Lex Nederbragt

Image of Lex Nederbragt
Norwegian version of this page
Phone +47-22844132
Username
Visiting address Blindernveien 31 None 0371 OSLO
Postal address Postboks 1066 Blindern 0316 OSLO

Background

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 Atlantic cod genome.

At CEES, I work on the genomics of atlantic cod and other species. For my 20% associate professor position at the department of Informatics, I teach analysis of sequencing data and (co-)supervise PhD and master students. I lead the Advisory Council for eInfrastructure (fagrådet for eInfrastruktur) at UiO.

I am a lead bioinformatician at the Norwegian Sequencing Centre and the most senior bioinformatician at CEES. I teach bioinformatics at the master/PHD level, and programming/modelling for first year bachelor students in Biosciences.

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

 

Tags: Atlantic cod, Ecological genomics, Evolutionary Ecology, Genomics, Population genomics, Programming, Amplicon high throughput sequencing, Bioinformatics, Biology, Comparative genomics, DNA sequence analysis, DNA sequencing, Evolution, Evolutionary biology, Evolutionary genomics, Fish, Genes, Genetics, Genome, High-throughput sequencing, Life Science, Phylogenomics, Pyrosequencing, 454 sequencing

Publications

  • Elgvin, Tore Oldeide; Trier, Cassandra Nicole; Tørresen, Ole Kristian; Hagen, Ingerid; Lien, Sigbjørn; Nederbragt, Alexander Johan; Ravinet, Mark Simon Paul; Jensen, Henrik & Sætre, Glenn-Peter (2017). The genomic mosaicism of hybrid speciation. Science Advances.  ISSN 2375-2548.  3 . doi: 10.1126/sciadv.1602996 Full text in Research Archive
  • Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman; Holden, Lars; Holden, Marit; Grytten, Ivar; Rand, Knut Dagestad; Drabløs, Finn Sverre; Johansen, Morten; Mora, Antonio M.; Lund-Andersen, Christin; Fromm, Bastian; Eskeland, Ragnhild; Gabrielsen, Odd Stokke; Ferkingstad, Egil; Nakken, Sigve; Bengtsen, Mads; Nederbragt, Alexander Johan; Thorarensen, Hildur Sif; Andreas Akse, Johannes; Glad, Ingrid Kristine; Hovig, Johannes Eivind & Sandve, Geir Kjetil (2017). GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome . GigaScience.  ISSN 2047-217X. . doi: 10.1093/gigascience/gix032
  • Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Reinar, William Brynildsen; Grove, Harald; Miller, Jason R.; Walenz, Brian; Knight, James; Ekholm, Jenny M.; Peluso, Paul; Edvardsen, Rolf; Tooming-Klunderud, Ave; Skage, Morten; Lien, Sigbjørn; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2017). An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics.  ISSN 1471-2164.  18:95, s 1- 23 . doi: 10.1186/s12864-016-3448-x Full text in Research Archive
  • Wilson, Greg; Brian, Jennifer; Cranston, Karen; Kitzes, Justin; Nederbragt, Alexander Johan & Teal, Tracy K (2017). Good enough practices in scientific computing. PloS Computational Biology.  ISSN 1553-734X.  13(6) . doi: https://doi.org/10.1371/journal.pcbi.1005510
  • Frank, Jeremy A.; Pan, Yao; Tooming-Klunderud, Ave; Eijsink, Vincent; McHardy, Alice C; Nederbragt, Alexander Johan & Pope, Phillip (2016). Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports.  ISSN 2045-2322.  6 . doi: 10.1038/srep25373 Full text in Research Archive
  • Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter; Nome, Torfinn; Hvidsten, Torgeir Rhoden; Leong, Jong; Minkley, David R.; Zimin, Aleksey; Grammes, Fabian; Grove, Harald; Gjuvsland, Arne Bjørke; Walenz, Brian; Hermansen, Russell A.; von Schalburg, Kristian R.; Rondeau, Eric; Genova, Alex Di; Antony Samy, Jeevan Karloss; Vik, Jon Olav; Vigeland, Magnus Dehli; Caler, Lis; Grimholt, Unni; Jentoft, Sissel; Våge, Dag Inge; de Jong, Pieter J.; Moen, Thomas; Baranski, Matthew; Palti, Yniv; Smith, Douglas W.; Yorke, James A.; Nederbragt, Alexander J.; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd; Jiang, Xuanting; Fan, Dingding; Hu, Yan; Liberles, David A.; Vidal, Rodrigo; Iturra, Patricia; Jones, Steven J.M.; Jonassen, Inge; Maass, Alejandro; Omholt, Stig William & Davidson, William S (2016). The Atlantic salmon genome provides insights into rediploidization. Nature.  ISSN 0028-0836.  533(7602), s 200- 205 . doi: 10.1038/nature17164
  • Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Star, Bastiaan; Snipen, Lars-Gustav; Hansen, Thomas F; Baalsrud, Helle Tessand; Nederbragt, Alexander Johan; Hanel, Reinhold; Salzburger, Walter; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2016). Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics.  ISSN 1061-4036.  48(10), s 1204- 1210 . doi: 10.1038/ng.3645
  • Solbakken, Monica Hongrø; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Seppola, Marit; Gregers, Tone Fredsvik; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2016). Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. Scientific Reports.  ISSN 2045-2322.  6 . doi: 10.1038/srep25211 Full text in Research Archive
  • Star, Bastiaan; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd; Pampoulie, Christophe & Jentoft, Sissel (2016). Genomic characterization of the Atlantic cod sex-locus. Scientific Reports.  ISSN 2045-2322.  6, s 1- 9 . doi: 10.1038/srep31235
  • Tørresen, Ole Kristian; Rise, Matthew L.; Jin, Xingkun; Star, Bastiaan; MacKenzie, Simon; Jakobsen, Kjetill Sigurd; Nederbragt, Alexander Johan & Jentoft, Sissel (2016). An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming, In Simon MacKenzie & Sissel Jentoft (ed.),  Genomics in Aquaculture.  Elsevier.  ISBN 9780128014189.  3.  s 45 - 72
  • Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2016). The new era of genome sequencing using high-throughput sequencing technology: Generation of the first version of the Atlantic cod genome, In Simon MacKenzie & Sissel Jentoft (ed.),  Genomics in Aquaculture.  Elsevier.  ISBN 9780128014189.  1.  s 1 - 20
  • Crusoe, Michael R.; Alameldin, Hussien F.; Awad, Sherine; Boucher, Elmar; Caldwell, Adam; Cartwright, Reed; Amanda, Charbonneau; Constantinides, Bede; Edvenson, Greg; Fay, Scott; Fenton, Jacob; Fenzl, Thomas; Fish, Jordan; Garcia-Gutierrez, Leonor; Garland, Phillip; Gluck, Jonathan; González, Iván; Guermond, Sarah; Guo, Jiarong; Gupta, Aditi; Herr, Joshua R.; Howe, Adina; Hyer, Alex; Härpfer, Alex; Irber, Luiz; Kidd, Rhys; Lin, David; Lippi, Justin; Mansour, Tamer; McA'Nulty, Pamela; McDonald, Eric; Mizzi, Jessica; Murray, Kevin D.; Nahum, Joshua R.; Nanlohy, Kaben; Nederbragt, Alexander Johan; Ortiz-Zuazaga, Humberto; Ory, Jeramia; Pell, Jason; Pepe-Ranney, Charles; Russ, Zachary N.; Schwarz, Erich; Scott, Camille; Seaman, Josiah; Sievert, Scott; Simpson, Jared; Skennerton, Connor T.; Spencer, James; Srinivasan, Ramakrishnan; Standage, Daniel; Stapleton, James A.; Steinman, Susan R.; Stein, Joe; Taylor, Benjamin; Trimble, Will; Wiencko, Heather L.; Wright, Michael; Wyss, Brian; Zhang, Qingpeng; zyme, en & Brown, C. Titus (2015). The khmer software package: enabling efficient nucleotide sequence analysis. F1000 Research.  