$ whoami

FARUK DUBE, PhD

Bioinformatics Scientist · SciLifeLab / Uppsala University

# Vaginal microbiome multi-omics · virome tool benchmarking · parasite drug-resistance genomics · reproducible pipelines

# Research since 2013 in Uganda, Sweden and the USA

[github] [email] [linkedin] [papers] [sciframe]

$ cat about.txt

CURRENT POSITION
Bioinformatics Scientist @ SciLifeLab / Uppsala University
FOCUS
Multi-omics of the vaginal microbiome in bacterial vaginosis; benchmarking tools that identify viruses in vaginal metagenomes; drug resistance in parasitic nematodes
APPROACH
End-to-end: raw sequencing data → statistical modelling → publication-ready outputs, with code and data released alongside the 2026 papers
8
peer-reviewed papers
5
first or co-first author
2
preprints (bioRxiv 2026)
1
submitted (PLOS ONE)

$ git log --since=2026-01-01

  1. release: hpc-digest, weekly Slack charts of a group's HPC compute and storage use
  2. submitted: Parascaris β-tubulin haplotypes and benzimidazole resistance (PLOS ONE); code & data public
  3. preprint: Benchmarking virus identification tools on vaginal metagenomes, bioRxiv
  4. release: C. elegans Atlas, an interactive 3D anatomy explorer
  5. paper: Multi-omics of bacterial vaginosis (co-first author), npj Women's Health
  6. preprint: PLAGUE, improved-confidence plasmid reconstruction from short-read assemblies, bioRxiv
  7. analysis: MetaPhlAn 4 vs VIRGO2 for Gardnerella species resolution

$ git log --oneline --graph

* 2024–now Bioinformatics Scientist — SciLifeLab / Uppsala University & SLU # Multi-omics, ML models, metagenomics, pangenomics, 5+ concurrent projects
* 2023 Visiting Scholar — Northwestern University, USA # 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
* 2018–2019 Research Engineer — Swedish Veterinary Agency # NGS pipelines, antimicrobial resistance surveillance
* 2016–2018 MSc Infection Biology — Uppsala University # Infectious pathogens and their biology
* 2013–2016 Lab Technologist — Makerere University / Walter Reed Project, Uganda # USAID pandemic surveillance, data coordination across Africa

$ ./list_skills.sh

→ Genomics & Multi-Omics

WGS · RNA-seq · Metagenomics · Viromics
Metabolomics · GWAS/QTL · Pangenomics
PacBio HiFi amplicon haplotyping

→ Pipeline Engineering

Nextflow DSL2 · nf-core
Docker/Singularity · SLURM/HPC · GPU

→ Machine Learning & AI

scikit-learn · PyTorch
CNN / LSTM / Transformers / GNN

→ Programming & Data

R · Python · Bash · SQL
JavaScript · Django · REST APIs · Git

→ Data Visualization

ggplot2 · ggtree · matplotlib
seaborn · publication figures

→ Multi-Omics Integration

DIABLO · MOFA2 · DESeq2
QIIME2 · phyloseq · Kraken2 · MetaPhlAn

$ find ~/projects/ -type d

$ ls ./microbiome-and-virome/

* Vaginal VirBench

bioRxiv 2026

Benchmarking virus identification tools on vaginal metagenomes

  • Tests 14 tools across five evaluations: controlled genome fragments, simulated viral spike-ins, real assemblies, RCA-enriched viromes, and an independent cohort
  • Built on 13 assemblies from South African adolescents; the tool ranking held in an independent 30-sample Swedish cohort, MiTCH (Spearman ρ = 0.952)
  • geNomad and VIBRANT led with opposite errors: VIBRANT made 8 false viral calls and found 22% of viral contigs; geNomad made 201 and found 33%
PythonNextflowGPUcontainers
→ repo → preprint

