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Showing results 1-50 of 71 << Previous 1 2    Next >>

2019
1 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 ;Volume 4. p. 701-736
UiO Untitled
 
2 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 ;Volume 47.(4) p. e21-
OUS UiO Untitled
 
3 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 ;Volume 15.(2) p. 1-13
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4 Kanduri, Srinivasa Kalyana Chakravarthi; Bock, Christoph; Gundersen, Sveinung; Hovig, Eivind; Sandve, Geir Kjetil.
Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinformatics 2019 ;Volume 35.(9) p. 1615-1624
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2018
5 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 ;Volume 19.(481) p. -
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6 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 ;Volume 128.(6) p. 2642-2650
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7 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 ;Volume 46.(1) p. W186-W193
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8 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 ;Volume 13.(12) p. 1-17
UiO Untitled
 
2017
9 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
 
10 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 ;Volume 7.(1) p. -
AHUS NTNU OUS UiO Untitled
 
11 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 ;Volume 18. p. -
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12 Holden, Lars; Jullum, Martin; Sandve, Geir Kjetil.
Statistical modeling of repertoire overlap in entire sampling spaces. : Norsk Regnesentral 2017 15 p. NR-notat(SAMBA/13/2017)
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13 Kanduri, Chakravarthi; Domanska, Diana; Hovig, Eivind; Sandve, Geir Kjetil.
Genome build information is an essential part of genomic track files. Genome Biology 2017 ;Volume 18.(1)
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14 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 ;Volume 18.(1) p. 1-14
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15 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 ;Volume 18:263. p. 1-8
UiO Untitled
 
16 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 ;Volume 199.((2)) p. 782-791
OUS UiO Untitled
 
17 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 ;Volume 12.(12) p. -
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18 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 ;Volume 6.(7) Suppl. https://academic.oup p. 1-12
NR NTNU OUS UiO Untitled
 
2016
19 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 ;Volume 32.(11) p. 1743-1745
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20 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
21 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 ;Volume 10.(4) p. -
NR NTNU OUS UiO Untitled
 
22 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 ;Volume 10.(7)
NTNU OUS UiO Untitled
 
23 Ferkingstad, Egil; Holden, Lars; Sandve, Geir Kjetil F..
Monte Carlo Null Models for Genomic Data. Statistical Science 2015 ;Volume 30.(1) p. 59-71
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24 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
 
25 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 ;Volume 10.(3) p. -
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26 Mora Ortiz, Antonio Carlos; Sandve, Geir Kjetil; Gabrielsen, Odd Stokke; Eskeland, Ragnhild.
In the loop: promoter-enhancer interactions and bioinformatics. Briefings in Bioinformatics 2015 p. -
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27 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 ;Volume 10.(4) p. -
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2014
28 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 ;Volume 23.(4) p. 942-948
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29 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 ;Volume 46.(9) p. 964-972
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30 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 ;Volume 30.(11) p. 1620-1622
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31 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 ;Volume 15.(1)
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32 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
 
33 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
 
34 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
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35 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
36 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 ;Volume 41.(W1) p. W133-W141
NORCE NR NTNU OUS UiB UiO UiT Untitled
 
37 Ferkingstad, Egil; Holden, Lars; Sandve, Geir Kjetil.
Monte Carlo null models for genomic data. 2013 Joint Statistical Meetings; 2013-08-05
NR UiO Untitled
 
38 Ferkingstad, Egil; Holden, Lars; Sandve, Geir Kjetil.
Monte Carlo null models in ecology. Oslo: Norsk Regnesentral 2013 6 p. NR-notat(SAMBA/20/13)
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39 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 ;Volume 11.(163) p. -
NTNU UiO Untitled
 
40 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 ;Volume 6:45.
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41 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 ;Volume 41.(10) p. 5164-5174
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42 Sandve, Geir Kjetil; Nekrutenko, Anton; Taylor, James; Hovig, Johannes Eivind.
Ten Simple Rules for Reproducible Computational Research. PloS Computational Biology 2013 ;Volume 9.(10)
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2012
43 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 ;Volume 67.(1) p. 33-40
OUS UiO Untitled
 
44 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 ;Volume 7.(3)
UiO Untitled
 
45 Disanto, Giulio; Sandve, Geir Kjetil; Berlanga-Taylor, Antonio; Ragnedda, Giammario; Morahan, Julia; Watson, Corey T; Giovannoni, Gavin; Ebers, Georg C; Ramagopalan, Sreeram V.
Vitamin D receptor binding, chromatin states and association with multiple sclerosis. Human Molecular Genetics 2012 ;Volume 21.(16) p. 3575-3586
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46 Watson, Corey T; Disanto, Giulio; Sandve, Geir Kjetil; Breden, Felix; Giovannoni, Gavin; Ramagopalan, Sreeram V.
Age-Associated Hyper-Methylated Regions in the Human Brain Overlap with Bivalent Chromatin Domains. PLoS ONE 2012 ;Volume 7.(9)
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2011
47 Sandve, Geir Kjetil; Gundersen, Sveinung; Rydbeck, Halfdan; Glad, Ingrid Kristine; Holden, Lars; Holden, Marit; Liestøl, Knut; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Johansen, Morten; Nygaard, Vegard; Tøstesen, Eivind; Frigessi, Arnoldo; Hovig, Eivind.
The differential disease regulome. BMC Genomics 2011 ;Volume 12. p. 353-
NR NTNU OUS UiO Untitled
 
48 Gundersen, Sveinung; Kalaš, Matúš; Abul, Osman; Frigessi, Arnoldo; Hovig, Eivind; Sandve, Geir Kjetil.
Identifying elemental genomic track types and representing them uniformly. BMC Bioinformatics 2011 ;Volume 12.
NORCE NR OUS UiB UiO Untitled
 
49 Sandve, Geir Kjetil Ferkingstad; Ferkingstad, Egil; Nygård, Ståle.
Sequential Monte Carlo multiple testing. Bioinformatics 2011 ;Volume 27.(23) p. 3235-3241
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2010
50 Sandve, Geir Kjetil; Gundersen, Sveinung; Rydbeck, Halfdan; Glad, Ingrid Kristine; Holden, Lars; Holden, Marit; Liestøl, Knut; Clancy, Trevor; Ferkingstad, Egil; Johansen, Morten; Nygaard, Vegard; Tøstesen, Eivind; Frigessi, Arnoldo; Hovig, Eivind.
The Genomic HyperBrowser: inferential genomics at the sequence level. Genome Biology 2010 ;Volume 11.(12)
NR OUS UiO Untitled
 
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