ISSN 2046-1402.  s 1- 12 . doi: 10.12688/f1000research.6924.1
  • Brembu, Tore; Winge, Per; Tooming-Klunderud, Ave; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd & Bones, Atle M. (2014). The chloroplast genome of the diatom Seminavis robusta: New features introduced through multiple mechanisms of horizontal gene transfer. Marine Genomics.  ISSN 1874-7787.  16(1), s 17- 27 . doi: 10.1016/j.margen.2013.12.002
  • Hermansen, Jo Skeie; Haas, Fredrik; Trier, Cassandra Nicole; Bailey, Richard Ian; Nederbragt, Alexander Johan; Marzal, Alfonso & Sætre, Glenn-Peter (2014). Hybrid speciation through sorting of parental incompatibilities in Italian sparrows. Molecular Ecology.  ISSN 0962-1083.  23(23), s 5831- 5842 . doi: 10.1111/mec.12910
  • Siddiqui, Huma; Lagesen, Karin; Nederbragt, Alexander Johan; Eri, Lars Magne; Jeansson, Stig & Jakobsen, Kjetill Sigurd (2014). Pathogens in Urine from a Female Patient with Overactive Bladder Syndrome Detected by Culture-Independent High Throughput Sequencing: A Case Report. Open Microbiology Journal.  ISSN 1874-2858.  8, s 148- 153 . doi: 10.2174/1874285801408010148
  • Star, Bastiaan; Nederbragt, Alexander Johan; Hansen, Marianne Helén Selander; Skage, Morten; Gilfillan, Gregor Duncan; Bradbury, Ian R.; Pampoulie, Christophe; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2014). Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA. PLoS ONE.  ISSN 1932-6203.  9(3) . doi: 10.1371/journal.pone.0089676 Full text in Research Archive
  • Tooming-Klunderud, Ave; Sogge, Hanne; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Lagesen, Karin; Glöckner, Gernot; Hayes, Paul K; Rohrlack, Thomas & Jakobsen, Kjetill Sigurd (2013). From Green to Red: Horizontal Gene Transfer of the Phycoerythrin Gene Cluster between Planktothrix Strains. Applied and Environmental Microbiology.  ISSN 0099-2240.  79(21), s 6803- 6812 . doi: 10.1128/AEM.01455-13 Full text in Research Archive
  • Espelund, Mari; Minge, Marianne Aastebøl; Gabrielsen, Tove M; Nederbragt, Alexander Johan; Shalchian-Tabrizi, Kamran; Otis, Christian; Turmel, Monique; Lemieux, Claude & Jakobsen, Kjetill Sigurd (2012). Genome Fragmentation Is Not Confined to the Peridinin Plastid in Dinoflagellates. PLoS ONE.  ISSN 1932-6203.  7(6) . doi: 10.1371/journal.pone.0038809 Full text in Research Archive
  • Logares, Ramiro; Haverkamp, Thomas Hendricus Augustus; Kumar, Surendra; Lanzén, Anders; Nederbragt, Alexander Johan; Quince, Christopher & Kauserud, Håvard (2012). Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches. Journal of Microbiological Methods.  ISSN 0167-7012.  91(1), s 106- 113 . doi: 10.1016/j.mimet.2012.07.017
  • Siddiqui, Huma; Lagesen, Karin; Nederbragt, Alexander Johan; Jeansson, Stig & Jakobsen, Kjetill Sigurd (2012). Alterations of microbiota in urine from women with interstitial cystitis. BMC Microbiology.  ISSN 1471-2180.  12(205) . doi: 10.1186/1471-2180-12-205 Full text in Research Archive
  • Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Paulsen, Jonas; Solbakken, Monica Hongrø; Sharma, Animesh; Wetten, Ola Frang; Lanzén, Anders; Winer, Roger; Knight, James; Vogel, Jan-Hinnerk; Aken, Bronwen; Andersen, Øivind; Lagesen, Karin; Tooming-Klunderud, Ave; Edvardsen, Rolf; Kirubakaran, G. Tina; Espelund, Mari; Nepal, Chirag; Previti, A. Christopher; Karlsen, Bård Ove; Moum, Truls; Skage, Morten; Berg, Paul Ragnar; Gjøen, Tor; Kuhl, Heiner; Thorsen, Jim; Malde, Ketil; Reinhardt, Richard; Du, Lei; Johansen, Steinar Daae; Searle, Steve; Lien, Sigbjørn; Nilsen, Frank; Jonassen, Inge; Omholt, Stig W; Stenseth, Nils Christian & Jakobsen, Kjetill Sigurd (2011). The genome sequence of Atlantic cod reveals a unique immune system. Nature.  ISSN 0028-0836.  477(7363), s 207- 210 . doi: 10.1038/nature10342 Full text in Research Archive
  • Brede, Dag Anders; Snipen, Lars-Gustav; Ussery, David Wayne; Nederbragt, Alexander Johan & Nes, Ingolf (2011). Complete Genome Sequence of the Commensal Enterococcus faecalis 62, Isolated from a Healthy Norwegian Infant. Journal of Bacteriology.  ISSN 0021-9193.  193(9), s 2377- 2378 . doi: 10.1128/JB.00183-11
  • Gabrielsen, Tove M; Minge, Marianne Aastebøl; Espelund, Mari; Tooming-Klunderud, Ave; Patil, Viswanath; Nederbragt, Alexander Johan; Otis, Christian; Turmel, Monique; Shalchian-Tabrizi, Kamran; Lemieux, Claude & Jakobsen, Kjetill Sigurd (2011). Genome Evolution of a Tertiary Dinoflagellate Plastid. PLoS ONE.  ISSN 1932-6203.  6(4), s e19132 . doi: 10.1371/journal.pone.0019132
  • Siddiqui, Huma; Nederbragt, Alexander Johan; Lagesen, Karin; Jeansson, Stig & Jakobsen, Kjetill Sigurd (2011). Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons. BMC Microbiology.  ISSN 1471-2180.  11 . doi: 10.1186/1471-2180-11-244
  • Løvoll, Marie Therese; Wiik-Nielsen, Jannicke; Sørensen, Søren Grove; Faller, Randi; Wiik-Nielsen, Christer R.; Kristoffersen, Anja Bråthen; Poppe, Trygve; Jung, J.; Jung, Joonil; Pedamallu, CS; Nederbragt, Alexander Johan; Sekhar Pedamallu, Chandra; Meyerson, M; Rimstad, Espen; Meyerson, Matthew & Tengs, Torstein (2010). A novel totivirus and piscine reovirus (PRV) in Atlantic salmon (Salmo salar) with cardiomyopathy syndrome (CMS). Virology Journal.  ISSN 1743-422X.  7 . doi: 10.1186/1743-422X-7-309
  • Nederbragt, Alexander Johan; Rounge, Trine Ballestad; Kausrud, Kyrre & Jakobsen, Kjetill Sigurd (2010). Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads. Sequencing.  ISSN 2090-0325.  2010 . doi: 10.1155/2010/782465
  • Wetten, Ola Frang; Nederbragt, Alexander Johan; Wilson, Robert; Jakobsen, Kjetill Sigurd; Edvardsen, Rolf & Andersen, Øivind (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.  ISSN 1471-2148.  10 . doi: 10.1186/1471-2148-10-315
  • Johansen, Steinar; Coucheron, Dag-Hugo; Andreassen, morten; Karlsen, Bård Ove; Furmanek, T; Jorgensen, TE; Jørgensen, Tor Erik; Emblem, A; Emblem, Åse; Breines, Ragna; Nordeide, JT; Moum, Truls; Nederbragt, AJ; Stenseth, Nils Christian & Jakobsen, KS (2009). Large-scale sequence analyses of Atlantic cod. New Biotechnology.  ISSN 1871-6784.  25(5), s 263- 271 . doi: 10.1016/j.nbt.2009.03.014

