Lex Nederbragt

• Reinar, William Brynildsen; Tørresen, Ole K.; Nederbragt, Lex; Matschiner, Michael; Jentoft, Sissel & Jakobsen, Kjetill Sigurd (2023). Teleost genomic repeat landscapes in light of diversification rates and ecology. Mobile DNA. ISSN 1759-8753. 14(1), s. 1–12. doi: 10.1186/s13100-023-00302-9. Fulltekst i vitenarkiv
• Eliassen, June Edvarda; Bøe, Maria Vetleseter; Nederbragt, Lex; Berg, Marthe Mjøen & Gregers, Tone Fredsvik (2022). Motivasjon for beregningsorientert biologi og sammenhengen med matematikk R2 fra videregående opplæring. Nordic Journal of STEM Education. ISSN 2535-4574. 4(2), s. 58–70. doi: 10.5324/njsteme.v4i2.4026. Fulltekst i vitenarkiv
• Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan & Sandve, Geir Kjetil (2020). Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods. BMC Genomics. ISSN 1471-2164. 21. doi: 10.1186/s12864-020-6685-y. Fulltekst i vitenarkiv
• Khelik, Ksenia; Sandve, Geir Kjetil; Nederbragt, Alexander Johan & Rognes, Torbjørn (2020). NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics. ISSN 1471-2105. 21(1). doi: 10.1186/s12859-020-3414-0. Fulltekst i vitenarkiv
• Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F. & Guo, Baocheng [Vis alle 9 forfattere av denne artikkelen] (2019). A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome . Genome Biology and Evolution (GBE). ISSN 1759-6653. 11(11), s. 3291–3308. doi: 10.1093/gbe/evz240. Fulltekst i vitenarkiv
• Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2019). Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Computational Biology. ISSN 1553-734X. 15(2), s. 1–13. doi: 10.1371/journal.pcbi.1006731. Fulltekst i vitenarkiv
• Varadharajan, Srinidhi; Sandve, Simen Rød; Gillard, Gareth Benjamin; Tørresen, Ole K.; Mulugeta, Teshome Dagne & Hvidsten, Torgeir Rhoden [Vis alle 11 forfattere av denne artikkelen] (2018). The grayling genome reveals selection on gene expression regulation after whole-genome duplication. Genome Biology and Evolution (GBE). ISSN 1759-6653. 10(10), s. 2785–2800. doi: 10.1093/gbe/evy201. Fulltekst i vitenarkiv
• Tørresen, Ole K.; Brieuc, Marine Servane; Solbakken, Monica Hongrø; Sørhus, Elin; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd [Vis alle 9 forfattere av denne artikkelen] (2018). Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics. ISSN 1471-2164. 19(240), s. 1–17. doi: 10.1186/s12864-018-4616-y. Fulltekst i vitenarkiv
• Jørgensen, Tor Erik; Karlsen, Bård Ove; Emblem, Åse; Breines, Ragna; Andreassen, morten & Rounge, Trine Ballestad [Vis alle 15 forfattere av denne artikkelen] (2018). Mitochondrial genome variation of Atlantic cod. BMC Research Notes. ISSN 1756-0500. 11:397, s. 1–7. doi: 10.1186/s13104-018-3506-3. Fulltekst i vitenarkiv
• Lie, Kai Kristoffer; Tørresen, Ole K.; Solbakken, Monica Hongrø; Rønnestad, Ivar; Tooming-Klunderud, Ave & Nederbragt, Alexander Johan [Vis alle 8 forfattere av denne artikkelen] (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. ISSN 1471-2164. 19(186), s. 1–17. doi: 10.1186/s12864-018-4570-8. Fulltekst i vitenarkiv
• Rand, Knut Dagestad; Grytten, Ivar; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2017). Coordinates and intervals in graph-based reference genomes. BMC Bioinformatics. ISSN 1471-2105. 18:263, s. 1–8. doi: 10.1186/s12859-017-1678-9. Fulltekst i vitenarkiv
• Khelik, Ksenia; Lagesen, Karin; Sandve, Geir Kjetil; Rognes, Torbjørn & Nederbragt, Alexander Johan (2017). NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinformatics. ISSN 1471-2105. 18(1), s. 1–14. doi: 10.1186/s12859-017-1748-z. Fulltekst i vitenarkiv
• 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: 10.1371/journal.pcbi.1005510. Fulltekst i vitenarkiv
• Elgvin, Tore Oldeide; Trier, Cassandra Nicole; Tørresen, Ole Kristian; Hagen, Ingerid; Lien, Sigbjørn & Nederbragt, Alexander Johan [Vis alle 9 forfattere av denne artikkelen] (2017). The genomic mosaicism of hybrid speciation. Science Advances. ISSN 2375-2548. 3, s. 1–16. doi: 10.1126/sciadv.1602996. Fulltekst i vitenarkiv
• Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman & Holden, Lars [Vis alle 25 forfattere av denne artikkelen] (2017). GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome. GigaScience. ISSN 2047-217X. 6(7), s. 1–12. doi: 10.1093/gigascience/gix032. Fulltekst i vitenarkiv Vis sammendrag

  Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. Findings: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Conclusions: Through a combination of streamlined data acquisition, interoperable representation of dataset collections and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no

• Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Reinar, William Brynildsen; Grove, Harald & Miller, Jason R. [Vis alle 16 forfattere av denne artikkelen] (2017). An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics. ISSN 1471-2164. 18, s. 1–23. doi: 10.1186/s12864-016-3448-x. Fulltekst i vitenarkiv
• Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole Kristian; Star, Bastiaan; Snipen, Lars-Gustav & Hansen, Thomas F [Vis alle 13 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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. Fulltekst i vitenarkiv
• Tørresen, Ole Kristian; Rise, Matthew L.; Jin, Xingkun; Star, Bastiaan; MacKenzie, Simon & Jakobsen, Kjetill Sigurd [Vis alle 8 forfattere av denne artikkelen] (2016). An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming. I MacKenzie, Simon & Jentoft, Sissel (Red.), Genomics in Aquaculture. Elsevier. ISSN 9780128014189. s. 45–72. doi: 10.1016/B978-0-12-801418-9.00003-2.
• 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. I MacKenzie, Simon & Jentoft, Sissel (Red.), Genomics in Aquaculture. Elsevier. ISSN 9780128014189. s. 1–20. doi: 10.1016/B978-0-12-801418-9.00001-9.
• Lien, Sigbjørn; Koop, Ben F; Sandve, Simen Rød; Miller, Jason R.; Kent, Matthew Peter & Nome, Torfinn [Vis alle 45 forfattere av denne artikkelen] (2016). The Atlantic salmon genome provides insights into rediploidization. Nature. ISSN 0028-0836. 533(7602), s. 200–205. doi: 10.1038/nature17164. Fulltekst i vitenarkiv
• Solbakken, Monica Hongrø; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Seppola, Marit; Gregers, Tone Fredsvik & Jakobsen, Kjetill Sigurd [Vis alle 7 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv Vis sammendrag

  Genome sequencing of the teleost Atlantic cod demonstrated loss of the Major Histocompatibility Complex (MHC) class II, an extreme gene expansion of MHC class I and gene expansions and losses in the innate pattern recognition receptor (PRR) family of Toll-like receptors (TLR). In a comparative genomic setting, using an improved version of the genome, we characterize PRRs in Atlantic cod with emphasis on TLRs demonstrating the loss of TLR1/6, TLR2 and TLR5 and expansion of TLR7, TLR8, TLR9, TLR22 and TLR25. We find that Atlantic cod TLR expansions are strongly influenced by diversifying selection likely to increase the detectable ligand repertoire through neo- and subfunctionalization. Using RNAseq we find that Atlantic cod TLRs display likely tissue or developmental stage-specific expression patterns. In a broader perspective, a comprehensive vertebrate TLR phylogeny reveals that the Atlantic cod TLR repertoire is extreme with regards to losses and expansions compared to other teleosts. In addition we identify a substantial shift in TLR repertoires following the evolutionary transition from an aquatic vertebrate (fish) to a terrestrial (tetrapod) life style. Collectively, our findings provide new insight into the function and evolution of TLRs in Atlantic cod as well as the evolutionary history of vertebrate innate immunity.

