Battistuzzi Lab · Oakland University · Michigan, USA
Microbial pangenomics · phylogenomics · molecular clocks · astrobiology · reproducible bioinformatics
I am a doctoral researcher in the Biological and Biomedical Sciences PhD program at Oakland University, working in the Battistuzzi Lab. My research asks how microbial genomes diversify across populations and deep evolutionary time, and how analytical choices in pangenomics influence the evolutionary histories we reconstruct.
My current work combines population-scale pangenomics, core and accessory genome analysis, phylogenomics, and molecular-clock inference. I am particularly interested in connecting genome variation with the microbial Tree of Life and with questions about ancient and extreme life that are relevant to astrobiology.
I also build reproducible research software and teaching tools so that genome-scale analyses are easier to inspect, test, and reuse.
A curated, literature-backed guide to microbial pangenomics, covering genome quality control, annotation, gene-cluster and graph pangenomes, downstream analysis, visualization, databases, reproducible workflows, and an annotated reading list.
Explore the resource → · Visit my research portfolio →
My doctoral research examines how pangenome construction choices, core-gene definitions, taxonomic sampling, and genome diversity affect microbial phylogenetic reconstruction. The broader goal is to connect population-level genome variation with deeper evolutionary relationships across prokaryotes.
I use phylogenomic alignments and divergence-time methods to study evolutionary timing across microbial lineages. This includes evaluating how genome sampling and marker selection influence time-calibrated evolutionary hypotheses.
A parallel research direction explores how microbial evolutionary history, extremophile biology, and genomic signatures can inform questions about ancient life, environmental resilience, and biosignature interpretation.
These projects form the main public software ecosystem I am developing around microbial comparative genomics.
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A genome cohort curation toolkit for NCBI microbial assemblies. It supports genome retrieval, GCA/GCF assembly-record reconciliation, metadata extraction, quality filtering, and optional close-genome relatedness checks. Focus: genome acquisition and curation |
An evidence-aware framework for microbial species delineation using ANI, alignment fraction, genome quality, GTDB taxonomic context, dereplication, and phylogenomic evidence. Focus: species-boundary evidence |
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A reproducible Nextflow workflow for microbial gene-family pangenomics and core-genome phylogenomics. Roary is the default pangenome engine, with Panaroo available as an alternative route. Focus: pangenome to phylogeny |
An ordination workbench for microbial pangenome presence/absence matrices using PCA, Jaccard PCoA, metadata-aware visualization, and gene-cluster loadings. Focus: genome-level gene-content structure |
| Project | Purpose |
|---|---|
| PanGenome Openness Estimator | Heaps' law, genome accumulation curves, and permutation-based pangenome openness analysis |
| roary-pangenome-figure-atlas | Static and interactive visualization of Roary gene presence/absence data |
| FORGE Slurm Lab | Interactive learning resources for Slurm, modules, Conda, and HPC workflows |
| BLab Slurm Builder | A lightweight helper for composing Slurm job scripts |
| Rosalind Bioinformatics | Algorithmic bioinformatics problem solving and reproducible code examples |
| Awesome Microbial Pangenomics | Curated literature, software, data resources, and learning guidance for microbial pangenomics |
AbGradCon 2026, oral presentation accepted
Reconstructing the Microbial Tree of Life Using Population-Scale Pangenome Phylogenomics
University of Arizona, Tucson · September 14-18, 2026
AbSciCon 2026, poster presentation
Reconstructing the Microbial Tree of Life Using Population-Scale Pangenome Phylogenomics
Madison, Wisconsin · May 18, 2026
Graduate Research Conference, Oakland University
Oral presentation on population-scale pangenome phylogenomics and microbial Tree of Life reconstruction
Provost Graduate Student Research Award, Oakland University, Winter 2026
$1,500 research award for Assessing the Impact of Population-Scale Pangenome Choices on Microbial Phylogenies
Sigma Xi Travel Award, 2026
Travel support for presenting research at AbSciCon 2026
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Bilal, M., & Battistuzzi, F. U. (2026). Pangenomes: Unveiling Genetic Diversity Across Populations and Beyond. Encyclopedia of Evolutionary Biology, 2nd edition, Vol. 2, 294-306. Elsevier.
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Kanwal, M., Basheer, A., Bilal, M., et al. (2024). In silico vaccine design for Yersinia enterocolitica: A comprehensive approach to enhanced immunogenicity, efficacy, and protection. International Immunopharmacology, 143, 113241.
| Area | Tools and methods |
|---|---|
| Pangenomics | Roary, Panaroo, PIRATE, PPanGGOLiN, gene presence/absence analysis |
| Phylogenomics | IQ-TREE, MAFFT, MUSCLE, core-gene concatenation, model selection |
| Molecular clocks | MCMCTree, RelTime, divergence-time calibration |
| Genome comparison | FastANI, GTDB-Tk, dRep, CheckM2 |
| Programming | Python, R, Bash, Linux |
| Reproducible workflows | Nextflow, Snakemake, Conda, GitHub Actions |
| HPC | Slurm, array jobs, large-scale genome analysis |
| Visualization | Matplotlib, Seaborn, Plotly, ggplot2, ggtree, ComplexHeatmap, Shiny, Gnuplot, iTOL, interactive HTML reporting |
I serve as a graduate assistant at Oakland University and have taught laboratory courses in genetics and introductory biology. My teaching emphasizes experimental reasoning, clear data interpretation, and reproducible computational analysis.
I also serve as President of the Association of Graduate and Professional Students at Oakland University for 2026-27 and have contributed to graduate training activities through the NSF NRT DAMOS program in data analytics and multi-omics science.
PhD, Biological and Biomedical Sciences
Oakland University, Michigan, USA · in progress
MPhil, Biotechnology
University of Sargodha, Pakistan · 2021-2023
BS, Biotechnology
University of Sargodha, Pakistan · 2017-2021
microbial evolution pangenomics phylogenomics molecular clocks Tree of Life extremophiles astrobiology comparative genomics reproducible bioinformatics HPC
I am interested in collaborations involving microbial pangenomics, genome evolution, phylogenomics, molecular clocks, astrobiology, and reproducible computational biology.
Email: mbilal@oakland.edu
Google Scholar: scholar.google.com/citations?user=nQycrykAAAAJ
LinkedIn: linkedin.com/in/itsmbilal88
Portfolio: mbilal-ou.github.io
GitHub: github.com/mbilal-OU
Profile design evidence: benchmark and decisions
Live public contribution calendar. The squares update as new qualifying GitHub contributions are recorded.