Nabil-Fareed Alikhan

Bioinformatics · Microbial Genomics · Software Development

Nabil-Fareed Alikhan

Bioinformatician, developer, and academic leader with 15+ years' experience in microbial genomics, open-source software, and collaborative science.

Email:nabil@happykhan.comWebsite:happykhan.comGitHub:happykhan

Education

2010–2015
PhD in Microbiology
University of Queensland, Australia
2009
BSc (Hons, 1st Class) in Microbiology
University of Queensland
2004–2008
BSc in Biochemistry & Bachelor of Information Technology
University of Queensland

Professional Experience

2024–Present
Senior Bioinformatician
The Centre for Genomic Pathogen Surveillance (CGPS), University of Oxford, UK
Leading development and integration of pathogen genomics platforms for global public health surveillance.
2018–2023
Bioinformatics Scientific Programmer – Interim Head of Informatics
Quadram Institute Bioscience, Norwich, UK
2016–2018
Senior Research Fellow in Pathogen Bioinformatics
University of Warwick, UK
Integrated ancient metagenomes into EnteroBase and sequenced/analyzed 10,000 modern S. enterica genomes.
2014–2016
Research Fellow in Genomics of Bacterial Pathogens
University of Warwick, UK
Co-developed EnteroBase (enterobase.warwick.ac.uk) for big-data genomic analysis of enteric pathogens and adapted robotic genotyping for high-throughput sequencing library preparation.
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.

Funding & Grants

2022
QIB Cloud Renewal£1.49M
BBSRC
2021
RonaQC SARS-CoV-2 QC Tool£40k
UKRI/COG-UK
Role: Co-PI
2022
Microbial Bioinformatics Hackathon 2022£10k
BBSRC
Role: Co-PI
2020
CLIMB-BIG-DATA; A Cloud Infrastructure for Big-Data Microbial Bioinformatics£1.9M
MRC
Role: Inherited on appointment as Interim Head of Informatics
2022
UK Food Safety Research Network£1.6M
BBSRC
Role: Inherited on appointment as Interim Head of Informatics

Invited Talks

Jan 2026
Pathogenesis of enteric pathogens; a genomic approach
The Festival of Genomics & Biodata 2026 — ExCel, London, UK
Sept 2025
PathogenWatch / AMRwatch for Food Safety
Global Microbial Identifier 15 (GMI15) Conference 2025 — University of Melbourne, Australia.
Jul 2025
Open Data, Open Minds; Bioinformatics & Big Data lessons from COVID-19 and beyond
Centre for Systems Health and integrated Metabolic Research (SHIMR) Research Symposium 2025 — Nottingham Trent University, UK
Dec 2022
Our complicated relationship with microbes and how genomics can help
Irish Computational Biology and Genomics Symposium 2022 — National University of Ireland, Ireland
Jul 2022
ESCMID: Moving beyond single species outbreaks
ESCMID-ESGEM — Virtual
Sept 2022
EnteroBase - Platforms for molecular epidemiology
13th International Meeting on Microbial Epidemiological Markers (IMMEM XIII) — Bath, UK
Nov 2019
Understanding Drivers of Antimicrobial Resistance in the Food Chain
AMR Workshop 2019 — Guangzhou, China

Teaching & Supervision

2025-present
PhD co-supervisor (Wa Ode Dwi Daningrat), University of Oxford
2021–2024
Bioinformatics lead and board member of the Microbes, Microbiomes and Bioinformatics Doctoral Training Partnership (MMBDTP)
2021
PhD student placement (Madeline Iseminger), Quadram Institute Bioscience
2021
PhD student placement (Winnie Lai), Quadram Institute Bioscience
2019–2021
PhD advisory team (Ebenezer Foster-Nyarko), Quadram Institute Bioscience
2018
Supervising a MRC DTP Mini-project student (Stephen Li), University of Warwick
2017
Lecturing a Student Selected component ‘Infection – from bench to bedside’, University of Warwick
2015
Tutoring a Student Selected component ‘Infection – from bench to bedside’, University of Warwick
2013
Tutor BIOL3004 – Genomics & Bioinformatics, University of Queensland

