN, Makonde HM, Bosire CM, Mzee SS, Mwamburi SM, Kibiti CM, '' Isolation and morphological characterization of endophytic fungi isolated from mangrove plants along the Kenyan coastline'' African Journal of Microbiology Research. 14, No. 10, (2020): Pp 594-607. DOI: 10.5897/AJMR2020. 9402.
22. Muwawa EM, Makonde HM, Obieze CC, Jefwa JM, Kahindi JHP, Khasa DP, ''Isolation, characterization and biotechnological potential of tropical culturable rhizospheric fungi from four mangrove species in Kenya'' African Journal of Microbiology Research. Vol. 14, No. 9, (2020): Pp. 541-554. DOI: 10.5897/AJMR2020.9394.
23. Muwawa EM, Makonde HM, Jefwa JM, Kahindi JHP, Khasa DP, ''Molecular identification of bacterial isolates from the rhizospheres of four mangrove species in Kenya'' African Journal of Microbiology Research. Vol. 14, No. 9, (2020): Pp. 525-535. DOI: 10.5897/AJMR2020.9393.
24. Micah KL, Faith JT, Meshack AO, Huxley MM, “Modulation of Aflatoxin Production by Interaction of Aspergillus Species from Eastern Kenya.” IOSR Journal of Environmental Science, Toxicology and Food Technology (IOSR-JESTFT). Vol. 13, No. 11, (2019): Pp. 01-07. DOI: 10.9790/2402-1311010107.
25. Omondi GO, Malala JB, Msanzu JB, Omukhango AC, Kamau GG, Makonde HM, Chimbevo LM, ‘’Growth Performance, Metabolic Efficiency and Nutrient Utilization of BALB/C Mice Fed with Diet Made from Leftovers from Cocos nucifera Pulp,’’ American Journal of BioScience. Vol. 7, No. 1, (2019): pp. 1-6. doi: 10.11648/j.ajbio.20190701.11.
26. Kawaka F, Makonde H, Dida M, Opala P, Ombori O, Maingi J, Muoma J. ‘’Genetic diversity of symbiotic bacteria nodulating common bean (Phaseolus vulgaris) in western Kenya.’’ PLoS ONE 13, no. 11 (2018): e0207403. doi.org/10.1371/journal. pone.0207403.
27. Muhonja CN, Magoma G, Imbuga M, Makonde HM. “Molecular Characterization of Low-Density Polyethene (LDPE) Degrading Bacteria and Fungi from Dandora Dumpsite, Nairobi, Kenya,” International Journal of Microbiology, Article ID 4167845, (2018): 10 pages. doi.org/10.1155/2018/4167845.
28. Muhonja CN, Makonde HM, Magoma G, Imbuga M. ‘’Biodegradability of polyethylene by bacteria and fungi from Dandora dumpsite Nairobi-Kenya.’’ PLoS ONE 13, no. 7 (2018): e0198446. doi.org/10.1371/journal.pone.0198446.
29. Josiah O. Kuja, Huxley M. Makonde, Hamadi I. Boga, Anne T.W. Muigai, Jun Uetake. ‘’Phylogenetic diversity of prokaryotes on the snow-cover of Lewis glacier in Mount Kenya.’’ African Journal of Microbiology Research 12, no 24. (2018): 574-579. DOI: 10.5897/AJMR2017.8750.
30. Odilia Atamba Salano, Huxley Mae Makonde, Remmy Wekesa Kasili, Hamadi Iddi Boga. ‘’Isolation and characterization of fungi from a hot-spring on the shores of Lake Bogoria, Kenya.’’ Journal of Yeast and Fungal Research 9, no. 1 (2018): 1-13. DOI: 10.5897/JYFR2018.0182.
31. Christine W. Njiru, Huxley M. Makonde, John M. Kahindo, Edwin O. Matoka and Charles M. Matoka. "Bio-prospecting of macro-algae for potential industrial dyes." African Journal of Biotechnology 17, no. 26 (2018): 804-810. DOI: 10.5897/AJB2018.16460.
32. Odilia Atamba Salano, Huxley Mae Makonde, Remmy Wekesa Kasili, Laura Nyawira Wangai, Mildred Pauline Nawiri and Hamadi Iddi Boga. "Diversity and distribution of fungal communities within the hot springs of soda lakes in the Kenyan rift valley." African Journal of Microbiology Research 11, no. 19 (2017): 764- 775. DOI: 10.5897/AJMR2017.8510.
