Nabil-Fareed Alikhan, PhD
Senior Bioinformatician | Microbial Genomics | Scientific Software
More than 15 years building genomic analysis software, data platforms and computing systems for pathogen surveillance and research. Contributions include EnteroBase, GrapeTree, BRIG, PathogenWatch and AMRwatch, as well as national SARS-CoV-2 genomic surveillance, large-scale quality control and international programme delivery.
Email: nabil@happykhan.comWebsite: happykhan.comGitHub: happykhanLinkedIn: nabil-fareed-alikhanLocation: Oxford, UK
Expertise
- Genomics: Microbial population and comparative genomics; genomic surveillance; antimicrobial resistance; assembly quality control; benchmarking; biological interpretation. Research record (Google Scholar, 2 September 2026): h-index 30 and 12,364 citations.
- Software and data: Python since 2009; Flask and APIs; SQL; JavaScript and TypeScript; React; Java; WebAssembly; scientific web applications and biological databases.
- Computing and workflows: Linux and HPC; Nextflow DSL2; SLURM; Docker and Apptainer; practical AWS Batch and ECR; reproducible scientific workflows.
- Leadership and delivery: Bioinformatics teams and services; cross-partner delivery; technical planning; stakeholder communication; mentoring; curriculum development and practical training.
Experience
Senior Bioinformatician
Jan 2024 to presentCentre for Genomic Pathogen Surveillance, University of Oxford | Oxford, UK
- Work within the PathogenWatch and AMRwatch development teams; built and benchmarked E. coli and Salmonella analysis containers and integrated BactScout and QualiBact quality controls into PathogenWatch.
- Designed QualiBact, deriving versioned assembly-quality thresholds from 2,440,377 assemblies across 307 bacterial species and testing how failed QC changes AMR detection.
- Coordinate bioinformatics delivery across GHRU2 partner sites, including proficiency testing across five international organisations.
- Translate genomic-surveillance methods into practice through draft WHO AMR guidance, PATH-SAFE national recommendations and training in PathogenWatch, Microreact and genomic epidemiology.
Bioinformatics Scientific Programmer | Interim Head of Informatics (May to Dec 2023)
Dec 2018 to Dec 2023Quadram Institute Bioscience | Norwich, UK
- Served as Interim Head of Informatics from May to December 2023, leading a five-person bioinformatics service and taking responsibility for computational infrastructure.
- Built and ran COG-UK bioinformatics infrastructure supporting the release of more than 80,000 SARS-CoV-2 genomes; managed staff covering processing, analysis and weekly reporting to the DHSC and Foreign Office.
- Led technical planning as PI for the £1.49 million BBSRC QIB Cloud Renewal capital award.
- First author on a multi-centre evaluation of the ARTIC sequencing method using data from more than 3,600 clinical samples; also contributed to the PHA4GE metadata standard adopted by NCBI BioSample.
- First-authored a 2022 population-genomics study tracing AMR-carrying Salmonella across Brazilian poultry and UK food and clinical contexts.
Senior Research Fellow in Pathogen Bioinformatics
Dec 2016 to Dec 2018University of Warwick | Coventry, UK
- Integrated ancient metagenomes into EnteroBase and co-authored SPARSE, a method for reconstructing microbial strains from metagenomic sequence data.
- Co-developed cgMLST schemes and first-authored the 2018 EnteroBase paper analysing population structure across more than 100,000 Salmonella genomes.
Research Fellow in Genomics of Bacterial Pathogens
Dec 2014 to Dec 2016University of Warwick | Coventry, UK
- Developed EnteroBase middleware and APIs in Python and Flask, designed its database and contributed JavaScript and Jinja views for large-scale bacterial population analysis.
- Co-developed GrapeTree for interactive exploration of large genomic datasets and continue to maintain the software.
Research Associate
2008 to 2009School of Chemistry and Molecular Biosciences, University of Queensland | Brisbane, Australia
- Administered and supported Linux and macOS workstations and servers used to share bacterial-genomics data for the Beatson Microbial Genomics group.
- Developed automated bioinformatics pipelines, including parallelised execution on HPC clusters.
Software portfolio
- PathogenWatch and AMRwatch: Development team member; built species-specific analysis containers and integrated genomic quality controls. pathogen.watch
- EnteroBase: Developed its Python and Flask middleware and APIs, designed the database and contributed JavaScript and Jinja views. enterobase.warwick.ac.uk
- GrapeTree: Co-developed and continue to maintain an interactive tool for exploring large genomic datasets. github.com/achtman-lab/GrapeTree
- BRIG: Created and continue to maintain a Java desktop application for comparative-genome visualisation. github.com/happykhan/BRIG
- RonaQC, BRIGX and GenomicX: Develop RonaQC, BRIGX and GenomicX applications using TypeScript, React and WebAssembly. genomicx.org
Professional leadership and engagement
- Invited speaking: Invited speaker at conferences and professional meetings on microbial genomics, genomic surveillance and scientific software.
- Conference and community leadership: Organised or co-organised five microbial bioinformatics conferences, meetings and hackathons between 2020 and 2025, including the 8th and 12th Microbial Bioinformatics Hackathons.
- People development: Managed or supervised five staff during QIB's SARS-CoV-2 programme and trained two bioinformaticians in SARS-CoV-2 genomics.
- Curriculum leadership: Bioinformatics Lead and board member for MMBDTP from 2021 to 2024; designed and delivered practical training across partner institutions.
Education
- PhD in Microbiology, University of Queensland, 2010 to 2015
- BSc (Hons, First Class) in Microbiology, University of Queensland, 2009
- BSc in Biochemistry and Bachelor of Information Technology, University of Queensland, 2004 to 2008