Introduction to Bioinformatics

An introduction to bioinformatics at APAF

One of the main focuses of our group has been the development of a data analysis pipeline for label free experiments with complex experimental design, motivated by a series of drought stress experiments involving multiple conditions ran by researchers at CBMS Macquarie University.

In the previous years we developed a series of bioinformatics and statistical analyses to partially automate the annotation and provide a starting point to the analysis of such data sets, and 2010-2011 saw the publication of two of the resulting articles [1-2] in the Journal “Proteomics”. These efforts have continued more recently with forays into gene ontology based functional analysis, likewise aimed at multi-condition complex experiments. Some yet unpublished work using this approach has shown promise so far, and won one of the student poster prizes at the recent Lorne proteomics conference [3].

We also have Ingenuity Pathway Analysis (IPA) software available for human, mice and some yeast signalling pathways. If you require IPA software to be used with results from your samples please let us know.

Dr. Dana Pascovici

[1] Mirzaei, M., Pascovici, D., Keighley, T., George, I., Voelckel, C., Heenan, P. B. and Haynes, P. A. (2011), Shotgun proteomic profiling of five species of New Zealand Pachycladon. PROTEOMICS, 11: 166–171. doi: 10.1002/pmic.200900816
[2] Gammulla, C. G., Pascovici, D., Atwell, B. J. and Haynes, P. A. (2010), Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low-temperature stress. PROTEOMICS, 10: 3001–3019. doi: 10.1002/pmic.201000054
[3] Mirzaei, M., Pascovici, D., Keighley, T., Atwell, B.J. and Haynes, P.A., Differential Regulation of Aqualporins and Small GTPases proteins in rice leaves subjected to drought stress and recovery, winning student poster at the Lorne Proteomics Conference, 2011.