Curriculum Vitae
Email: nabil@happykhan.comWebsite: happykhan.comGitHub: happykhanLinkedIn: nabil-fareed-alikhanScholar: profileORCID: 0000-0002-1243-0767
📄 See my publications
Senior bioinformatician and microbial genomicist with more than 15 years' experience developing scientific software, analysing pathogen populations and delivering genomic-surveillance programmes.
30
H-Index
12,364
Citations
15
Years Experience
94,150
Software Downloads
Citation metrics verified on Google Scholar, 2 September 2026
Education
PhD in Microbiology
University of Queensland, Australia
2010–2015
Thesis: Escherichia coli virulence: a genomic approach
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
Employment
2024 – Present
Senior Bioinformatician
The Centre for Genomic Pathogen Surveillance (CGPS), University of Oxford, UK
Develop pathogen-genomics software, analytical methods and training for international genomic-surveillance programmes.
May 2023 – Dec 2023
Interim Head of Informatics
Quadram Institute Bioscience, Norwich, UK
Dec 2018 – Apr 2023
Bioinformatics Scientific Programmer
Quadram Institute Bioscience, Norwich, UK
2016 – 2018
Senior Research Fellow in Pathogen Bioinformatics
University of Warwick, UK
Analysed bacterial population genomics and integrated metagenomic data into large-scale surveillance infrastructure.
2014 – 2016
Research Fellow in Genomics of Bacterial Pathogens
University of Warwick, UK
Developed scientific software and data infrastructure for large-scale bacterial population analysis.
Mar 2009 – Nov 2009
Research Associate
School of Chemistry and Molecular Biosciences, University of Queensland, Australia
System administration and technical support for Linux/MacOSX workstations. Developed automated bioinformatics pipelines for the Beatson Microbial Genomics group.
Nov 2008 – Jan 2009
Research Associate
School of Chemistry and Molecular Biosciences, University of Queensland, Australia
Programmed software pipelines for bioinformatics, especially parallelization on high-performance computer clusters. Server administration for sharing bacterial genomics data.
Research Software & Infrastructure
PathogenWatch and AMRwatch | Development-team member
Built species-specific analysis containers, integrated genomic quality controls and developed automated interpretation of AMRFinderPlus outputs. · Project
QualiBact | Designer and developer
Created a species-aware bacterial assembly-quality framework benchmarked on 2,440,377 assemblies across 307 species. · Project
EnteroBase and GrapeTree | Developer and co-developer
Developed EnteroBase middleware, APIs and database design; co-developed and continue to maintain GrapeTree. · Project
BRIG | Creator and maintainer
Created and continue to maintain the Java desktop application for comparative-genome visualisation. · Project
RonaQC and GenomicX | Developer and maintainer
Develop browser-based scientific software using TypeScript, React and WebAssembly. · Project
Skills
Bioinformatics & Analysis
Microbial population and comparative genomics
Genomic surveillance and antimicrobial resistance
Genome assembly, read mapping and phylogenetics
Assembly quality control, validation and benchmarking
Biological interpretation and scientific communication
Scientific Software & Data
Python since 2009
Flask, REST APIs and SQL
JavaScript, TypeScript and React
Java and WebAssembly
Scientific web applications and biological databases
Infrastructure & Workflows
Linux and HPC since 2008–2009
Nextflow DSL2 and SLURM
Docker and Apptainer
AWS Batch and ECR
Reproducible workflows and parallel execution
Leadership, Teaching & Engagement
Bioinformatics team and service management
Cross-partner programme delivery
Mentoring, supervision and curriculum development
Practical training and invited speaking
Public-health and international stakeholder engagement