Academic Service

2026
Technical Group Member
UKHSA TARZET Invasive Meningococcal Disease Technical Group
2022–present
Founder and Administrator
mstdn.science (science-focused Mastodon instance)
2026–present
Editorial Board Member
Microbial Genomics (MGen)
2021–2024
Board Member
Microbes Microbiomes & Bioinformatics DTP
2019–present
PHA4GE Infrastructure Working Group
PHA4GE
2020–2023
Treasurer
QIB Postdoc Society
2019–2024
Internal grant reviewer
Quadram Institute Bioscience
2015-2018
Equality & Diversity Committee Member
University of Warwick
2015–present
Supervisor for PhD and MRes projects
Various

Skills

  • Bioinformatics & Analysis: De novo Assembly, Read Mapping, Population Genomics, Comparative Genome Analysis, Phylogenetics, IQTree, RAxML, Statistics (Python/R), Linux & CLI
  • Programming & Development: Python, JavaScript, Java, Bash, Perl, Flask, SQL, HTML/CSS, PHP, Full-Stack Development
  • Infrastructure & Workflows: HPC, Nextflow, Docker, Cloud Computing, Database Design, Linux Server Administration, Workflow Parallelization
  • Leadership & Management: Scientific Team Leadership, Grant Writing & Costing, Project Management, Mentoring & Supervision, Strategic Planning
  • Policy & Engagement: Public Health Stakeholder Engagement, Science Communication, Policy Translation, International Collaboration

Organised Meetings

Sept 2025
12th Microbial Bioinformatics Hackathon
14th edition of the International Meeting on Microbial Epidemiological Markers, Porto, Portugal
May 2025
Applied Bioinformatics & Public Health Microbiology
Wellcome Genome Campus, UK and Virtual
Sept 2021
CampyUK goes global 2021
Virtual
Apr 2020
Micro Binfie Virtual Conference 2020
Virtual
Sept 2022
8th Microbial Bioinformatics Hackathon
Bath, UK

