Date: January 2018


I am a self-taught bioinformatician with a firm background in biology. In my work, I analyse data from high-throughput sequencing instruments, specialising in de novo assembly of small and large genomes. I had a central role in the sequencing and assembly of the first version of the Atlantic cod genome.

I work at the Centre for Ecological and Evolutionary Synthesis (CEES) Dept. of Biosciences, Univ. of Oslo, on the genomics of Atlantic cod and other species, as well as on new methods to represent (reference) genomic information. For my 20% associate professor position at the department of Informatics (Univ. of Oslo), I teach analysis of sequencing data and (co-)supervise PhD and master students.

I am a lead bioinformatician at the Norwegian Sequencing Centre and the most senior bioinformatician at CEES. As lead instructor for the bioinformatics course I teach, I manage the volunteer teachers and helpers.

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.

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 My presentations can be found on slideshare (, and I am active on twitter (@lexnederbragt).

Research and Professional Experience

  • 2013- Associate Professor (20%), Dept of Informatics, University of Oslo, Norway
  • 2005- Postdoct. Res. Fellow, Researcher, Senior Engineer, Dept. of Biosciences, Univ. of Oslo, Norway
  • 2003-2005 Senior Scientist, Lingvitae AS, Oslo, Norway
  • 2002-2003 Postdoctoral research project University of Hawaii, USA


  • 2014-2015 Foundation programme Teaching and Learning in Higher Education (‘Pedagogisk basiskompetanse’): Common part (‘fellesdelen’, 50 hours) + 37.5 hours in small modules
  • 1997-2001 PhD Biology, Utrecht Grad. School of Developmental Biology, Utrecht University, Netherlands
  • 1990-1996 BSc & MSc Biology, Utrecht University, Netherlands

Grants that I am listed on as collaborator

European Research council

  • ERC Consolidator Grant: CICHLIDX, an integrative approach towards the understanding of an adaptive radiation of East African cichlid fishes (PI: Walter Salzburger, Univ. of Basel)

Research Council of Norway

  • REPEAT: Evolutionary and functional importance of simple repeats in the genome ‘Toppforsk’ project (PI: Kjetill Jakobsen)
  • Aqua Genome Project (PI: Kjetill Jakobsen)
  • Norwegian Sequencing Centre Research Infrastructure, phase II (PI: Kjetill Jakobsen, Univ. of Oslo)
  • CodReseq: Translating the cod genome for aquaculture (PI: Kjetill Jakobsen)
  • Haddoc, assessment of long-term effects of oil exposure on early life stages of Atlantic haddock (PI: Sonic Meier, Inst. of Marine Research)
  • Genome dynamics in early eukaryotic evolution: importance of enigmatic lineages (PI: Russel Orr, Univ. of Oslo)
  • The genomic and physiological basis of invasiveness in a harmful house-invader (InHouse) (PI: Inger Skrede, Univ. of Oslo)

Teaching and teaching material

Courses organised

Contributions to university courses

  • MBV-INF4410/9410 Bioinformatics for Molecular Biology (Univ. of Oslo): lecture on “The bioinformatics of sequencing and assembling genomes”, and “What does it mean to do bioinformatics?”, 2013-2016
  • BIO9905MERG1 - Bioinformatics for Metagenomic Analyses and Environmental Sequencing (Univ. of Oslo): lectures on “Next Generation Sequencing techniques and data relevant for metagenomics analyses” and “Assembly of metagenomes”, 2011
  • BIO2120 Evolusjonsbiologi (Univ. of Oslo): lectures on “Evolution and Development” and “Evolution of Genes and Genomes”; group work, 2006 - 2007
  • Erasmus ICP course Marine Cell Biology (Observatoire Oceanologique, Banyuls-sur-mer, France): lectures on “Fundamental aspects of development” and “Cell cycle changes during development”, 2000

Contributions to workshops

Software and Data Carpentry

Software Carpentry and Data Carpentry are teaching researchers in science, engineering, medicine, and related disciplines worldwide computing and data analysis skills through short workshops using volunteer instructors. I am a certified instructor of and organize and lead workshops in Norway and Sweden. Together with Karin Lagesen and with support from the Science Library (UiO), we have established Software and Data Carpentry at the University of Oslo, see, organising workshops more and more frequently, and increasing the number of certified instructors. I am also a certified instructor trainer, which enables me to give workshops for researchers that want to become instructors for Software or Data Carpentry.