View all works in Cristin

  • Eide, Marta; Puntervoll, Pål; Lille-Langøy, Roger; Goldstone, Jared V.; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Rydbeck, Halfdan; Jakobsen, Kjetill Sigurd; Stegeman, John; Goksøyr, Anders & Karlsen, Odd Andre (2016). Chemical warfare in the marine environment: genomic survey of the Atlantic cod (Gadus morhua) defensome reveals the absence of an important xenosensor.
  • Nederbragt, Alexander Johan (2016). Doing bioinformatics: a user’s perspective .
  • Nederbragt, Alexander Johan (2016). Genomic variation detection in Atlantic cod using long reads .
  • Nederbragt, Alexander Johan (ed.) (2016). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
  • Nederbragt, Alexander Johan (2016). SMRTwishes for SMRTsoftware for SMRTreads - a user’s perspective.
  • Nederbragt, Alexander Johan (2016). The new Atlantic cod reference genome.
  • Nederbragt, Alexander Johan & Lagesen, Karin (2016). The Carpentry effort at the University of Oslo.
  • Nederbragt, Alexander Johan (2015). A New, High Quality Reference Genome Assembly For Atlantic Cod.
  • Nederbragt, Alexander Johan (2015). Active learning strategies for bioinformatics teaching.
  • Nederbragt, Alexander Johan (2015). Bioinformatics breakout : Recent experiences from Oslo.
  • Nederbragt, Alexander Johan (ed.) (2015). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
  • Nederbragt, Alexander Johan (2015). Local, central or cloud Why we chose to build our e-infrastructure for sequence analysis embedded in the university of Oslo HPC cluster.
  • Star, Bastiaan; Jentoft, Sissel; Matschiner, Michael; Nederbragt, Alexander Johan; Kjesbu, Olav Sigurd; Berg, Paul Ragnar; Bradbury, Ian R.; Pampoulie, Christophe; Hansen, Marianne Helén Selander; Skage, Morten; Jakobsen, Kjetill Sigurd & Stenseth, Nils Christian (2015). Does historic DNA provide genomic evidence for recent selection in Atlantic cod?.
  • Brynildsen, William; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2014). Genomic sequence repeats in fish genomes.
  • Matschiner, Michael; Star, Bastiaan; Berg, Paul Ragnar; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Hansen, Marianne Helén Selander; Skage, Morten; Kjesbu, Olav Sigurd; Stenseth, Nils Christian; Jakobsen, Kjetill Sigurd & Jentoft, Sissel (2014). Population differentiation and local adaptation in Atlantic cod.
  • Nederbragt, Alexander Johan (2014). Assembly – before and after .
  • Nederbragt, Alexander Johan (2014). Coding & Best Practice in Programming: Why it matters so much in the NGS era .
  • Nederbragt, Alexander Johan (ed.) (2014). In between lines of code - a blog about biology, sequencing, bioinformatics and more .
  • Nederbragt, Alexander Johan (2014). Mix and match: using multiple sequencing technologies and assemblers for the new Atlantic cod genome.
  • Nederbragt, Alexander Johan (2014). The why and how of long reads for de novo genome assembly.
  • Nederbragt, Alexander Johan (2014). The why and how of long reads for de novo genome assembly.
  • Nederbragt, Alexander Johan; Walenz, Brian; Tørresen, Ole Kristian; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Miller, Jason Rafe (2014). Towards correction-free assembly of raw PacBio reads .
  • Tørresen, Ole Kristian; Jentoft, Sissel; Star, Bastiaan; Sandve, Geir Kjetil F.; Skage, Morten; Hansen, Marianne Helén Selander; Tooming-Klunderud, Ave; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2014). A new, high quality reference genome assembly for Atlantic cod.
  • Tørresen, Ole Kristian; Walenz, Brian; Grove, Harald; Lien, Sigbjørn; Knight, James; Star, Bastiaan; Lagesen, Karin; Sandve, Geir Kjetil F.; Skage, Morten; Hansen, Marianne Helén Selander; Klunderud, Ave Tooming; Miller, Jason Rafe; Jentoft, Sissel; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2014). A new, high quality reference genome assembly for Atlantic cod.
