Month: August 2013

Magnets!

Whoa, Torben really raised the bar for the scientific rigor and quality of this blog. A bar that I will happily swoop well under without it even grazing the top of my head.

The last couple of months have largely focused around preparing for our Early Stage Assessments, which entails a short report and a viva consolidating what we have been doing since we started and what our plans for the next two years are. Sounds fun right? It’s actually not. It is however a good opportunity to think about what has worked, what hasn’t and the direction our research is going in.

A network approach to integrate different –omics data

My everyday commute to uni is approximately 1 hour, so I try to use this time efficiently by reading relevant literature for my PhD project.  Inspired by a paper from Kuchel et al. in 2010 I developed a network approach to integrate different -omics data, such as gene expression data (transcriptomics) and NMR and/or MS data (metabolomics). My initial approach is outlined in this blog post.

Creating a differential gene co-expression network

Suppose you have gene expression data from a disease group and a healthy control group, and you create a gene co-expression network (where nodes represent genes and edges represent high absolute correlation values), such that high correlated gene profiles in the control group are represented by green edges, red edges represent high correlations in the disease phenotype and black edges are drawn of two gene profiles are correlated in both, control and disease phenotype.

It’s hard

On the occasional instant that I decide to return home, be it only for those couple days a year that I feel equipped enough to be haunted again by that small town I grew up in, I continuously get asked the question – ‘so what are you up to now’?

I start with the polite, ‘oh hello stranger, long time no see’ – stranger being the key word, you know for those former secondary school class comrades of yours that you only still vaguely recognize through a certain social networking website. ‘Still in London mate, but doing a PhD now’… Awkward silence now, as they decide where such a position ranks against a proper job.

The Three Mantras

Well, I guess its my turn again 🙂 . In the past few weeks we have been preparing for our early stage review. Initially it felt it was just one of those milestones one has to jump through but how wrong I was. It has allowed me to rethink the aims of my project and to think about the best means of executing them.

I have also been thinking about what makes a great scientist over the past few weeks and it has become evident to me that everyone has their own way of getting there. However, there are three things that no professional scientist can ever avoid.