Cristin

2020
1.	du Pré, Fleur; Blazevski, Jana; Dewan, Alisa Elinsdatter; Stamnæs, Jorunn; Kanduri, Srinivasa Kalyana Chakravarthi; Sandve, Geir Kjetil; Johannesen, Marie Kongshaug; Lindstad, Christian Borgen; Hnida, Kathrin; Fugger, Lars; Melino, Gerry; Qiao, Shuo-Wang; Sollid, Ludvig Magne. B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2. Journal of Experimental Medicine (JEM) 2020 ;Volum 217:e20190860..(2) s. 1-14 OUS UiO Untitled

2.	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

3.	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. - OUS UiO Untitled

4.	Weber, Cédric R.; Akbar, Rahmad; Yermanos, Alexander; Pavlovic, Milena; Snapkov, Igor; Sandve, Geir Kjetil; Reddy, Sai T.; Greiff, Victor. immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Bioinformatics 2020 ;Volum 36.(11) s. 3594-3596 UiO Untitled
2019
5.	Brown, Alex; Snapkov, Igor; Akbar, Rahmad; Pavlovic, Milena; Miho, Enkelejda; Sandve, Geir Kjetil; Greiff, Victor. Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires. Molecular Systems Design & Engineering 2019 ;Volum 4.(4) s. 701-736 UiO Untitled

6.	Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit; Mathelier, Anthony. A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research 2019 ;Volum 47.(4) s. e21- OUS UiO Untitled

7.	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 UiO Untitled

8.	Kanduri, Srinivasa Kalyana Chakravarthi; Bock, Christoph; Gundersen, Sveinung; Hovig, Eivind; Sandve, Geir Kjetil. Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinformatics 2019 ;Volum 35.(9) s. 1615-1624 OUS UiO Untitled

9.	Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana; Holden, Lars; Gheorghe, Marius; Mathelier, Anthony; Glad, Ingrid Kristine; Sandve, Geir Kjetil. Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics 2019 s. 1-8 NR OUS UiO Untitled

10.	Snir, Omri; Kanduri, Srinivasa Kalyana Chakravarthi; Lundin, Knut Erik Aslaksen; Sandve, Geir Kjetil; Sollid, Ludvig Magne. Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production. United European Gastroenterology journal 2019 ;Volum 0.(0) s. 1-9 OUS UiO Untitled
2018
11.	Domanska, Diana Ewa; Kanduri, Srinivasa Kalyana Chakravarthi; Simovski, Boris; Sandve, Geir Kjetil. Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. BMC Bioinformatics 2018 ;Volum 19.(481) s. - UiO Untitled

12.	Risnes, Louise Fremgaard; Christophersen, Asbjørn; Dahal-Koirala, Shiva; Neumann, Ralf Stefan; Sandve, Geir Kjetil; Sarna, Vikas Kumar; Lundin, Knut Erik Aslaksen; Qiao, Shuo Wang; Sollid, Ludvig Magne. Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease. Journal of Clinical Investigation 2018 ;Volum 128.(6) s. 2642-2650 OUS UiO Untitled

13.	Simovski, Boris; Kanduri, Srinivasa Kalyana Chakravarthi; Gundersen, Sveinung; Titov, Dmytro; Domanska, Diana Ewa; Bock, Christoph; Bossini-Castillo, Lara; Chikina, Maria; Favorov, Alexander; Layer, Ryan M.; Mironov, Alexandre A.; Quinlan, Aaron R.; Sheffield, Nathan C.; Trynka, Gosia; Sandve, Geir Kjetil. Coloc-stats: A unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Research 2018 ;Volum 46.(1) s. W186-W193 OUS UiO Untitled

14.	Yao, Ying; Zia, Asima; Wyrozemski, Lukasz Adam; Lindeman, Ida; Sandve, Geir Kjetil; Qiao, Shuo Wang. Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments. PLOS ONE 2018 ;Volum 13.(12) s. 1-17 UiO Untitled
2017
15.	Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix; Lirussi, Lisa; Sengupta, Tanima; Tekin, Nuriye Basdag; Jobert, Laure; Alexandrov, Ludmil B.; Galashevskaya, Anastasia; Rada, Christina; Sandve, Geir Kjetil; Rognes, Torbjørn; Krokan, Hans Einar; Nilsen, Hilde Loge. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. 6th EU-US Conference on Repair of endogenous DNA damage; 2017-09-24 - 2017-09-28 AHUS NTNU UiO Untitled

16.	Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix; Lirussi, Lisa; Sengupta, Tanima; Tekin, Nuriye Basdag; Jobert, Laure; Alexandrov, Ludmil B.; Galashevskaya, Anastasia; Rada, Cristina; Sandve, Geir Kjetil; Rognes, Torbjørn; Krokan, Hans Einar; Nilsen, Hilde Loge. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. Scientific Reports 2017 ;Volum 7.(1) s. - AHUS NTNU OUS UiO Untitled

