Career Profile

I’m Will Rowe, a computational biologist currently working in in the Loman Lab on the ARTIC Network and COG-UK consortium projects.

I work on algorithmic bioinformatics and genomics. I develop algorithms for a range of applications; incorporating the latest advances in data sketching, machine learning and graph theory into my scientific software and biological research portfolio. I apply my algorithmic work to biological problems, such as: real-time genomic epidemiology of viral outbreaks, gene dynamics in the gut microbiome, and antimicrobial resistance gene surveillance.

My future research strategy focusses on making large-scale genomic research accessible and tractable at pace with advances in sequencing technologies; and applying this to global public health problems such as antimicrobial resistance. This includes developing algorithms for indexing, augmenting and querying genomic data collections using tiered computing infrastructure; ranging from low-cost laptops, phones and chips, through to cloud and high-performance computing.

I’m a strong proponent of open science and will continue to release open source software, teaching materials and research.

Employment Record

Postdoctoral Research Associate

2019 - present
Institute of Microbiology and Infection

University of Birmingham

Visiting scientist

2019 - present
Science and Technology Facilities Council

UK Research and Innovation

Computational biologist

2017 - 2019
Hartree Centre (IBM/Science and Technology Facilities Council)

UK Research and Innovation

Postdoctoral Research Associate

2016 - 2017
Institute of Integrative Biology

University of Liverpool

Trainee Clinical Scientist

2015 - 2016
Addenbrooke’s Hospital (Cambridge University Hospitals)

National Health Service

Funding, Papers & Software



Reservoirs of mobile antibiotic resistance genes in the gut microbiome of preterm infants

Dragons Den funding

Institute of Integrative Biology funding scheme; competitively awarded during PostDoc


2 rounds of competitive funding, awarded during PhD


466 citations, h-index 13. Please click on the abstract links for more information. Data last scraped from Google Scholar on 14.1.2021.

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
CV Pulford, BM Perez-Sepulveda, R Canals, JA Bevington, RJ Bengtsson, ...
Nature Microbiology, 1-12, 2020 - abstract
Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity
E Volz, V Hill, JT McCrone, A Price, D Jorgensen, Á O’Toole, J Southgate, ...
Cell, 2020 - abstract
Increased risk of SARS-CoV-2 infection in staff working across different care homes: enhanced CoVID-19 outbreak investigations in London care Homes
SN Ladhani, JY Chow, R Janarthanan, J Fok, E Crawley-Boevey, ...
Journal of Infection 81 (4), 621-624, 2020 - abstract
Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020
E Alm, EK Broberg, T Connor, EB Hodcroft, AB Komissarov, ...
Eurosurveillance 25 (32), 2001410, 2020 - abstract
An integrated national scale SARS-CoV-2 genomic surveillance network
The Lancet Microbe, 2020 - abstract
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
L du Plessis, JT McCrone, AE Zarebski, V Hill, C Ruis, B Gutierrez, ...
Science, 2020 - abstract
Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
AP Carrieri, N Haiminen, S Maudsley-Barton, LJ Gardiner, B Murphy, ...
bioRxiv, 2020 - abstract
Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom
JG Chappell, T Tsoleridis, G Clark, L Berry, N Holmes, C Moore, M Carlile, ...
medRxiv, 2020 - abstract
Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
AJ Page, AE Mather, T Le-Viet, EJ Meader, NF Alikhan, GL Kay, ...
medRxiv, 2020 - abstract
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
BM Perez-Sepulveda, D Heavens, CV Pulford, AV Predeus, R Low, ...
bioRxiv, 2020 - abstract
Explainable AI reveals key changes in skin microbiome associated with menopause, smoking, aging and skin hydration
AP Carrieri, N Haiminen, S Maudsley-Barton, LJ Gardiner, B Murphy, ...
bioRxiv, 2020 - abstract
When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data
WPM Rowe
Genome biology 20 (1), 199, 2019 - abstract
Streaming histogram sketching for rapid microbiome analytics
WPM Rowe, AP Carrieri, C Alcon-Giner, S Caim, A Shaw, K Sim, JS Kroll, ...
Microbiome 7 (1), 1-13, 2019 - abstract
A fast machine learning workflow for rapid phenotype prediction from whole shotgun metagenomes
AP Carrieri, WPM Rowe, M Winn, EO Pyzer-Knapp
Proceedings of the AAAI Conference on Artificial Intelligence 33, 9434-9439, 2019 - abstract
The diversity, evolution and ecology of Salmonella in venomous snakes
CV Pulford, N Wenner, ML Redway, EV Rodwell, HJ Webster, R Escudero, ...
PLoS neglected tropical diseases 13 (6), e0007169, 2019 - abstract
Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
R Canals, DL Hammarlöf, C Kröger, SV Owen, WY Fong, ...
PLoS biology 17 (1), e3000059, 2019 - abstract
Indexed variation graphs for efficient and accurate resistome profiling
WPM Rowe, MD Winn
Bioinformatics 34 (21), 3601-3608, 2018 - abstract
Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa
PM Ashton, SV Owen, L Kaindama, WPM Rowe, CR Lane, L Larkin, ...
Genome medicine 9 (1), 1-13, 2017 - abstract
Overexpression of antibiotic resistance genes in hospital effluents over time
WPM Rowe, C Baker-Austin, DW Verner-Jeffreys, JJ Ryan, C Micallef, ...
Journal of Antimicrobial Chemotherapy 72 (6), 1617-1623, 2017 - abstract
Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule?
DW Verner-Jeffreys, T Brazier, RY Perez, D Ryder, RM Card, TJ Welch, ...
FEMS Microbiology Ecology 93 (4), fix015, 2017 - abstract
Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa
PM Ashton, SV Owen, L Kaindama, WPM Rowe, C Lane, L Larkin, S Nair, ...
BioRxiv, 139576, 2017 - abstract
Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
W Rowe, DW Verner-Jeffreys, C Baker-Austin, JJ Ryan, DJ Maskell, ...
Water Science and Technology 73 (7), 1541-1549, 2016 - abstract
Antimicrobial resistance gene monitoring in aquatic environments (thesis)
W Rowe
University of Cambridge, 2016 - abstract
Search engine for antimicrobial resistance: a cloud compatible pipeline and web interface for rapidly detecting antimicrobial resistance genes directly from sequence data
W Rowe, KS Baker, D Verner-Jeffreys, C Baker-Austin, JJ Ryan, ...
PloS one 10 (7), e0133492, 2015 - abstract
Host subtraction, filtering and assembly validations for novel viral discovery using next generation sequencing data
GM Daly, RM Leggett, W Rowe, S Stubbs, M Wilkinson, ...
PLoS One 10 (6), e0129059, 2015 - abstract
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant
HH Al-Balool, D Weber, Y Liu, M Wade, K Guleria, PLP Nam, J Clayton, ...
Genome research 21 (11), 1788-1799, 2011 - abstract


