Graeme Fox

Graeme Fox

🧬 Research Fellow Bioinformatician
πŸ“ DeepSEQ, The University of Nottingham
πŸŽ“ PhD in Ecological Genetics (Manchester Metropolitan University)
πŸŽ“ MSc (Conservation Biology) & BSc (Hons) (Biological Sciences) (The University of Liverpool)

About

I am currently a research fellow at The University of Nottingham based within DeepSEQ; the bioinformatics and genomics core facility.

🧬

Genomics

Next-generation sequencing technologies and applications

πŸ”¬

Bioinformatics

Computational approaches to biological questions

🌿

Ecological Genetics

Conservation and ecological applications

I have a very general interest in genomics and bioinformatics, with particular focus on ecological genetics. My work involves using cutting edge next-generation sequencing technologies and bioinformatics approaches to answer a broad range of biological questions.

My previous roles have included research and training at the NEOF facility at The University of Sheffield, and roles involving the use of genomics and bioinformatics approaches for diet analysis in A. mellifera, and qPCR approaches to describe changes in the gut microbiome of B. terrestris. My PhD and role as a research associate at Manchester Metropolitan University involved various next-generation sequencing methods and applications in conservation and ecology.

I also have experience as a research technician at The University of Manchester in both the soil ecology group and genomics core facility.

Published Work

2025

George Day, Thomas Bolderstone, Greg J. Conway, Tony Cross, Tony Davis, Matilda Dolan, Mervyn Greening, Colin Neale, Ian Nicholson, Kim Nicholson, Ann Ward, Nik Ward, Graeme Fox, Ewan Harney, Helen Hipperson, Kathryn Maher, Jamie Thompson, Rachel Tucker, Dean Waters, Kate L. Durrant, Terry Burke, Jon Slate, Kathryn E. Arnold
The Genomic Signature of Demographic Decline in a Long-Distance Migrant in a Range-Extreme Population
Molecular Ecology e17805
Simon Deacon, Inswasti Cahyani, Nadine Holmes, Graeme Fox, Rory Munro, Satrio Wibowo, Thomas Murray, Hannah Mason, Mark Housley, Daniel Martin, Abdi Sharif, Areeba Patel, Robert Goldspring, Sebastian Brandner, Felix Sahm, Stuart Smith, Simon Paine, Matthew Loose
ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis
Neuro-Oncology 2025;, noaf103
Nash, A., Lee, IN., Fox, G. et al.
An evaluation of spraying as a delivery method for human mesenchymal stem cells suspended in low-methyl pectin solutions
Stem Cell Res Ther 16, 246
Patel, A., GΓΆbel, K., Ille, S. et al.
Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors
Nature Medicine

2024

George Day, Graeme Fox, Helen Hipperson, Kathryn H. Maher, Rachel Tucker, Gavin J. Horsburgh, Dean Waters, Kate L. Durant, Terry Burke, Jon Slate, Kathryn E. Arnold
Revealing the Demographic History of the European Nightjar (Caprimulgus europaeus)
Ecology and Evolution. Volume 14, Issue 10 October 2024 e70460

2022

Graeme Fox, Latha R. Vellaniparambil, Loreto Ros, Joshua Sammy, Richard F. Preziosi, Jennifer K. Rowntree
Complex urban environments provide Apis mellifera with a richer plant forage than suburban and more rural landscapes
Ecology and Evolution. Volume 12, Issue 11 e9490
Steven, W.J. Canty, John Paul Kennedy, Graeme Fox, Kenan Matterson, Vanessa L. GonzΓ‘lez, Mayra L. NΓΊΓ±ez-Vallecillo, Richard F. Preziosi & Jennifer K. Rowntree
Mangrove diversity is more than fringe deep
Scientific Reports 12, Article Number 1695 (2022)

2021

Alex Williams, Holly Langridge, Angela L. Straathof, Graeme Fox, Howbeer Muhammadali, Katherine A. Hollywood, Royston Goodacre & Franciska T. de Vries
Comparing root exudate collection techniques: An improved hybrid method.
Soil Biology and Biochemistry. 161 (2021).
Steven, W.J. Canty, Graeme Fox, Jennifer K. Rowntree, Richard F. Preziosi
Genetic structure of a remnant Acropora cervicornis population.
Scientific Reports. 11:3523 (2021)

2020

Milena Benavides-Serrato, Yully Fernanda Contreras-Rueda, Lina M. Barrios-Gardelis, Graeme Fox, Thomas D. Hughes, NΓ©stor Hernando Campos-Campos, Richard F. Preziosi
Isolation and characterization of 17 polymorphic microsatellite loci for a sea urchin (Echinometra lucunter: Echinometridae).
Rev. Acad. Colomb. Cienc. Ex. Fis. Nat. 44(172): 759-767 (2020).

