Lab Members

Fiona Whelan, Senior Lecturer, 2023 Lister Prize, 2024 UKRI Future Leaders Fellow (she/her)

Fiona is a bioinformatician, microbiologist, and evolutionary biologist at the University of Manchester. Previously, Fiona was an Anne McLaren Fellow at the University of Nottingham and a MSCA Postdoctoral Fellow (2018-20) in James McInerney's research group investigating gene co-occurrence patterns in microbial pangenomes. Fiona conducted her Ph.D. research on the human microbiome and cystic fibrosis in the laboratory of Dr. Michael G. Surette at McMaster University as a CIHR Doctoral and Cystic Fibrosis Canada scholar. Fiona also worked as a MSc with Dr. Dawn Bowdish, also at McMaster University, investigating the evolutionary history of a family of immune cell receptors with support from a Ontario Graduate Scholarship. When not in the lab, Fiona enjoys being outdoors - hiking, camping, swimming, running etc.!

Michelle Hardman, Postdoctoral Research Associate

Michelle is a Postdoctoral Research Associate in the Whelan Lab. Previously, she was at Swansea University, where she studied the effects of Manuka honey on cystic fibrosis (CF) pathogens using in vivo models. Prior to that, Michelle completed her PhD on CF microbiomes at Manchester Metropolitan University, where she also worked part-time as a microbiology teaching technician. In her free time, she enjoys cooking, walking, and spending time with friends and family.

Melissa Lawson, Postdoctoral Research Associate

Mel is a Postdoctoral Research Associate in the Whelan lab. Previously, she was the Director of Translational Biology (in vivo) at Microbiotica Ltd in Cambridge. Prior to this she was a Postdoctoral Research Associate with Profs Richard Grencis and Ian Roberts examining interactions between the host immune system, gut microbiome and intestinal parasites. From 2014-2018 Mel researched the impact of infant milk diets on shaping the early life gut microbiome as a Postdoctoral associate and MSCA postdoctoral fellow (2015-2017) in Prof Lindsay Hall’s lab at the Quadram Institute Bioscience in Norwich. Mel completed her PhD in Immunology in the laboratories of Profs Kathy McCoy and Andrew Macpherson examining the role of IgA on intestinal bacteria, and she has degrees in Pathobiology (MSc) and microbiology (BSc) from the University of Guelph, Canada. In her free time, Mel likes spending time outdoors with her family, yoga and cooking.

Francis Gyapong, NERC Envision DTP student (he/him)

Francis is a PhD student at the University of Nottingham having started in October 2023. He is an ENVISION DTP scholar who will work in the Whelan lab on The effects of environmental metals on the spread of antimicrobial resistance genes in the stickleback skin microbiome.. The project is co-supervised by Dr. Whelan, Prof. Andrew MacColl, and Dr. Hanna Hartikainen, and will include wet lab techniques and bioinformatic approaches. Before beginning his PhD, Francis earned a Master of Philosophy in Molecular Cell Biology of Infectious Pathogens in which he studied the microbes resident on face masks during the COVID-19 era and used the model organism Galleria mellonella to investigation the pathogenecity of isolated microbes. Francis likes music and video games outside of the lab!

Hannah Jones, Research Assistant (she/her)

Hannah is a research assistant at the University of Manchester. Previously, Hannah worked as a scientist at a microbiology-based contract research organisation, testing in vitro devices designed to remove biofilms within the wound care industry. She also worked at QIAGEN developing in vitro cancer diagnostic assays using digital PCR. Hannah conducted a BSc in Biological and Medical sciences and an MSc in International Public Health, where she investigated the microvascular system of sepsis patients in a hospital in Malawi. In the Whelan lab, Hannah will be investigating the strain diversity and microbe interaction in the cystic fibrosis lung microbiome. Out of work Hannah enjoys reading, hiking and weightlifting.