Software Carpentry workshops taught

  • University of Oslo: 2012, 2013, 2015, 2016, 2017
  • Netherlands eScience Centre: 2017
  • University of Bergen: 2014
  • Science for Life Laboratory, Stockholm, Sweden 2014

Software/Data Carpentry instructor retreat

I gave a session on Interactive learning techniques, recording:

Selected blog posts

“A new 1st semester bachelor course ‘Introduction to Computational Modelling for the Biosciences’”

“Developments in high throughput sequencing – July 2016 edition”

“Active learning strategies for bioinformatics teaching” (2015)

“On graph-based representations of a (set of) genomes” (2015)

“On the benefits of ‘open’ for teaching” (2014)



Selected repositories:

Invited Seminars

Slide decks:

Selected presentations:

“Genomic variation detection in Atlantic cod using long reads”, SMRT Scientific Symposium, Leiden, The Netherlands, 2016

“Local, central or cloud: why we chose to build our e-infrastructure for sequence analysis embedded in the university of Oslo HPC cluster” workshop “e-infrastructures for Massively Parallel Sequencing”, Uppsala, 2015

“Coding & Best Practice in Programming: Why it matters so much in the NGS era”, SeqAhead Scientific Meeting 2014 “NGS Data after the Gold Rush”, Norwich, 2014

“Experiences with Combining PacBio with Short Read Technology for Improved de novo Assembly of Complex Genomes”, 4th Next Generation Sequencing Congress, London 2012

Professional and Community Service

Grant Panels and Reviewing

  • The Resource Allocation Committee for CPU and storage access at National HPC facilities (UNINETT Sigma2 AS), Norway (2014-)

Advisory boards

  • Secretary, Executive Council ‘The Carpentries’ (Software and Data Carpentry) (2018-)
  • Leader, Advisory Council (‘fagråd’) eInfrastructure, University of Oslo (2016-)
  • Leader of the board, Digital Life Norway Research School (2016-)
  • MicrobesNG Microbial Genome Sequencing service and Open Strain Archive, Univ. of Birmingham, External Advisory Board (2014-)

Manuscript Reviewing

Open reviews: Publons

Reviewer for Nature Methods, Nature Scientific Data, Bioinformatics, BMC Bioinformatics, BMC Genomics, Animal Genetics, Gigascience

Volunteer activies

  • Leader, ‘kodeklubben Bærum’ (code club), offering coding classes to children from 8 to 14 (2016-)
  • Board member of the residential condominium ‘Hiltonåsen’, Slependen, Norway (2009-2015)

Research Mentoring

Graduate Students

  • Co-supervisor PhD students, Univ. of Oslo since 2008, 2 finished, 3 ongoing

Undergraduate Researchers

  • Main supervisor MSc students, Univ. of Oslo since 2014, 3 finished, 1 ongoing
  • Co-supervisor MSc students, Univ. of Oslo since 2013, 3 finished


  • Dutch: first language, excellent oral/written
  • English: excellent oral/written
  • Norwegian: good oral/written
  • German: conversational

List of publications


Tørresen, O. K., Brieuc, M. S. O., Solbakken, M. H., Sørhus, E., Nederbragt, A. J., Jakobsen, K. S., Meier, S., Edvardsen, R. B., & Jentoft, S. (2017). Genomic architecture of codfishes featured by expansions of innate immune genes and short tandem repeats. BioRxiv, 163949.

Varadharajan, S., Sandve, S. R., Tørresen, O. K., Lien, S., Vollestad, L. A., Jentoft, S., Nederbragt, A. J., & Jakobsen, K. S. (2017). The grayling genome reveals selection on gene expression regulation after whole genome duplication. BioRxiv, 153270.

Peer-reviewed publications

Elgvin, T. O., Trier, C. N., Tørresen, O. K., Hagen, I. J., Lien, S., Nederbragt, A. J., Ravinet, M., Jensen, H., & Sætre, G.-P. (2017). The genomic mosaicism of hybrid speciation. Science Advances, 3(6), e1602996.

Khelik, K., Lagesen, K., Sandve, G. K., Rognes, T., & Nederbragt, A. J. (2017). NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinformatics, 18, 338.

Rand, K. D., Grytten, I., Nederbragt, A. J., Storvik, G. O., Glad, I. K., & Sandve, G. K. (2017). Coordinates and intervals in graph-based reference genomes. BMC Bioinformatics, 18, 263.

