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Items: 46

1.

Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production.

Snir O, Kanduri C, Lundin KEA, Sandve GK, Sollid LM.

United European Gastroenterol J. 2019 Dec;7(10):1399-1407. doi: 10.1177/2050640619862461. Epub 2019 Jul 3.

2.

B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2.

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.

J Exp Med. 2020 Feb 3;217(2). pii: e20190860. doi: 10.1084/jem.20190860.

PMID:
31727780
3.

A map of direct TF-DNA interactions in the human genome.

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A.

Nucleic Acids Res. 2019 Aug 22;47(14):7715. doi: 10.1093/nar/gkz582. No abstract available.

4.

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes.

Grytten I, Rand KD, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK.

PLoS Comput Biol. 2019 Feb 19;15(2):e1006731. doi: 10.1371/journal.pcbi.1006731. eCollection 2019 Feb.

5.

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis.

Domanska D, Kanduri C, Simovski B, Sandve GK.

BMC Bioinformatics. 2018 Dec 14;19(1):481. doi: 10.1186/s12859-018-2438-1.

6.

A map of direct TF-DNA interactions in the human genome.

Gheorghe M, Sandve GK, Khan A, Chèneby J, Ballester B, Mathelier A.

Nucleic Acids Res. 2019 Feb 28;47(4):e21. doi: 10.1093/nar/gky1210. Erratum in: Nucleic Acids Res. 2019 Aug 22;47(14):7715.

7.

Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments.

Yao Y, Zia A, Wyrożemski Ł, Lindeman I, Sandve GK, Qiao SW.

PLoS One. 2018 Dec 5;13(12):e0208484. doi: 10.1371/journal.pone.0208484. eCollection 2018.

8.

Colocalization analyses of genomic elements: approaches, recommendations and challenges.

Kanduri C, Bock C, Gundersen S, Hovig E, Sandve GK.

Bioinformatics. 2019 May 1;35(9):1615-1624. doi: 10.1093/bioinformatics/bty835.

9.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

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.

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474.

10.

Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease.

Risnes LF, Christophersen A, Dahal-Koirala S, Neumann RS, Sandve GK, Sarna VK, Lundin KE, Qiao SW, Sollid LM.

J Clin Invest. 2018 Jun 1;128(6):2642-2650. doi: 10.1172/JCI98819. Epub 2018 May 14.

11.

Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy.

Salvatore S, Domanska D, Wood M, Nordeng H, Sandve GK.

PLoS One. 2017 Dec 28;12(12):e0190101. doi: 10.1371/journal.pone.0190101. eCollection 2017.

12.

Genome build information is an essential part of genomic track files.

Kanduri C, Domanska D, Hovig E, Sandve GK.

Genome Biol. 2017 Sep 14;18(1):175. doi: 10.1186/s13059-017-1312-1.

13.

Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1.

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.

Sci Rep. 2017 Aug 3;7(1):7199. doi: 10.1038/s41598-017-07314-5.

14.

NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences.

Khelik K, Lagesen K, Sandve GK, Rognes T, Nederbragt AJ.

BMC Bioinformatics. 2017 Jul 12;18(1):338. doi: 10.1186/s12859-017-1748-z.

15.

High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease.

Roy B, Neumann RS, Snir O, Iversen R, Sandve GK, Lundin KEA, Sollid LM.

J Immunol. 2017 Jul 15;199(2):782-791. doi: 10.4049/jimmunol.1700169. Epub 2017 Jun 9.

16.

Coordinates and intervals in graph-based reference genomes.

Rand KD, Grytten I, Nederbragt AJ, Storvik GO, Glad IK, Sandve GK.

BMC Bioinformatics. 2017 May 18;18(1):263. doi: 10.1186/s12859-017-1678-9.

17.

The rainfall plot: its motivation, characteristics and pitfalls.

Domanska D, Vodák D, Lund-Andersen C, Salvatore S, Hovig E, Sandve GK.

