I am a post-doctoral Research Associate at the Virology Division in the Department of Pathology at the University of Cambridge working with Dr. Andrew Firth.
Biography
I have previously completed a Computational Genomics and Training (CGAT) fellowship at the University of Oxford and a PhD in endogenous retroviral evolution at the University of Nottingham.
Research
My main research focus is detecting novel and under-researched RNA viruses in non-model organisms, particularly insects and other arthropods, and characterising their evolution. I am also interested in software development for computational biology and have developed the tool CIAlign (github.com/KatyBrown/CIAlign) for cleaning and visualising multiple sequence alignments.
Publications
Key publications:
Identification of RNA Virus–Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets
Molecular Biology and Evolution
2023-04-04 | Journal article
Contributors: Ingrida Olendraite; Katherine Brown; Andrew E Firth; Thomas Leitner
Identification of RNA virus-derived RdRp sequences in publicly available transcriptomic datasets
2022-10-18 | Preprint
Contributors: Ingrida Olendraite; Katherine Brown; Andrew E. Firth
A novel map of human p53 response elements uncovers evidence of selection pressures and variants similar to Li-Fraumeni Syndrome mutations
medRxiv
2022-09-29 | Preprint
Contributors: Ping Zhang; Katherine Brown; David Barnes; Isaac Kitchen-Smith; David Sims; Adrienne Flanagan; Solange De Noon; Peter Van Loo; Steven Hargreaves; Will Cross et al.
Women in the European Virus Bioinformatics Center
Viruses
2022-07 | Journal article | Author
DOI: 10.3390/v14071522
Contributors: Franziska Hufsky; Abecasis AB; Patricia Agudelo-Romero; Magda Bletsa; Katherine Brown; Claudia Claus; Stefanie Deinhardt-Emmer; Li Deng; Caroline C. Friedel; Maria Ines Gismondi et al.
Evaluating ribosomal frameshifting in CCR5 mRNA decoding
Nature
2022-04-21 | Journal article
CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments
Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression
Germline and Somatic Genetic Variants in the p53 Pathway Interact to Affect Cancer Risk, Progression, and Drug Response
Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression
2021-11-19 | Preprint
Contributors: Georgia M. Cook; Katherine Brown; Pengcheng Shang; Yanhua Li; Lior Soday; Adam M. Dinan; Charlotte Tumescheit; A. P. Adrian Mockett; Ying Fang; Andrew E. Firth et al.
Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus
pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread
PLOS Pathogens
2021-08-16 | Journal article
Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection
PLOS Pathogens
2021-06-17 | Journal article
pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread
2021-04-13 | Preprint
Contributors: Tomasz H. Benedyk; Julia Muenzner; Viv Connor; Yue Han; Katherine Brown; Kaveesha J. Wijesinghe; Yunhui Zhuang; Susanna Colaco; Guido A. Stoll; Owen S. Tutt et al.
CIAlign - A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments
2020-09-16 | Preprint
Contributors: Charlotte Tumescheit; Andrew E. Firth; Katherine Brown
Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus
2020-08-11 | Preprint
Contributors: Chris H. Hill; Georgia M. Cook; Sawsan Napthine; Anuja Kibe; Katherine Brown; Neva Caliskan; Andrew E. Firth; Stephen C. Graham; Ian Brierley
Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression
Scientific Reports
2019-12 | Journal article
ICTV Virus Taxonomy Profile: Solinviviridae
CGAT-core: a python framework for building scalable, reproducible computational biology workflows
F1000Research
2019-04-04 | Journal article
ICTV Virus Taxonomy Profile: Polycipiviridae
Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma
Transcriptional and Translational Landscape of Equine Torovirus
Is gibbon ape leukaemia virus still a threat?
Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates
Characterisation of a group of endogenous gammaretroviruses in the canine genome
The Veterinary Journal
2013-04 | Journal article
Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing.
Virology
2012-10-11 | Journal article
Teaching and Supervisions
Teaching:
2024/2025:
- Foundations of phylogenetic inference - Training Lead, Trainer
2022/2023:
- SARS-CoV-2 Genomics - Training Lead
2021/2022:
- SARS-CoV-2 Genomics - Training Lead