* MiTCH: Multi-Omics of Bacterial Vaginosis

npj Women's Health 2026

How vaginal microbes and metabolites relate to bacterial vaginosis (co-first author)

  • Integrates shotgun metagenomics and targeted LC-MS metabolomics from 111 Swedish women (29 with BV, 82 controls) using DIABLO and MOFA2
  • Builds a Gardnerella pangenome from 61 metagenome-assembled genomes and links genes to metabolites
  • Analysis code, processed data, figures and supplementary tables are public; reads on ENA (PRJEB108308)
RDIABLOMOFA2MetaPhlAn 4LC-MS
→ repo → paper

* MetaPhlAn 4 vs VIRGO2 for Gardnerella

analysis

How two reference databases represent Gardnerella species

  • MetaPhlAn 4 co-bins G. piotii with G. pickettii and G. swidsinskii with G. leopoldii; its G. vaginalis row sums seven GTDB species clusters
  • VIRGO2 labels piotii, swidsinskii and leopoldii separately
  • A database-content comparison, not a read-level accuracy test; reproduces in about a minute from precomputed outputs
PythonMetaPhlAn 4VIRGO2GTDB
→ repo

$ ls ./parasite-drug-resistance/

* Parascaris β-Tubulin & Benzimidazole Resistance

submitted

How β-tubulin genes differ between resistant and susceptible P. univalens

  • Sequences all seven β-tubulin genes as long PacBio HiFi amplicons from pooled eggs of a resistant and a susceptible farm, resolving 243 haplotypes
  • Nextflow DSL2 pipeline from HiFi reads to haplotypes, variants and identity matrices (pbaa, pbmm2, FreeBayes, bcftools)
  • R code regenerates every figure and table, then checks them against the numbers in the manuscript; reads on ENA (PRJEB102621)
Nextflow DSL2PacBio HiFiFreeBayesR
→ repo → Zenodo

* Gene Co-Expression Networks in P. univalens

PLOS ONE 2024

Tissue-specific response to ivermectin

  • RNA-seq of the anterior end and intestine of 28 adult worms exposed to ivermectin in vitro
  • Consensus network from 10 inference methods in Seidr, with Leiden module detection
  • Found seven modules associated with ivermectin response and 219 core genes
RSeidrLeidenDESeq2
→ repo → paper

* Ivermectin Response in C. elegans

PLOS ONE 2023

Transcriptomics integrated with abamectin QTL

  • Nextflow RNA-seq workflow: QC, rRNA removal, trimming and Salmon quantification, ready for DESeq2 or edgeR
  • Manhattan plots of GWA mappings after ivermectin exposure (AndersenLab data), with a rug plot of genes implicated in resistance
NextflowSalmonRGWAS/QTL
→ RNA-seq pipeline → mapping plots → paper

$ ls ./pipelines/

* PLAGUE

bioRxiv 2026

PLasmid Assembly Genetic Unit Evaluator: improved-confidence plasmid reconstruction from short-read assemblies

  • Post-processes MOB-suite output to cut false-positive plasmid calls from fragmented, low-coverage assemblies
  • Checks circularity, reads spanning a candidate's two ends, and total coverage; optional plasmid copy-number estimates
  • Screens plasmids for antimicrobial-resistance genes with Abricate
Nextflow DSL2MOB-suiteAbricateSingularity/Docker
→ repo → preprint

* StagNF

in development

A Nextflow reimplementation of part of the StaG-mwc metagenomics workflow

  • Quality control (fastp), host removal (Bowtie2), taxonomic profiling (MetaPhlAn) and a MultiQC report
  • Profiles for UPPMAX, generic SLURM and SGE clusters
NextflowMetaPhlAnHPC
→ repo

$ ls ./tools-and-web-apps/

* PhDplanner

live

A free toolkit for doctoral students in Sweden

  • Courses360: searchable index of 1,000+ doctoral courses from over half of Sweden's universities
  • Defence Planner: turns a defence date into a milestone timeline with email reminders
  • LinkedPapers: maps how publications connect through citations and semantic similarity from one DOI
  • Sciframe: scientific figure editor (below)
Web App
→ phdplanner.com

