“Pathogen genomics is no longer a luxury—it is now an essential tool for public health security in Africa.”
Dr. John Nkengasong (Founding Director, Africa CDC)
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About me
About me
Dr. Julien A. Nguinkal is a bioinformatician from Cameroon currently working at the Bernhard Nocht Institute for Tropical Medicine as a Senior Bioinformatician, where he supports the East African Community’s regional One Health program. His work focuses on using epidemiological and genomic data to better detect, track, and understand infectious diseases, especially in areas with limited laboratory resources.
He develops workflows and analysis pipelines that help identify disease-causing pathogens, monitor antimicrobial resistance, and respond quickly to outbreaks. He works closely with mobile and fixed laboratories in East and Central Africa and provides training to local scientists and public health professionals. Over the past few years, he has supported genomic research on diseases such as mpox, cholera, and Cryptosporidium.
Julien is passionate about applying data and technology to improve public health. He maintains a strong interest in strengthening public health genomics in Africa through collaborative research, training, and the integration of bioinformatics into routine surveillance frameworks.
Education
Education
Ph.D. Bioinformatics
Ph.D. Bioinformatics
University of Rostock | Rostock, Germany
(2017 - 2021)
Development of genomic resources and genetic tools for precision pikeperch farming through high-throughput sequencing and computational genomics
Advisors: Prof. Tom Goldammer, Prof. Olaf Wolkenhauer.
M.Sc. Bioinformatics
M.Sc. Bioinformatics
University of Jena | Jena, Germany
(2015 - 2017)
Biomarkers Prediction in Candida spp. Infections Based on Dual Time Course RNA-Seq
Advisors: Prof. Reinhard Guthke, Dr. Jörg Linde.
B.Sc. Bioinformatics & Genome Research
B.Sc. Bioinformatics & Genome Research
University of Bielefeld | Bielefeld, Germany
(2009 - 2013)
Development and Evaluation of Analysis Pipelines for High-Throughput Identification of Post-translationally Modified Proteins
Advisor: Prof. Alexander Goesmann
Certifications and Specialized Training
Bioinformatics Pipeline Development with Nextflow — ecSeq Bioinformatics, Leipzig, Germany — Oct. 2022
AI-assisted Data Analysis for Genomics — Berlin Institute of Medical Systems Biology (BIMSB) / MDC Platform for Bioinformatics and Omics Data Science, Berlin, Germany — March 2025
Technical Skillset
Technical Skillset
Genomics & Public Health Bioinformatics
Genomics & Public Health Bioinformatics
NGS Workflow Development
▸ End-to-end pipelines for Illumina, PacBio & Nanopore data
▸ De novo genome assembly, polishing, and annotation
▸ Reference-based mapping, variant calling, consensus building
▸ Quality control and contamination detectionAMR Surveillance & Genomic Epidemiology
▸ AMR gene prediction: AMRFinderPlus, ResFinder, CARD
▸ Phylogenetic reconstruction: IQ-TREE, RAxML, FastTree
▸ Transmission mapping: Microreact, Nextstrain, GrapeTree
▸ Metadata integration: iTOL, Pathogenwatch, ExcelR, R/tidyverse
▸ Genomic clustering and outbreak detection
Metagenomics & Microbiome Analysis
▸ Taxonomic classification: MetaPhlAn, Kraken2, Centrifuge, Kaiju
▸ Resistome and virulome profiling: RGI, AbritaMR, resfinder
▸ 16S/ITS pipelines: DADA2, QIIME2
▸ Environmental and wastewater metagenomics
▸ Visualization: Krona, Pavian, phyloseq, ggplot2
💻 Programming & Scripting
💻 Programming & Scripting
Toolbox:
Github Linux Latex RStudio VS Code
Quarto RMarkdown JupyterLab
HPC SLURM Nextflow Snakemake
Coding:
Python: Biopython, pandas, scipy, scikit-learn, matplotlib
R: Bioconductor, Knitr, caret, tidymodels, tidyverse, tidyomics, shiny
Misc: BASH, Julia, SQL, Terra
Publications
Publications
A selection of my publications is presented below.
📖Peer-Reviewed Journal Articles
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.
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.
📝Preprints
Nguinkal JA, Zoclanclounon YAB, Brunner RM, Goldammer T.
Haplotype-resolved telomere-to-telomere assembly of the African catfish (Clarias gariepinus). bioRxiv. 2023.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 Ag 2024 Abstract.
📘 Theses
Nguinkal JA. Development of genomic resources and tools for precision farming of pikeperch through high-throughput sequencing and computational genomics [Dissertation]. Rostock (DE): University of Rostock; 2021. Available from: https://doi.org/10.18453/rosdok_id00004127
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. 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.
Sholarly Track Record Board
Sholarly Track Record Board
📖Journal Articles & Preprints
Published: 16 (First-author: 8),
Corresponding: 6
Submitted/Under-review: 4
Preprints: 3
In-preparation: 5
🎤Conference & Seminars
Invited Talks: 4
Keynote Lectures: 1
Oral Presentations: 6
Seminar Talks: 10
Poster Presentations: 5
Travel Grants: 2
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