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2023
1 Nederbragt, Lex.
Cognitive Load: what is it and how can we take it in consideration when teaching?. iEarth Digital Learning Forum; 2023-09-28 - 2023-09-28
UiO Untitled
 
2 Reinar, William Brynildsen; Tørresen, Ole K.; Nederbragt, Lex; Matschiner, Michael; Jentoft, Sissel; Jakobsen, Kjetill Sigurd.
Teleost genomic repeat landscapes in light of diversification rates and ecology. Mobile DNA 2023 ;Volum 14.(1) s. 1-12
UiO Untitled
 
2022
3 Eliassen, June Edvarda; Bøe, Maria Vetleseter; Nederbragt, Lex; Berg, Marthe Mjøen; Gregers, Tone Fredsvik.
Motivasjon for beregningsorientert biologi og sammenhengen med matematikk R2 fra videregående opplæring. Nordic Journal of STEM Education 2022 ;Volum 4.(2) s. 58-70
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4 Nederbragt, Lex.
Carpentry@UiO: Workshops for basic skills in programming and datamanagement at The University of Oslo (UiO). CarpentryCon 2022, Panel discussion: The Carpentries Regional Subcommunities: Activities, Challenges, and Opportunities; 2022-08-01 - 2022-08-12
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5 Nederbragt, Lex; Lemma, Roza Berhanu; Belova, Tatiana; Cheneby, Jeanne; Ibrahim, Mohamed; Akdeniz, Byram Cevdet; Rossini, Roberto.
Oslo Bioinformatics Workshop Week 2022. Center for Bioinformatics, The Faculty of Mathematics and Natural Sciences, UiO https://www.mn.uio.no/sbi/english/events/oslo-bioinformatics-week-2022/ 2022
UiO Untitled
 
2021
6 Eliassen, June Edvarda; Bøe, Maria Vetleseter; Nederbragt, Lex; Gregers, Tone Fredsvik.
Motivasjon for beregningsorientert biologi og sammenhengen med matematikk R2 fra videregående opplæring. MNT konferansen 2021; 2021-03-15 - 2021-03-16
UiO Untitled
 
7 Nederbragt, Lex.
Using Jupyter for teaching programming to bachelor students in Bioscience. iearth digitale laeringsforum; 2021-06-03 - 2021-06-03
UiO Untitled
 
2020
8 Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan; Sandve, Geir Kjetil.
Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods. BMC Genomics 2020 ;Volum 21.
UiO Untitled
 
9 Khelik, Ksenia; Sandve, Geir Kjetil; Nederbragt, Alexander Johan; Rognes, Torbjørn.
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics 2020 ;Volum 21.(1) s. -
UiO OUS Untitled
 
10 Nederbragt, Alexander Johan; Harris, Rayna Michelle; Hill, Alison Presmanes; Wilson, Greg.
Ten quick tips for teaching with participatory live coding. PLoS Computational Biology 2020 ;Volum 16.(9) s. 1-7
UiO Untitled
 
2019
11 Fyhn, Marianne; Malthe-Sørenssen, Anders; Mørken, Knut Martin; Nederbragt, Alexander Johan; Odden, Tor Ole; Sundnes, Joakim.
Beregningsorientering og utdanningsutvikling. Presentasjon for delegasjon fra Norges teknisk naturvitenskapelige universitet; 2019-09-24 - 2019-09-24
UiO Untitled
 
12 Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine; Sandve, Geir Kjetil.
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Computational Biology 2019 ;Volum 15.(2) s. 1-13
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13 Nederbragt, Alexander Johan.
Learning from the Carpentries. CarpentryConnect Manchester 2019; 2019-06-25 - 2019-06-27
UiO Untitled
 
14 Varadharajan, Srinidhi; Rastas, Pasi; Löytynoja, Ari; Matschiner, Michael; Calboli, Federico C. F.; Guo, Baocheng; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd; Merilä, Juha.
A High-Quality Assembly of the Nine-Spined Stickleback (Pungitius pungitius) Genome. Genome Biology and Evolution (GBE) 2019 ;Volum 11.(11) s. 3291-3308
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2018
15 Jørgensen, Tor Erik; Karlsen, Bård Ove; Emblem, Åse; Breines, Ragna; Andreassen, morten; Rounge, Trine Ballestad; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd; Nymark, Marianne; Ursvik, anita; Coucheron, Dag H; Jakt, Lars Martin; Nordeide, Jarle Tryti; Moum, Truls Borg; Johansen, Steinar Daae.
Mitochondrial genome variation of Atlantic cod. BMC Research Notes 2018 ;Volum 11:397. s. 1-7
NORD UiT UiO NLSH Untitled
 
