Career Profile
I’m Will Rowe, a software engineer currently working at GRAIL in the UK engineering team. I mainly work on software for running our clinical trials but I also contribute to the machine learning classifier and bioinformatics pipeline teams.
I like to work on algorithmic bioinformatics and “big data” problems, developing algorithms for a range of applications and incorporating the latest advances in data sketching, machine learning and graph theory into my software and research portfolio. I apply my algorithmic work to biological problems, such as: featurisation of genetic markers for population screening, real-time genomic epidemiology of viral outbreaks, gene dynamics in the gut microbiome, and antimicrobial resistance gene surveillance.
Employment Record
Skills & Strengths
Programming:
Go, C, CPP, Python, Typescript, BASH
Reproducibility:
LSF, NextFlow, Conda, git
Visualisation:
Jupyter, R, MatLab
Web design:
React, WASM, HTML5, CSS, Django
Cloud computing:
Docker, AWS, Terraform
Machine Learning:
RF, ANN, regression etc.
Software, Papers & Funding
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:
GROOT
Identification of Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling).
HULK
A tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
5044 citations, h-index 28. Please click on the abstract links for more information. Data last scraped from Google Scholar on 14.6.2024.
First author papers:
When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data
Genome biology 20, 1-12, 2019 - abstract
Streaming histogram sketching for rapid microbiome analytics
Microbiome 7, 1-13, 2019 - abstract
Indexed variation graphs for efficient and accurate resistome profiling
Bioinformatics 34 (21), 3601-3608, 2018 - abstract
Overexpression of antibiotic resistance genes in hospital effluents over time
Journal of Antimicrobial Chemotherapy 72 (6), 1617-1623, 2017 - abstract
Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
Water Science and Technology 73 (7), 1541-1549, 2016 - abstract
Antimicrobial resistance gene monitoring in aquatic environments (thesis)
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
PLoS One 10 (7), e0133492, 2015 - abstract
Contributor papers (hidden, click to expand):
Succinate utilisation by Salmonella is inhibited by multiple regulatory systems
PLoS genetics 20 (3), e1011142, 2024 - abstract
Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes
Journal of Hospital Infection 135, 28-36, 2023 - abstract
Salmonella succinate utilisation is inhibited by multiple regulatory systems
bioRxiv, 2022.12. 21.521472, 2022 - abstract
How to sequence 10,000 bacterial genomes and retain your sanity: an accessible, efficient and global approach
Access Microbiology 4 (5), po0645, 2022 - abstract
Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission
Clinical Microbiology and Infection 28 (1), 93-100, 2022 - abstract
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
The Lancet Infectious Diseases 22 (1), 35-42, 2022 - abstract
CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance
Genome biology 22, 1-21, 2021 - abstract
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
Genome biology 22, 1-18, 2021 - abstract
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells
Iscience 24 (11), 2021 - abstract
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant
Science 374 (6574), eabl9551, 2021 - abstract
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B. 1.1. 7
Cell reports 35 (13), 2021 - abstract
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
Microbial genomics 7 (6), 000589, 2021 - abstract
Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom
Journal of General Virology 102 (6), 001595, 2021 - abstract
Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B. 1.1. 7: an ecological study
The Lancet Public Health 6 (5), e335-e345, 2021 - abstract
Genome-Wide Identification and Expression Analysis of SOS Response Genes in Salmonella enterica Serovar Typhimurium
Cells 10 (4), 943, 2021 - abstract
Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
Nature microbiology 6 (3), 327-338, 2021 - abstract
Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Scientific reports 11 (1), 4565, 2021 - abstract
Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
Science 371 (6530), 708-712, 2021 - abstract
Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity
Cell 184 (1), 64-75. e11, 2021 - abstract
Increased risk of SARS-CoV-2 infection in staff working across different care homes: enhanced CoVID-19 outbreak investigations in London care Homes
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
Eurosurveillance 25 (32), 2001410, 2020 - abstract
An integrated national scale SARS-CoV-2 genomic surveillance network
The Lancet. Microbe 1 (3), e99, 2020 - abstract
nCoV-2019 novel coronavirus bioinformatics protocol
Artic Network, 2020 - abstract
When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data
Genome biology 20, 1-12, 2019 - abstract
Streaming histogram sketching for rapid microbiome analytics
Microbiome 7, 1-13, 2019 - abstract
A fast machine learning workflow for rapid phenotype prediction from whole shotgun metagenomes
Proceedings of the AAAI Conference on Artificial Intelligence 33 (01), 9434-9439, 2019 - abstract
The diversity, evolution and ecology of Salmonella in venomous snakes
PLoS neglected tropical diseases 13 (6), e0007169, 2019 - abstract
Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
PLoS biology 17 (1), e3000059, 2019 - abstract
Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity
Microbial Cell Factories 17, 1-13, 2018 - abstract
Indexed variation graphs for efficient and accurate resistome profiling
Bioinformatics 34 (21), 3601-3608, 2018 - abstract
International phase I study protocol to develop a patient-reported outcome measure for adolescents and adults receiving gender-affirming treatments (the GENDER-Q)
BMJ open 8 (10), e025435, 2018 - abstract
Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa
Genome medicine 9, 1-13, 2017 - abstract
Overexpression of antibiotic resistance genes in hospital effluents over time
Journal of Antimicrobial Chemotherapy 72 (6), 1617-1623, 2017 - abstract
Salmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in …
BioRxiv, 139576, 2017 - abstract
Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule?
FEMS Microbiology Ecology 93 (4), fix015, 2017 - abstract
Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
Water Science and Technology 73 (7), 1541-1549, 2016 - abstract
Antimicrobial resistance gene monitoring in aquatic environments (thesis)
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
PLoS One 10 (7), e0133492, 2015 - abstract
Host subtraction, filtering and assembly validations for novel viral discovery using next generation sequencing data
PloS one 10 (6), e0129059, 2015 - abstract
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant
Genome research 21 (11), 1788-1799, 2011 - abstract
BBSRC (CoI)
£724612
Reservoirs of mobile antibiotic resistance genes in the gut microbiome of preterm infants
Dragons Den funding
£4000
Institute of Integrative Biology funding scheme; competitively awarded during PostDoc
GlaxoSmithKline
£34000
2 rounds of competitive funding, awarded during PhD
Teaching, Leadership & Speaking
Genomics Masters module
2016-2017
Designed and taught content (lectures and workshops) for a module of the LIFE708 Masters degree at the University of Liverpool
Bioinformatics supervision
2016-2017
Provided bioinformatic supervision for PhD students at the University of Liverpool
Bioinformatics workshops
2016-2018
Organised and ran weekly bioinformatics workshops for the institute
HiPy
2016-2018
Assisted at university-wide Python workshops as an instructor
Editorial board member
2019 - 2021
Journal of Open Source Software
Balti and Bioinformatics
2019 - 2021
This is a 1-day conference that attracts ~75 delegates per year. I organised and chaired this year’s event
Grant reviewer
2019 - 2021
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
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.
ABPHM
2019
Oral talk at the Applied Bioinformatics & Public Health Microbiology conference, Hinxton
Doherty Institute
2018
Invited seminar at the Doherty Institute, University of Melbourne
SMBE
2018
Lightning talk for the Genome Evolution in Pathogen Transmission and Disease conference, Kyoto
Genome Science
2018
Invited oral talk for the Genome Science conference, Nottingham
COMMET
2017
Invited oral talk for Community Network in Metagenomics conference, Warwick
BSAC
2016
Oral talk for British Society of Antimicrobial Chemotherapy confernce. London