$ cat about.txt
CURRENT POSITION
Bioinformatics Scientist @ SciLifeLab / Uppsala University
Bioinformatics Scientist @ SciLifeLab / Uppsala University
FOCUS
Scalable pipelines and ML frameworks for multi-omics & pathogen genomics
Scalable pipelines and ML frameworks for multi-omics & pathogen genomics
APPROACH
End-to-end: raw sequencing data → statistical modelling → publication-ready outputs
End-to-end: raw sequencing data → statistical modelling → publication-ready outputs
IMPACT
7 papers · 500+ samples processed · 15+ researchers trained · 3 continents
7 papers · 500+ samples processed · 15+ researchers trained · 3 continents
$ git log --oneline --graph
* 2024-now Bioinformatics Scientist — SciLifeLab / Uppsala University & SLU
# Multi-omics, ML models, metagenomics, pangenomics, 5+ concurrent projects
# Multi-omics, ML models, metagenomics, pangenomics, 5+ concurrent projects
* 2023 Visiting Scholar — Northwestern University, USA
# GWAS & QTL pipelines for drug resistance genomics
# GWAS & QTL pipelines for drug resistance genomics
* 2019-2024 PhD Biomedical Sciences — Swedish University of Agricultural Sciences
# Bioinformatics & drug resistance in parasites, 4 first-author papers
# Bioinformatics & drug resistance in parasites, 4 first-author papers
* 2018-2019 Research Engineer — Swedish Veterinary Agency
# NGS pipelines, antimicrobial resistance surveillance
# NGS pipelines, antimicrobial resistance surveillance
* 2016-2018 MSc Infection Biology — Uppsala University
# Infectious pathogens and their biology
# Infectious pathogens and their biology
* 2013-2016 Lab Technologist — Makerere University / Walter Reed Project, Uganda
# USAID pandemic surveillance, data coordination across Africa
# USAID pandemic surveillance, data coordination across Africa
$ ./list_skills.sh
→ Genomics & Multi-Omics
→ Pipeline Engineering
Nextflow DSL2 · nf-core
Docker/Singularity · SLURM/HPC · GPU
Docker/Singularity · SLURM/HPC · GPU
→ Machine Learning & AI
scikit-learn · PyTorch
CNN / LSTM / Transformers / GNN
CNN / LSTM / Transformers / GNN
→ Programming & Data
R · Python · Bash · SQL
Django · REST APIs · Git
Django · REST APIs · Git
→ Data Visualization
ggplot2 · ggtree · matplotlib
seaborn · publication figures
seaborn · publication figures
→ Multi-Omics Integration
DIABLO · MOFA2 · DESeq2
QIIME2 · phyloseq · Kraken2
QIIME2 · phyloseq · Kraken2
$ find ~/projects/ -type d
$ ls ./research-pipelines/
* Viral Benchmarking Pipeline
Modular pipeline integrating deep learning models (CNN, LSTM, Transformers, GNN) with GPU-accelerated inference for comprehensive virus identification benchmarking.
* High-Throughput Transcriptomic Pipeline
Automated differential expression analysis with integrated QC for transcriptomic profiling across multiple experimental systems — sweet potato viral challenge and cell line parasite response.
* Virome-Microbiome Analysis Workflow
Automated pipelines for public health surveillance integrating viral and microbial community profiling with external data sources.
* GWAS Pipeline for Drug Resistance
Association mapping and QTL analysis workflows with reproducible visualization for genomic studies of drug resistance in parasites.
* Gene Co-Expression Network Analysis
Consensus network construction using 10 inference algorithms with Leiden module detection, identifying core responsive genes across parasitic, bacterial, and viral pathogen datasets.
$ ls ./ml-and-multi-omics/
* Multi-Omics Microbiome Platform
Integrated shotgun metagenomics, targeted LC-MS metabolomics, and Gardnerella pangenomics using supervised and unsupervised multi-omics methods for community-level characterization of bacterial vaginosis.
* ML Models for Vaginal Microbiome
Computational tools for biomarker identification and clinical prediction from microbiome data using machine learning classification models.
$ ls ./web-apps/
* PhD Planner — phdplanner.com
Courses360: Search and recommendations across 700+ courses from 16 Swedish universities.
DefencePlanner: Milestone tracking with automated email reminders for PhD defence planning.
LinkedPapers: Interactive citation graph, paper search, and reading lists.
DefencePlanner: Milestone tracking with automated email reminders for PhD defence planning.
LinkedPapers: Interactive citation graph, paper search, and reading lists.
$ grep -r "Dube F" ~/publications/
2025 Adero J, ..., Dube F, et al. Virus-Specific Defense Responses in Sweetpotato. Biology, 14(11):1541.
→ DOI
2024 Dube F et al. Gene co-expression network analysis in P. univalens following ivermectin exposure. PLoS One, 19(2):e0298039.
→ DOI
2023 Valeckova E, ..., Dube F, et al. Intestinal colonization with C. jejuni affects broiler gut microbiota. Front Microbiol, 14:1205797.
→ DOI
2023 Dube F et al. Transcriptomics of ivermectin response in C. elegans: integrative QTL mapping. PLoS One, 18(5):e0285262.
→ DOI
2022 Dube F et al. Ivermectin-induced gene expression changes in P. univalens and C. elegans. Parasit Vectors, 15(1):158.
→ DOI
2021 Dube F et al. Benzylpenicillin-producing T. erinacei and MRSA on European hedgehogs. BMC Microbiol, 21(1):212.
→ DOI
2020 Martin F, Dube F, et al. Transcriptional responses in P. univalens after anthelminthic exposure. Parasit Vectors, 13(1):342.
→ DOI
# +3 manuscripts in preparation
$ cat contact_info.txt
→ Email: farukmeddie@gmail.com
→ GitHub: github.com/ruqse
→ LinkedIn: linkedin.com/in/farukdube
→ Instagram: instagram.com/farukdube
# Open to: Research collaborations · Consulting opportunities · Interesting problems
Metabolomics · GWAS/QTL · Pangenomics