Career Profile

I’m Will Rowe, a computational biologist working in microbial genomics.

I write software to analyse metagenomic data. My main areas of interest are in identifying genetic variation within microbiomes using variation graphs, as well classifying microbiome samples using data sketching methods and machine learning.

Experience

Postdoctoral Research Associate

2019 - present
University of Birmingham

Working in the Loman Lab on the ARTIC network project. Projects include:

  • developing software for real-time molecular epidemiology

Computational biologist

2017 - 2019
UK Research and Innovation

Developing and implementing algorithms for the analysis of genomic and metagenomic data. Projects included:

  • computational methods for microbiome classification tasks
  • identification of antibiotic resistance genes and mobile genetic elements
  • metagenomic pipeline development

Postdoctoral Research Associate

2016 - 2017
University of Liverpool

Designing analysis pipelines, software and computational workflows to analyse, visualise and store large-scale genomic and transcriptomic data.

Trainee Clinical Scientist

2015 - 2016
National Health Service

Utilising bioinformatics and genomic sequencing to facilitate the identification of pathogenic variants in patient genome data.

Grants, Software & Publications

GRANTS:

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

SOFTWARE:

Here are a selection of my most recent projects. Please click on the links to find out more or visit my GitHub page.

Baby GROOT

appromiately weighted variation graphs for haplotype identification
a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples (a.k.a. Resistome Profiling).
a tool that creates small, fixed-size sketches from streaming microbiome sequencing data, enabling rapid metagenomic dissimilarity analysis.
A pipeline for Detecting Resistome Associated taXa

PUBLICATIONS:

Co-first author publications are indicated by *. Please visit Google Scholar for the most current list.

When The Levee Breaks: a practical guide to sketching algorithms for processing the flood of genomic data
Will Rowe
Genome Biology. 2019
The diversity, evolution and ecology of Salmonella in venomous snakes
Caisey Victoria Pulford, Nicolas Wenner, Martha L Redway, Ella V Rodwell, Hermione J Webster, Roberta Escudero, Carsten Kröger, Rocío Canals, Will Rowe, Javier Lopez, Neil Hall, Paul D Rowley, Dorina Timofte, Robert A Harrison, Kate S Baker, Jay C. D. Hinton
PLOS Neglected Tropical Diseases. 2019
A Fast Machine Learning Workflow for Rapid Phenotype Prediction from Whole Shotgun Metagenomes
Anna Paola Carrieri, Will Rowe*, Martyn D Winn, Edward O Pyzer-Knapp
IAAI. 2019
Streaming histogram sketching for rapid microbiome analytics
Will Rowe*, Anna Paola Carrieri, Cristina Alcon-Giner, Shabhonam Caim, Alex Shaw, Kathleen Sim, J Simon Kroll, Lindsay Hall, Edward O Pyzer-Knapp, Martyn D Winn
Microbiome. 2019
Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
Rocío Canals, Disa L Hammarlöf, Carsten Kröger, Siân V Owen, Wai Yee Fong, Lizeth Lacharme-Lora, Xiaojun Zhu, Nicolas Wenner, Sarah E Carden, Jared Honeycutt, Denise M Monack, Robert A Kingsley, Philip Brownridge, Roy R Chaudhuri, Will Rowe, Alexander V Predeus, Karsten Hokamp, Melita A Gordon, Jay CD Hinton
PLoS biology. 2019
Indexed variation graphs for efficient and accurate resistome profiling
Will Rowe, Martyn Winn
Bioinformatics. 2018
Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa
Philip M Ashton, Siân V Owen, Lukeki Kaindama, Will Rowe, Chris R Lane, Lesley Larkin, Satheesh Nair, Claire Jenkins, Elizabeth M de Pinna, Nicholas A Feasey, Jay CD Hinton, Timothy J Dallman
Genome medicine. 2017
Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule?
David W Verner-Jeffreys, Thomas Brazier, Ramon Y Perez, David Ryder, Roderick M Card, Timothy J Welch, Rowena Hoare, Thao Ngo, Nikki McLaren, Richard Ellis, Kerry L Bartie, Stephen W Feist, Will Rowe, Alexandra Adams, Kim D Thompson
FEMS microbiology ecology. 2017
Overexpression of antibiotic resistance genes in hospital effluents over time
Will Rowe, Craig Baker-Austin, David W Verner-Jeffreys, Jim J Ryan, Duncan J Maskell, Gareth P Pearce
Journal of Antimicrobial Chemotherapy. 2017
Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment
Will Rowe, David W Verner-Jeffreys, Craig Baker-Austin, Jim J Ryan, Duncan J Maskell, Gareth P Pearce
Water Science and Technology. 2016
Search engine for antimicrobial resistance: a cloud compatible pipeline and web interface for rapidly detecting antimicrobial resistance genes directly from sequence data
Will Rowe, Kate S Baker, David Verner-Jeffreys, Craig Baker-Austin, Jim J Ryan, Duncan Maskell, Gareth Pearce
PLoS One. 2015
Host subtraction, filtering and assembly validations for novel viral discovery using next generation sequencing data
Gordon M Daly, Richard M Leggett, Will Rowe, Samuel Stubbs, Maxim Wilkinson, Ricardo H Ramirez-Gonzalez, Mario Caccamo, William Bernal, Jonathan L Heeney
PLoS One. 2015
Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant
Haya H Al-Balool, David Weber, Yilei Liu, Mark Wade, Kamlesh Guleria, Pitsien Lang Ping Nam, Jake Clayton, Will Rowe, Jonathan Coxhead, Julie Irving, David J Elliott, Andrew G Hall, Mauro Santibanez-Koref, Michael S Jackson
Genome research. 2011

Teaching & Engagement

TEACHING:

Genomics Masters module

2017
designed and taught content (lectures and workshops) for a module of the LIFE708 Masters degree at the University of Liverpool

ENGAGEMENT:

Bioinformatics workshops

2016-2018
organised and ran weekly bioinformatics workshops at the Institute of Integrative Biology

HiPy

2016-2018
assisted at university-wide Python workshops as an instructor

SPEAKING:

ABPHM

2019
oral talk at the Applied Bioinformatics & Public Health Microbiology conference

Doherty Institute

2018
invited seminar at the Doherty Institute, University of Melbourne

Society for Molecular Biology & Evolution

2018
lightning talk for the Genome Evolution in Pathogen Transmission and Disease conference Kyoto

Genome Science

2018
oral talk for the Genome Science conference

COMMET

2017
invited oral talk for Community Network in Metagenomics conference

BSAC conference

2016
oral talk for British Society of Antimicrobial Chemotherapy confernce

Skills

Programming:
Go, C, Python, BASH

Reproducibility:
LSF, NextFlow, Conda, git

Visualisation:
Jupyter, R, MatLab

Web design:
HTML5, CSS, Django, JS

Cloud computing:
Docker, AWS

Machine Learning:
RF, ANN, regression etc.