All of my software is open sourced and available via my GitHub repositories. My software is actively maintained, with strong community engagement in the form of GitHub issues, project forking and pull requests. My software is also packaged for Conda, Brew and BaseSpace. I also contribute to open source projects such as ARTIC Network, BioConda, JOSS and HiPy.

Here are my current GitHub stats and a selection of my most recent projects:

ARTIC tools

A set of tools for viral amplicon schemes
GitHub stars GitHub top language GitHub last commit bioconda

ARTIC pipeline

A pipeline for working with virus sequencing data sequenced with nanopore
GitHub stars GitHub top language GitHub last commit bioconda
IPFS-backed database for recording and distributing sequencing data
GitHub stars GitHub top language GitHub last commit


Appromiately weighted variation graphs for haplotype identification
GitHub stars GitHub top language GitHub last commit
Identification of Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling).
GitHub stars GitHub top language GitHub last commit bioconda
A tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
GitHub stars GitHub top language GitHub last commit bioconda
A pipeline for Detecting Resistome Associated taXa
GitHub stars GitHub top language GitHub last commit bioconda

Teaching, Leadership & Speaking

Teaching & Engagement

Genomics Masters module

Designed and taught content (lectures and workshops) for a module of the LIFE708 Masters degree at the University of Liverpool

Bioinformatics supervision

Provided bioinformatic supervision for PhD students at the University of Liverpool

Bioinformatics workshops

Organised and ran weekly bioinformatics workshops for the institute


Assisted at university-wide Python workshops as an instructor

Leadership, Professional & Collegial Experience

Editorial board member

2019 -
Journal of Open Source Software

Balti and Bioinformatics

2019 -
This is a 1-day conference that attracts ~75 delegates per year. I organised and chaired this year’s event

Grant reviewer

2019 -
I reviewed a grant application for the Auckland Medical Research Foundation, New Zealand.

Publication reviewer

2015 -
I review for a number of journals including JOSS, PLoS One and Microbial Ecology.

Captain of Boats

2012 - 2013
Magdalene College, University of Cambridge

MCR Social Secretary

2012 - 2013
Magdalene College, University of Cambridge

Industrial Collaboration

UKRI Innovation Return on Research

2017 - 2019
As part of the IROR programme, I consulted with several companies and research institutes (incl. Unilever, Rothamsted Research, Quadram Institute) to deliver high performance computing solutions for genomics applications. This resulted in several pieces of software being commercially licensed and registered as intellectual property.

Industrial Collaborative Award in Science and Engineering (ICASE)

2011 - 2015
As part of my PhD training, I spent several months in the labs of the Centre for Environment, Fisheries and Aquaculture Science, and GlaxoSmithKline, enacting knowledge transfer, data generation and report production focussed on antimicrobial resistance gene dynamics in the environment.



Oral talk at the Applied Bioinformatics & Public Health Microbiology conference, Hinxton

Doherty Institute

Invited seminar at the Doherty Institute, University of Melbourne


Lightning talk for the Genome Evolution in Pathogen Transmission and Disease conference, Kyoto

Genome Science

Invited oral talk for the Genome Science conference, Nottingham


Invited oral talk for Community Network in Metagenomics conference, Warwick


Oral talk for British Society of Antimicrobial Chemotherapy confernce. London

Skills & Stats

Go, C, CPP, Python, BASH

LSF, NextFlow, Conda, git

Jupyter, R, MatLab

Web design:
HTML5, CSS, Django, JS

Cloud computing:
Docker, AWS

Machine Learning:
RF, ANN, regression etc.