Sandve group

Publications 2022

Sandve GK, Greiff V (2022)
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking
Bioinformatics, 38 (21), 4994-4996
DOI 10.1093/bioinformatics/btac612, PubMed 36073940

Grytten I, Dagestad Rand K, Sandve GK (2022)
KAGE: fast alignment-free graph-based genotyping of SNPs and short indels
Genome Biol, 23 (1), 209
DOI 10.1186/s13059-022-02771-2, PubMed 36195962

Rognes T, Scheffer L, Greiff V, Sandve GK (2022)
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching
Bioinformatics, 38 (17), 4230-4232
DOI 10.1093/bioinformatics/btac505, PubMed 35852318

Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V (2022)
Reference-based comparison of adaptive immune receptor repertoires
Cell Rep Methods, 2 (8), 100269
DOI 10.1016/j.crmeth.2022.100269, PubMed 36046619

Olstad EW, Nordeng HME, Sandve GK, Lyle R, Gervin K (2022)
Low reliability of DNA methylation across Illumina Infinium platforms in cord blood: implications for replication studies and meta-analyses of prenatal exposures
Clin Epigenetics, 14 (1), 80
DOI 10.1186/s13148-022-01299-3, PubMed 35765087

Kanduri C, Pavlović M, Scheffer L, Motwani K, Chernigovskaya M, Greiff V, Sandve GK (2022)
Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification
Gigascience, 11
DOI 10.1093/gigascience/giac046, PubMed 35639633

Dahal-Koirala S, Balaban G, Neumann RS, Scheffer L, Lundin KEA, Greiff V, Sollid LM, Qiao SW, Sandve GK (2022)
TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences
Brief Bioinform, 23 (2)
DOI 10.1093/bib/bbab566, PubMed 35062022

Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V (2022)
In silico proof of principle of machine learning-based antibody design at unconstrained scale
MAbs, 14 (1), 2031482
DOI 10.1080/19420862.2022.2031482, PubMed 35377271

Publications 2021

Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V (2021)
Individualized VDJ recombination predisposes the available Ig sequence space
Genome Res, 31 (12), 2209-24 (in press)
DOI 10.1101/gr.275373.121, PubMed 34815307

Pavlovic M, Scheffer L, Motwani K, Kanduri C, Kompova R, Vazov N, Waagan K, Bernal FLM, Costa AA, Corrie B, Akbar R, Al Hajj GS, Balaban G, Brusko TM, Chernigovskaya M, Christley S, Cowell LG, Frank R, Grytten I, Gundersen S, Haff IH, Hovig E, Hsieh PH, Klambauer G, Kuijjer ML et al. (2021)
The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires
Nat. Mach. Intell., 3 (11), 936-+
DOI 10.1038/s42256-021-00413-z

Yao Y, Wyrozżemski Ł, Lundin KEA, Sandve GK, Qiao SW (2021)
Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq
PLoS One, 16 (10), e0258029
DOI 10.1371/journal.pone.0258029, PubMed 34618841

Lemma RB, Ledsaak M, Fuglerud BM, Sandve GK, Eskeland R, Gabrielsen OS (2021)
Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB
Sci Rep, 11 (1), 9008
DOI 10.1038/s41598-021-88516-w, PubMed 33903675

Dahal-Koirala S, Risnes LF, Neumann RS, Christophersen A, Lundin KEA, Sandve GK, Qiao SW, Sollid LM (2021)
Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs
Front Immunol, 12, 639672
DOI 10.3389/fimmu.2021.639672, PubMed 33927715

Akbar R, Robert PA, Pavlović M, Jeliazkov JR, Snapkov I, Slabodkin A, Weber CR, Scheffer L, Miho E, Haff IH, Haug DTT, Lund-Johansen F, Safonova Y, Sandve GK, Greiff V (2021)
A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding
Cell Rep, 34 (11), 108856
DOI 10.1016/j.celrep.2021.108856, PubMed 33730590

Balaban G, Grytten I, Rand KD, Scheffer L, Sandve GK (2021)
Ten simple rules for quick and dirty scientific programming
PLoS Comput Biol, 17 (3), e1008549
DOI 10.1371/journal.pcbi.1008549, PubMed 33705383

Kanduri C, Sandve GK, Hovig E, De S, Layer RM (2021)
Editorial: Genomic Colocalization and Enrichment Analyses
Front Genet, 11, 617876
DOI 10.3389/fgene.2020.617876, PubMed 33574832

Publications 2020

Yao Y, Zia A, Neumann RS, Pavlovic M, Balaban G, Lundin KEA, Sandve GK, Qiao SW (2020)
T cell receptor repertoire as a potential diagnostic marker for celiac disease
Clin Immunol, 222, 108621
DOI 10.1016/j.clim.2020.108621, PubMed 33197618

Weber CR, Akbar R, Yermanos A, Pavlović M, Snapkov I, Sandve GK, Reddy ST, Greiff V (2020)
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Bioinformatics, 36 (11), 3594-3596
DOI 10.1093/bioinformatics/btaa158, PubMed 32154832

Grytten I, Rand KD, Nederbragt AJ, Sandve GK (2020)
Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods
BMC Genomics, 21 (1), 282
DOI 10.1186/s12864-020-6685-y, PubMed 32252628

Khelik K, Sandve GK, Nederbragt AJ, Rognes T (2020)
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
BMC Bioinformatics, 21 (1), 66
DOI 10.1186/s12859-020-3414-0

du Pré MF, Blazevski J, Dewan AE, Stamnaes J, Kanduri C, Sandve GK, Johannesen MK, Lindstad CB, Hnida K, Fugger L, Melino G, Qiao SW, Sollid LM (2020)
B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2
J Exp Med, 217 (2)
DOI 10.1084/jem.20190860, PubMed 31727780

Publications 2019

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A (2019)
A map of direct TF-DNA interactions in the human genome
Nucleic Acids Res, 47 (14), 7715
DOI 10.1093/nar/gkz582, PubMed 31251803

Brown AJ, Snapkov I, Akbar R, Pavlovic M, Miho E, Sandve GK, Greiff V (2019)
Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires
Mol. Syst. Des. Eng., 4 (4), 701-736
DOI 10.1039/c9me00071b

Snir O, Kanduri C, Lundin KEA, Sandve GK, Sollid LM (2019)
Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production
United European Gastroenterol J, 7 (10), 1399-1407
DOI 10.1177/2050640619862461, PubMed 31839965

Kanduri C, Bock C, Gundersen S, Hovig E, Sandve GK (2019)
Colocalization analyses of genomic elements: approaches, recommendations and challenges
Bioinformatics, 35 (9), 1615-1624
DOI 10.1093/bioinformatics/bty835, PubMed 30307532

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A (2019)
A map of direct TF-DNA interactions in the human genome
Nucleic Acids Res, 47 (4), e21
DOI 10.1093/nar/gky1210, PubMed 30517703

Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK (2019)
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
PLoS Comput Biol, 15 (2), e1006731
DOI 10.1371/journal.pcbi.1006731, PubMed 30779737

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

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

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

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

Publications 2017

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

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

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

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

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

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

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

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

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

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

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

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

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

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
DOI 10.1214/14-STS484

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

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

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

Publications 2013

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

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

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

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

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

Publications 2012

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

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

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

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

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

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

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

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