Nabil-Fareed Alikhan, PhD - Curriculum Vitae
🎓 Education
PhD in Microbiology, University of Queensland, Australia (2010 – 2015)
Thesis: "Escherichia coli virulence: a genomic approach"
Primary Supervisor: Scott Beatson
BSc (Hons, 1st Class) in Microbiology, University of Queensland (2009)
Thesis: "Comparative genome analysis of Escherichia coli VR50"
BSc in Biochemistry & Bachelor of Information Technology, University of Queensland (2004-2008)
🎤 Invited Speaker
- Irish Computational Biology and Genomics Symposium 2022 - National University of Ireland, Galway (1-2 Dec 2022)
- ESCMID: Moving beyond single species outbreaks - Virtual (7 Jul 2022)
- 13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII) - Bath, UK (14-17 Sept 2022)
- Understanding Drivers of Antimicrobial Resistance in the Food Chain - Guangzhou, China (19 Nov 2019)
📢 Selected Oral Presentations
- Platforms for genomic surveillance of FBD pathogens - Africa CDC Food borne pathogen group, Virtual (16 Jun 2022)
- Bioinformatics Gotchas - 3rd ARTICNetwork and CLIMB-BIG-DATA joint workshop, Virtual (13-14 Jan 2022)
- SARS-CoV-2 sequencing in East Anglia - COG-Together event, Cambridge, UK (14 Oct 2021)
- Building better infrastructure for a brave new world - Balti and Bioinformatics, Birmingham, UK (14 Nov 2019)
- Deciphering ancient microbes with modern population genomic databases - 8th International Symposium on Biomolecular Archaeology, Max Planck Institute, Jena, Germany (18-21 Sept 2018)
- Understanding genomic landscapes in EnteroBase with cgMLST & GrapeTree - QI Keynote Lecture, Quadram Institute, Norwich, UK (9 Aug 2018)
- EnteroBase: Bacterial population genomics in the era of big-data - ENA facilities Day 2017, EBI, Hinxton, UK (25 Oct 2017)
- Scalable and user-friendly workflows for Molecular Epidemiology using EnteroBase - 11th International Meeting on Microbial Epidemiological Markers, Estoril, Portugal (9-12 Mar 2016)
- EnteroBase: A Powerful, User-Friendly Online Resource - 1st ASM Conference on Rapid NGS Bioinformatic Pipelines, Washington DC, USA (24-27 Sept 2015)
🧠 Skills
Bioinformatics
De novo assembly, population genomics, phylogenetics (IQTree, RAxML), statistics (Python, R), and Linux systems.
Software Development
Full-stack development in Python (Flask), JavaScript, Java, Bash & Perl.
Created and maintained EnteroBase (>800 k genomes, 1.6 k+ users), GrapeTree, and BRIG.
Experience with HPC & Nextflow workflows, databases (SQL), HTML & PHP.
Leadership & Collaboration
Project leadership, strategic grant planning, cross-institute training, and international coordination through PHA4GE and COG-UK.
💡 Grants
- QIB Cloud Renewal – £1.49 M (BBSRC PI)
- RonaQC SARS-CoV-2 QC Tool – £40 k (UKRI/COG-UK, Co-PI)
- Microbial Bioinformatics Hackathon 2022 – £10 k (BBSRC, Co-PI)
- CLIMB-BIG-DATA; A Cloud Infrastructure for Big-Data Microbial Bioinformatics - £1.9 M (MRC, Inherited on appointment as Interim Head of Informatics)
- UK Food Safety Research Network - £1.6 M (BBSRC, Inherited on appointment as Interim Head of Informatics)
📚 Publications
H-index 28 | > 11369 citations
Full, searchable publication list: happykhan.com/publications
Key works include:
- Zhou et al. (2020) GrapeTree: visualization of genomic relationships among 100 k pathogens. Genome Research
- Alikhan et al. (2011) BRIG: BLAST Ring Image Generator. BMC Genomics
- Achtman et al. (2021) Genomic diversity of Salmonella enterica – 10 K Genomes Project. Wellcome Open Res.
🎤 Selected Talks
- Keynote, Irish Computational Biology & Genomics Symposium (2022)
- IMMEM XIII, Bath (2022) – Microbial epidemiology & bioinformatics
- Balti & Bioinformatics, Birmingham (2019) – Infrastructure for open genomics
🧩 Service & Teaching
- Board Member, Microbes Microbiomes & Bioinformatics DTP (2021–)
- PHA4GE Infrastructure Working Group (2019–)
- Treasurer, QIB Postdoc Society (2020–2023)
- Internal grant reviewer, Quadram Institute (2019–)
- Supervisor for PhD and MRes projects (2015–present)
🌐 Contact
📧 nabil@happykhan.com 🌍 happykhan.com 💻 github.com/happykhan
Last updated: November 2025