About Lex Nederbragt

I am a Senior Lecturer (‘Førstelektor’) at the Department of Biosciences, University of Oslo. I am also head of education and training for the Centre for Bioinformatics, Dept. of Informatics, Univ. of Oslo.

At the Dept. of Biosciences, I lead the implementation of Computing in Science Education in the bachelor degree. As part of that I organise the first-semester course “Introduction to Computational Modelling for the Biosciences” (BIOS1100), teaching new Bioscience students mathematical modeling of biological problems using Python.

For the Centre for Bioinformatics, I develop and coordinate a portfolio of credited courses as well as workshops for master and PhD students and other staff.

I am a self-taught bioinformatician with a firm background in biology. My research at the Centre for Ecological and Evolutionary Synthesis (CEES) at the Dept. of Biosciences is on new methods to represent (reference) genomic information. I previously had a central role in the sequencing and assembly of the Atlantic cod genome. I lead the Advisory Council for eInfrastructure (fagrådet for eInfrastruktur) at UiO.

I am a Software Carpentry instructor, teaching computational lab skills to scientists in the Nordic countries. I am an advocate of open source software, and reproducible computational biology. I share my work not only through publications, but also on my science blog at lexnederbragt.com. My presentations can be found on figshare and slideshare, and I am active on twitter (@lexnederbragt).

I have an analytical mind that loves problem solving. I value honesty and professionalism, and dislike hype. I believe that sharing and openness will further science more than competition. I choose impact over impact factor.

Manuscripts I am most proud of

Patella engrailed and dpp

Nederbragt, A. J., Loon, A. E. van, & Dictus, W. J. A. G. (2002). Expression of Patella vulgata Orthologs of engrailed and dpp-BMP2/4 in Adjacent Domains during Molluscan Shell Development Suggests a Conserved Compartment Boundary Mechanism. Developmental Biology, 246(2), 341–355. https://doi.org/10.1006/dbio.2002.0653

In my mind, the highlight paper from my PhD, which was in ‘evo-devo’, evolutionary developmental biology. We showed expression of Engrailed and Dpp orthologs in early limpet development. The cells expressing these genes were on opposite sides of the border of the developing shell. We coupled that observation to the expression in cells at other borders in developing embryos.

Atlantic cod genome I

Star, B., Nederbragt, A. J., Jentoft, S., Grimholt, U., Malmstrøm, …, Omholt, S. W., Stenseth, N. C., & Jakobsen, K. S. (2011). The genome sequence of Atlantic cod reveals a unique immune system. Nature, 477(7363), 207–210. https://doi.org/10.1038/nature10342

We were able to use the Roche/454 GS FLX in a tru team-based effort to sequence the genome of the Atlantic Cod, the eukaryote first genome sololey sequenced using ‘next-generation’ technologies to be accepted into the Ensembl database. The genome showed that Atlantic cod has an unusual immune system, the first genome to show lack of key genes that ‘everyone’ thought vertebrates could not do without.

Atlantic cod genome II

Tørresen, O. K., Rise, M. L., Jin, X., Star, B., MacKenzie, S., Jakobsen, K. S., Nederbragt, A. J., & Jentoft, S. (2016). 3 - An improved version of the Atlantic cod genome and advancements in functional genomics: Implications for the future of cod farming. In Genomics in Aquaculture (pp. 45–72). San Diego: Academic Press. Retrieved from http://www.sciencedirect.com/science/article/pii/B9780128014189000032

My first last-author publication. A lot of work, with all available seuqencing technologies (at the time), many bioinformatics analyses led to a very complete Atlantic cod genome. I am proud to have contributed to making the Atlantic Cod genome continue to be a valuable resource to the community.

Good enough practices

Wilson, G., Bryan, J., Cranston, K., Kitzes, J., Nederbragt, L., & Teal, T. K. (2017). Good enough practices in scientific computing. PLOS Computational Biology, 13(6), e1005510. https://doi.org/10.1371/journal.pcbi.1005510

A true team effort, written by members of my favorite community, the Carpentries. A companion text to the ‘Best practices’ paper, meant to present strategies that researchers can (and we feel, should) adopt, but also will keep using once they have adopted them.

Lessons

I am also proud to have contributed to several Carpentries lessons.

LICENSE NOTICE. Unless prevented by existing licenses or otherwise, I release the material on this blog under a CC0 license. Feel free to use the material for the greater good. The license does not require a reference to the source, but I would appreciate it.