Mailund on the Internet

I’m off to Leipzig to visit Svante Pääbo’s group at the Max-Planck Institute there, to try to get in on future Neanderthal analysis.

The first Neanderthal paper should be out soon(ish) so of course it is too late to get in on that, but we hope to be able to use our CoalHMM methodology on future data.

I don’t know how much I will be able to blog while away, so you might not hear from me for a few days… we will see.

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There’s an intersting interview with Svante Pääbo here. In case you’ve been living under a rock the last few years: Svante Pääbo is running the Neanderthal genome sequencing program.

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Yeah, I know I’m a day late with my list of the blog posts I found interesting during the week, but yesterday was my birthday and I didn’t spend it at the computer.

Human evolution

1. A burst of segmental duplications in the genome of the African great ape ancestor (Nature)
   1. Did burst of gene duplication set stage for human evolution? (Science Daily)
   2. A burst of DNA duplication in the ancestor of humans, chimps and gorillas (Not exactly rocket science)
   3. Is human uniqueness a matter of copy number? (Gene expression)
2. How diverse were early hominoids? (Greg Laden)

Neanderthal genome

1. Neanderthal DNA revealed (partially) on Darwin’s 200th birthday (Genome Canada blogs)
2. What makes us human? Neanderthal genome holds clues (Wired)
3. Neanderthal genome gets a first draft (Scientific blogging)

Teaching

1. The mystery of the $150 textbooks (Statistical modeling)
   1. The economics of textbooks (Me!)
   2. More on those $150 textbooks (Statistical modeling)
   3. Hey, nobody offered me $8000 (Statistical modeling)

Publishing

1. Impact factors and Physical Review Letters (Biocurious)
2. Hypocrisy inside open access journals (The secret microbe)

3. Commenting on scientific articles (Nascent)

4. Google Peer Review!? (A blog around the clock)

R Programming

1. Our new R package: R2jags (Statistical modeling)

2. Find information about R with Rseek.org (Revolutions)

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It is Sunday, so it is time for me to list the blog posts I found interesting this week.

This week I’ve had a bit of a fight with creationism, so I’ve read some blog posts on that, but I am not going to dignify the discussion with linking to them here.

Instead it will just be the usual list of programming and bioinformatics links.

Enjoy!

Bioinformatics

• The curse of BLAST (bbgm)
• Neaderthal genome will be released (Greg Laden)
• Cryptic variation in the human mutation rate (PLoS Biology)
  • Mutation patterns in the human genome are more variable than expected (Greg Laden)

Programming

• Getters and setters in Python (Eli Bendersky)
• A (brief) introduction to Python-Core development (Jesse Noller)
• Fancy debugging with gdb (emacs-fu)
• Python threads and the global interpreter lock (Jesse Noller)
• An Interview With Adam Olsen, Author of Safe Threading (Jesse Noller)

Statistics

• Different meanings of Bayesian statistics (Statistical Modeling, Causal Inference, and Social Science)
• McCloskey et al on significance testing in economics (Statistical Modeling, Causal Inference, and Social Science)

Blogging

• University professors turn to the blogosphere, for classes and recognition (A blog around the clock)
• Do you comment on your own blog? (A blog around the clock)

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This is so cool!

I can’t wait to get my hands on the Neanderthal and run it through our CoalHMM analysis!

Yeah, we are pretty swamped with worn on that project already, but this will just be so cool I can’t wait.

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