Simovski, B., Vodak, D., Gundersen, S., Domanska, D., Abdulrahman Azab, Holden, L., Holden, M., Grytten, I., Rand, K., Drablos, F., Johansen, M., Mora, A., Lund-Andersen, C., Fromm, B., Eskeland, R., Gabrielsen, O. S., Ferkingstad, E., Sigve Nakken, Bengtsen, M., Nederbragt, A. J., Thorarensen, H. S., Akse, J. A., Glad, I., Hovig, E., & Sandve, G. K. (2017a). Gsuite HyperBrowser version2.0b. GigaScience Database.

Simovski, B., Vodák, D., Gundersen, S., Domanska, D., Azab, A., Holden, L., Holden, M., Grytten, I., Rand, K., Drabløs, F., Johansen, M., Mora, A., Lund-Andersen, C., Fromm, B., Eskeland, R., Gabrielsen, O. S., Ferkingstad, E., Nakken, S., Bengtsen, M., Nederbragt, A. J., Sif Thorarensen, H., Andreas Akse, J., Glad, I., Hovig, E., & Sandve, G. K. (2017b). GSuite HyperBrowser: Integrative analysis of dataset collections across the genome and epigenome. GigaScience.

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.

Malmstrøm, M., Matschiner, M., Tørresen, O. K., Star, B., Snipen, L. G., Hansen, T. F., Baalsrud, H. T., Nederbragt, A. J., Hanel, R., Salzburger, W., Stenseth, N. C., Jakobsen, K. S., & Jentoft, S. (2016). Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics, 48(10), 1204–1210.

Star, B., Nederbragt, A. J., Jentoft, S., Grimholt, U., Malmstrøm, M., Gregers, T. F., Rounge, T. B., Paulsen, J., Solbakken, M. H., Sharma, A., Wetten, O. F., Lanzén, A., Winer, R., Knight, J., Vogel, J.-H., Aken, B., Andersen, Ø., Lagesen, K., Tooming-Klunderud, A., Edvardsen, R. B., Tina, K. G., Espelund, M., Nepal, C., Previti, C., Karlsen, B. O., Moum, T., Skage, M., Berg, P. R., Gjøen, T., Kuhl, H., Thorsen, J., Malde, K., Reinhardt, R., Du, L., Johansen, S. D., Searle, S., Lien, S., Nilsen, F., Jonassen, I., 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.

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.

Book chapters

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

Tørresen, O. K., Star, B., Jentoft, S., Jakobsen, K. S., & Nederbragt, A. J. (2016). 1 - The new era of genome sequencing using high-throughput sequencing technology: Generation of the first version of the Atlantic cod genome. In Genomics in Aquaculture (pp. 1–20). San Diego: Academic Press. Retrieved from

Software publications

Crusoe, M. R., Alameldin, H. F., Awad, S., Boucher, E., Caldwell, A., Cartwright, R., Charbonneau, A., Constantinides, B., Edvenson, G., Fay, S., Fenton, J., Fenzl, T., Fish, J., Garcia-Gutierrez, L., Garland, P., Gluck, J., González, I., Guermond, S., Guo, J., Gupta, A., Herr, J. R., Howe, A., Hyer, A., Härpfer, A., Irber, L., Kidd, R., Lin, D., Lippi, J., Mansour, T., McA’Nulty, P., McDonald, E., Mizzi, J., Murray, K. D., Nahum, J. R., Nanlohy, K., Nederbragt, A. J., Ortiz-Zuazaga, H., Ory, J., Pell, J., Pepe-Ranney, C., Russ, Z. N., Schwarz, E., Scott, C., Seaman, J., Sievert, S., Simpson, J., Skennerton, C. T., Spencer, J., Srinivasan, R., Standage, D., Stapleton, J. A., Steinman, S. R., Stein, J., Taylor, B., Trimble, W., Wiencko, H. L., Wright, M., Wyss, B., Zhang, Q., zyme, en, & Brown, C. T. (2015). The khmer software package: Enabling efficient nucleotide sequence analysis. F1000Research.