16 Lie, Kai Kristoffer; Tørresen, Ole K.; Solbakken, Monica Hongrø; Rønnestad, Ivar; Tooming-Klunderud, Ave; Nederbragt, Alexander Johan; Jentoft, Sissel; Sæle, Øystein.
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 2018 ;Volum 19.(186) s. 1-17
HAVFORSK UiO UiB Untitled
 
17 Nederbragt, Alexander Johan.
Programmering og modellering i biovitenskapsutdanning. Undervisningsseminar for NT-fak, Univ. i Tromsø; 2018-01-08 - 2018-01-08
UiO Untitled
 
18 Reinar, William Brynildsen; Tørresen, Ole K.; Matschiner, Michael; Jentoft, Sissel; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd.
The impact of repetitive DNA on speciation rates in teleost fish. SMBE 2018; 2018-07-08 - 2018-07-12
UiO Untitled
 
19 Tørresen, Ole K.; Brieuc, Marine Servane; Solbakken, Monica Hongrø; Sørhus, Elin; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd; Meier, Sonnich; Edvardsen, Rolf; Jentoft, Sissel.
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats. BMC Genomics 2018 ;Volum 19.(240) s. 1-17
UiO HAVFORSK Untitled
 
20 Varadharajan, Srinidhi; Sandve, Simen Rød; Gillard, Gareth Benjamin; Tørresen, Ole K.; Mulugeta, Teshome Dagne; Hvidsten, Torgeir Rhoden; Lien, Sigbjørn; Vøllestad, Leif Asbjørn; Jentoft, Sissel; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd.
The grayling genome reveals selection on gene expression regulation after whole-genome duplication. Genome Biology and Evolution (GBE) 2018 ;Volum 10.(10) s. 2785-2800
NMBU UiO Untitled
 
2017
21 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.
The genomic mosaicism of hybrid speciation. Science Advances 2017 ;Volum 3. s. 1-16
NTNU UiO NMBU Untitled
 
22 Khelik, Ksenia; Lagesen, Karin; Sandve, Geir Kjetil; Rognes, Torbjørn; Nederbragt, Alexander Johan.
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinformatics 2017 ;Volum 18.(1) s. 1-14
OUS VETINST UiO Untitled
 
23 Nederbragt, Alexander Johan.
How I got infected by fish genomics - and how you can too. Eijkman lecture; 2017-03-24 - 2017-03-24
UiO Untitled
 
24 Nederbragt, Alexander Johan.
Software Carpentry og Data Carpentry: opplæring i bruk og deling av forskningsdata – for forskere, av forskere, ved UiO. NARMA Vårkonferanse 2017; 2017-03-28 - 2017-03-29
UiO Untitled
 
25 Nederbragt, Alexander Johan.
Teaching Researchers Basic Skills for Computational Research: the Software Carpentry Model. 2017 Nordic eInfrastructure Collaboration conference; 2017-05-29 - 2017-06-01
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26 Rand, Knut Dagestad; Grytten, Ivar; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine; Sandve, Geir Kjetil.
Coordinates and intervals in graph-based reference genomes. BMC Bioinformatics 2017 ;Volum 18:263. s. 1-8
UiO Untitled
 
27 Sandve, Simen Rød; Hvidsten, Torgeir Rhoden; Lien, Sigbjørn; Rori, Rohlfs; Jakobsen, Kjetill Sigurd; Nome, Torfinn; Varadharajan, Srinidhi; Nederbragt, Alexander Johan; Vøllestad, Leif Asbjørn.
Evolution after whole genome duplication - insights from the salmonids. Evolution Conference; 2017-06-22
UiO NMBU Untitled
 
28 Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman; Holden, Lars; Holden, Marit; Grytten, Ivar; Rand, Knut Dagestad; Drabløs, Finn; Johansen, Morten; Mora Ortiz, Antonio Carlos; Lund-Andersen, Christin; Fromm, Bastian; Eskeland, Ragnhild; Gabrielsen, Odd Stokke; Ferkingstad, Egil; Nakken, Sigve; Bengtsen, Mads; Nederbragt, Alexander Johan; Thorarensen, Hildur Sif; Akse, Johannes Andreas; Glad, Ingrid Kristine; Hovig, Johannes Eivind; Sandve, Geir Kjetil.
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome. GigaScience 2017 ;Volum 6.(7) Suppl. https://academic.oup s. 1-12
NTNU UiO OUS NR Untitled
 
29 Tennøe, Simen; Mobarhan, Milad; Dragly, Svenn-Arne; Solbrå, Andreas Våvang; Nederbragt, Alexander Johan.
Teaching modelling to first-year biology students. 2017 International Conference on Computational Science and Engineering - Software, Education, and Biomedical applications; 2017-10-23 - 2017-10-25
UiO Untitled
 
30 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.
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod. BMC Genomics 2017 ;Volum 18. s. 1-23
UIA NMBU UiO HAVFORSK Untitled
 