Prima Lesaso, MSc Bioinformatics and Systems Biology student (she/her)

Prima is a postgraduate student at the University of Manchester having started in September 2024. She is currently undertaking her first master’s project in the Whelan Lab, exploring the lung microbiome of people with cystic fibrosis via metagenomic analyses. The project is being supervised by Dr. Whelan and is being done entirely in silico. Prior to this, Prima earned a Bachelor’s of Science in Biological Sciences with an honours in Biotechnology at the University of Edinburgh, where the focus of her final year project was to conduct a meta-analysis of the Komagataella phaffii transcriptome in order to decipher its codon usage bias. This project was done under the supervision of Dr Giovanni Stracquadanio as well as current PhD candidate Anima Sutradhar. Outside of the lab, Prima is a massive jazz head and enjoys gardening, puzzles and being around animals.

Jacky You, MSc Bioinformatics and Systems Biology student

Jacky previously studied Biomedical Engineering (BEng) at University College London, with a particular focus on data analytics and programming in the medical and healthcare field. His final year project looked at evaluating different Machine Learning models that diagnose the disease Necrotising Enterocolitis from the abdominal X-rays of pre-term infants. Prior to this, Jacky participated in the pilot Research Internship scheme with the Royal Academy of Engineering, where he investigated a novel method to measure the biomechanics of the cornea using a bespoke imaging system. In his free time, Jacky likes cooking and hiking near Manchester.

Kaiwen Xiao, MSc Infection Biology student

You?

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Alumni

Rebecca Wallis Downham, Harry Smith Vacation Scholar (2022-23)

Rebecca is an undergraduate studying Biotechnology with a year in Computer Science at the University of Nottingham. As part of the Excel in Science programme, she is completing an internship investigating the effectiveness of different medias for growing bacteria isolated from the cystic fibrosis lung microbiome. Rebecca is keen to develop her skills and knowledge for a career in research and is super excited to be doing this in the Whelan lab!

Peter Anthony Oyom, BBSRC DTP Rotation student (2023)

Peter is a first year PhD student on the BBSRC Doctoral Training Partnership who began his rotation in the Whelan lab in October 2023. He will be studying the genomic diversity of the Prairie Epidemic Strain of iPseudomonas aeruginosa isolated from individuals with cystic fibrosis using a combination of microbiology assays and bioinformatics tools. Peter’s passion for microbiology arose from his work in clinical diagnostic laboratories, which motivated him to pursue an MSc in Clinical and Molecular Microbiology at the University of Nottingham. After graduating, Peter worked as an assistant technical officer with the NHS, and later became a registered biomedical scientist. Peter loves learning and has a broad interest in areas related to the microbiome, antimicrobial resistance and One Health. When away from work, he enjoys fiction novels, art and exploring natural environments.

Lily Moran, SREP undergraduate (2023)

Lily is a 4th year student at the University of Nottingham, and is currently undertaking a integrated Biochemistry Msci. She is with the Whelan lab as part of the School of Life Sciences Summer Research Experience programme, gaining experience in areas relating to both microbiology and data analysis. Her work focuses on investigating relationships between members of the Cystic Fibrosis lung microbiome, with the aim of identifying potential mutually-dependent species from sequencing data.

Iremide Sanyaolu, Wellcome Trust Biomedical Vacation Scholarship student (2023)

Iremide is a Microbiology undergraduate student at Trinity College Dublin. Iremide is interested in all things Microbiology particularly in the areas of anti-microbial resistance and microbial pathogenesis. In the Whelan lab, Iremide will be investigating the interactions between Staphylococcus species in the cystic fibrosis lung microbiome as well as using bioinformatics tools such as R programming for data analysis. Iremide is enthusiastic about participating in the research project at the Whelan lab, developing essential skills and hands-on experience that will assist in a career in research.

Katie Hodson, BBSRC DTP rotation student (2023)

Katie is currently in the first year of her PhD at the University of Nottingham and is completing a BBSRC DTP rotation in the Whelan lab. Katie is working on the competitive lottery model of microbiome assembly and is using a mixture of bioinformatics and wet lab work to investigate competition between bacteria in the cystic fibrosis lung microbiome. Before beginning her PhD, Katie completed an MRes in Molecular Genetics in which she researched non-canonical DNA replication in the archaeon Haloferax volcanii. Outside of the lab, Katie enjoys climbing and playing guitar!

Arooj Qamar, MSc Student (2020-22)

Arooj obtained her BSc from the University of Toronto in molecular biology, immunology and disease. Before deciding to pursue a Masters, Arooj worked as a Data Analyst for investment companies, and as a lab technician at UofT where she looked at disease resistance phenotypes in greenhouse crops. Arooj is now interested in combining the two experiences of wet lab biology and data analytics to pursue scientific questions in her MSc at Toronto Metropolitan University. Arooj is co-supervised between Dr. Whelan and Professor McPhee, investigating the molecular evolution of virulence in Shigella by exploring gene co-occurrence patterns in Shigella subgroups.

Luc Davies, MSc Student (2022)

Luc is currently undertaking an MSc in Bioinformatics at the University of Nottingham hoping to advance his analytical, statistical and computing skills having previously completed a BSc in Biology where he took a great interest studying genetics, particularly those related to infectious bacteria. Luc is currently working on his thesis which involves analysing large volumes of sequencing data taken from cystic fibrosis lung cultures in the hope of discovering and explaining patterns of co-occurrence in anti-microbial resistance genes in addition to compiling his work into a scalable and reusable Python-based pipeline.

Alexis Ayuketah, NSURP Undergraduate (2021-22)

Alexis joined the lab as a rising junior at the University of Maryland, studying Neuroscience on a pre-medicine track with an aim to achieve her MD/PhD in graduate school. Though her interests currently include molecular neuroscience and medicine, she still has interest in other fields, those of which include microbiology. In the Whelan Lab as an NSURP Mentee, she is currently studying species-species interactions in the cystic fibrosis microbiome, working with DNA sequencing data and the R programming language. When she is not in the lab, she loves to bake and play piano, guitar, or sing!

Odunayo Ogunnowo, BBSRC DTP Magnify Studentship student (2022)

Odunayo is an undergraduate Biomedical Science student at Nottingham Trent University. Odunayo has an interest in microbiology and medicine and is currently toying with the idea of doing both! She is very excited to spend her summer at the Whelan lab completing her research project on the interactions between Staphylococcus aureus and other members of the cystic fibrosis sputum microbiome with which she hopes to gain a wide range of skills in and out of the laboratory. Odunayo is always open to learn and try new things and is confident that the Whelan lab is the place to do so!

Jess O'Shea, BBSRC DTP Rotation student (2021)

Jess joined the lab as a BBSRC DTP rotation student at The University of Nottingham. Before joining the Whelan lab, Jess work in the medical manufacturing industry, specialising in microbiological environmental sampling, quality control and assurance, health and safety and medical device regulation. Jess previously was involved in research into Klebsiella bacteriophage and other alternative antimicrobials to combat antimicrobial resistance. In the Whelan lab, Jess was using bioinformatic tools like R to determine potential competition between microbes of the cystic fibrosis lung.

Gabriela Herrero, NSURP Undergraduate (2020)

Gabriela joined the lab as a senior at the University of Puerto Rico at Mayagüez studying Industrial Microbiology. Before joining the Whelan lab, Gabriela worked in the microbiology laboratory on research which focuses on describing the fungi present on the skin of Boa constrictors in Puerto Rico. Sadly, due to the pandemic, that project is on hold. In the Whelan lab, Gabriela was an NSURP mentee conducting a virtual bioinformatic project investigating species co-occurrence patterns in the lung microbiome of individuals with cystic fibrosis.

Robert Alston, NSURP Undergraduate (2020)

Robert joined the lab as a senior at North Carolina Central University studying Pharmaceutical Sciences. Robert's interests include looking at how the immune systems function can be improved upon naturally, with the use of plants and/or plant derived pharmaceuticals. With the current COVID 19 pandemic, his on-campus summer internship was canceled. As a NSURP mentee, Robert was investigating whether there are quantitative differences in the microbiota found in the lower respiratory tract of cystic fibrosis patients when they are in an exacerbated vs. stable state. He is also investigating whether these differences are universal or patient specific.