About Me

I’m Lilly, a postdoctoral researcher in the Sheppard Lab within the INEOS Oxford Institute of Antimicrobial Research at the University of Oxford. I previously completed my PhD as part of The Wellcome Trust - University of Nottingham & University of Birmingham Joint 4 Year PhD Training Programme for Antimicrobials & Antimicrobial Resistance under the supervision of Professor Alan McNally and Dr. Nicole Wheeler. My research focuses on the evolution of multidrug resistance (MDR) in Escherichia coli, using a combination of comparative and functional genomic approaches to disentangle the evolutionary processes that can result in multidrug resistant phenotypes.

Beyond my research, I sit on my department’s Equality, Diversity, and Inclusion and Biology Research Staff Network Committees. I am also part of the Microbiology Society’s Early Career Microbiologists' Forum Executive Committee as the Publishing Panel representative and was previously elected as the Audit, Risk, and Evalutation representative.

Interests
  • Bioinformatics
  • Microbial evolutionary genomics
  • Pangenomics
  • Antimicrobial resistance
Education
  • PhD Microbiology & Infection, 2020-2023

    University of Birmingham

  • MRes Antimicrobials & Antimicrobial Resistance, 2019 - 2020

    University of Birmingham

  • MSc Mathematical Medicine & Biology, 2018 - 2019

    University of Nottingham

  • BSc Mathematics, 2015 - 2018

    Univeristy of Bimringham

Skills

Bioinformatics
Programming

python

Data analysis and visualisation

Teaching Experience

 
 
 
 
 
Instructor
Mar 2023 – Mar 2023 University of Birmingham
As part of a team, delivered a 5-day intensive course introducing the basics of microbial genomics with whole class teaching, demonstrations and 1-2-1 support.
 
 
 
 
 
Assistant Instructor
Jun 2021 – Jul 2021 Zoom
Assisted in delivering a 5 day online workshop teaching the basics of python to agricultural researchers in Africa as part of the BiXCoP programme.

Accomplish­ments

Coursera
Machine Learning
See certificate

Presentations

Poster Presentation: Distinct evolutionary trajectories in the Escherichia coli pangenome
Poster Presentation: Escherichia coli pangenome evolution is independent of phylogeny
Poster Presentation: Mining the Escherichia coli pangenome for lineage-specific metabolism

Recent Publications

Quickly discover relevant content by filtering publications.
(2022). GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes. Microbial Genomics.

DOI

(2022). Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microbial Genomics.

DOI

(2022). Prokaryote pangenomes are dynamic entities. Current Opinion in Microbiology.

DOI

(2021). The role of potentiating mutations in the evolution of pandemic Escherichia coli clones. EJCMID.

DOI

(2021). Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility. MGen.

DOI

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