• Frank, Jeremy A.; Pan, Yao; Tooming-Klunderud, Ave; Eijsink, Vincent; McHardy, Alice C & Nederbragt, Alexander Johan [Vis alle 7 forfattere av denne artikkelen] (2016). Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports. ISSN 2045-2322. 6. doi: 10.1038/srep25373. Fulltekst i vitenarkiv
• Crusoe, Michael R.; Alameldin, Hussien F.; Awad, Sherine; Boucher, Elmar; Caldwell, Adam & Cartwright, Reed [Vis alle 61 forfattere av denne artikkelen] (2015). The khmer software package: enabling efficient nucleotide sequence analysis. F1000 Research. ISSN 2046-1402. s. 1–12. doi: 10.12688/f1000research.6924.1.
• 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.
• Hermansen, Jo Skeie; Haas, Fredrik; Trier, Cassandra Nicole; Bailey, Richard Ian; Nederbragt, Alexander Johan & Marzal, Alfonso [Vis alle 7 forfattere av denne artikkelen] (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.
• Star, Bastiaan; Nederbragt, Alexander Johan; Hansen, Marianne Helén Selander; Skage, Morten; Gilfillan, Gregor Duncan & Bradbury, Ian R. [Vis alle 10 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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.
• Tooming-Klunderud, Ave ; Sogge, Hanne; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Lagesen, Karin & Glöckner, Gernot [Vis alle 9 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
• 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. Fulltekst i vitenarkiv
• Logares, Ramiro; Haverkamp, Thomas Hendricus Augustus; Kumar, Surendra; Lanzén, Anders; Nederbragt, Alexander Johan & Quince, Christopher [Vis alle 7 forfattere av denne artikkelen] (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.
• Espelund, Mari; Minge, Marianne Aastebøl; Gabrielsen, Tove M; Nederbragt, Alexander Johan; Shalchian-Tabrizi, Kamran & Otis, Christian [Vis alle 9 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv

Se alle arbeider i Cristin

• Nederbragt, Lex (2023). Cognitive Load: what is it and how can we take it in consideration when teaching?
• Nederbragt, Lex (2022). Carpentry@UiO: Workshops for basic skills in programming and datamanagement at The University of Oslo (UiO).
• Nederbragt, Lex; Lemma, Roza Berhanu; Belova, Tatiana; Cheneby, Jeanne; Ibrahim, Mohamed & Akdeniz, Byram Cevdet [Vis alle 7 forfattere av denne artikkelen] (2022). Oslo Bioinformatics Workshop Week 2022. Vis sammendrag

  December 7th-13th 2022 will see the very first Oslo Bioinformatics Workshop Week at the University of Oslo, Norway. This event is organised by the Student Committee of the Centre for Bioinformatics at UiO, in collaboration with the ISCB Regional Student group in Norway. These workshops are open to the scientific community in Oslo and the surrounding area.

• Eliassen, June Edvarda; Bøe, Maria Vetleseter; Nederbragt, Lex & Gregers, Tone Fredsvik (2021). Motivasjon for beregningsorientert biologi og sammenhengen med matematikk R2 fra videregående opplæring.
• Nederbragt, Lex (2021). Using Jupyter for teaching programming to bachelor students in Bioscience.
• Nederbragt, Alexander Johan; Harris, Rayna Michelle; Hill, Alison Presmanes & Wilson, Greg (2020). Ten quick tips for teaching with participatory live coding. PLoS Computational Biology. ISSN 1553-734X. 16(9), s. 1–7. doi: 10.1371/journal.pcbi.1008090. Fulltekst i vitenarkiv
• Fyhn, Marianne; Malthe-Sørenssen, Anders; Mørken, Knut Martin; Nederbragt, Alexander Johan; Odden, Tor Ole & Sundnes, Joakim (2019). Beregningsorientering og utdanningsutvikling.
• Nederbragt, Alexander Johan (2019). Learning from the Carpentries.
• Nederbragt, Alexander Johan (2018). Programmering og modellering i biovitenskapsutdanning.
• Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan & Jakobsen, Kjetill Sigurd (2018). The impact of repetitive DNA on speciation rates in teleost fish.
• Tennøe, Simen; Mobarhan, Milad; Dragly, Svenn-Arne; Solbrå, Andreas Våvang & Nederbragt, Alexander Johan (2017). Teaching modelling to first-year biology students. Vis sammendrag