* Sciframe

live

A free browser editor for scientific figures, slides, posters and graphical abstracts

  • Built from 32,000+ open-licensed illustrations, PDB protein structures and PubChem molecules
  • Runs in the browser with no installation; part of the PhDplanner toolkit
Web AppPDBPubChem
→ open Sciframe

* C. elegans Atlas

live

An interactive 3D explorer of C. elegans anatomy

  • Two views: whole body (Virtual Worm / OpenWorm) and neural EM (NeuroSC meshes)
  • Search structures, then inspect, focus or isolate them; spread anatomy apart to see it clearly
JavaScriptWebGLVite
→ explore the atlas → repo

* hpc-digest

MIT

Weekly Slack digests of a research group's compute and storage use on an HPC cluster

  • Compute: month-to-date core-hours per user per Slurm account, used vs allocated, and whether usage is ahead of the month's pace
  • Storage: CephFS quota gauges for files and bytes per project, plus who holds the files and who holds the bytes
  • Runs as self-resubmitting Slurm jobs and needs no admin rights
PythonSlurmCephFSSlack API
→ repo

$ grep -r "Dube F" ~/publications/ | sort -r

  1. 2026
    Dube F, Happel A-U, Jaspan HB, Warchavchik Hugerth L. Benchmarking virus identification tools on vaginal metagenomes. bioRxiv (preprint) first author
    → DOI → code
  2. 2026
    Tydén E, Martin F, Dube F. Novel β-tubulin mutations and haplotype restructuring associated with benzimidazole resistance in Parascaris univalens. PLOS ONE (submitted)
    → code
  3. 2026
    Shabana H*, Dube F*, et al. Multi-omics investigation of metabolomic and microbial features in bacterial vaginosis. npj Women's Health 4:26 *co-first author
    → DOI → code
  4. 2026
    Kozubal K, Dube F, et al. PLAGUE: Improved confidence plasmid reconstruction from short read assemblies. bioRxiv (preprint)
    → DOI → code
  5. 2025
    Adero J, ..., Dube F, et al. Virus-specific defense responses in sweetpotato: transcriptomic insights into resistance and susceptibility to SPFMV, SPCSV, and SPVD. Biology 14(11):1541
    → DOI
  6. 2024
    Dube F, Delhomme N, et al. Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure. PLOS ONE 19(2):e0298039 first author
    → DOI → code
  7. 2023
    Valečková E, ..., Dube F, et al. Intestinal colonization with Campylobacter jejuni affects broiler gut microbiota composition but is not inhibited by daily intake of Lactiplantibacillus plantarum. Front Microbiol 14:1205797
    → DOI
  8. 2023
    Dube F, Hinas A, et al. Transcriptomics of ivermectin response in Caenorhabditis elegans: integrating abamectin quantitative trait loci and comparison to the ivermectin-exposed DA1316 strain. PLOS ONE 18(5):e0285262 first author
    → DOI → code
  9. 2022
    Dube F, Hinas A, et al. Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro. Parasit Vectors 15(1):158 first author
    → DOI
  10. 2021
    Dube F, Söderlund R, et al. Benzylpenicillin-producing Trichophyton erinacei and methicillin resistant Staphylococcus aureus carrying the mecC gene on European hedgehogs – a pilot-study. BMC Microbiol 21(1):212 first author
    → DOI
  11. 2020
    Martin F, Dube F, et al. Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole. Parasit Vectors 13(1):342
    → DOI

$ cat contact_info.txt

emailfarukmeddie@gmail.com
githubgithub.com/ruqse
linkedinlinkedin.com/in/farukdube
instagraminstagram.com/farukdube

# Open to: research collaborations · consulting · microbiomes, reproducible workflows and research tools