CV
I aspire to seek a deeper scientific understanding of pathogens, hosts and habitats through bioinformatics and computational analysis of big biological and genomic data, and promoting open reproducible scientific research.
Basics
| Name | Gilbert Kibet-Rono |
| Label | Genomics & Bioinformatics Research Associate |
| kibet.gilbert.r@gmail.com | |
| Url | https://kibet-gilbert.github.io |
| Github | https://github.com/kibet-gilbert |
| Summary | I am a bioinformatician focusing on pathogen genomics: NGS sequencing, high-throughput analysis, and open, reproducible scientific research. |
Work
-
2020.08 - Present Kenya
Research Associate, Genomics & Bioinformatics
International Livestock Research Institute (ILRI)
Metagenomic, viral, bacterial, wastewater and single-cell NGS analysis.
- Library preparation and sequencing using Illumina and ONT platforms.
- Bioinformatics Pipeline development (Nextflow, Linux, git & GitHub)
- Bioinformatics Analysis in a local HPC cluster and using SLURM
- Data management, curation and submission to NCBI, GISAID.
- Statistical analysis with R & Python, visualization, manuscript drafting.
Volunteer
-
2020.01 - 2021.01 Remote
Fellow
ASAPbio
Co-developed a ten-hour open course on preprints in life sciences.
- Updated and Updloaded the content to ASAPbio's GitHub repo
- I advocate for open science and preprints among early-career researchers
Education
Awards
- 2019.08.01
The CODATA-RDA Research Data Science Travel Grant
H3ABioNet
Awarded to attend The CODATA-RDA Research Data Science Advanced Workshop on Bioinformatics at the Abdus Salam International Centre for Theoretical Physics (ICTP).
- 2019.11.01
H3ABionet ISCB–ASBCB Conference Travel Grant
H3ABioNet
Training and travel support for bioinformatics workshops in Africa.
- 2020.01.01
Publications
-
2023.11.01 Genomic Epidemiology of SARS-CoV-2 Lineages in Kenya, 2020–2022
Journal of Virology
Sequencing and analysis of over 1,200 SARS-CoV-2 genomes in East Africa revealing regional spread and variant emergence.
-
2022.07.01 Wastewater-based Surveillance of Pathogens and AMR Genes in Nairobi
bioRxiv
Developed a metagenomic pipeline and analyzed community-level prevalence of key antimicrobial resistance markers.
Skills
| Genomics | |
| NGS Library Prep | |
| Illumina | |
| ONT | |
| Variant Calling | |
| AMR Profiling |
| Bioinformatics | |
| Nextflow | |
| Snakemake | |
| Linux | |
| HPC | |
| MultiQC | |
| BLAST | |
| IQ-TREE |
| Data Science | |
| R | |
| ggplot2 | |
| Python | |
| pandas | |
| Plotly | |
| Altair |
Languages
| English | |
| Fluent |
| Swahili | |
| Native speaker |
Interests
| Pathogen Genomics | |
| SARS-CoV-2 | |
| AMR Surveillance | |
| Zoonotic Viruses | |
| Wastewater Analysis |
| Computational Reproducibility | |
| Open Science | |
| Pipelines | |
| GitHub Actions | |
| FAIR Data |
References
| Dr. Samuel Oyola | |
| Principal Scientist and Genomics lead at ILRI. |
Projects
- 2023.06 - Present
Wastewater Pathogen and AMR surveillance through shotgun metagenomics
I develop and maintain a Nextflow pipeline for processing 1000+ samples on Slurm HPC; includes QC, assembly, taxonomy, AMR profiling.
- Modular design with BioContainers
- MultiQC integration