Publications
Publications
📖 Peer-Reviewed Journal Articles
Katee SM, et al. (incl. Nguinkal JA). Expanding African biodiversity genomics to meet global biodiversity goals. Nature Reviews Biodiversity. 2026 Mar 23:1-5.
Nguinkal JA, Melo AM, Nzoyikorera N, Jurgen M, Affara M, Gehre F. Evaluation of optimal pooling strategies for Mpox virus genomic surveillance using the Illumina Viral Surveillance Panel on the iSeq100 platform in outbreak settings. BMJ Public Health. 2026 Mar 10;4(1).
Mapunda LA, Beyanga M, Moremi N, Hakizimana JN, Kamori D, Chacha A, Mgimba E, Mrosso D, Mwafulango AE, Mushumbusi J, Ndunguru F. , Nguinkal JA, et.al Genomic Insights into Marburg Virus Strains from 2023 and 2025 Outbreaks in Kagera, Tanzania. Emerging infectious diseases.;32(1).
Oludele H, Shardow AL, Apaflo M, Ibekwe J, Baeti P, Nguinkal JA, Awe O. Genomic landscape of HIV-1 drug resistance in Africa: a comprehensive analysis of mutation trends, subtype diversity, and therapeutic implications (1990–2024). Briefings in Bioinformatics. 2025 Dec 12;26(Suppl 1):i14.
Molina A, Ihorimbere T, Nzoyikorera N, Nambozo EJ, Namubiru S, Nabadda S, Pimundu G, Githii SM, Nykwe GA, Abias AG, Msigwa FL., Nguinkal JA, et.al. Strategies and challenges in containing antimicrobial resistance in East Africa: a focus on laboratory-based surveillance. Antimicrobial Resistance & Infection Control. 2025 Nov 7;14(1):134.
Trojnacki A, Nguinkal JA, May J, Rainer K, Duscher GG, Winkelmayer L, Ungureanu A, Jaho E, Vlachostergiou A, Suciu G, Stalidi C. Assessing rapid response mobile laboratory (RRML) capacities in Europe and Africa to improve One Health disease surveillance activities and pandemic preparedness across two continents. One Health Outlook. 2025 Oct 23;7(1):53. https://doi.org/10.1186/s42522-025-00180-6
Nguinkal JA*, Gehre F, Lagu HI, Achol E, Nzeyimana E, Kiiru JN, Nyandwi J, Dumo GW, Moremi N, Nabadda SN, Mukagatare I. A Capacity Strengthening Model towards Self-reliant and Sustainable One-Health Workforce in six East African Community Partner States. Frontiers in Public Health. 2025 Jul 24;13:1636817. https://doi.org/10.3389/fpubh.2025.1636817
Sone B, Ambe LA, Ampama MN, Ajohkoh C, Che D, Nguinkal JA, Taubert A, Hermosilla C, Kamena F. Prevalence and Molecular Characterization of Cryptosporidium Species in Diarrheic Children in Cameroon. Pathogens. 2025; 14(3):287.https://pmc.ncbi.nlm.nih.gov/articles/PMC11945035/pdf/pathogens-14-00287.pdf
Nguinkal JA*, Zoclanclounon YAB, Molina A, Roba A, Nyakio NM, Lokamar PN, Nzoyikorera N, Ihorimbere T, Nyandwi J, Aguer MA, et al. Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community. BMC Public Health. 2024; 24(1):1500.https://link.springer.com/article/10.1186/s12889-024-18990-0
Nguinkal JA, Zoclanclounon YAB, Brunner RM, Chen Y, Goldammer T.
Haplotype-resolved and near-T2T genome assembly of the African catfish (Clarias gariepinus). Scientific Data. 2024; 11(1):1095.https://www.nature.com/articles/s41597-024-03906-9
Gehre F, Nzeyimana E, Lagu HI, Achol E, Nguinkal JA, et al.
Rapid regional mobile laboratory response and genomic monkeypox virus (MPXV) surveillance in seven East African Community partner states. Eurosurveillance. 2024; 29(35):2400541.https://pmc.ncbi.nlm.nih.gov/articles/PMC11484336/
Kanyerezi S, Guerfali FZ, Anzaku AA, Babaleye OA, Calvert-Joshua T, Nguinkal JA, et al. Wastewater metagenomics in Africa: Opportunities and challenges. PLOS Global Public Health. 2024; 4(12):e0004044.https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0004044
Clols-Fuentes J, Nguinkal JA, Unger P, Kreikemeyer B, Palm HW.
Bacterial Communities From Two Freshwater Aquaculture Systems in Northern Germany. Environmental Microbiology Reports. 2024; 16(6):e70062.
Clols-Fuentes J, Nguinkal JA, Unger P, Kreikemeyer B, Palm HW.
Bacterial community in African catfish (Clarias gariepinus) recirculating aquaculture systems under different stocking densities. Frontiers in Marine Science. 2023; 10:10.https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2023.1073250/full
Hildebrand MC, Rebl A, Nguinkal JA, Palm HW, Baßmann B.
Effects of Fe-DTPA on health and welfare of the African catfish (Clarias gariepinus). Water. 2023; 15(2):299.
Verleih M, Visnovska T, Nguinkal JA, Rebl A, Goldammer T, Andreassen R.
