Welcome to the website of Kat Holt and her microbial genomics lab, based at the University of Melbourne.

To see what we get up to in the lab, check out the blog posts on recent papers. Lab members are listed here.


The Lab

We are a computational and genome sequencing lab in the Department of Biochemistry and Molecular Biology (School of Biomedical Sciences, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne), located in the Bio21 Institute. We work closely with collaborators in other research, public health and hospital labs to develop projects and generate data. We have recently set up in-house sequencing capacity for 16S and whole genome sequencing using Illumina MiniSeq and Oxford Nanopore platforms. We then use a combination of phylogenetics, sequence analysis, comparative genomics, spatiotemporal analysis and epidemiological methods to analyse and interpret the data. Much of this is done using high performance computing. See research areas and fundingpublications and blog posts (to the right) for more.

We publish open access wherever we can (usually with preprints available before peer review, links on the right), deposit all data in public databases and release open source code.

Info on current and past group members are here. Some recent highlights from lab members include:

  • Jane Hawkey was awarded her PhD and graduated in December 2017. She was also awarded a Victoria Fellowship in Life Sciences from the Victorian state government, to undertake a research visit to Cambridge in 2018.
  • Ryan Wick won a 2015 national innovation award for his Bandage (assembly graph viewer) software package, and in 2017 was invited to speak about his hybrid long/short read assembler Unicycler at the Oxford Nanopore user meetings in London and New York.
  • Claire Gorrie won the 2015 People’s Choice Award for her 3 Minute Thesis presentation and was selected to give a TEDx talk in October 2017. She is now working at the MDU Public Health lab while putting the final touches on her thesis.
  • Sebastian Duchêne joined the lab in June 2016 as a Mackenzie Postdoctoral Fellow, and was also awarded a 2017 Dyason Fellowship and 2017 Computational Biology Hallmark Initiative seed funding grant.
  • Kelly Wyres secured a 2017 Early Career Researcher grant from the University of Melbourne.
  • Zoe Dyson and Margaret Lam took out the prizes for best talk and best poster at the 2016 Faculty of Medicine postdoc symposium, and together with Danielle Ingle were awarded 2017 Early Career Researcher Collaborative grants from the School of Biomedical Sciences.
  • Danielle Ingle completed her PhD in the lab and graduated in March 2017. While we were sad to see her leave the lab, we are thrilled that she has commenced a postdoc at ANU and MDU working on the COMPARE project, and we will get to continue working with her as a collaborator!

Students interested in joining the lab should first read about graduate research programmes at the University of Melbourne and contact Kat to discuss potential projects.


Kat Holt – Bio

Kat is currently a Viertel Senior Medical Research Fellow, HHMI-Gates International Research Scholar and Associate Professor at the University Of Melbourne.

She has a double degree BA/BSc from the University of Western Australia, majoring in Biochemistry, Applied Statistics and Philosophy, with Honours in Genetics (focusing on plant gene expression). After a short stint in the Bioinformatics Division at the Walter and Eliza Hall Institute, Kat went to the University of Cambridge to undertake a PhD in Molecular Biology at the Wellcome Trust Sanger Institute. There she studied the genomics of typhoid fever, under the supervision of Gordon Dougan, Julian Parkhill and Duncan Maskell.

In 2010 Kat returned to Australia to take up an NHMRC Early Career Fellowship in the Department of Microbiology and Immunology at the University of Melbourne. While working as a research fellow, she also undertook a Masters in Epidemiology at the University of Melbourne, graduating in 2011.

In late 2012, Kat was recruited to a lab head position in the Department of Biochemistry and Molecular Biology at the University of Melbourne, and established a lab in the Bio21 Institute.

In addition to being named a Howard Hughes Medical Institute and Gates Foundation International Research Scholar and Viertel Foundation Senior Medical Research fellow, Kat has been awarded the Australian Academy of Science’s Gottschalk Medal for early career medical research (2017), a Georgina Sweet Award for Women in Quantitative Biomedical Science (2016), L’Oréal-UNESCO Rising Talents Fellowship (2015), the NHMRC Research Excellence Award for the Top-Ranked Career Development Fellow (2014) and L’Oréal For Women In Science Australia & NZ Fellowship (2013).

A list of Kat’s publications can be found via Google Scholar, and blog posts on recent papers are collated here. Kat is also a Senior Editor of the journal Microbial Genomics, published by the UK’s Microbiology Society.

Kat (centre) and lab members at AMIGOS in Sydney, April 2015

Kat (centre) and lab members at AMIGOS in Sydney, April 2015