33. Huxley Mae Makonde, Romano Mwirichia, Edith Mnyazi Muwawa, Hans-Peter Klenk and Hamadi Iddi Boga. “Fungal diversity and community structure in gut, mound and surrounding soil of fungus-cultivating termites.” African Journal of Microbiology Research 11, no. 12 (2017): 504-515. DOI: 10.5897/AJMR2017.8484.
34. Mwakio E, Chimbevo M, Malala J, Makonde H, Kahindo J, Awadh M, Msanzu J, “A Comparative Study on Microbiological and Physico-chemical Properties of Three Local Alcoholic Beverages Produced and Consumed in Mombasa County, Kenya.” Microbiology Research Journal International. 20. 1-9 (2017). DOI: 10.9734/MRJI/2017/28061.
35. Anne K. Kambura, Romano K. Mwirichia, Remmy W. Kasili, Edward N. Karanja, Huxley M. Makonde, Hamadi I. Boga. “Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya.” BMC Microbiology 16 (2016):136. DOI 10.1186/s12866-016-0748-x
36. Edith M. Muwawa,Nancy L.M. Budambula, Zipporah L. Osiemo, Hamadi I. Boga, Huxley M. Makonde. “Isolation and characterization of some gut microbial symbionts from fungus-cultivating termites (Macrotermes and Odontotermes spp.).” African Journal of Microbiology Resaerch 10, no. 26 (2016): 994-1004. Doi.org/10.5897/AJMR2016.8060.
37. Anne K. Kambura, Romano K. Mwirichia, Remmy W. Kasili, Edward N. Karanja, Huxley M. Makonde, Hamadi I. Boga. “Diversity of fungi in sediment and water sampled fromthe hot springs in Lake Magadi and Little Magadi in Kenya.” African Journal of Microbiology Research 10, no. 10 (2016): 330-338. DOI:10.5897/AJMR2015.7879.
- Ali Shee, Mariam Maku Swaleh, Laila Uweso Abubakar, Huxley Mae Makonde, Saeed Mutta Mwaguni, Daniel Munga, Mumini Ndenge Dzoga and Cyrilus Otulo Wandera. (2025). Microalgae and Black Soldier Fly Larvae as Sustainable Methods for Decentralized Sewage Treatment in Sub-Saharan Africa. IntechOpen. doi: 10.5772/intechopen.1007746
Postgraduate supervision
Grants & projects
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Seedings Lab Equipment Grant 2024
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SolCoolDry Project Phase II: Development of Milkfish (Chanos chanos) and Kimarawali (Stolephorus delecatulus) Solar Drying-Cooling Technology, Value Addition and Quality Assurance. 2023
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Evaluation of Properties of Silk fibers for Medical Applications in Kenya 2022
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Internationalization at home: integrating collaborative online international learning (coil) and virtual exchanges in higher education institutions in Kenya. 2022
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Design and Installation of a Performance Evaluation and Control System for the Hybrid Modified Solar Assisted Biogas Production Energy Plant at the Technical University of Mombasa. 2021
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Development of an Online Platform-Based system to Improve the Quality of Education Through Continuous Course and Lecturer Evaluation. 2021
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Antibiotics in Food and Environment: Occurrence, Role in Formation and transfer of Resistant Genes and their removal from Waste water using Green Adsorbents from Locally available Materials 2020
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Germplasm Conservation of Indigenous Edible Mushrooms to Diversify Nutritious and Safe Food Sources in Kenya 2020
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SolCoolDry Project Phase I: Development of Milkfish (Chanos chanos) and Kimarawali (Stolephorus delecatulus) Solar Drying-Cooling Technology, Value Addition and Quality Assurance – SolCoolDry: 2019
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Mitigating the Adverse Health Effects of Aflatoxins by Reducing Human Consumption: A Value Chain approach. 2018
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Optimization of marine cage culture systems for Rabbitfish (Siganus argenteus) and Tilapia (Oreochromis niloticus) in Kwale and Kilifi Counties. 2018
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Microbial Biodiversity, Biogeography and their potential for nutrients cycling and waste Bioremediation in mangrove ecosystem. 2015
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Screening for cellulases for Biofuel production. 2010
Leadership & professional experience
Current Position
- Associate Professor of Biotechnology, Department of Chemistry and Biological Sciences, TUM - May 2024 to present.
- Dean, School of Pure ans Applied Sciences, Technical University of Mombasa (TUM) - Septmeber 2025 to present.
- Previously Dean, School of Applied and Health Sciences, Technical University of Mombasa (TUM) - April 2023 to Septemebr 2025.
Previous Academic and Administrative Positions
- Chairperson, Department of Pure & Applied Sciences, TUM - 2018–2022.
- Acting Dean, School of Applied & Health Sciences, TUM - served on several occasions.
