Geir Kjetil Sandve

  • Post. doc.
 

Author network for Geir Kjetil Sandve by COREMINE medical


Publications 2018

Domanska D, Kanduri C, Simovski B, Sandve GK (2018)
Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis
BMC Bioinformatics, 19 (1), 481
DOI 10.1186/s12859-018-2438-1, PubMed 30547739

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A (2018)
A map of direct TF-DNA interactions in the human genome
Nucleic Acids Res (in press)
DOI 10.1093/nar/gky1210, PubMed 30517703

Kanduri C, Bock C, Gundersen S, Hovig E, Sandve GK (2018)
Colocalization analyses of genomic elements: approaches, recommendations and challenges
Bioinformatics (in press)
DOI 10.1093/bioinformatics/bty835, PubMed 30307532

Risnes LF, Christophersen A, Dahal-Koirala S, Neumann RS, Sandve GK, Sarna VK, Lundin KE, Qiao SW, Sollid LM (2018)
Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease
J Clin Invest, 128 (6), 2642-2650
DOI 10.1172/JCI98819, PubMed 29757191

Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK (2018)
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
Nucleic Acids Res, 46 (W1), W186-W193
DOI 10.1093/nar/gky474, PubMed 29873782

Yao Y, Zia A, Wyrożemski Ł, Lindeman I, Sandve GK, Qiao SW (2018)
Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments
PLoS One, 13 (12), e0208484
DOI 10.1371/journal.pone.0208484, PubMed 30517183

Publications 2017

Alsøe L, Sarno A, Carracedo S, Domanska D, Dingler F, Lirussi L, SenGupta T, Tekin NB, Jobert L, Alexandrov LB, Galashevskaya A, Rada C, Sandve GK, Rognes T, Krokan HE, Nilsen H (2017)
Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1
Sci Rep, 7 (1), 7199
DOI 10.1038/s41598-017-07314-5, PubMed 28775312

Domanska D, Vodák D, Lund-Andersen C, Salvatore S, Hovig E, Sandve GK (2017)
The rainfall plot: its motivation, characteristics and pitfalls
BMC Bioinformatics, 18 (1), 264
DOI 10.1186/s12859-017-1679-8, PubMed 28521741

Kanduri C, Domanska D, Hovig E, Sandve GK (2017)
Genome build information is an essential part of genomic track files
Genome Biol, 18 (1), 175
DOI 10.1186/s13059-017-1312-1, PubMed 28911336

Khelik K, Lagesen K, Sandve GK, Rognes T, Nederbragt AJ (2017)
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences
BMC Bioinformatics, 18 (1), 338
DOI 10.1186/s12859-017-1748-z, PubMed 28701187

Rand KD, Grytten I, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2017)
Coordinates and intervals in graph-based reference genomes
BMC Bioinformatics, 18 (1), 263
DOI 10.1186/s12859-017-1678-9, PubMed 28521770

Roy B, Neumann RS, Snir O, Iversen R, Sandve GK, Lundin KEA, Sollid LM (2017)
High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease
J Immunol, 199 (2), 782-791
DOI 10.4049/jimmunol.1700169, PubMed 28600290

Salvatore S, Domanska D, Wood M, Nordeng H, Sandve GK (2017)
Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy
PLoS One, 12 (12), e0190101
DOI 10.1371/journal.pone.0190101, PubMed 29284043

Simovski B, Vodák D, Gundersen S, Domanska D, Azab A, Holden L, Holden M, Grytten I, Rand K, Drabløs F, Johansen M, Mora A, Lund-Andersen C, Fromm B, Eskeland R, Gabrielsen OS, Ferkingstad E, Nakken S, Bengtsen M, Nederbragt AJ, Thorarensen HS, Akse JA, Glad I, Hovig E, Sandve GK (2017)
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
Gigascience, 6 (7), 1-12
DOI 10.1093/gigascience/gix032, PubMed 28459977

Publications 2016

Børnich C, Grytten I, Hovig E, Paulsen J, Čech M, Sandve GK (2016)
Galaxy Portal: interacting with the galaxy platform through mobile devices
Bioinformatics, 32 (11), 1743-5
DOI 10.1093/bioinformatics/btw042, PubMed 26819474