Published lesson materials

Achterberg, H., Adams, J., Adelman, J., Allen, J., Aranda, J., Bae, S., Banaszkiewicz, P., Barmby, P., Barr, E., Beitey, D., Bekolay, T., Berghold, J., Bjørnstad, M., Blischak, J., Boissonneault, M., Bosley, C., Bostroem, A., Boughton, A., Brase, R., Brown, A., Brown, K., Cabunoc Mayes, A., Carroll, I., Chase, J., Childs, S., Choi, J., Clare, R., Clayton, S., Cock, P., Connell, M., Corvellec, M., Coudrat, T., Dale, R., Davis, M., Davis, N., Davison, A., Demichelis, R., Devenyi, G. A., Dolson, E., Dotson, D., Duchesne, L., Duckles, J., Emonet, R., Endsley, K. A., Fauchereau, N., Ford, T., Förstner, K., Gonzalez, I., Gosmann, J., Gosset, J., Gray, J., Greshake, B., Guillou, S., Haley, M., Hames, S., Hamrick, J. B., Hannon, E., Hansen, M., Hertweck, K., Hinsen, K., Hjelm, J., Hodges, T., Howard, D., Irving, D., Jackson, M., Jolly, B., Jones, N., Joyce, B., Ketcheson, D., King, W. T., Klerke, S., Ko, L., Kwong, A., Laken, B., Lapp, H., Latornell, D., Leeman, J. R., Leyder, J.-C., Ligtenberg, W., Lin, J., Lonsdale, A., Manhaes Savio, A., May, R., Mazur, D., Michonneau, F., Mills, B., Mughal, Z., Nederbragt, L., Neufeld, R., O’Leary, A., Obeng, A., Ory, J., Osiecka, N., Pipitone, J., Pińska, A., Poisot, T., Pomorski, P., Raghupathy, N., Rathgeber, F., Rawls, M., Richie-Halford, A., Riley, J., Robitaille, T., Rokem, A., Roswell, M., Sadjadi, M., Sales de Andrade, E., Schmeier, S., Sheneman, L., Shiffer, A., Shkurti, A., Silva, R., Soranzo, N., Spence, E., Srinath, A., Staneva, V., Stapleton, J., Stucky, B., Taylor, C., Teal, T., Telenczuk, B., Thomas, I., Thorne, B., Torres, G., Tröndle, T., Upani, J., Vahtras, O., Helm, E. van der, Walsh, A., Walter, N., Weitzel, D., Wheeler, D., White, E., Williamson, E. P., Willmore, F., Wilson, A., Wilson, G., Xiao, X., & Zonca, A. (2017, February). Software Carpentry: Programming with Python. Retrieved from

Ahmadia, A., Allen, J., Appling, A., Aubin, S., Bachant, P., Baird, D., Banaszkiewicz, P., Barmby, P., Batut, B., Bekolay, T., Belkin, M., Blischak, J., Bonsma, M., Borrelli, J., Boughton, A., Bouquin, D., Brauning, R., Brett, M., Brown, A., Cabunoc Mayes, A., Charlesworth, J., Charlton, B., Chen, D., Christensen, G., Collings, R., Corvellec, M., Davis, M., Devenyi, G. A., Dolson, E., Duchesne, L., Duckles, J., Emonet, R., Estève, L., Farsarakis, E., Fauber, B., Fouilloux, A., Förstner, K., Geiger, S., Gonzalez, I., Guarinello, M., Guillou, S., Hadwin, J., Haeni, M., Haessig, P., Hannah, N., Hansen, M., Harihareswara, S., Heilmaier, A., Heroux, M., Hertweck, K., Hilboll, A., Hinsen, K., Huang, D., Ismiraldi, Y., Jackson, M., Jacobs, C., Jarecka, D., Johnston, L. W., Jones, D., Jędrzejewski-Szmek, Z., Kelly, T., King, W. T., Kluyver, T., Konrad, B., Kuzak, M., Küderle, A., Labrie, K., Lapp, H., Latornell, D., Laufersweiler, M., LeBauer, D., Lee, K., Liffers, M., Llebot, C., Loucks, C., Ma, K., Marwaha, K., May, R., Michonneau, F., Mills, B., Mueller, A., Munk, M., Nagraj, V., Nederbragt, L., Nunez-Iglesias, J., O’Brien, B., O’Leary, A., Olsson, C., Panitz, M., Pawsey, C., Pfenninger, S., Pipitone, J., Poisot, T., Preney, P., Rice, T., Riemer, K., Rio Deiros, D., Robinson, N., Rockenberger, A., Rohl, A., Rokem, A., Sacks, B., Sarahan, M., Schmeier, S., Schmider, H., Shellito, P., Shriwise, P. C., Silva, R., Smithyman, B., Soranzo, N., Steinbach, P., Stevens, S., Stueker, O., Stuermer, B., Timbers, T., Traphagen, D., Tröndle, T., Walt, A. van der, Vandervalk, S., Watson, G., Weaver, B., Wheelhouse, M., White, E., Williamson, E. P., Wilson, G., Wu, S., & Zhang, Q. (2017a, February). Software Carpentry: Version Control with Git. Retrieved from