BMC Bioinformatics. 2017 May 18;18(1):264. doi: 10.1186/s12859-017-1679-8.

18.

GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.

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.

Gigascience. 2017 Jul 1;6(7):1-12. doi: 10.1093/gigascience/gix032.

19.

Galaxy Portal: interacting with the galaxy platform through mobile devices.

Børnich C, Grytten I, Hovig E, Paulsen J, Čech M, Sandve GK.

Bioinformatics. 2016 Jun 1;32(11):1743-5. doi: 10.1093/bioinformatics/btw042. Epub 2016 Jan 27.

20.

In the loop: promoter-enhancer interactions and bioinformatics.

Mora A, Sandve GK, Gabrielsen OS, Eskeland R.

Brief Bioinform. 2016 Nov;17(6):980-995. Epub 2015 Nov 19. Review.

21.

c-Myb Binding Sites in Haematopoietic Chromatin Landscapes.

Bengtsen M, Klepper K, Gundersen S, Cuervo I, Drabløs F, Hovig E, Sandve GK, Gabrielsen OS, Eskeland R.

PLoS One. 2015 Jul 24;10(7):e0133280. doi: 10.1371/journal.pone.0133280. eCollection 2015.

22.

ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets.

Rydbeck H, Sandve GK, Ferkingstad E, Simovski B, Rye M, Hovig E.

PLoS One. 2015 Apr 16;10(4):e0123261. doi: 10.1371/journal.pone.0123261. eCollection 2015.

23.

EBNA2 binds to genomic intervals associated with multiple sclerosis and overlaps with vitamin D receptor occupancy.

Ricigliano VA, Handel AE, Sandve GK, Annibali V, Ristori G, Mechelli R, Cader MZ, Salvetti M.

PLoS One. 2015 Apr 8;10(4):e0119605. doi: 10.1371/journal.pone.0119605. eCollection 2015.

24.

Transcriptionally active regions are the preferred targets for chromosomal HPV integration in cervical carcinogenesis.

Christiansen IK, Sandve GK, Schmitz M, Dürst M, Hovig E.

PLoS One. 2015 Mar 20;10(3):e0119566. doi: 10.1371/journal.pone.0119566. eCollection 2015.

25.

Human somatic cell mutagenesis creates genetically tractable sarcomas.

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.

Nat Genet. 2014 Sep;46(9):964-72. doi: 10.1038/ng.3065. Epub 2014 Aug 17. Erratum in: Nat Genet. 2014 Dec;46(12):1372. Iszvak, Zsuzsanna [corrected to Izsvák, Zsuzsanna.

PMID:
25129143
26.

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.

Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F; FANTOM consortium.

BMC Genomics. 2014 Mar 26;15:120. doi: 10.1186/1471-2164-15-120.

27.

HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.

Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E.

Bioinformatics. 2014 Jun 1;30(11):1620-2. doi: 10.1093/bioinformatics/btu082. Epub 2014 Feb 7.

28.

Ten simple rules for reproducible computational research.

Sandve GK, Nekrutenko A, Taylor J, Hovig E.

PLoS Comput Biol. 2013 Oct;9(10):e1003285. doi: 10.1371/journal.pcbi.1003285. Epub 2013 Oct 24. No abstract available.

29.

Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression.

Handel AE, Sandve GK, Disanto G, Handunnetthi L, Giovannoni G, Ramagopalan SV.

BMC Med Genomics. 2013 Oct 30;6:45. doi: 10.1186/1755-8794-6-45.

30.

Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease.

Handel AE, Sandve GK, Disanto G, Berlanga-Taylor AJ, Gallone G, Hanwell H, Drabløs F, Giovannoni G, Ebers GC, Ramagopalan SV.

BMC Med. 2013 Jul 12;11:163. doi: 10.1186/1741-7015-11-163.

31.

The Genomic HyperBrowser: an analysis web server for genome-scale data.