  • Loman, N.; Hadfield, James & Nederbragt, Alexander Johan (2013). Seqbench: Open-source benchmarking of sequence platforms and software.
  • Nederbragt, Alexander Johan (2013). High Throughput Sequencing technologies.
  • Nederbragt, Alexander Johan (2013). High Throughput Sequencing technologies at the Norwegian Sequencing Centre with a focus on genome assembly.
  • Nederbragt, Alexander Johan (2013). Improving and validating the Atlantic Cod genome assembly using error-corrected as well as raw PacBio reads .
  • Nederbragt, Alexander Johan (2013). Lessons learned from assembling the Atlantic cod genome.
  • Nederbragt, Alexander Johan (2013). Repeat after me: Is our research reproducible (enough)?.
  • Nederbragt, Alexander Johan (2013). The IPython Notebook: an introduction, and hands-on/live demo.
  • Nederbragt, Alexander Johan (2013). The IPython Notebook: an introduction, and hands-on/live demo.
  • Nederbragt, Alexander Johan (2013). Using PacBio Reads to Improve and Validate the Assembly of the Complex Atlantic Cod Genome.
  • Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Miller, Jason Rafe; Walenz, Brian; Jentoft, Sissel & Jakobsen, Kjetill Sigurd (2013). Improving the Atlantic cod genome using long-read PacBio in combination with 454 and Illumina sequencing data.
  • Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Skage, Morten; Tooming-Klunderud, Ave; Hansen, Marianne Helén Selander; Jentoft, Sissel; Omholt, Stig W; Lien, Sigbjørn & Jakobsen, Kjetill Sigurd (2012). The long jump: Long distance mate pairs and long PacBio reads for the Salmon Genome Project.
  • Nederbragt, Alexander Johan (2012). A different kettle of fish entirely: bioinformatic challenges and solutions for whole de novo genome assembly of Atlantic cod and Atlantic salmon .
  • Nederbragt, Alexander Johan (2012). Experiences with Combining PacBio with Short Read Technology for Improved de novo Assembly of Complex Genomes.
  • Nederbragt, Alexander Johan (2012). Experiences with Combining PacBio with Short Read Technology for Improved de novo Assembly of Complex Genomes.
  • Nederbragt, Alexander Johan (2012). High-throughput sequencing og behovet for tungregneressurser.
  • Nederbragt, Alexander Johan (2012). How and why I use blogging and twitter for science.
  • Nederbragt, Alexander Johan (ed.) (2012). In between lines of code - a blog about biology, sequencing, bioinformatics and more .
  • Nederbragt, Alexander Johan (2012). New High Throughput Sequencing technologies at the Norwegian Sequencing Centre - and beyond.
  • Nederbragt, Alexander Johan (2012). New High Throughput Sequencing technologies at the Norwegian Sequencing Centre - and beyond.
  • Nederbragt, Alexander Johan (2012). The best of both worlds - Combining PacBio with short read technology for improved de novo genome assembly.
  • Nederbragt, Alexander Johan (2012). The bioinformatics of sequencing and assembling genomes - with a focus on the Atlantic cod and salmon genome projects.
  • Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Khelik, Ksenia; Lagesen, Karin; Rounge, Trine Ballestad; Star, Bastiaan; Tina, Kirubakaran G.; Berg, Paul Ragnar; Rognes, Torbjørn; Jentoft, Sissel; Winer, Roger; Dewar, Ken & Jakobsen, Kjetill Sigurd (2012). Challenges and Opportunities for Improving the Atlantic Cod Genome Assembly and Annotation.
  • Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Lagesen, Karin; Khelik, Ksenia; Rognes, Torbjørn; Jentoft, Sissel & Jakobsen, Kjetill Sigurd (2012). Improving the cod genome with the use of multi-platform sequencing data.
  • Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin; Gregers, Tone Fredsvik; Rounge, Trine Ballestad; Solbakken, Monica Hongrø; Paulsen, Jonas; Lagesen, Karin; Tooming-Klunderud, Ave; Tina, Kirubakaran G.; Espelund, Mari; Skage, Morten; Berg, Paul Ragnar; Omholt, Stig W; Stenseth, Nils Christian & Jakobsen, Kjetill Sigurd (2011). The genome of Atlantic cod reveals a unique immune system.
  • Brembu, Tore; Winge, Per; Sparstad, Torfinn; Klunderud, Ave Tooming; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd & Bones, Atle M. (2011). Genomprosjektet på kiselalgen Seminavis robusta.
  • Brembu, Tore; Winge, Per; Sparstad, Torfinn; Klunderud, Ave Tooming; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd & Bones, Atle M. (2011). The Seminavis robusta genome project.
  • Løvoll, Marie Therese; Wiik-Nielsen, Jannicke; Grove, Søren; Wiik-Nielsen, Christer R.; Kristoffersen, Anja Bråthen; Jung, J.; Pedamallu, CS; Nederbragt, Alexander Johan; Meyerson, Matthew; Rimstad, Espen & Tengs, Torstein (2011). Totivirus og reovirus i laks med kardiomyopatisyndrom (CMS).
  • Nederbragt, Alexander Johan (2011). How to sequence a large eukaryotic genome and how we sequenced the cod genom.
  • Nederbragt, Alexander Johan (ed.) (2011). In between lines of code - a blog about biology, sequencing, bioinformatics and more .
  • Nederbragt, Alexander Johan (2011). Next generation sequencing: research opportunities and bioinformatic challenges.
  • Nederbragt, Alexander Johan; Lagesen, Karin & Malmstrøm, Martin (2011). Bioinformatic analysis of genomic data.
  • Rounge, Trine Ballestad & Nederbragt, Alexander Johan (2011). The Atlantic Cod Genome Project.
  • Nederbragt, Alexander Johan (ed.) (2010). An assembly of reads, contigs and scaffolds: a blog on all things newbler and beyond .
  • Nederbragt, Alexander Johan (2010). How you can use the GS FLX (454) for your project, and why it does not have to be very expensive.
  • Nederbragt, Alexander Johan (2010). Sekvensering, genotyping of bioinformatikk.
  • Nederbragt, Alexander Johan (2010). Sequencing the cod genome - with a focus on bioinformatic analyses.
  • Nederbragt, Alexander Johan (2010). The Norwegian High-Throughput Sequencing Centre - The 454 GS FLX node.
  • Nederbragt, Alexander Johan (2010). The Norwegian High-Throughput Sequencing Centre - The Illumina Genome Analyzer II (GAII) node.
  • Nederbragt, Alexander Johan (2010). The Norwegian Sequencing Centre at the University of Oslo and what it can do for the microbial science community at MatNat.
  • Nederbragt, Alexander Johan & Tooming-Klunderud, Ave (2010). From next generation reads to genomes: experiences gained from different genome projects.
  • Grimholt, Unni; Malmstrøm, Martin; Nederbragt, Alexander Johan; Rounge, Trine Ballestad; Jentoft, Sissel; Tooming-Klunderud, Ave; Star, Bastiaan; Skage, Morten; Gaup, Hege Junita & Jakobsen, Kjetill Sigurd (2009). The lack of cod MHC class II.
  • Grimholt, Unni; Nederbragt, Alexander Johan; Rounge, Trine Ballestad; Malmstrøm, Martin; Star, Bastiaan; Tooming-Klunderud, Ave; Skage, Morten; Jentoft, Sissel; Gaup, Hege Junita; Bakke, Hege; Solbakken, Monica Hongrø & Jakobsen, Kjetill Sigurd (2009). The cod genome project.
  • Jakobsen, Kjetill Sigurd; Rounge, Trine Ballestad; Nederbragt, Alexander Johan & Star, Bastiaan (2009). Sequencing of the cod genome: progress and perspectives.
  • Nederbragt, Alexander Johan (2009). High-Throughput Sequencing Services at the University of Oslo.
  • Nederbragt, Alexander Johan (2009). Overview of the cod assembly.
  • Nederbragt, Alexander Johan (2009). Processing high throughput sequence data from environmental samples using MEGAN.
  • Nederbragt, Alexander Johan (2009). The Cod Genome project.
  • Nederbragt, Alexander Johan (2009). The cod genome project.

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Published May 26, 2011 9:54 PM - Last modified May 30, 2017 11:11 AM

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