17.	Domanska, Diana Ewa; Vodak, Daniel; Christin, Lund-Andersen; Salvatore, Stefania; Hovig, Eivind; Sandve, Geir Kjetil. The rainfall plot: Its motivation, characteristics and pitfalls. BMC Bioinformatics 2017 ;Volum 18. s. - NR OUS UiO Untitled

18.	Holden, Lars; Jullum, Martin; Sandve, Geir Kjetil. Statistical modeling of repertoire overlap in entire sampling spaces. : Norsk Regnesentral 2017 15 s. NR-notat(SAMBA/13/2017) NR UiO Untitled

19.	Kanduri, Chakravarthi; Domanska, Diana; Hovig, Eivind; Sandve, Geir Kjetil. Genome build information is an essential part of genomic track files. Genome Biology 2017 ;Volum 18.(1) OUS UiO Untitled

20.	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 UiO VETINST Untitled

21.	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

22.	Roy, Bishnudeo; Neumann, Ralf Stefan; Snir, Omri; Iversen, Rasmus; Sandve, Geir Kjetil; Lundin, Knut Erik Aslaksen; Sollid, Ludvig Magne. High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease. Journal of Immunology 2017 ;Volum 199.((2)) s. 782-791 OUS UiO Untitled

23.	Salvatore, Stefania; Domanska, Diana Ewa; Wood, Mollie; Nordeng, Hedvig Marie Egeland; Sandve, Geir Kjetil. Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy. PLOS ONE 2017 ;Volum 12.(12) s. - FHI UiO Untitled

24.	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 NR NTNU OUS UiO Untitled
2016
25.	Børnich, Claus; Grytten, Ivar; Hovig, Johannes Eivind; Paulsen, Jonas; Cech, Martin; Sandve, Geir Kjetil. Galaxy Portal: Interacting with the galaxy platform through mobile devices. Bioinformatics 2016 ;Volum 32.(11) s. 1743-1745 OUS UiO Untitled

26.	Simovski, Boris; Drabløs, Finn Sverre; Gundersen, Sveinung; Johansen, Morten; Domanska, Diana Ewa; Azab, Abdulrahman; Sandve, Geir Kjetil; Hovig, Johannes Eivind. The Genomic HyperBrowser. European Conference on Computational Biology; 2016-09-03 - 2016-09-07 NTNU UiO Untitled
2015
27.	Rydbeck, Halfdan; Sandve, Geir Kjetil F.; Ferkingstad, Egil; Simovski, Boris; Rye, Morten Beck; Hovig, Johannes Eivind. ClusTrack: Feature extraction and similarity measures for clustering of genome-wide data sets. PLOS ONE 2015 ;Volum 10.(4) s. - NR NTNU OUS UiO Untitled

28.	Bengtsen, Mads; Klepper, Kjetil; Gundersen, Sveinung; Cuervo Torre, Ignacio; Drabløs, Finn; Hovig, Johannes Eivind; Sandve, Geir Kjetil F.; Gabrielsen, Odd Stokke; Eskeland, Ragnhild. c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PLOS ONE 2015 ;Volum 10.(7) NTNU OUS UiO Untitled

29.	Ferkingstad, Egil; Holden, Lars; Sandve, Geir Kjetil F.. Monte Carlo Null Models for Genomic Data. Statistical Science 2015 ;Volum 30.(1) s. 59-71 NR UiO Untitled

30.	Ferkingstad, Egil; Sandve, Geir Kjetil F.; Holden, Lars. Monte Carlo null models for genomic data. Statistikkseminar ved Institutt for matematiske fag, NTNU; 2015-04-09 NR NTNU UiO Untitled

31.	Kraus, Hanne Irene; Sandve, Geir Kjetil F.; Schmitz, Martina; Dürst, Matthias; Hovig, Johannes Eivind. Transcriptionally active regions are the preferred targets for chromosomal HPV integration in cervical carcinogenesis. PLOS ONE 2015 ;Volum 10.(3) s. - AHUS OUS UiO Untitled

32.	Mora Ortiz, Antonio Carlos; Sandve, Geir Kjetil; Gabrielsen, Odd Stokke; Eskeland, Ragnhild. In the loop: promoter-enhancer interactions and bioinformatics. Briefings in Bioinformatics 2015 s. - UiB UiO Untitled

33.	Ricigliano, Vito A. G.; Handel, Adam E; Sandve, Geir Kjetil F.; Annibali, Viviana; Ristori, Giovanni; Mechelli, Rosella; Cader, M.Zameel; Salvetti, Marco. EBNA2 binds to genomic intervals associated with multiple sclerosis and overlaps with vitamin D receptor occupancy. PLOS ONE 2015 ;Volum 10.(4) s. - UiO Untitled
2014
34.	Disanto, Giulio; Sandve, Geir Kjetil; Ricigliano, Vito AG; Pakpoor, Julia; Berlanga-Taylor, Antonio; Handel, Adam E; Kuhle, Jens; Holden, Lars; Watson, Corey T; Giovannoni, Gavin; Handunnetthi, Lahiru; Ramagopalan, Sreeram V. DNase hypersensitive sites and association with multiple sclerosisxs. Human Molecular Genetics 2014 ;Volum 23.(4) s. 942-948 NR UiO Untitled