- Acting departmental leadership roles - undertook acting responsibilities within the department as required.
- Academic staff member at TUM - engaged in teaching, research, postgraduate supervision, curriculum development, and academic programme implementation.
Major Leadership and Professional Roles
- Provides strategic academic and administrative leadership as Dean, overseeing teaching, research, quality assurance, staff and resource management, and institutional development.
- Led departmental operations as Chairperson, coordinating academic activities, staff responsibilities, and programme delivery.
- Contributed to curriculum development for undergraduate, master's, and doctoral programmes in biotechnology, biochemistry, and related disciplines.
- Served on Boards of Management at Kwale High School, Ribe Boys’ High School, and Chang’ombe Secondary School, including chairing academic committees.
- Served as an IFBA Global Mentor in biosafety and biosecurity.
- Participated in international academic leadership and internationalisation initiatives, including the DIES programme.
- Contributed to research leadership, grant development, postgraduate supervision, research collaboration, and institutional capacity building.
Awards & memberships
Awards and Scholarships
- Awarded a DAAD PhD scholarship (2010–2012)
- Fully funded RUFORUM MSc Biotechnology scholarship (2007–2009).
Professional Memberships & Committees
- Member of the DAAD Scholarship Selection Committee.
- Member of the Kenya DAAD Scholars Association (KDSA).
- Member of the Bioethics Society of Kenya (BSK).
- Treasurer KDSA, TUM Chapter.
- Member of the International Federation of Biosafety Associations (IFBA).
- Member of Biorisk Management Association of Kenya (BMAK).
- Member of Western Indian Ocean Marine Science Association (WIOMSA).
- Member of American Society for Microbiology (ASM).
- Committee member of the Kenya DAAD Scholars Association (KDSA) (2015-2018).
- Member of the TUM Ethical Review Committee (ERC) (2018-2022).
- Member of Regional Student Group (RSG-Africa) of the International Society for Computational Biology (ISCB) from 2008-2013.
Editorial and Reviewer Roles
- Peer reviewer for journals including PLOS ONE, International Journal of Microbiology, Journal of Insect Science, Folia Microbiologica, and other microbiology and genetics journals.
- Reviewer of African Research Initiative for Scientific Excellence (ARISE) grant applications.
- External subject expert for academic programme validation at Maasai Mara University and external examiner of postgraduate theses.
Consultancy and Professional Service
- Provides academic and scientific expertise through grant and proposal review, curriculum validation, postgraduate examination, and facilitation of research administration and grant-writing workshops.
Industry and Community Engagement
- Contributes to collaborative research on marine fish processing and preservation, aquaculture, food safety, aflatoxin mitigation, waste bioremediation, and environmental sustainability.
- Supports research capacity building, scientific training, stakeholder engagement, and university–industry and international research collaboration.
Key achievements
Research and Scientific Advancement
- Published extensively in peer-reviewed scientific journals, contributing to knowledge in microbial diversity, metagenomics, molecular biology, and biotechnology.
- Led and participated in funded research on microbial biodiversity, mangrove ecosystem functioning, bioremediation, antimicrobial resistance, indigenous edible mushrooms, aflatoxin mitigation, and marine aquaculture.
- Advanced research into bioactive compounds from microorganisms and marine organisms, with potential environmental, industrial, food safety, and public health applications.
Innovation and Technology Development
- Contributed to the development of solar drying and cooling technologies for marine fish, focusing on value addition, preservation, and quality assurance.
- Supported innovation through multidisciplinary research collaborations and TUM’s Research and Innovation Week.
Leadership and Institutional Development
- Provides strategic academic and administrative leadership currently as Dean of the School of Pure and Applied Sciences, and prevoiuosly as Dean of the School of Applied and Health Sciences at TUM.
- Previously served as Chairperson of the Department of Pure and Applied Sciences, contributing to academic governance, staff development, and teaching and research standards.
- Promotion of internationalisation, institutional partnerships, and research capacity building through initiatives supported by DAAD and other partners.
Policy and Governance
- Contributes to institutional policy implementation, quality assurance, resource management, and academic programme development.
- Serves on secondary-school Boards of Management, chairing academic committees and contributing to educational governance, policy review, budgeting, and performance oversight.
Industry and Community Impact
- Contributes to research addressing food safety, aflatoxin exposure, sustainable fisheries, aquaculture, waste management, and environmental conservation.
- Supports postgraduate research training and mentorship, having supervised PhD and master's students to completion.
- Facilitation of scientific proposal-writing, research administration, and capacity-building workshops, strengthening research skills and collaboration among academics and researchers.
