Highlights
The actual blog posts are an unholy mix of very different topics and have very differing length and general usefulness.
On this page I will try to list some of my longer posts; those that are not exactly "news" items but can also be interesting days after I wrote them.
Association mapping
- What is association mapping? (posted Dec 8 2007)
- Association mapping and local genealogies (posted Feb 27 2008)
Genome analysis
- How much for that genome? (posted Sep 20 2008)
- Framework for whole genome sequencing (posted Oct 10 2008)
- Playing with spatial queries in MySQL (posted Jan 22 2009)
- Building a database for CoalHMM results (posted Mar 25 2009)
High performance computing
- Let's kill desktop computing (posted Jan 22 2008)
- Some thoughts on grid computing... (posted Oct 8 2008)
- Genome Technology interview on parallelism and R (posted Oct 15 2008)
Programming
- GSL and C++ (posted May 27 2008)
- Profiling Python (posted Sep 23 2008)
- Trying out Boost.Test (posted Oct 8 2008)
- Yet another Newick parser (posted Jan 19 2009)
Phylogenetics
- How deterministic is neighbour-joining anyway? (posted Jul 23 2008)
- On gene trees and species trees (posted Feb 12 2009)
Research life
- Thoughts on peer-reviewing (posted Feb 24 2008)
- Postdoc life vs PI life (posted May 9 2008)
- I guess I've been lucky (posted May 17 2008)
Speciation
- Mapping human genetic ancestry (posted Jan 30 2008)
- Estimating local ancestry (posted Feb 26 2008)
- On segment lengths, going back in time, in the coalescence process. Part 1: The ancestry of a single species (posted Feb 23 2009)
- On segment lengths, going back in time, in the coalescence process. Part 2: The ancestry of two species (posted Feb 27 2009)
Statistical alignment
- Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes (posted Jan 9 2008)
- Uncertainty in inferred alignments (posted Mar 3 2008)
- Heads or tails and reliable alignments (posted Mar 23 2008)
Statistics
- The problem with p-values (posted Jan 28 2009)
- What is a p-value? (posted Jul 1 2009)
- True positives and false positives (posted Jul 2 2009)
- True positives and large sample sizes (posted Jul 5 2009)
- The problem with confidence intervals (posted Aug 7 2009)
Teaching
- Learning how to teach and hating it (posted Mar 8 2008)
- Programming for (non-computer) scientists (posted Jun 6 2008)
- Teaching programming in bioinformatics (posted Sep 16 2008)
- Why do we need a separate class for teaching programming in bioinformatics? (posted Sep 19 2008)
- First week of Applied Programming (posted Nov 5 2008)