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.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41. doi: 10.1093/nar/gkt342. Epub 2013 Apr 30.

32.

Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements.

Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E.

Nucleic Acids Res. 2013 May 1;41(10):5164-74. doi: 10.1093/nar/gkt227. Epub 2013 Apr 9.

33.

Age-associated hyper-methylated regions in the human brain overlap with bivalent chromatin domains.

Watson CT, Disanto G, Sandve GK, Breden F, Giovannoni G, Ramagopalan SV.

PLoS One. 2012;7(9):e43840. doi: 10.1371/journal.pone.0043840. Epub 2012 Sep 24.

34.

Vitamin D receptor binding, chromatin states and association with multiple sclerosis.

Disanto G, Sandve GK, Berlanga-Taylor AJ, Ragnedda G, Morahan JM, Watson CT, Giovannoni G, Ebers GC, Ramagopalan SV.

Hum Mol Genet. 2012 Aug 15;21(16):3575-86. doi: 10.1093/hmg/dds189. Epub 2012 May 16.

35.

Genomic regions associated with multiple sclerosis are active in B cells.

Disanto G, Sandve GK, Berlanga-Taylor AJ, Morahan JM, Dobson R, Giovannoni G, Ramagopalan SV.

PLoS One. 2012;7(3):e32281. doi: 10.1371/journal.pone.0032281. Epub 2012 Mar 2.

36.

Identifying elemental genomic track types and representing them uniformly.

Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK.

BMC Bioinformatics. 2011 Dec 30;12:494. doi: 10.1186/1471-2105-12-494.

37.

Sequential Monte Carlo multiple testing.

Sandve GK, Ferkingstad E, Nygård S.

Bioinformatics. 2011 Dec 1;27(23):3235-41. doi: 10.1093/bioinformatics/btr568. Epub 2011 Oct 13.

38.

Increased expression of IRF4 and ETS1 in CD4+ cells from patients with intermittent allergic rhinitis.

Bruhn S, Barrenäs F, Mobini R, Andersson BA, Chavali S, Egan BS, Hovig E, Sandve GK, Langston MA, Rogers G, Wang H, Benson M.

Allergy. 2012 Jan;67(1):33-40. doi: 10.1111/j.1398-9995.2011.02707.x. Epub 2011 Sep 15.

39.

The differential disease regulome.

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.

BMC Genomics. 2011 Jul 7;12:353. doi: 10.1186/1471-2164-12-353.

40.

The Genomic HyperBrowser: inferential genomics at the sequence level.

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.

Genome Biol. 2010;11(12):R121. doi: 10.1186/gb-2010-11-12-r121. Epub 2010 Dec 23.

41.

Segmentation of DNA sequences into twostate regions and melting fork regions.

Tøstesen E, Sandve GK, Liu F, Hovig E.

J Phys Condens Matter. 2009 Jan 21;21(3):034109. doi: 10.1088/0953-8984/21/3/034109. Epub 2008 Dec 17.

PMID:
21817254
42.

Compo: composite motif discovery using discrete models.

Sandve GK, Abul O, Drabløs F.

BMC Bioinformatics. 2008 Dec 8;9:527. doi: 10.1186/1471-2105-9-527.

43.

Assessment of composite motif discovery methods.

Klepper K, Sandve GK, Abul O, Johansen J, Drablos F.

BMC Bioinformatics. 2008 Feb 26;9:123. doi: 10.1186/1471-2105-9-123.

44.

Improved benchmarks for computational motif discovery.

Sandve GK, Abul O, Walseng V, Drabløs F.

BMC Bioinformatics. 2007 Jun 8;8:193.

45.

A methodology for motif discovery employing iterated cluster re-assignment.

Abul O, Drabløs F, Sandve GK.

Comput Syst Bioinformatics Conf. 2006:257-68.

46.

A survey of motif discovery methods in an integrated framework.

Sandve GK, Drabløs F.

Biol Direct. 2006 Apr 6;1:11.

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