Emma Hobbs

PhD Candidate

Originally from England, Emma obtained a BSc (Hons) in Biochemistry from the University of Surrey. Her undergraduate degree included a 12-month industrial placement at GlaxoSmithKline’s Medical Research Centre (Hertfordshire, England), working within the Protein and Cellular Sciences department to design and generate candidate protein targets. Afterwards, in September 2019 Emma moved to St Andrews as a PhD student under the joint supervision of Dr Tracey Gloster (St Andrews), Dr Leighton Pritchard (Strathclyde) and Dr Sean Chapman (James Hutton).

Emma’s research focuses on data mining genomes to identify carbohydrate processing enzymes (CAZymes) for industrial exploitation in biofuel production. Specifically, Emma uses bioinformatics techniques to data-mine fungal genomes to identify potential plant cell-wall degrading enzymes. Emma is also exploring the evolution of CAZomes (all CAZymes within genomes of interest) in plant pathogenic and non-pathogenic bacteria. Understanding these repertoires of enzymes may influence the design of enzyme cocktails for industrial degradation of biomass, and elucidate the evolutionary arms race between plant host and pathogen.

Emma’s laboratory work includes:

  • Using X-ray crystallography techniques to resolve the structural fold of novel plant cell-wall degrading enzymes
  • Design enzymatic assays to
  • Use synthetic biology approaches to optimise CAZymes carbohydrate processing properties of potential use in biofuel production.

In addition to her research, Emma has helped at several Software Carpentry workshops, hosted by the Industrial Biotechology Innovation Centre (iBioIC) and the Software Sustainability Institute (SSI).

Outside university, Emma frequently goes hiking in the Scottish wilderness, knits and plays video games.

Education/Academic Qualifications and Experience

Doctorate of Philosophy (PhD)
University of St Andrews
University of Strathclyde
James Hutton Institute
Sept 2019 - Dec 2023

Laboratory Demonstrator
University of St Andrews
Sept 2022 - Sept 2023

PhD Industrial Placement
Bright Ascensions
Dundee, Scotland
July 2021-Oct 2021

Bachelor of Science (BSc, (Hons) - Biochemistry
University of Surrey
Sept 2015 - July 2019

Industrial Placement
GlaxoSmith Kline
Stevenage, Hertfordshire, England

Supervisors

  • Tracey Gloster (University of St Andrews)
  • Leighton Pritchard (University of Strathclyde)
  • Sean Chapman (James Hutton Institute)

Research Output

Software

Packages and repositories Emma has developed during her PhD:

cazy_webscraper - DOI: 10.5281/zenodo.6343936
A tool to retrieve annotation, sequence, structure, genomic and taxonomic data from the CAZy, NCBI, UniProt, RSCB PDB and GTDB databases, and build a local SQLite3 CAZyme database.

pyrewton - DOI: 10.5281/zenodo.3876218
A Python package for the independent and comprehensive evaluation of CAZyme classifications, and the creation of a comprehensive CAZome database (a database cataloguing proteomic data for all CAZymes within the genomes of species of interest).

cazomevolve - DOI: 10.5281/zenodo.6614827
A Python package to explore the evolution of CAZomes, including the identification of networks of co-evolving CAZy families in genomes of interest.

saintBioutils - DOI: DOI: 10.5281/6541551
A collection of miscellenaious functions for bioinformatics tools and analyses

Publications

Hobbs, Emma E. M.; Pritchard, Leighton; Chapman, Sean; Gloster, Tracey M. (2021): cazy_webscraper: For creating a local CAZyme database. figshare. Poster. doi.org/10.6084/m9.figshare.14370860

Hobbs, Emma E. M.; Gloster, Tracey M.; Chapman, Sean; Pritchard, Leighton (2021): Comprehensive evaluation of CAZyme prediction tools in fungal and bacterial species. figshare. Poster. doi.org/10.6084/m9.figshare.14370836

Hobbs, Emma E. M.; Pritchard, Leighton; Gloster, Tracey M.; Chapman, Sean (2021): cazy_webscraper - getting started. figshare. Poster. doi.org/10.6084/m9.figshare.14370869

Email: eemh1@st-andrews.ac.uk
ORDIC
GitHub
LinkedIn
Gloster Laboratory website