Publications

  • Pathogenwatch: A Public Health Platform for Rapid Interpretation of Pathogen Genomics. Alikhan, et al.. medRxiv (2026).
  • Considerations for Compute Infrastructure for Pathogen Sequence Analysis. Lagesen, et al.. VeriXiv 3 (2026).
  • Monitoring Antimicrobial Resistance Trends from Global Genomics Data: Amr.Watch. David, et al.. PLOS Global Public Health 5 (2025).
  • Monitoring of Vaccine Targets and Interventions Using Global Genome Data: vaccines. watch. David, et al.. Preprint (2025).
  • PATH-SAFE Consortium Recommendations for Genomic Surveillance of Food-Borne Diseases Escherichia coli and Listeria monocytogenes. Gally, et al.. FSA Research and Evidence (2025).
  • Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine. Ereqat, et al.. Pathogens 13 (2024).
  • Genomic Diversity and Epidemiological Significance of Non-Typhoidal Salmonella Found in Retail Food Collected in Norfolk, UK. Bloomfield, et al.. Microbial Genomics 9 (2023).
  • Investigation of Hospital Discharge Cases and SARS-CoV-2 Introduction into Lothian Care Homes. Cotton, et al.. Journal of Hospital Infection 135 (2023).
  • Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals. Castillo-Bravo, et al.. Microbiology Spectrum 10 (2022).
  • Dynamics of Salmonella Enterica and Antimicrobial Resistance in the Brazilian Poultry Industry and Global Impacts on Public Health. Alikhan, et al.. PLOS Genetics 18 (2022).
  • Characterising the Persistence of RT-PCR Positivity and Incidence in a Community Survey of SARS-CoV-2. Eales, et al.. Wellcome Open Research 7 (2022).
  • Future-Proofing and Maximizing the Utility of Metadata: The PHA4GE SARS-CoV-2 Contextual Data Specification Package. Griffiths, et al.. GigaScience 11 (2022).
  • Replacement of the Alpha Variant of SARS-CoV-2 by the Delta Variant in Lebanon between April and June 2021. Merhi, et al.. Microbial Genomics 8 (2022).
  • Naming the Unnamed: Over 65,000 Candidatus Names for Unnamed Archaea and Bacteria in the Genome Taxonomy Database. Pallen, et al.. International Journal of Systematic and Evolutionary Microbiology 72 (2022).
  • Combined Epidemiological and Genomic Analysis of Nosocomial SARS-CoV-2 Infection Early in the Pandemic and the Role of Unidentified Cases in Transmission. Snell, et al.. Clinical Microbiology and Infection 28 (2022).
  • Hospital Admission and Emergency Care Attendance Risk for SARS-CoV-2 Delta (B.1.617.2) Compared with Alpha (B.1.1.7) Variants of Concern: A Cohort Study. Twohig, et al.. The Lancet Infectious Diseases 22 (2022).
  • Benchmark Datasets for SARS-CoV-2 Surveillance Bioinformatics. Xiaoli, et al.. PeerJ 10 (2022).
  • The Impact of Viral Mutations on Recognition by SARS-CoV-2 Specific T Cells. de Silva, et al.. iScience 24 (2021).
  • Genomic Diversity of Escherichia Coli from Healthy Children in Rural Gambia. Foster-Nyarko, et al.. PeerJ 9 (2021).
  • Genomic Diversity of Salmonella Enterica -The UoWUCC 10K Genomes Project. Achtman, et al.. Wellcome Open Research 5 (2021).
  • Defining the Analytical and Clinical Sensitivity of the ARTIC Method for the Detection of SARS-CoV-2. Alikhan, et al.. Preprint (2021).
  • CoronaHiT: High-Throughput Sequencing of SARS-CoV-2 Genomes. Baker, et al.. Genome Medicine 13 (2021).
  • Extensive Microbial Diversity within the Chicken Gut Microbiome Revealed by Metagenomics and Culture. Gilroy, et al.. PeerJ 9 (2021).
  • Changes in Symptomatology, Reinfection, and Transmissibility Associated with the SARS-CoV-2 Variant B.1.1.7: An Ecological Study. Graham, et al.. The Lancet Public Health 6 (2021).
  • Invasive Atypical Non-Typhoidal Salmonella Serovars in The Gambia. Kanteh, et al.. Microbial Genomics 7 (2021).
  • Recurrent Emergence of SARS-CoV-2 Spike Deletion H69/V70 and Its Role in the Alpha Variant B.1.1.7. Meng, et al.. Cell Reports 35 (2021).
