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Bioinformatics Training

 

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
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
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687

CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments

PeerJ
2022-03-15 | Journal article
Part of ISSN: 2167-8359

Ribosome profiling of porcine reproductive and respiratory syndrome virus reveals novel features of viral gene expression

eLife
2022-02-28 | Journal article
Part of ISSN: 2050-084X

Germline and Somatic Genetic Variants in the p53 Pathway Interact to Affect Cancer Risk, Progression, and Drug Response

Cancer Research
2021 | Journal article
Part of ISSN: 0008-5472

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

Nucleic Acids Research
2021-11-18 | Journal article
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread

PLOS Pathogens
2021-08-16 | Journal article
Part of ISSN: 1553-7374

Manipulation of the unfolded protein response: A pharmacological strategy against coronavirus infection

PLOS Pathogens
2021-06-17 | Journal article
Part of ISSN: 1553-7374

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
Part of ISSN: 2045-2322

ICTV Virus Taxonomy Profile: Solinviviridae

Journal of General Virology
2019-05-01 | Journal article
Part of ISSN: 0022-1317
Part of ISSN: 1465-2099

CGAT-core: a python framework for building scalable, reproducible computational biology workflows

F1000Research
2019-04-04 | Journal article
Part of ISSN: 2046-1402

ICTV Virus Taxonomy Profile: Polycipiviridae

Journal of General Virology
2019-04-01 | Journal article
Part of ISSN: 0022-1317
Part of ISSN: 1465-2099

Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma

Journal of Virology
2018-10-17 | Journal article
Part of ISSN: 0022-538X
Part of ISSN: 1098-5514

Transcriptional and Translational Landscape of Equine Torovirus

Journal of Virology
2018-06-27 | Journal article
Part of ISSN: 0022-538X
Part of ISSN: 1098-5514

Is gibbon ape leukaemia virus still a threat?

Mammal Review
2017-01 | Journal article
Part of ISSN: 0305-1838

Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates

Journal of Virology
2014-11-01 | Journal article
Part of ISSN: 0022-538X
Part of ISSN: 1098-5514

Characterisation of a group of endogenous gammaretroviruses in the canine genome

The Veterinary Journal
2013-04 | Journal article
Part of ISSN: 1090-0233

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