  The field of biology relies heavily on computations. This is not well reflected in education and the current undergraduate curriculum has little computational content. This results in a discontinuity between the education received by the students and the problems they face after graduation. The end result is that the students are not equipped to meet the requirements of modern research nor the tasks awaiting them in the industry. To remedy this problem, a new course, BIOS 1100 - Introduction to Modelling in Biology, will be held for the first time at the University of Oslo in fall 2017. Currently, no available book combines biology and programming at an introductory level in a satisfactory way. Most textbooks teach both topics separately or expect the reader to know either biology or programming from before. We have therefore written our own textbook to be used as curriculum in this course. This book aims to teach programming and modelling to first year biology students through examples from biology. The book is based on a philosophy of just-in-time teaching where the programming concepts are introduced just when they are needed to solve the problem in hand. This puts the programming content in an unusual order in comparison to the traditional computer science curriculum while keeping the biology students motivated by the problems they solve. The examples are mainly from the three branches of biology: population dynamics, bioinformatics and evolution. The purpose is to give biology students a practical understanding of programming and mathematical models. This will enable the understanding of mathematical models and encourage critical thinking. Programming allows much more realistic and inspiring problems to be addressed, enabling students to work on current research topics early on. The textbook is written using DocOnce (created by Hans Petter Langtangen), which enables us to compile the book to both LaTeX/PDF, HTML and Jupyter Notebooks.

