I provide bioinformatics support within the Food Innovation and Health Institute Strategic Programme. My role involves developing analytical strategies and actively contributing to the data analysis of studies across three key areas:
- Analysis of genome wide human transcriptomic databases generated by RNA-sequencing from in vitro experiments with cell models and biopsy tissues collected from human intervention studies,
- Plant genomic analysis with a major focus on RNA-sequencing analyses of wheat and brassica, and
- Metagenomics and metatranscriptomic analysis of human gut microbiota.
I trained as a Computer Scientist, starting with a Bachelor’s in Engineering from the ITCH II, followed by a MSc in the subject of content-based image retrieval from CENIDET. During my PhD at the University of East Anglia, my research focused on the subject of colour constancy, specifically regarding illuminant estimation. Finally, I have postdoctoral experience in bioinformatics from my post at the Earlham Institute where I performed analyses of transcriptomics and metabolomics data, applying statistical methods and machine learning approaches.
Anuradha Ravi, Perla Troncoso-Rey, Jennifer Ahn-Jarvis, Kendall R. Corbin, Suzanne Harris, Hannah Harris, Alp Aydin, Gemma L. Kay, Thanh Le Viet, Rachel Gilroy, Mark J. Pallen, Andrew J. Page, Justin O’Grady, Frederick J. Warren (2021) Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies2021-05-11, DOI: 10.1101/2021.05.11.441322 [pre-print]
Mikhaela Neequaye, Sophia Stavnstrup, Wendy Harwood, Tom Lawrenson, Penny Hundleby, Judith Irwin, Perla Troncoso-Rey, Shikha Saha, Maria H. Traka, Richard Mithen, and Lars Østergaard (2021) CRISPR-Cas9-Mediated Gene Editing of MYB28 Genes Impair Glucoraphanin Accumulation of Brassica oleracea in the Field, https://doi.org/10.1089/crispr.2021.0007
Mikhaela Neequaye, Shikha Saha, Martin Trick, Burkhard Steuernagel, Perla Troncoso-Rey, Frans van den Bosch, Pauline Stephenson, Maria H Traka, Lars Østergaard, Richard Mithen (2020) The Effect of Introgression of an R2R3 MYB Transcription Factor on Sulphur Metabolism in Brassica oleracea, https://doi.org/10.1101/2020.08.02.232819 [pre-print]
Pippa J. Gunn,Camilla Pramfalk,Val Millar,Thomas Cornfield,Matthew Hutchinson,Elspeth M. Johnson,Shilpa R. Nagarajan,Perla Troncoso-Rey,Richard F. Mithen,Katherine E. Pinnick,Maria H. Traka,Charlotte J. Green,Leanne Hodson (2020) Modifying nutritional substrates induces macrovesicular lipid droplet accumulation and metabolic alterations in a cellular model of hepatic steatosis, https://doi.org/10.14814/phy2.14482
Maria H Traka, Antonietta Melchini, Jack Coode-Bate, Omar Al Kadhi, Shikha Saha, Marianne Defernez, Perla Troncoso-Rey, Helen Kibblewhite, Carmel M O’Neill, Federico Bernuzzi, Laura Mythen, Jackie Hughes, Paul W Needs, Jack R Dainty, George M Savva, Robert D Mills, Richard Y Ball, Colin S Cooper, Richard F Mithen (2019) Transcriptional changes in prostate of men on active surveillance after a 12-mo glucoraphanin-rich broccoli intervention—results from the Effect of Sulforaphane on prostate CAncer PrEvention (ESCAPE) randomized controlled trial, AJCN, https://doi.org/10.1093/ajcn/nqz012.
Al Kadhi O., Traka M., Melchini A., Troncoso-Rey P., Jurkowski W., Defernez M., Pachori P., Mills R. D., Ball R. Y., Mithen R.(2017) Increased transcriptional and metabolic capacity for lipid metabolism in the peripheral zone of the prostate may underpin its increased susceptibility to cancer, Oncotarget 8 84902-84916 doi: 10.18632/oncotarget.17926