  • Large-Scale Sequencing of SARS-CoV-2 Genomes from One Region Allows Detailed Epidemiology and Enables Local Outbreak Management. Page, et al.. Microbial Genomics 7 (2021).
  • REACT-1 Round 11 Report: Low Prevalence of SARS-CoV-2 Infection in the Community Prior to the Third Step of the English Roadmap out of Lockdown. Riley, et al.. Preprint (2021).
  • REACT-1 Round 12 Report: Resurgence of SARS-CoV-2 Infections in England Associated with Increased Frequency of the Delta Variant. Riley, et al.. Preprint (2021).
  • SARS-CoV-2 Variants of Concern Dominate in Lahore, Pakistan in April 2021. Sarwar, et al.. Microbial Genomics 7 (2021).
  • Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Volz, et al.. Cell 184 (2021).
  • Gambian Poultry Isolates from Hyperendemic Group of AMR Escherichia coli Strains in Sub-Saharan Africa. Foster-Nyarko, et al.. Access Microbiology 2 (2020).
  • Non-Human Primates in the Gambia Harbour Human-Associated Pathogenic Escherichia coli Strains. Foster-Nyarko, et al.. Access Microbiology 2 (2020).
  • ICTV Virus Taxonomy Profile: Herelleviridae. Barylski, et al.. Journal of General Virology 101 (2020).
  • Evolution of Salmonella enterica Serotype Typhimurium Driven by Anthropogenic Selection and Niche Adaptation. Bawn, et al.. PLOS Genetics 16 (2020).
  • Emergence of Human-Adapted Salmonella enterica Is Linked to the Neolithization Process. Key, et al.. Nature Ecology & Evolution 4 (2020).
  • Rapid Mycobacterium Tuberculosis Spoligotyping from Uncorrected Long Reads Using Galru. Page, et al.. Preprint (2020).
  • Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan. Rasheed, et al.. Microorganisms 8 (2020).
  • The EnteroBase User's Guide, with Case Studies on Salmonella Transmissions, Yersinia Pestis Phylogeny, and Escherichia Core Genomic Diversity. Zhou, et al.. Genome Research 30 (2020).
  • Within-Host Diversity and Vertical Transmission of Group B Streptococcus Among Mother-infant Dyads in The Gambia. Foster-Nyarko, et al.. Preprint (2019).
  • Multiple Evolutionary Trajectories for Non-O157 Shiga Toxigenic Escherichia coli. Alikhan, et al.. Preprint (2019).
  • Genome-Wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems. Chen, et al.. Cell Reports 29 (2019).
  • A Genomic Overview of the Population Structure of Salmonella. Alikhan, et al.. PLoS genetics 14 (2018).
  • Principles of Systems Biology, No. 31. Cho, et al.. Cell Systems 7 (2018).
  • Comparative Analysis of Core Genome MLST and SNP Typing within a European Salmonella Serovar Enteritidis Outbreak. Pearce, et al.. International Journal of Food Microbiology 274 (2018).
  • Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes. Zhou, et al.. Preprint 10812 (2018).
  • GrapeTree: Visualization of Core Genomic Relationships among 100,000 Bacterial Pathogens. Zhou, et al.. Genome Research 28 (2018).
  • Pan-Genome Analysis of Ancient and Modern Salmonella Enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. Zhou, et al.. Current Biology 28 (2018).
  • Comparison of Classical Multi-Locus Sequence Typing Software for next-Generation Sequencing Data. Page, et al.. Microbial Genomics 3 (2017).
  • Mechanisms Involved in Acquisition of bla\textsubscriptNDM Genes by IncA/C2 and IncFIIY Plasmids. Wailan, et al.. Antimicrobial Agents and Chemotherapy 60 (2016).
  • Molecular Analysis of Asymptomatic Bacteriuria Escherichia coli Strain VR50 Reveals Adaptation to the Urinary Tract by Gene Acquisition. Beatson, et al.. Infection and Immunity 83 (2015).
  • BLAST Ring Image Generator (BRIG): Simple Prokaryote Genome Comparisons. Alikhan, et al.. BMC genomics 12 (2011).
  • Genome Sequence of the Emerging Pathogen Aeromonas caviae. Beatson, et al.. Journal of Bacteriology 193 (2011).