Publications 2015

Bengtsen M, Klepper K, Gundersen S, Cuervo I, Drabløs F, Hovig E, Sandve GK, Gabrielsen OS, Eskeland R (2015)
c-Myb Binding Sites in Haematopoietic Chromatin Landscapes
PLoS One, 10 (7), e0133280
DOI 10.1371/journal.pone.0133280, PubMed 26208222

Christiansen IK, Sandve GK, Schmitz M, Dürst M, Hovig E (2015)
Transcriptionally active regions are the preferred targets for chromosomal HPV integration in cervical carcinogenesis
PLoS One, 10 (3), e0119566
DOI 10.1371/journal.pone.0119566, PubMed 25793388

Ferkingstad E, Holden L, Sandve GK (2015)
Monte Carlo Null Models for Genomic Data
Stat. Sci., 30 (1), 59-71

Mora A, Sandve GK, Gabrielsen OS, Eskeland R (2015)
In the loop: promoter-enhancer interactions and bioinformatics
Brief Bioinform, 17 (6), 980-995
DOI 10.1093/bib/bbv097, PubMed 26586731

Ricigliano VA, Handel AE, Sandve GK, Annibali V, Ristori G, Mechelli R, Cader MZ, Salvetti M (2015)
EBNA2 binds to genomic intervals associated with multiple sclerosis and overlaps with vitamin D receptor occupancy
PLoS One, 10 (4), e0119605
DOI 10.1371/journal.pone.0119605, PubMed 25853421

Rydbeck H, Sandve GK, Ferkingstad E, Simovski B, Rye M, Hovig E (2015)
ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets
PLoS One, 10 (4), e0123261
DOI 10.1371/journal.pone.0123261, PubMed 25879845

Publications 2014

Molyneux SD, Waterhouse PD, Shelton D, Shao YW, Watling CM, Tang QL, Harris IS, Dickson BC, Tharmapalan P, Sandve GK, Zhang X, Bailey SD, Berman H, Wunder JS, Izsvák Z, Lupien M, Mak TW, Khokha R (2014)
Human somatic cell mutagenesis creates genetically tractable sarcomas
Nat Genet, 46 (9), 964-72
DOI 10.1038/ng.3065, PubMed 25129143

Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E (2014)
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Bioinformatics, 30 (11), 1620-2
DOI 10.1093/bioinformatics/btu082, PubMed 24511080

Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F, FANTOM consortium (2014)
Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines
BMC Genomics, 15, 120
DOI 10.1186/1471-2164-15-120, PubMed 24669905

Publications 2013

Handel AE, Sandve GK, Disanto G, Berlanga-Taylor AJ, Gallone G, Hanwell H, Drabløs F, Giovannoni G, Ebers GC, Ramagopalan SV (2013)
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
BMC Med, 11, 163
DOI 10.1186/1741-7015-11-163, PubMed 23849224

Handel AE, Sandve GK, Disanto G, Handunnetthi L, Giovannoni G, Ramagopalan SV (2013)
Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression
BMC Med Genomics, 6, 45
DOI 10.1186/1755-8794-6-45, PubMed 24171864

Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E (2013)
Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements
Nucleic Acids Res, 41 (10), 5164-74
DOI 10.1093/nar/gkt227, PubMed 23571755

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E (2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data
Nucleic Acids Res, 41 (Web Server issue), W133-41
DOI 10.1093/nar/gkt342, PubMed 23632163

Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013)
Ten simple rules for reproducible computational research
PLoS Comput Biol, 9 (10), e1003285
DOI 10.1371/journal.pcbi.1003285, PubMed 24204232

Publications 2012

Disanto G, Sandve GK, Berlanga-Taylor AJ, Morahan JM, Dobson R, Giovannoni G, Ramagopalan SV (2012)
Genomic regions associated with multiple sclerosis are active in B cells
PLoS One, 7 (3), e32281
DOI 10.1371/journal.pone.0032281, PubMed 22396755