• Nederbragt, Alexander Johan (2017). How I got infected by fish genomics - and how you can too.
• Nederbragt, Alexander Johan (2017). Software Carpentry og Data Carpentry: opplæring i bruk og deling av forskningsdata – for forskere, av forskere, ved UiO.
• Nederbragt, Alexander Johan (2017). Teaching Researchers Basic Skills for Computational Research: the Software Carpentry Model.
• Sandve, Simen Rød; Hvidsten, Torgeir Rhoden; Lien, Sigbjørn; Rori, Rohlfs; Jakobsen, Kjetill Sigurd & Nome, Torfinn [Vis alle 9 forfattere av denne artikkelen] (2017). Evolution after whole genome duplication - insights from the salmonids.
• Nederbragt, Alexander Johan (2016). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
• Nederbragt, Alexander Johan (2016). Doing bioinformatics: a user’s perspective.
• Nederbragt, Alexander Johan (2016). SMRTwishes for SMRTsoftware for SMRTreads - a user’s perspective.
• Nederbragt, Alexander Johan (2016). Genomic variation detection in Atlantic cod using long reads.
• Nederbragt, Alexander Johan (2016). The new Atlantic cod reference genome.
• Nederbragt, Alexander Johan & Lagesen, Karin (2016). The Carpentry effort at the University of Oslo.
• Eide, Marta; Puntervoll, Pål; Lille-Langøy, Roger; Goldstone, Jared V.; Tørresen, Ole Kristian & Nederbragt, Alexander Johan [Vis alle 11 forfattere av denne artikkelen] (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 (2015). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
• Star, Bastiaan; Jentoft, Sissel; Matschiner, Michael; Nederbragt, Alexander Johan; Kjesbu, Olav Sigurd & Berg, Paul Ragnar [Vis alle 12 forfattere av denne artikkelen] (2015). Does historic DNA provide genomic evidence for recent selection in Atlantic cod?
• Nederbragt, Alexander Johan (2015). Bioinformatics breakout : Recent experiences from Oslo.
• Nederbragt, Alexander Johan (2015). Active learning strategies for bioinformatics teaching.
• Nederbragt, Alexander Johan (2015). A New, High Quality Reference Genome Assembly For Atlantic Cod.
• 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.
• Brynildsen, William; Tørresen, Ole Kristian; Jakobsen, Kjetill Sigurd & Nederbragt, Alexander Johan (2014). Genomic sequence repeats in fish genomes.
• Tørresen, Ole Kristian; Jentoft, Sissel; Star, Bastiaan; Sandve, Geir Kjetil F.; Skage, Morten & Hansen, Marianne Helén Selander [Vis alle 9 forfattere av denne artikkelen] (2014). A new, high quality reference genome assembly for Atlantic cod.
• Nederbragt, Alexander Johan (2014). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
• 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; 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; Walenz, Brian; Grove, Harald; Lien, Sigbjørn; Knight, James & Star, Bastiaan [Vis alle 15 forfattere av denne artikkelen] (2014). A new, high quality reference genome assembly for Atlantic cod.
• Matschiner, Michael; Star, Bastiaan; Berg, Paul Ragnar; Tørresen, Ole Kristian; Nederbragt, Alexander Johan & Hansen, Marianne Helén Selander [Vis alle 11 forfattere av denne artikkelen] (2014). Population differentiation and local adaptation in Atlantic cod.
• Nederbragt, Alexander Johan (2014). The why and how of long reads for de novo genome assembly.
• 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 (2013). Repeat after me: Is our research reproducible (enough)?
• Nederbragt, Alexander Johan (2013). Using PacBio Reads to Improve and Validate the Assembly of the Complex Atlantic Cod Genome.
• 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). The IPython Notebook: an introduction, and hands-on/live demo.
• Nederbragt, Alexander Johan (2013). Lessons learned from assembling the Atlantic cod genome.
• Nederbragt, Alexander Johan (2013). High Throughput Sequencing technologies.
• Nederbragt, Alexander Johan (2013). The IPython Notebook: an introduction, and hands-on/live demo.
• 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 at the Norwegian Sequencing Centre with a focus on genome assembly.
• 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.
• Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Lagesen, Karin; Khelik, Ksenia; Rognes, Torbjørn & Jentoft, Sissel [Vis alle 7 forfattere av denne artikkelen] (2012). Improving the cod genome with the use of multi-platform sequencing data.
• Nederbragt, Alexander Johan (2012). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
• 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). The bioinformatics of sequencing and assembling genomes - with a focus on the Atlantic cod and salmon genome projects.
• 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). The best of both worlds - Combining PacBio with short read technology for improved de novo genome assembly.
• Nederbragt, Alexander Johan (2012). New High Throughput Sequencing technologies at the Norwegian Sequencing Centre - and beyond.
• Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Skage, Morten; Tooming-Klunderud, Ave ; Hansen, Marianne Helén Selander & Jentoft, Sissel [Vis alle 9 forfattere av denne artikkelen] (2012). The long jump: Long distance mate pairs and long PacBio reads for the Salmon Genome Project.
• Nederbragt, Alexander Johan (2012). New High Throughput Sequencing technologies at the Norwegian Sequencing Centre - and beyond.
• Nederbragt, Alexander Johan (2012). How and why I use blogging and twitter for science.
• Nederbragt, Alexander Johan; Tørresen, Ole Kristian; Khelik, Ksenia; Lagesen, Karin; Rounge, Trine Ballestad & Star, Bastiaan [Vis alle 13 forfattere av denne artikkelen] (2012). Challenges and Opportunities for Improving the Atlantic Cod Genome Assembly and Annotation.
• Star, Bastiaan; Nederbragt, Alexander Johan; Jentoft, Sissel; Grimholt, Unni; Malmstrøm, Martin & Gregers, Tone Fredsvik [Vis alle 18 forfattere av denne artikkelen] (2011). The genome of Atlantic cod reveals a unique immune system.
• Nederbragt, Alexander Johan (2011). In between lines of code - a blog about biology, sequencing, bioinformatics and more.
• Nederbragt, Alexander Johan; Lagesen, Karin & Malmstrøm, Martin (2011). Bioinformatic analysis of genomic data.
• Nederbragt, Alexander Johan (2011). How to sequence a large eukaryotic genome and how we sequenced the cod genom.
• Rounge, Trine Ballestad & Nederbragt, Alexander Johan (2011). The Atlantic Cod Genome Project.
• Nederbragt, Alexander Johan (2011). Next generation sequencing: research opportunities and bioinformatic challenges.

Se alle arbeider i Cristin