Oral Presentations

May 2026
Genomics Costing Tool web application
Eastern Europe Central Asia (EECA) Genomics and Sequencing Community of Practice — Virtual
Apr 2026
Genomics Costing Tool web application
PulseNet Middle East Monthly APHL Webinar Series — Virtual
Apr 2026
Practical public health surveillance strategies and bridging the gap to use of mobile genetic elements
China-Bath Symposium of Genomic Epidemiology and Mobile Genetic Elements — Milner Centre for Evolution, University of Bath, UK
Feb 2026
QualiBact - Quality control advice for all
PHA4GE Data Standards Working Group Seminar Series — Virtual
Oct 2025
QualiBact
ESGEM AMR Seminar — Virtual
Sept 2025
12th Microbial Bioinformatics Hackathon
14th International Meeting on Microbial Epidemiological Markers (IMMEM XIV) — Porto, Portugal
Nov 2024
Mastering Microreact and Data-Flo for Advanced Data Visualization
UKHSA Science Group Scientific Seminars — Virtual
Oct 2024
A novel format for capturing cell organisation
ASM Conference on Rapid Applied Microbial NGS and Bioinformatic Pipelines (ASMNGS 2024) — Washington D.C., USA
Jan 2023
Dynamics of Salmonella enterica and antimicrobial resistance in the Brazilian poultry industry and global impacts on public health
US CDC Foodborne Division Seminar — Virtual
Jun 2022
Platforms for genomic surveillance of FBD pathogens
Africa CDC Food borne pathogen group — Virtual
Jan 2022
Bioinformatics Gotchas
3rd ARTICNetwork and CLIMB-BIG-DATA joint workshop on COVID-19 data analysis — Virtual
Oct 2021
SARS-CoV-2 sequencing in East Anglia
COG-Together event — Cambridge, UK
Jan 2021
Bioinformatics Gotchas
ARTICnetwork and CLIMB-BIG-DATA joint workshop on COVID-19 data analysis — Virtual
Nov 2019
Building better infrastructure for a brave new world
Balti and Bioinformatics — Birmingham, UK
Sept 2018
Deciphering ancient microbes with modern population genomic databases
8th International Symposium on Biomolecular Archaeology 2018. Max Planck Institute (Jena) — Germany
Aug 2018
Understanding genomic landscapes in EnteroBase with cgMLST & GrapeTree
QI Keynote Lecture — Quadram Institute, Norwich, United Kingdom
Apr 2018
Tackling ‘Big Data’ challenges in microbial genomics with EnteroBase.
1st Warwick Postdoctoral Science Symposium — University of Warwick, United Kingdom
Oct 2017
EnteroBase: Bacterial population genomics in the era of big-data
ENA facilities Day 2017 — EBI, Hinxton, United Kingdom
Mar 2016
Scalable and user-friendly workflows for Molecular Epidemiology using EnteroBase
11th International Meeting on Microbial Epidemiological Markers — Estoril, Portugal
Sept 2015
EnteroBase: A Powerful, User-Friendly Online Resource for Analysing Genomic Variation
1st ASM Conference on Rapid NGS Bioinformatic Pipelines for Enhanced Molecular Epidemiologic Investigation of Pathogens — Washington DC, USA
Sept 2014
Genomic analysis of E. coli O157:H7 associated with increased excretion, or 'super-shedding', in cattle
Genetics and Genomics Seminar series — University of Queensland, Brisbane, Australia
Oct 2013
Comparative genomics of non-O157 Shiga toxigenic E. coli
Division of Microbiology and Infection Seminar Series — University of Warwick, Coventry, United Kingdom
Jul 2013
Comparative genomics of non-O157 Shiga toxigenic E. coli
Genetics and Genomics Seminar series — University of Queensland, Australia
Nov 2012
Comparative genomics of non-O157 Shiga-toxigenic Escherichia coli reveals distinct lineages with multiple approaches to achieve pathogenesis
8th Annual SCMB Research Students Symposium — University of Queensland, Brisbane, Australia
Jul 2012
Visualising bacterial genome comparisons of next-generation sequencing datasets using BRIG
Microbial Informatics Workshop at the Australian Society for Microbiology 2012 Annual Scientific Meeting — Brisbane, Australia
Mar 2012
The BLAST Ring Image Generator: simple prokaryote genome comparisons
ASM QLD Becton Dickinson Student Award — University of Queensland, Australia

Conference Posters

Oct 2022
Online quality control of SARS-CoV-2 data with RonaQC
ASM Conference on Rapid Applied Microbial NGS and Bioinformatics Pipelines — Baltimore, USA
Mar 2022
Large scale SARS-CoV-2 genome sequencing to aid COVID-19 pandemic management
QIB Trustees Event — Norwich, UK
Sept 2018
Understanding genomic landscapes in EnteroBase with cgMLST & GrapeTree
ASM Conference on Rapid Applied Microbial NGS and Bioinformatics Pipelines — Washington DC
Oct 2013
Comparative genomics of non-O157 Enterohaemorrhagic Escherichia coli.
10th International Meeting on Microbial Epidemiological Markers — Paris, France
Jul 2012
Analysis and visualisation of genome comparisons within a large scale genomic study of Shiga-Toxin Producing E. coli.
The Australian Society for Microbiology 2012 Annual Scientific Meeting — Brisbane, Australia
Nov 2010
BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons.
6th Annual SCMB Research Students Symposium — University of Queensland, St Lucia, QLD
Nov 2009
Interactive Genome Orthology Resource (IGOR): A novel approach to comparing genomes
5th Annual SCMB Research Students Symposium — University of Queensland, St Lucia, QLD