I’m a PhD candidate at La Trobe University in Melbourne. I completed my undergrad degree in Psychological Science, and I’m now delving into the exciting world of biology and ‘omic data’. My research focuses on investigating the biological mechanisms underlying ocular growth control and the development of myopia (short-sightedness). With my submission date (almost) in sight, I’ve started this blog to chronicle my successes and failures as I explore ways to analyse, interpret, and display my data.
For more about my research, check out ResearchGate or click on the publication links below.
Publications
Murphy, M., Riddell, N., Crewther, D.P., Simpson, D., & Crewther, S.G. (2018). Temporal whole field sawtooth flicker without a spatial component elicits a myopic shift following optical defocus irrespective of waveform direction in chicks. PeerJ, 7, e6277.
Giummarra, L., Crewther, S.G., Riddell, N., Murphy, M., & Crewther, D.P. (2018). Pathway analysis identifies altered mitochondrial metabolism, neurotransmission, structural pathways and complement cascade in retina/RPE/choroid in chick model of form-deprivation myopia. PeerJ, 6, e5048.
Riddell, N., Faou, P., Crewther, S.G. (2018). Short term optical defocus perturbs normal developmental shifts in retina/RPE protein abundance. BMC Developmental Biology, 18, 18.
Riddell, N., Faou, P., Murphy, M., Giummarra, L., Downs, R., & Crewther, S.G. (2017). The retina/RPE proteome in chick myopia and hyperopia models: commonalities with inherited and age-related ocular pathologies. Molecular Vision, 23, 872-888.
Riddell, N., & Crewther, S. G. (2017). Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets. Scientific Reports, 7, 9719.
Riddell, N., & Crewther, S. G. (2017). Integrated comparison of GWAS, transcriptome, and proteomics studies highlights similarities in the biological basis of animal and human myopia. Investigative Ophthalmology & Visual Science, 58(1), 660-669.
Riddell, N., Giummarra, L., Hall, N. E., & Crewther, S. G. (2016). Bidirectional expression of metabolic, structural, and immune pathways in early myopia and hyperopia. Frontiers in Neuroscience, 10.
Riddell, N., Hugrass, L., Jayasuriya, J., Crewther, S. G., & Crewther, D. P. (2016). An asymmetric outer retinal response to drifting sawtooth gratings. Journal of Neurophysiology, 115(5), 2349-2358.
Dear Nina,
ReplyDeleteI hope you are doing well. I found your blog very informative. I'm new to R and I need a bit of help. I'm interested in GOPlot (chord diagram) and I'd like to use it to illustrate overlapping genes across 5 different animals, so basically I have 5 columns (each column contains numnber of genes that interact with one or more columns).
I managed to import the file into R as CSV but it didn't go well when I wanted to have it done! what do you suggest?
Many thanks,
Saleh
Hi Saleh,
ReplyDeleteIf you want to use the GOplot package just replace the gene ontology information with your species names when formatting the files (take a look at the GOplot tutorial - https://wencke.github.io/ - for examples). Alternatively, you could try a more flexible generator like circos (http://circos.ca/) that might be better suited to your data. If you have issues, email me an example and I'll try to get it working for you (nina.riddell@gmail.com).
Cheers,
Nina
hii nina...I was also trying to make chord diagram for my gene ontology data...but facing problem in making proper input file format..please can you share your input file so that i can understand where is problem...and how the matrix should be formed...please help me...
ReplyDeleteDear Pooja,
DeleteFor your query, I think the best tool can support you is Circos. Please find this fantastic tool here: http://circos.ca/