2014 in Review

A bit past due, but I like to do these year in review posts, even if just for myself. A lot of time it seems that I spend too much time doing absurd tasks like formatting text or figuring out some silly web application or file format, so it’s nice to see that it does come to something tangible in the end.

Papers

2014 was slowish, compared to 2013, but I have a few big things in the pipeline (one accepted, another in minor revisions, and the second edition of our book incorporating all errata and some other improvements is almost done).

Still, several projects I was involved with finally got their papers out in 2014:

  1. Metagenomic insights into the human gut resistome and the forces that shape it by Kristoffer Forslund, Shinichi Sunagawa, Luis Pedro Coelho, and Peer Bork in Bioessays (2014)DOI:10.1002/bies.201300143

We looked at the presence of antibiotic resistance potential and how it correlates with animal antibiotic usage across countries.

  1. Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo by Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Neves D, Aresta-Branco F, Ferreira FR, Guegan F, Coelho LP, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. in Mol Microbiol, 2014 Jun 19. DOI:10.1111/mmi.12677
  2. A community effort to assess and improve drug sensitivity prediction algorithms by James C Costello, Laura M Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P Menden, Nicholas J Wang, Mukesh Bansal, Muhammad Ammad-ud-din, Petteri Hintsanen, Suleiman A Khan, John-Patrick Mpindi, Olli Kallioniemi, Antti Honkela, Tero Aittokallio, Krister Wennerberg, NCI DREAM Community, James J Collins, Dan Gallahan, Dinah Singer, Julio Saez-Rodriguez, Samuel Kaski, Joe W Gray & Gustavo Stolovitzky in Nature BiotechnologyDOI:10.1038/nbt.2877
  3. A community computational challenge to predict the activity of pairs of compounds by Mukesh Bansal, Jichen Yang, Charles Karan, Michael P Menden, James C Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, Rui Zhong, Beibei Chen, Minsoo Kim, Tao Wang, Laura M Heiser, Ronald Realubit, Michela Mattioli, Mariano J Alvarez, Yao Shen, NCI-DREAM Community, Daniel Gallahan, Dinah Singer, Julio Saez-Rodriguez, Yang Xie, Gustavo Stolovitzky & Andrea Califano in Nature Biotechnology DOI:10.1038/nbt.3052

Blogposts

The most read blog post during 2014 was (Why Python is Better than Matlab for Scientific Software)[https://metarabbit.wordpress.com/2013/10/18/why-python-is-better-than-matlab-for-scientific-software/].

For the posts written in 2014, the most read was this comment on modernity, which had a less-read follow-up.

The post that was hardest to write was talking about an academic dry spell.

Other

I did a bit of traveling, giving talks in Leuven, Paris, and San Sebastian, and teaching software carpentry in, Denmark, Cyprus and Jordan. San Sebastian was a fantastic place (I had never really gotten the appeal of the independently wealthy life until I visited San Sebastian).

Another interesting thing I did was a webcast on linear regression, including the funky kind, in Python. It was an interesting experience, maybe I’ll do it again.

Most importantly

Normally, I try to leave my personal life out of this blog (and the public internets), but 2014 was also remarkable for the birth of our second daughter, Sarah.

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