Jamie McGowan
Postdoctoral Scientist - Earlham Institute
I am a postdoc in the Swarbreck Group at the Earlham Institute. I am working on sequencing protist genomes as part of the Darwin Tree of Life Project (DToL), which aims to sequence the genomes of all ~70,000 eukaryotic species in Britain and Ireland. My main interests are in the broad areas of evolutionary genomics and bioinformatics. I am particularly interested in microbial/single-celled eukaryotes (protists) as these include the most under sampled, diverse lineages of eukaryotes and some of the most devastating pathogens.
Prior to joining the Earlham Institute, I carried out my PhD research at Maynooth University with Dr David Fitzpatrick. Here, I applied a mix of bioinformatics, genomics, and proteomics techniques to study genomic evolution in Phytophthora and other oomycete species. These microbial pathogens represent one of the biggest threats to global food security and natural ecosystems. I also obtained a first-class honours BSc degree in Biology and Computer Science from Maynooth University.
Research Interests
Education
| Year | University | Degree | Subject |
|---|---|---|---|
| 2016 - 2020 | Maynooth University | PhD | Bioinformatics and Evolutionary Genomics |
| 2012 - 2016 | Maynooth University | BSc (Double Honours) | Biology and Computer Science (First Class Honours) |
Publications
Multiple Independent Genetic Code Reassignments of the UAG Stop Codon in Phyllopharyngean Ciliates
Jamie McGowan, Thomas A. Richards, Neil Hall, David Swarbreck
bioRxiv Preprint
Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids
Jamie McGowan, Estelle S. Kilias, Elisabet Alacid, James Lipscombe, Benjamin H. Jenkins, Karim Gharbi, Gemy G. Kaithakottil, Iain C. Macaulay, Seanna McTaggart, Sally D. Warring, Thomas A. Richards, Neil Hall, David Swarbreck
PLOS Genetics
F-box receptor mediated control of substrate stability and subcellular location organizes cellular development of Aspergillus nidulans
Özlem Sarikaya Bayram, Özgür Bayram, Betim Karahoda, Cindy Meister, Anna M. Köhler, Sabine Thieme, Nadia Elramli, Dean Frawley, Jamie McGowan, David A. Fitzpatrick, Kerstin Schmitt, Leandro Jose de Assis, Oliver Valerius, Gustavo H. Goldman, Gerhard H. Braus
PLOS Genetics
Genome of Pythium myriotylum Uncovers an Extensive Arsenal of Virulence-Related Genes among the Broad-Host-Range Necrotrophic Pythium Plant Pathogens
Paul Daly, Dongmei Zhou, Danyu Shen, Yifan Chen, Taiqiang Xue, Siqiao Chen, Qimeng Zhang, Jinfeng Zhang, Jamie McGowan, Feng Cai, Guan Pang, Nan Wang, Taha Majid Mahmood Sheikh, Sheng Deng, Jingjing Li, Hüseyin Okan Soykam, Irem Kara, David A. Fitzpatrick, Irina S. Druzhinina, Günseli Bayram Akcapinar, Lihui Wei
Microbiology Spectrum
Dual-transcriptomic, microscopic, and biocontrol analyses of the interaction between the bioeffector Pythium oligandrum and the Pythium soft-rot of ginger pathogen Pythium myriotylum
Paul Daly, Siqiao Chen, Taiqiang Xue, Jingjing Li, Taha M. Sheikh, Qimeng Zhang, Xuehai Wang, Jinfeng Zhang, David Fitzpatrick, Jamie McGowan, Xiujuan Shi, Sheng Deng, Min Jiu, Dongmei Zhou, Irina Druzhinina, Lihui Wei
Frontiers in Microbiology
Genomic diversity, chromosomal rearrangements, and interspecies hybridization in the Ogataea polymorpha species complex
Sara J. Hanson, Eoin Ó Cinnéide, Letal I. Salzberg, Kenneth H. Wolfe, Jamie McGowan, David A. Fitzpatrick, Kate Matlin
G3: Genes, Genomes, Genetics
Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae
Jamie McGowan, Richard O'Hanlon, Rebecca A Owens, David A Fitzpatrick
Microorganisms
Recent Advances in Oomycete Genomics
Jamie McGowan, David A Fitzpatrick
Advances in Genetics
Characterisation of three Novel β-1, 3 glucanases from the Medically Important House Dust Mite Dermatophagoides pteronyssinus (airmid).
Rose Waldron, Jamie McGowan, Natasha Gordon, E Bruce Mitchell, David A Fitzpatrick, Sean Doyle
Insect Biochemistry and Molecular Biology
Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23
Eoin O'Connor, Jamie McGowan, Charley GP McCarthy, Anica Amini, Helen Grogan, David A Fitzpatrick
G3: Genes, Genomes, Genetics
Control of Development, Secondary Metabolism and Light-Dependent Carotenoid Biosynthesis by the Velvet Complex of Neurospora crassa
Ozlem Sarikaya Bayram, Anne Dettmann, Betim Karahoda, Nicola M Moloney, Tereza Ormsby, Jamie McGowan, Sara Cea-Sanchez, Alejandro Miralles-Duran, Guilherme TP Brancini, Eva M Luque, David A Fitzpatrick, David Canovas, Luis M Corrochano, Sean Doyle, Eric U Selker, Stephan Seiler, Ozgur Bayram
Genetics
Proteome and Allergenome of the European House Dust Mite Dermatophagoides pteronyssinus
Rose Waldron, Jamie McGowan, Natasha Gordon, Charley McCarthy, E Bruce Mitchell, David A Fitzpatrick
PLOS One
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB)
Jamie McGowan, Kevin P Byrne, David A Fitzpatrick
Genome Biology and Evolution (GBE)
Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal
Jamie McGowan, David A Fitzpatrick
mSphere
Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite
Rose Waldron, Jamie McGowan, Natasha Gordon, Charley McCarthy, E Bruce Mitchell, Sean Doyle, David A Fitzpatrick
Genome Announcements
Tools
OGOB - Oomycete Gene Order Browser
A curated database that facilitates comparative genomic and syntenic analyses of oomycete species
OGOBBUSCO Phylogenomics
A simple Python pipeline to construct species phylogenies using BUSCO proteins/genes with supermatrix and supertree appraoches
GitHubSkimSeqQC Pipeline
A snakemake pipeline for QC of low-coverage skim-sequencing of genome and transcriptome data
GitHubCoassembly Pipeline
A snakemake pipeline to generate and QC genome (co)assemblies and transcriptome alignment
GitHubAssembly Kmer Clustering
A Python/R tool to visualise and cluster contigs from a genome assembly. Useful for metagenomes or contaminated assemblies
GitHubOomycete Networks
An interactive website to explore sequence similarity networks of oomycete effector proteins
Oomycete Networks