Category: Computational Genomics

You are into tumor evolution? And got a fancy model? Want to battle with the best?

Then check out the ICGC-TCGA DREAM Somatic Mutation Calling – Tumour Heterogeneity Challenge (SMC-Het).

These are the days of Big Science, my friend. You can’t just have a short name …

Quick recap: Last time we talked about tumor evolution and I presented a toy example to introduce key concepts. I also introduced the intra-tumor phylogeny problem: Given a sample of the genomes of clones in a tumour, reconstruct its `life history’. This problem consists of two sub-problems: (1)identification of clones, and (2) inferring evolutionary relationships between clones.

This problem falls into the general area of reconstructing phylogenetic trees — so how does inferring clonal trees compare to classical phylogenetic methods?

“Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer’s life history is encrypted in the somatic mutations present,”

write Nik-Zainal et al in the abstract of their 2012 Cell paper `The life history of 21 breast cancers‘. The key figure of their paper shows a phylogenetic tree of tumor development in a patient. The paper contains lots of computational work on analyzing and interpreting mutations based on deep-sequencing data, but –a big surprised but— the very last step of putting together the tree was done manually. Half the paper is describing the reasoning that Peter Campbell and his group used to condense all the evidence they had gathered from genomic data into the tree – but there is no algorithm.

Welcome back! The last post discussed rules 1-3: the importance to do a postdoc, a concise CV and a unique research statement. Like the last post this one is inspired by a Career Development Workshop at ISMB 2012 that I contributed to (download the slides).

There is still one thing missing from a standard application pack:

4. Pretend you care! The teaching statement

Together with CV and research statement some places ask you to submit a teaching statement. So write one. But don’t be fooled, it’s pretty low on the priority list (for the hiring committee, even if maybe not for you). Academic employers want three things from you: money, papers, and … long time nothing … teaching. I’m not saying they won’t ask you to teach for many hours a week, but when it comes to you being evaluated its money and papers (in that order) which…

Starting your own group is one of the most important steps in your scientific career — and one of the hardest.

Being invited to a Career Development Workshop at ISMB 2012 made me write down some of the advice that I had got when I was on the jobmarket a few years ago (and even put some of it on slides).

In a diverse and interdisciplinary field like computational biology it is very quite hard to come up with general rules that fit everyone. This is why I went down the self-indulgent route and revisited the CV and research statement I had prepared 4 years ago. (You’ll find a copy in the slides.) Some things are Ok, some things I would improve now — you will see, I’ll comment on this later. Let’s start with the basics: