Date: June 2018

Summary

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.

Research and Professional Experience

  • 2018- Senior lecturer, Dept. of Biosciences and Dept of Informatics, University of Oslo, Norway
  • 2018- Head of education and training, Centre for Bioinformatics, Dept of Informatics, University of Oslo, Norway
  • 2013-2018 Associate Professor (20%), Dept of Informatics, University of Oslo, Norway
  • 2005-2018 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

Education

  • 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

Teaching and teaching material

Courses organised

BIOS1100 - Introduction to Computational Modelling in the Biosciences: http://www.uio.no/studier/emner/matnat/ibv/BIOS1100; new first-year bachelor course that I am coordinator and main teacher for; the course is the first implementation of the ‘Computing in Science Education’ project for the Biosciences study program, teaching python programming and modelling of real biological phenomena, 2017-

INF-BIO5121/9121 - High Throughput Sequencing technologies and bioinformatics analysis Univ. of Oslo: http://inf-biox121.readthedocs.org/en/2015/; I organise the course, coordinating with the five other teachers, and teach the assembly module: http://inf-biox121.readthedocs.org/en/2016/Assembly/, 2012-2016

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

Next-Gen Sequence Analysis Workshop ‘week 3’ (intermediate and advanced skills) (invited) 2015, Michigan State University http://angus.readthedocs.org/en/2015/week3.html Univ. California Davis Assembly Masterclass (invited) 2013 http://davis-assembly-masterclass-2013.readthedocs.org/en/latest/ De novo genome assembly, Univ. of Oslo, 2011 De novo genome assembly (invited), Univ. of Gothenburg, 2011

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 uio.no/carpentry, 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: https://www.youtube.com/watch?v=QptHJgzooU0.

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)

Selected blog posts

“A new 1st semester bachelor course ‘Introduction to Computational Modelling for the Biosciences’” https://flxlexblog.wordpress.com/2017/03/08/a-new-1st-semester-bachelor-course-introduction-to-computational-modelling-for-the-biosciences

“Developments in high throughput sequencing – July 2016 edition” https://flxlexblog.wordpress.com/2016/07/08/developments-in-high-throughput-sequencing-july-2016-edition/

“Active learning strategies for bioinformatics teaching” (2015) https://flxlexblog.wordpress.com/2015/08/31/active-learning-strategies-for-bioinformatics-teaching-2/

“On graph-based representations of a (set of) genomes” (2015) https://flxlexblog.wordpress.com/2015/04/09/on-graph-based-representations-of-a-set-of-genomes/

“On the benefits of ‘open’ for teaching” (2014) https://flxlexblog.wordpress.com/2014/11/04/on-the-benefits-of-open-for-teaching/

Software

Github: https://github.com/lexnederbragt

Selected repositories: RepSeq (Nederbragt et al 2010) https://github.com/lexnederbragt/RepSeq SequenceTools (scripts to work with DNA sequence and related files) https://github.com/lexnederbragt/sequencetools

Invited Seminars

Slide decks:

Selected presentations:

“Genomic variation detection in Atlantic cod using long reads”, SMRT Scientific Symposium, Leiden, The Netherlands, 2016 https://figshare.com/articles/Genomic_variation_detection_in_Atlantic_cod_using_long_reads/3413887

“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 https://www.youtube.com/watch?v=g5JtEQPEQiI

“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 http://www.slideshare.net/flxlex/140507-seq-aheadngscodingbestpractices

“Experiences with Combining PacBio with Short Read Technology for Improved de novo Assembly of Complex Genomes”, 4th Next Generation Sequencing Congress, London 2012 http://www.slideshare.net/flxlex/131014-cees-holmenreproducibility

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 https://publons.com/author/18712/alexander-j-nederbragt

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, 4 ongoing

Undergraduate Researchers Main supervisor MSc students, Univ. of Oslo since 2014, 4 finished, 1 ongoing Co-supervisor MSc students, Univ. of Oslo since 2013, 2 finished, 1 ongoing

Languages

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

List of publications

See also my Google Scholar profile or ORCID page.

Preprints

Grytten, I., Rand, K. D., Nederbragt, A. J., Storvik, G. O., Glad, I. K., & Sandve, G. K. (2018). Graph Peak Caller: Calling ChIP-Seq Peaks on Graph-based Reference Genomes. bioRxiv, 286823. https://doi.org/10.1101/286823

Khelik, K., Nederbragt, A. J., Sandve, G. K., & Rognes, T. (2018). NucMerge: Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads. bioRxiv, 483701. https://doi.org/10.1101/483701

Khelik, K., Sandve, G. K., Nederbragt, A. J., & Rognes, T. (2018). NucBreak: Location of structural errors in a genome assembly by using paired-end Illumina reads. bioRxiv. https://doi.org/10.1101/393488

Peer-reviewed publications

Jørgensen, T. E., Karlsen, B. O., Emblem, Å., Breines, R., Andreassen, M., Rounge, T. B., Nederbragt, A. J., Jakobsen, K. S., Nymark, M., Ursvik, A., Coucheron, D. H., Jakt, L. M., Nordeide, J. T., Moum, T., & Johansen, S. D. (2018). Mitochondrial genome variation of Atlantic cod. BMC Research Notes, 11, 397. https://doi.org/10.1186/s13104-018-3506-3

Lie, K. K., Tørresen, O. K., Solbakken, M. H., Rønnestad, I., Tooming-Klunderud, A., Nederbragt, A. J., Jentoft, S., & Sæle, Ø. (2018). Loss of stomach, loss of appetite? Sequencing of the ballan wrasse (Labrus bergylta) genome and intestinal transcriptomic profiling illuminate the evolution of loss of stomach function in fish. BMC Genomics, 19, 186. https://doi.org/10.1186/s12864-018-4570-8

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. (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics, 19. https://doi.org/10.1186/s12864-018-4616-y

Varadharajan, S., Sandve, S. R., Gillard, G. B., Tørresen, O. K., Mulugeta, T. D., Hvidsten, T. R., Lien, S., Asbjørn Vøllestad, L., Jentoft, S., Nederbragt, A. J., & Jakobsen, K. S. (2018). The Grayling Genome Reveals Selection on Gene Expression Regulation after Whole-Genome Duplication. Genome Biology and Evolution, 10(10), 2785–2800. https://doi.org/10.1093/gbe/evy201

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. https://doi.org/10.1126/sciadv.1602996

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. https://doi.org/10.1186/s12859-017-1748-z

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. https://doi.org/10.1186/s12859-017-1678-9

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. https://doi.org/10.5524/100292

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. https://doi.org/10.1093/gigascience/gix032

Tørresen, O. K., Star, B., Jentoft, S., Reinar, W. B., Grove, H., Miller, J. R., Walenz, B. P., Knight, J., Ekholm, J. M., Peluso, P., Edvardsen, R. B., Tooming-Klunderud, A., Skage, M., Lien, S., Jakobsen, K. S., & Nederbragt, A. J. (2017). An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics, 18(1), 95. https://doi.org/10.1186/s12864-016-3448-x

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

Frank, J. A., Pan, Y., Tooming-Klunderud, A., Eijsink, V. G. H., McHardy, A. C., Nederbragt, A. J., & Pope, P. B. (2016). Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports, 6, 25373. https://doi.org/10.1038/srep25373

Haverkamp, T. H., Tourasse, N. J., Nederbragt, A. J., Jakobsen, K. S., Kolstø, A.-B., & Økstad, O. A. (2016). Draft genomes of clinical Bacillus cereus isolates AH725 and B06.009 closely related to reference strains ATCC 14579 and ATCC 10987. bioRxiv, 073924. https://doi.org/10.1101/073924

Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., Hvidsten, T. R., Leong, J. S., Minkley, D. R., Zimin, A., Grammes, F., Grove, H., Gjuvsland, A., Walenz, B., Hermansen, R. A., Schalburg, K. von, Rondeau, E. B., Di Genova, A., Samy, J. K. A., Olav Vik, J., Vigeland, M. D., Caler, L., Grimholt, U., Jentoft, S., Inge Våge, D., Jong, P. de, Moen, T., Baranski, M., Palti, Y., Smith, D. R., Yorke, J. A., Nederbragt, A. J., Tooming-Klunderud, A., Jakobsen, K. S., Jiang, X., Fan, D., Hu, Y., Liberles, D. A., Vidal, R., Iturra, P., Jones, S. J. M., Jonassen, I., Maass, A., Omholt, S. W., & Davidson, W. S. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature, 533(7602), 200–205. https://doi.org/10.1038/nature17164

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. https://doi.org/10.1038/ng.3645

Solbakken, M. H., Tørresen, O. K., Nederbragt, A. J., Seppola, M., Gregers, T. F., Jakobsen, K. S., & Jentoft, S. (2016). Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. Scientific Reports, 6, 25211. https://doi.org/10.1038/srep25211

Star, B., Tørresen, O. K., Nederbragt, A. J., Jakobsen, K. S., Pampoulie, C., & Jentoft, S. (2016). Genomic characterization of the Atlantic cod sex-locus. Scientific Reports, 6, 31235. https://doi.org/10.1038/srep31235

Brembu, T., Winge, P., Tooming-Klunderud, A., Nederbragt, A. J., Jakobsen, K. S., & Bones, A. M. (2014). The chloroplast genome of the diatom Seminavis robusta: New features introduced through multiple mechanisms of horizontal gene transfer. Marine Genomics, 16, 17–27. https://doi.org/10.1016/j.margen.2013.12.002

Hermansen, J. S., Haas, F., Trier, C. N., Bailey, R. I., Nederbragt, A. J., Marzal, A., & Sætre, G.-P. (2014). Hybrid speciation through sorting of parental incompatibilities in Italian sparrows. Molecular Ecology, 23(23), 5831–5842. https://doi.org/10.1111/mec.12910

Nederbragt, A. J. (2014). On the middle ground between open source and commercial software - the case of the Newbler program. Genome Biology, 15(4), 113. https://doi.org/10.1186/gb4173

Röblitz, T., Saastad, O. W., Eide, H. A., Michalickova, K., Nederbragt, A. J., & Star, B. (2014). Scaling of Biological Data Work ows to Large HPC Systems - A Case Study in Marine Genomics -. Zenodo. https://doi.org/10.5281/zenodo.823031

Siddiqui, H., Lagesen, K., Nederbragt, A. J., Eri, L. M., Jeansson, S. L., & Jakobsen, K. S. (2014). Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-independent High Throughput Sequencing: A Case Report. The Open Microbiology Journal, 8(1). https://doi.org/10.2174/1874285801408010148

Star, B., Nederbragt, A. J., Hansen, M. H. S., Skage, M., Gilfillan, G. D., Bradbury, I. R., Pampoulie, C., Stenseth, N. C., Jakobsen, K. S., & Jentoft, S. (2014). Palindromic Sequence Artifacts Generated during Next Generation Sequencing Library Preparation from Historic and Ancient DNA. PLOS ONE, 9(3), e89676. https://doi.org/10.1371/journal.pone.0089676

Tooming-Klunderud, A., Sogge, H., Rounge, T. B., Nederbragt, A. J., Lagesen, K., Glöckner, G., Hayes, P. K., Rohrlack, T., & Jakobsen, K. S. (2013). From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains. Appl. Environ. Microbiol., 79(21), 6803–6812. https://doi.org/10.1128/AEM.01455-13

Espelund, M., Minge, M. A., Gabrielsen, T. M., Nederbragt, A. J., Shalchian-Tabrizi, K., Otis, C., Turmel, M., Lemieux, C., & Jakobsen, K. S. (2012). Genome Fragmentation Is Not Confined to the Peridinin Plastid in Dinoflagellates. PLOS ONE, 7(6), e38809. https://doi.org/10.1371/journal.pone.0038809

Logares, R., Haverkamp, T. H. A., Kumar, S., Lanzén, A., Nederbragt, A. J., Quince, C., & Kauserud, H. (2012). Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches. Journal of Microbiological Methods, 91(1), 106–113. https://doi.org/10.1016/j.mimet.2012.07.017

Siddiqui, H., Lagesen, K., Nederbragt, A. J., Jeansson, S. L., & Jakobsen, K. S. (2012). Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiology, 12(1), 205. https://doi.org/10.1186/1471-2180-12-205

Brede, D. A., Snipen, L. G., Ussery, D. W., Nederbragt, A. J., & Nes, I. F. (2011). Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant. Journal of Bacteriology, 193(9), 2377–2378. https://doi.org/10.1128/JB.00183-11

Gabrielsen, T. M., Minge, M. A., Espelund, M., Tooming-Klunderud, A., Patil, V., Nederbragt, A. J., Otis, C., Turmel, M., Shalchian-Tabrizi, K., Lemieux, C., & Jakobsen, K. S. (2011). Genome Evolution of a Tertiary Dinoflagellate Plastid. PLOS ONE, 6(4), e19132. https://doi.org/10.1371/journal.pone.0019132

Siddiqui, H., Nederbragt, A. J., Lagesen, K., Jeansson, S. L., & Jakobsen, K. S. (2011). Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiology, 11(1), 244. https://doi.org/10.1186/1471-2180-11-244

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. https://doi.org/10.1038/nature10342

Løvoll, M., Wiik-Nielsen, J., Grove, S., Wiik-Nielsen, C. R., Kristoffersen, A. B., Faller, R., Poppe, T., Jung, J., Pedamallu, C. S., Nederbragt, A. J., Meyerson, M., Rimstad, E., & Tengs, T. (2010). A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS). Virology Journal, 7(1), 309. https://doi.org/10.1186/1743-422X-7-309

Nederbragt, A. J., Rounge, T. B., Kausrud, K. L., & Jakobsen, K. S. (2010). Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads. Sequencing. Research article. https://doi.org/10.1155/2010/782465

Wetten, O. F., Nederbragt, A. J., Wilson, R. C., Jakobsen, K. S., Edvardsen, R. B., & Andersen, Ø. (2010). Genomic organization and gene expression of the multiple globins in Atlantic cod: Conservation of globin-flanking genes in chordates infers the origin of the vertebrate globin clusters. BMC Evolutionary Biology, 10(1), 315. https://doi.org/10.1186/1471-2148-10-315

Johansen, S. D., Coucheron, D. H., Andreassen, M., Karlsen, B. O., Furmanek, T., Jørgensen, T. E., Emblem, Å., Breines, R., Nordeide, J. T., Moum, T., Nederbragt, A. J., Stenseth, N. C., & Jakobsen, K. S. (2009). Large-scale sequence analyses of Atlantic cod. New Biotechnology, 25(5), 263–271. https://doi.org/10.1016/j.nbt.2009.03.014

Rounge, T. B., Rohrlack, T., Nederbragt, A. J., Kristensen, T., & Jakobsen, K. S. (2009). A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain. BMC Genomics, 10(1), 396. https://doi.org/10.1186/1471-2164-10-396

Siddiqui, H., Nederbragt, A. J., & Jakobsen, K. S. (2009). A solid-phase method for preparing human DNA from urine for diagnostic purposes. Clinical Biochemistry, 42(10), 1128–1135. https://doi.org/10.1016/j.clinbiochem.2009.03.010

Nederbragt, A. J., Balasingham, A., Sirevåg, R., Utkilen, H., Jakobsen, K. S., & Anderson-Glenna, M. J. (2008). Multiple-locus variable-number tandem repeat analysis of Legionella pneumophila using multi-colored capillary electrophoresis. Journal of Microbiological Methods, 73(2), 111–117. https://doi.org/10.1016/j.mimet.2008.02.007

Lespinet, O., Nederbragt, A. J., Cassan, M., Dictus, W. J., Loon, A. E. van, & Adoutte, A. (2002). Characterisation of two snail genes in the gastropod mollusc Patella vulgata. Implications for understanding the ancestral function of the snail-related genes in Bilateria. Development Genes and Evolution, 212(4), 186–195. https://doi.org/10.1007/s00427-002-0228-1

Nederbragt, A. J., Lespinet, O., Wageningen, S. V., Loon, A. E. V., Adoutte, A., & Dictus, W. J. A. G. (2002). A lophotrochozoan twist gene is expressed in the ectomesoderm of the gastropod mollusk Patella vulgata. Evolution & Development, 4(5), 334–343. https://doi.org/10.1046/j.1525-142X.2002.02020.x

Nederbragt, A. J., Loon, A. E. van, & Dictus, W. J. A. G. (2002a). Evolutionary biology: Hedgehog crosses the snail’s midline. Nature, 417(6891), 811–812. https://doi.org/10.1038/417811b

Nederbragt, A. J., Loon, A. E. van, & Dictus, W. J. A. G. (2002b). 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

Nederbragt, A. J., Welscher, P. te, Driesche, S. van den, Loon, A. E. van, & Dictus, W. J. (2002). Novel and conserved roles for orthodenticle/otx and orthopedia/otp orthologs in the gastropod mollusc Patella vulgata. Development Genes and Evolution, 212(7), 330–337. https://doi.org/10.1007/s00427-002-0246-z

Kooij, A. van der, Nederbragt, A. J., Goedemans, H. J., & Loon, A. van. (1996). The stringlike genes of the limpet Patella vulgata. Gene, 172(2), 261–265. https://doi.org/10.1016/0378-1119(96)00164-3

Thesis

Nederbragt, A. J. (2002, February). The evolution of developmental programs : A case study in the gastropod mollusc Patella vulgata (Dissertation). Retrieved from http://dspace.library.uu.nl/handle/1874/213

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. https://doi.org/10.1016/B978-0-12-801418-9.00003-2

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. https://doi.org/10.1016/B978-0-12-801418-9.00001-9

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. https://doi.org/10.12688/f1000research.6924.1

Published lesson materials

Wilson, G., Becker, E., McKay, S., Michonneau, F., Williams, J. J., Mayes, A. C., Silva, R., (hoytpr), P., Crosby, K., Nederbragt, L., NielInfante, Psomopoulos, F. E., Gourlé, H., (gaiusjaugustus), G., dbmarchant, Emonet, R., Cock, P., Banaszkiewicz, P., Teal, T., HLindsay, Thomas, A., Hamm, C., Allen, J., Jordan, K. L., EvanWill, Belkin, M., Pipitone, J., Young, N., Tang, M., Paudel, D., synesthesiam, Mills, B., Devenyi, G. A., Carroll, I., King, T. W., & gtehennepe. (2017, November). Data carpentry wrangling genomics lesson. https://doi.org/10.5281/zenodo.1064254

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 https://zenodo.org/record/278222#.WUvbc3XytE4

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 https://zenodo.org/record/278219#.WUvbgHXytE4

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 https://zenodo.org/record/278229#.WUvbfHXytE4

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 https://zenodo.org/record/278226#.WUvbd3XytE4

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 https://zenodo.org/record/278220#.WUvbbXXytE4