Ahmadia, A., Allen, J., Banaszkiewicz, P., Becker, E., Bekolay, T., Belkin, M., Blischak, J., Boughton, A., Bray, E., Cabunoc Mayes, A., Carroll, I., Crouch, S., Davis, M., Davis, N., Devenyi, G. A., Duckles, J., Emonet, R., Fortin, F.-A., Gonzalez, I., Hamm, C., Hansen, M., Harris, R. M., Henninger, F., Hertweck, K., Hinsen, K., Hodge, A., Jackson, M., King, W. T., Kitzes, J., Koch, C., Lang, D., Liversidge, T., Michonneau, F., Mills, B., Nederbragt, L., Nelson, E., O’Leary, A., Ortiz-Zuazaga, H., Patitsas, E., Pawlik, A., Perez, F., Pipitone, J., Poisot, T., Rokem, A., Silva, R., Steyn, J., Teal, T., Tröndle, T., Tweedie, F., Walt, A. van der, Vie, J.-J., Walker, J., Walsh, A., Weaver, B., White, E., Wilkerson, C., Williams, J., Williamson, E. P., Wilson, G., & Woo, K. (2017b, February). Software Carpentry: Instructor Training. Retrieved from

Aldazabal Mensa, I., Alexander, H., Allen, J., Alsheikh-Hussain, A., Attali, D., Baird, D., Baltzell, A., Banaszkiewicz, P., Barmby, P., Beagrie, R., Beane, G., Bedini, A., Bekolay, T., Belikov, E., Bell, J., Bill, B., Blin, K., Blischak, J., Boardman, S., Boissonneault, M., Bonnie, J., Boughton, A., Brase, R., Brown, A., Brunson, D., Bryk, J., Buske, O., Cabunoc Mayes, A., Carlise, M., Chen, D., Chung, K., Chung, K., Deveau, D., Devenyi, G. A., Doehle, P., Dolson, E., Doyle, M., Duckles, J., Emonet, R., Eyers, D., Fernandes, F., Fontenelle, H., Gacenga, F., Gardner, P., Gidden, M., Gonzalez, I., Gray, N., Guillou, S., Hagh, V. F., Hansen, M., Harstad, E., Hohenstein, T., Howe, A., Imamoglu, F., Irving, D., Jackson, M., Jane McTavish, E., Jennings, M., Jones, D., Jones, M. A., Keener, A., Keipert, K., Kelly, T., Kim, J. T., King, W. T., Koch, C., Konrad, B., Lake, S., Lang, D., Latornell, D., Lijnzaad, P., Ma, E., Mac, A., Madin, J., Magle, T., Mandel, M., Marini, C., Marwaha, K., Mashchenko, S., McCloy, D., Michonneau, F., Middleton, R., Milhans, J., Mills, B., Miotto, A., Mount, S., Nederbragt, L., Nielsen, D., Nielsen, D., Noga, K., O’Leary, A., Olson, R., Orr, A., Overgard Therkildsen, N., Palamartchouk, K., Perry, A., Peterson, M., Pipitone, J., Poisot, T., Pourreza, H., Povall, T., Richie-Halford, A., Ritchie, S., Rocha, C. B., Ross, N., Rydbeck, H., Sadjadi, M., Sanders, S., Schloss, P., Seyffert, B., Shattow, G., Silva, R., Simpkin, S., Simpson, J., Smith, B., Sobhani, A., Soranzo, N., Srinath, A., Standage, D., Staton, M., Steinbach, P., Stimberg, M., Telenczuk, B., Thoele, F., Timbers, T., Turner, S., Walt, A. van der, Schyndel, J. van, Vollmer, D., Linden, J. von der, Walker, A., Waterfall, J., Watson, G., White, E., Williamson, E. P., Willing, C., Wilson, G., Winston, D., Wolff, H., Young, L., & Zamparo, L. (2017, February). Software Carpentry: The Unix Shell. Retrieved from

Allen, J., Bachant, P., Banaszkiewicz, P., Bekolay, T., Blischak, J., Boissonneault, M., Boughton, A., Cabunoc Mayes, A., Capes, G., Devenyi, G. A., Digges, D., Duckles, J., Emonet, R., Fraser, A., Hansen, M., Hertweck, K., Irber, L., Jackson, M., King, W. T., Liu, G., Michonneau, F., Mills, B., Nederbragt, L., O’Leary, A., Pipitone, J., Poisot, T., Richie-Halford, A., Sherman, J., Silva, R., Smith, B., St-Onge, P.-L., Teucher, A., Williamson, E. P., & Wilson, G. (2017, February). Software Carpentry: Automation and Make. Retrieved from