2019

Graeme Fox, Richard F. Preziosi, Rachael A. Antwis, Fraser J. Combe, W. Edwin Harris, Ian R. Hartley, Andrew C. Kitchener, Selvino R. de Kort, Anne-Isola Nekaris, Milena Benavides-Serrato, Jennifer K. Rowntree
Multi-individual microsatellite identification: a multiple genome approach to microsatellite design (MiMi).
Molecular Ecology Resources (2019).

2018

Graeme Fox, Iulia Darolti, Jean-Denis Hibbitt, Richard F. Preziosi, John L. Fitzpatrick, Jennifer K. Rowntree
Genetic assessment of ex situ populations to aid species conservation and maintain heterozygosity in non-model species.
Journal of Zoo and Aquarium Research: 6(2): 50-56. (2018)
Combe F, Taylor-Cox E, Fox G, Sandri T, Davis N, Jones M, Cain B, Mallon D, Harris E
Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci).
Journal of Genetics. (2018)
Rachael Antwis, Sarah Griffiths, Xavier Harrison, ChΓ© Weldon, Michael Wood, Abigail Pretorius, Kevin Hopkins, Graeme Fox, and Richard Preziosi
Genetic Variability and Ontogeny Predict Microbiome Structure in a Disease-Challenged Montane Amphibian.
Multidisciplinary Journal of Microbial Ecology. (2018)
D'Cruze N, Singh B, Mookerjee A, Hunter K, Brassey CA, Rowntree J, Megson S, Fox G, Louies J, Sharath RS Macdonald DW
What's in a name? Wildlife traders evade authorities using code words.
Oryx: 52(1). 13-15 (2018)

2017

Ramirez K, Knight C, ... and de Vries F
Detecting macroecological patterns in bacterial communities across independent studies of global soils.
Nature Microbiology. (2017).
Madhura Castelino, Stephen Eyre, John Moat, Graeme Fox, Paul Martin, Pauline Ho, Mathew Upton & Anne Barton
Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform
BMC Microbiology 7. Article Number 23. (2017).

2016

Griffiths SM, Fox G, Briggs PJ, Donaldson IJ, Hood S, Richardson P, Leaver GW, Truelove NK & Preziosi RF
A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data.
Conservation Genetics Resources. (2016).
Moat J, Rizoulis A, Fox G & Upton M
Domestic shower hose biofilms contain fungal species capable of causing opportunistic infection.
Journal of Water and Health:14(4) (2016).

2015

Langarica-Fuentes A, Fox G, Robson GD
Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences.
Microbiology (2015).
Dr Madhura Castelino, MBBS, Stephen Eyre, PhD, John Moat, MSc, Graeme Fox, MSc, Paul Martin, MPhil, Umer Ijaz, PhD, Christopher Quince, PhD, Pauline Ho, PhD, Mathew Upton, PhD, Anne Barton, PhD
The skin microbiome in psoriatic arthritis: methodology development and pilot data.
The Lancet: 385(1): S27 (2015).

2014

Adrian Langarica-Fuentes, Pauline S Handley PhD, Ashley Houlden PhD, Graeme Fox, Geoffrey D Robson PhD
An investigation of the biodiversity of thermophilic and thermotolerant fungal species in composts using culture-based and molecular techniques.
Fungal Ecology: 11. 132-144. Elsevier. (2014).
Langarica-Fuentes, Adrian; Zafar, Urooj; Heyworth, Alan; Brown, Thomas; Fox, Graeme; Robson, Geoff.
Fungal succession in an in-vessel composting system characterised using DGGE and 454-pyrosequencing.
FEMS Microbiology Ecology:88. 296-308 (2014).

2013

David Penney PhD, Caroline Wadsworth; Graeme Fox; Sandra L Kennedy; Richard F Preziosi; Terence A Brown.
Absence of Ancient DNA in Sub-Fossil Insect Inclusions Preserved in 'Anthropocene' Colombian Copal.
PLOSONE: 8(9):e73150. (2013).

Achievements

πŸ’°

Grants

πŸ†

Awards

🎀

Conferences

πŸ“°

Media

πŸ’° Grants Awarded

November 2020 - Awarded a grant from the Eva Crane Trust for the project: "Healthy diet, healthy guts, healthy bees."

πŸ† Awards

February 2020 - Post-Graduate Research Paper Award (1st place) – Ecology and Environment Research Centre, Manchester Metropolitan University.

🎀 Conference Talks & Posters

December 2020 - British Ecological Society Annual Meeting 2020: Talk titled "A Hive of Activity – GIS and DNA sequencing reveal the effect urban spaces have on bee diet"

December 2019 - British Ecological Society Annual Meeting 2019: Talk titled "Why you should be using multiple genomes when developing new microsatellite markers. A new tool for a multiple genome approach to microsatellite design (MiMi)."

December 2016 - British Ecological Society Annual Meeting 2016: Poster titled "Ex situ conservation of the endangered undulate ray (Raja undulata)."

πŸ“° Work In The Press

Some work the department performed on trade in 'hatha jodi': a root believed to bring good luck in some cultures. Trade in the plant has been fuelling illicit trade in animal parts.

My work on captive populations of Raja undulata has been featured on BBC Earth and Manchester University News.