Disanto G, Sandve GK, Berlanga-Taylor AJ, Ragnedda G, Morahan JM, Watson CT, Giovannoni G, Ebers GC, Ramagopalan SV (2012)
Vitamin D receptor binding, chromatin states and association with multiple sclerosis
Hum Mol Genet, 21 (16), 3575-86
DOI 10.1093/hmg/dds189, PubMed 22595971

Watson CT, Disanto G, Sandve GK, Breden F, Giovannoni G, Ramagopalan SV (2012)
Age-associated hyper-methylated regions in the human brain overlap with bivalent chromatin domains
PLoS One, 7 (9), e43840
DOI 10.1371/journal.pone.0043840, PubMed 23028473

Publications 2011

Bruhn S, Barrenäs F, Mobini R, Andersson BA, Chavali S, Egan BS, Hovig E, Sandve GK, Langston MA, Rogers G, Wang H, Benson M (2011)
Increased expression of IRF4 and ETS1 in CD4+ cells from patients with intermittent allergic rhinitis
Allergy, 67 (1), 33-40
DOI 10.1111/j.1398-9995.2011.02707.x, PubMed 21919915

Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK (2011)
Identifying elemental genomic track types and representing them uniformly
BMC Bioinformatics, 12, 494
DOI 10.1186/1471-2105-12-494, PubMed 22208806

Sandve GK, Ferkingstad E, Nygård S (2011)
Sequential Monte Carlo multiple testing
Bioinformatics, 27 (23), 3235-41
DOI 10.1093/bioinformatics/btr568, PubMed 21998154

Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Drabløs F, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E (2011)
The differential disease regulome
BMC Genomics, 12, 353
DOI 10.1186/1471-2164-12-353, PubMed 21736759

Publications 2010

Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E (2010)
The Genomic HyperBrowser: inferential genomics at the sequence level
Genome Biol, 11 (12), R121
DOI 10.1186/gb-2010-11-12-r121, PubMed 21182759

Publications 2008

Klepper K, Sandve GK, Abul O, Johansen J, Drablos F (2008)
Assessment of composite motif discovery methods
BMC Bioinformatics, 9, 123
DOI 10.1186/1471-2105-9-123, PubMed 18302777

Lin TH, Ray P, Sandve GK, Uguroglu S, Xing EP (2008)
BayCis: A Bayesian hierarchical HMM for cis-regulatory module decoding in metazoan Genomes
Lect. Notes Bioinforma., 4955, 66-+

Sandve GK, Abul O, Drabløs F (2008)
Compo: composite motif discovery using discrete models
BMC Bioinformatics, 9, 527
DOI 10.1186/1471-2105-9-527, PubMed 19063744

Tøstesen E, Sandve GK, Liu F, Hovig E (2008)
Segmentation of DNA sequences into twostate regions and melting fork regions
J Phys Condens Matter, 21 (3), 034109
DOI 10.1088/0953-8984/21/3/034109, PubMed 21817254

Publications 2007

Abul O, Sandve GK, Drablos F (2007)
False discovery rates in identifying functional DNA motifs
PROCEEDINGS OF THE 7TH IEEE INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS AND BIOENGINEERING, VOLS I AND II, 387-+

Sandve GK, Abul O, Walseng V, Drabløs F (2007)
Improved benchmarks for computational motif discovery
BMC Bioinformatics, 8, 193
DOI 10.1186/1471-2105-8-193, PubMed 17559676

Publications 2006

Abul O, Drabløs F, Sandve GK (2006)
A methodology for motif discovery employing iterated cluster re-assignment
Comput Syst Bioinformatics Conf, 257-68
PubMed 17369644

Sandve GK, Drabløs F (2006)
A survey of motif discovery methods in an integrated framework
Biol Direct, 1, 11
DOI 10.1186/1745-6150-1-11, PubMed 16600018

Sandve GK, Nedland M, Syrstad OB, Eidsheim LA, Abul O, Drablos F (2006)
Accelerating motif discovery: Motif matching on parallel hardware
LECT NOTES COMPUT SC, 4175, 197-206

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