Discovery and Characterization of Conserved and Novel miRNAs in Pikeperch (Sander lucioperca). Int J Mol Sci. 2023; 25(1):189.https://www.mdpi.com/1422-0067/25/1/189
Djim-Adjim-Ngana K, Mbiakop BW, Oumar LA, Munshili Njifon HL, Tchinda Fossi C, Enyegue EL, Mouiche Mouliom MM, Fodouop Chegaing SP, Deweerdt L, Yanou NN, and Nguinkal JA*. Phenotypic characterization and epidemiology of extended-spectrum β-lactamase-producing Enterobacteriaceae strains from urinary tract infections in Garoua, Cameroon. Frontiers in Public Health. 2023 Jun 29;11:1187934. https://doi.org/10.3389/fpubh.2023.1187934
Nguinkal JA*, Verleih M, de Los Ríos-Pérez L, Brunner RM, Sahm A, Bej S, Rebl A, Goldammer T.
Comprehensive characterization of multitissue expression landscape, co-expression networks and positive selection in pikeperch. Cells. 2021; 10(9):2289.https://www.mdpi.com/2073-4409/10/9/2289
Schäfer N, Kaya Y, Rebl H, Stüeken M, Rebl A, Nguinkal JA, et al.
Characterization of stress and development key genes of pikeperch in vivo and in vitro. Fish Physiol Biochem. 2021; 47:515–532.https://link.springer.com/article/10.1007/s10695-021-00929-6
de Los Ríos-Pérez L, Nguinkal JA, Verleih M, Rebl A, Brunner RM, et al.
Ultra-high density SNP-based linkage map for chromosome-scale pikeperch genome assembly. Scientific Reports. 2020; 10(1):22335.
https://www.nature.com/articles/s41598-020-79358-z
Nguinkal JA*, Brunner RM, Verleih M, Rebl A, de Los Ríos-Pérez L, Schäfer N, Hadlich F, Stüeken M, Wittenburg D, Goldammer T.
The first highly contiguous genome assembly of pikeperch (Sander lucioperca). Genes. 2019; 10(9):708.
https://www.mdpi.com/2073-4425/10/9/708
📝 Preprints
Nguinkal JA, Zoclanclounon YAB, Brunner RM, Goldammer T.
Haplotype-resolved telomere-to-telomere assembly of the African catfish (Clarias gariepinus). bioRxiv. 2023.
El Allali A, Nguinkal JA, et al. Enabling Africa’s implementation of the Kunming-Montreal Global Biodiversity Framework through the African digital sequence information data bank. OSF.
📘 Theses
PhD Thesis
Nguinkal JA. Development of genomic resources and tools for precision farming of pikeperch through high-throughput sequencing and computational genomics [dissertation]. Rostock (DE): Universität Rostock; 2021. Available from: https://doi.org/10.18453/rosdok_id00004127
Msc Thesis
Nguinkal JA. Biomarkers prediction in Candida spp. infection based on RNA expression data [Master Thesis]. Jena (DE): University of Jena; 2017.
🎤 Conference Abstracts & Proceedings
🗣️ Invited Talk
Nguinkal JA. Uncovering Host Contexts of ARGs and MGEs Using Hi-C Assisted Metagenomics.
Seminar Talk, Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, South Africa, June 2025.
🗣️ Invited Talk
Nguinkal JA. Big Data Challenges in the Genomics Era: Handling Genomics Data with AI Technologies.
Workshop on AI, Bioinformatics & Big Data, University of Douala, Cameroon, June 2024.
📌 Poster Presentation
Nguinkal JA. Enhancing One Health Workforce Capabilities in the EAC Mobile Lab Network with Bioinformatics Training for Public Health Professionals 8th World One Health Congress, Cape Town, South Africa, Sept 2024.
Nguinkal JA, Zoclanclounon YAB, Brunner RM, Chen Y, Goldammer T.
The African Catfish (Clarias Gariepinus) Reference Genome – A Near Telomere-To-Telomere De Novo Chromosome-Level Assembly. AGBT 2024, Aug 2024.
🎤 Oral Presentation
Goldammer T, Nguinkal JA, Zoclanclounon YAB, Chen Y, Brunner RM.
The African Catfish (Clarias gariepinus) Reference Genome – A Near T2T Chromosome-Level Assembly.
AGBT Ag Meeting, Phoenix, Arizona, Feb. 2024.
📌 Poster Presentation
Nguinkal JA. Pathogen Data Crisis Amidst Communicable Diseases Threats: Strengthening Pathogen Genomics for Surveillance in the East African Community.
6th Biennial ASLM Conference, Cape Town, Dec 2023.
🐟 Oral/Poster Presentation
Nguinkal JA. Towards the Reference Genome Sequence and Annotation of Sander lucioperca (Pike-perch)
13th International Congress on the Biology of Fish - ICBF 2018, Calgary, Canada, 2018.
🎖️Grants & Awards
Early Career Scientist Grant Awards – 8th World One Health Congress, Sept. 2024, Cape Town, South Africa. Awarded a competitive travel grant worth €3000 for early career researchers to attend and present on Enhancing One Health Workforce Capabilities in the EAC Mobile Lab Network with Bioinformatics Training for Public Health Professionals at the 8th One Health Congress (2024). Contributed to panel discussions on "Unleashing the Power of Genomics for One Health".
🏫 Academic Service – Peer Review Activities
Reviewer, Scientific Reports (Nature Portfolio) - Since 2024
Reviewer, Scientific Data (Nature Portfolio) - Since 2024
Reviewer, BMJ Global Health - Since 2025