35.	Molyneux, Sam; Waterhouse, PD; Shelton, Dawne; Shao, Yang W; Watling, Christopher M; Tang, Qing-Lian; Harris, Isaac S; Dickson, Brendan C; Tharmapalan, Pirashaanthy; Sandve, Geir Kjetil F.; Zhang, Xiaoyang; Bailey, Swneke D; Berman, Hal; Wunder, Jay S; Iszvak, Zsuzsanna; Lupien, Mathieu; Mak, Tak W; Khokha, Rama. Human somatic cell mutagenesis creates genetically tractable sarcomas. Nature Genetics 2014 ;Volum 46.(9) s. 964-972 UiO Untitled

36.	Paulsen, Jonas; Sandve, Geir Kjetil F.; Gundersen, Sveinung; Lien, Tonje Gulbrandsen; Trengereid, Kai; Hovig, Johannes Eivind. HiBrowse: Multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics 2014 ;Volum 30.(11) s. 1620-1622 OUS UiO Untitled

37.	Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, H; Carninci, P; Forrest, A; Drabløs, Finn. Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC Genomics 2014 ;Volum 15.(1) NTNU STO UiO Untitled

38.	Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair; Drabløs, Finn. Chromatin data integrated with a human reference atlas of experimentally defined promoters reveal repressed promoters located in active chromatin. SocBiN Bioinformatics 2014; 2014-06-11 - 2014-06-13 NTNU UiO Untitled

39.	Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair; Drabløs, Finn. Repressed promoters in active chromatin. SocBiN Bioinformatics 2014; 2014-06-11 - 2014-06-13 NTNU UiO Untitled

40.	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. A new, high quality reference genome assembly for Atlantic cod. CEES Annual Student Conference; 2014-10-21 - 2014-10-22 UiO Untitled

41.	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. A new, high quality reference genome assembly for Atlantic cod. SocBiN Bioinformatics; 2014-06-11 - 2014-06-13 UiO NMBU Untitled
2013
42.	Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje Gulbrandsen; Rye, Morten Beck; Frigessi, Arnoldo; Hovig, Johannes Eivind. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research 2013 ;Volum 41.(W1) s. W133-W141 NORCE NR NTNU OUS UiB UiO UiT Untitled

43.	Ferkingstad, Egil; Holden, Lars; Sandve, Geir Kjetil. Monte Carlo null models for genomic data. 2013 Joint Statistical Meetings; 2013-08-05 NR UiO Untitled

44.	Ferkingstad, Egil; Holden, Lars; Sandve, Geir Kjetil. Monte Carlo null models in ecology. Oslo: Norsk Regnesentral 2013 6 s. NR-notat(SAMBA/20/13) NR UiO Untitled

45.	Handel, Adam E; Sandve, Geir Kjetil; Disanto, Giulio; Berlanga-Taylor, Antonio; Gallone, Anna; Hanwell, Heather EC; Drabløs, Finn; Giovannoni, Gavin; Ebers, Georg C; Ramagopalan, Sreeram V. Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. BMC Medicine 2013 ;Volum 11.(163) s. - NTNU UiO Untitled

46.	Handel, Adam E; Sandve, Geir Kjetil; Disanto, Giulio; Handunnetthi, Lahiru; Giovannoni, Gavin; Ramagopalan, Sreeram V. Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression. BMC Medical Genomics 2013 ;Volum 6:45. UiO Untitled

47.	Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf; Glad, Ingrid Kristine; Hovig, Johannes Eivind. Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Research 2013 ;Volum 41.(10) s. 5164-5174 NR OUS UiO Untitled

48.	Sandve, Geir Kjetil; Nekrutenko, Anton; Taylor, James; Hovig, Johannes Eivind. Ten Simple Rules for Reproducible Computational Research. PLoS Computational Biology 2013 ;Volum 9.(10) UiO Untitled
2012
49.	Bruhn, Sören; Barrenäs, Fredrik; Mobini, R; Andersson, B; Chavali, S.; Egan, B. S.; Hovig, Eivind; Sandve, Geir Kjetil; Langston, M. A.; Rogers, Gary; Wang, H.; Benson, Mikael. Increased expression of IRF4 and ETS1 in CD4(+) cells from patients with intermittent allergic rhinitis. Allergy. European Journal of Allergy and Clinical Immunology 2012 ;Volum 67.(1) s. 33-40 OUS UiO Untitled

50.	Disanto, Giulio; Sandve, Geir Kjetil; Berlanga-Taylor, Antonio; Morahan, Julia; Dobson, Ruth; Giovannoni, Gavin; Ramagopalan, Sreeram V. Genomic Regions Associated with Multiple Sclerosis Are Active in B Cells. PLOS ONE 2012 ;Volum 7.(3) UiO Untitled

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