31 Wilson, Greg; Brian, Jennifer; Cranston, Karen; Kitzes, Justin; Nederbragt, Alexander Johan; Teal, Tracy K.
Good enough practices in scientific computing. PLoS Computational Biology 2017 ;Volum 13.(6)
UiO Untitled
 
2016
32 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.
Chemical warfare in the marine environment: genomic survey of the Atlantic cod (Gadus morhua) defensome reveals the absence of an important xenosensor. 30th ESCBP Congress: Unraveling complexity: from molecules to ecosystems; 2016-09-04 - 2016-09-07
UiB UiO Untitled
 
33 Frank, Jeremy A.; Pan, Yao; Tooming-Klunderud, Ave; Eijsink, Vincent; McHardy, Alice C; Nederbragt, Alexander Johan; Pope, Phillip.
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports 2016 ;Volum 6. s. -
UiO NMBU Untitled
 
34 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.
The Atlantic salmon genome provides insights into rediploidization. Nature 2016 ;Volum 533.(7602) s. 200-205
NMBU VETINST UiO OUS UiB NTNU NOFIMA Untitled
 
35 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.
Evolution of the immune system influences speciation rates in teleost fishes. Nature Genetics 2016 ;Volum 48.(10) s. 1204-1210
UiO NMBU UIA HAVFORSK Untitled
 
36 Nederbragt, Alexander Johan.
Doing bioinformatics: a user’s perspective. Balti and Bioinformatics; 2016-09-28 - 2016-09-28
UiO Untitled
 
37 Nederbragt, Alexander Johan.
Genomic variation detection in Atlantic cod using long reads. SMRT Scientific Conference: Changing the World, One Molecule at a Time!; 2016-06-06 - 2016-06-07
UiO Untitled
 
38 Nederbragt, Alexander Johan.
In between lines of code - a blog about biology, sequencing, bioinformatics and more.
UiO Untitled
 
39 Nederbragt, Alexander Johan.
SMRTwishes for SMRTsoftware for SMRTreads - a user’s perspective. SMRT Informatics Developers Conference; 2016-06-08 - 2016-06-08
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40 Nederbragt, Alexander Johan.
The new Atlantic cod reference genome. ELIXIR Innovation and SME Forum: Data-Driven innovation in the aquaculture industries; 2016-05-12 - 2016-05-13
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41 Nederbragt, Alexander Johan; Lagesen, Karin.
The Carpentry effort at the University of Oslo. Miniseminar "Open Data Skills"; 2016-03-14
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42 Solbakken, Monica Hongrø; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Seppola, Marit; Gregers, Tone Fredsvik; Jakobsen, Kjetill Sigurd; Jentoft, Sissel.
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. Scientific Reports 2016 ;Volum 6.
UiT UiO UIA Untitled
 
43 Star, Bastiaan; Tørresen, Ole Kristian; Nederbragt, Alexander Johan; Jakobsen, Kjetill Sigurd; Pampoulie, Christophe; Jentoft, Sissel.
Genomic characterization of the Atlantic cod sex-locus. Scientific Reports 2016 ;Volum 6. s. 1-9
UIA UiO Untitled
 
44 Tørresen, Ole Kristian; Rise, Matthew L.; Jin, Xingkun; Star, Bastiaan; MacKenzie, Simon; Jakobsen, Kjetill Sigurd; Nederbragt, Alexander Johan; Jentoft, Sissel.
An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming. I: Genomics in Aquaculture. Elsevier 2016 ISBN 9780128014189. s. 45-72
UIA UiO Untitled
 
45 Tørresen, Ole Kristian; Star, Bastiaan; Jentoft, Sissel; Jakobsen, Kjetill Sigurd; Nederbragt, Alexander Johan.
The new era of genome sequencing using high-throughput sequencing technology: Generation of the first version of the Atlantic cod genome. I: Genomics in Aquaculture. Elsevier 2016 ISBN 9780128014189. s. 1-20
UIA UiO Untitled
 
2015
46 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.
The khmer software package: enabling efficient nucleotide sequence analysis. F1000 Research 2015 s. 1-12
UiO Untitled
 
47 Nederbragt, Alexander Johan.
A New, High Quality Reference Genome Assembly For Atlantic Cod. 9th European Zebrafish Meeting; 2015-06-28 - 2015-07-02
UiO Untitled
 
48 Nederbragt, Alexander Johan.
Active learning strategies for bioinformatics teaching. FEBS-IUBMB WORKSHOP ON EDUCATION IN MOLECULAR LIFE SCIENCES; 2015-09-18 - 2015-09-19
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49 Nederbragt, Alexander Johan.
Bioinformatics breakout : Recent experiences from Oslo. Pacific Biosciences user group meeting; 2015-11-09 - 2015-11-10
UiO Untitled
 
50 Nederbragt, Alexander Johan.
In between lines of code - a blog about biology, sequencing, bioinformatics and more.
UiO Untitled
 
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