Geir Kjetil Sandve

Image of Geir Kjetil Sandve
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Phone +47-22840861
Mobile phone +47-93853050
Room 4420
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Visiting address Department of Informatics Ole-Johan Dahls hus Gaustadalléen 23B 0373 Oslo
Postal address Postboks 1080 Blindern 0316 OSLO
Other affiliations Department for Informatics

I am an associate professor at the Biomedical Informatics Research Group (BMI) at the Department of informatics (IFI), University of Oslo (UiO). My current research is focused on genome analysis and coeliac disease. I previously worked on motif discovery in DNA. I also have a strong interest for teaching and supervision.

Research group 

We are a bioinformatics group located at the computer science department in Oslo. As a computational lab, our only asset is the codebases and accompanying experiences (competencies) we build up through research projects and learning activities. In line with this, our foremost priority is to create a working environment where all members learn, grow and enjoy their work. Our main approach to ensure high quality work is very traditional: working towards papers in leading peer-reviewed journals that will stand the test of time. In addition to this, we try to be deliberate in devising work processes and training activities that provides team members with a comprehensive selection of experiences for a career in bioinformatics or computer science.  

Who we are

Our group currently consists of three postdocs, two PhD students and a group leader:

We also have several associated members (co-supervised in the group):

  • Daniel Vodak
  • Ralf Neumann
  • Ying Yao
  • Eivind Gard Lund
  • Ksenia Khelik

Our research interests

We currently work on a variety of topics, including statistical genome analysis, graph-based genome representations, the adaptive immunity of celiac disease, epigenomics and pharmacoepidemiology (as reflected in recent publications).

Our approach to research

To do good science, one mainly needs to gain a unique research expertise and find the right research questions to address. This is in reality extremely challenging, touches on several dilemmas, and forms a main motivation for how we work in our group.

How we build a unique research competence:
- Try to be strategic in terms of long-term competence building when selecting research projects and collaborations
- Use team collaboration to allow each member to build a niche competence
- Emphasize reproducibility and reuse of code between projects
- Provide opportunities for both simple scripting and advanced software development

How we position ourselves to find good research questions:
- Work in areas of open and difficult problems
- Collaborate with biomedical groups that bring unique computational challenges

Our approach to training

An education at master level forms a good fundament for doing research, but much more is required to do good science. This is particularly apparent in an interdisciplinary field like bioinformatics. Many aspects are learnt best while doing real research. Other aspects are learnt more effectively through dedicated training. A main priority of our group is to establish infrastructure and work together so as to provide a comprehensive suite of learning opportunities for each member. We aim to provide the infrastructure and guidance to let every team member to get experience with:
- Appropriate programming styles to match the variety of scenarios relevant for computational science, ranging from rapid prototyping of small scripts to development of high quality code for large systems
- Effective software development processes, including use of empowering infrastructure and tools such as using tailored system setups and exploiting capabilities of IDEs.
- Software architecture and software design, as a distinct and often very useful phase prior to coding
- Computational modeling, specifically how to develop mathematically precise problem formulations and corresponding solutions for biomedical problems
- Practices that promote reproducibility of performed analyses and reuse of developed methodology
- Solving algorithmically challenging problems, including considerations of computational efficiency where necessary
- Writing grant applications
- Develop methodology and software in tight collaboration with peers, so as to get exposed to alternative ways of thinking and working at a very detailed level.
- Interact with a relevant international community, so as to ensure that one stays on top of ones field both with respect to science and technological developments

Tags: genome analysis, master tasks, bioinformatics

Publications

  • Domanska, Diana; Vodak, Daniel; Lund-Andersen, Christian; Salvatore, Stefania; Hovig, Eivind & Sandve, Geir Kjetil (2017). The rainfall plot: Its motivation, characteristics and pitfalls. BMC Bioinformatics.  ISSN 1471-2105.  18(1) . doi: 10.1186/s12859-017-1679-8
  • Roy, Bishnudeo; Neumann, Ralf Stefan; Iversen, Rasmus; Snir, Omri; Sandve, Geir Kjetil; Lundin, Knut Erik Aslaksen & Sollid, Ludvig Magne (2017). High-Throughput Single-Cell Analysis of B Cell Receptor Usage among Autoantigen-Specific Plasma Cells in Celiac Disease. Journal of Immunology.  ISSN 0022-1767. . doi: 10.4049/jimmunol.1700169
  • Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman; Holden, Lars; Holden, Marit; Grytten, Ivar; Rand, Knut Dagestad; Drabløs, Finn Sverre; Johansen, Morten; Mora, Antonio M.; Lund-Andersen, Christin; Fromm, Bastian; Eskeland, Ragnhild; Gabrielsen, Odd Stokke; Ferkingstad, Egil; Nakken, Sigve; Bengtsen, Mads; Nederbragt, Alexander Johan; Thorarensen, Hildur Sif; Andreas Akse, Johannes; Glad, Ingrid Kristine; Hovig, Johannes Eivind & Sandve, Geir Kjetil (2017). GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome . GigaScience.  ISSN 2047-217X. . doi: 10.1093/gigascience/gix032
  • Børnich, Claus; Grytten, Ivar; Hovig, Johannes Eivind; Paulsen, Jonas; Cech, Martin & Sandve, Geir Kjetil (2016). Galaxy Portal: Interacting with the galaxy platform through mobile devices. Bioinformatics.  ISSN 1367-4803.  32(11), s 1743- 1745 . doi: 10.1093/bioinformatics/btw042
  • Rydbeck, Halfdan; Sandve, Geir Kjetil F.; Ferkingstad, Egil; Simovski, Boris; Rye, Morten Beck & Hovig, Johannes Eivind (2015). ClusTrack: Feature extraction and similarity measures for clustering of genome-wide data sets. PLoS ONE.  ISSN 1932-6203.  10(4) . doi: 10.1371/journal.pone.0123261 Full text in Research Archive
  • Bengtsen, Mads; Klepper, Kjetil; Gundersen, Sveinung; Cuervo Torre, Ignacio; Drabløs, Finn; Hovig, Johannes Eivind; Sandve, Geir Kjetil F.; Gabrielsen, Odd Stokke & Eskeland, Ragnhild (2015). c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PLoS ONE.  ISSN 1932-6203.  10(7) . doi: 10.1371/journal.pone.0133280 Full text in Research Archive
  • Ferkingstad, Egil; Holden, Lars & Sandve, Geir Kjetil F. (2015). Monte Carlo Null Models for Genomic Data . Statistical Science.  ISSN 0883-4237.  30(1), s 59- 71 . doi: 10.1214/14-STS484
  • Kraus, Hanne Irene; Sandve, Geir Kjetil F.; Schmitz, Martina; Dürst, Matthias & Hovig, Johannes Eivind (2015). Transcriptionally active regions are the preferred targets for chromosomal HPV integration in cervical carcinogenesis. PLoS ONE.  ISSN 1932-6203.  10(3) . doi: 10.1371/journal.pone.0119566
  • Mora Ortiz, Antonio Carlos; Sandve, Geir Kjetil; Gabrielsen, Odd Stokke & Eskeland, Ragnhild (2015). In the loop: promoter-enhancer interactions and bioinformatics . Briefings in Bioinformatics.  ISSN 1467-5463. . doi: 10.1093/bib/bbv097
  • Ricigliano, Vito A. G.; Handel, Adam E; Sandve, Geir Kjetil F.; Annibali, Viviana; Ristori, Giovanni; Mechelli, Rosella; Cader, M.Zameel & Salvetti, Marco (2015). EBNA2 binds to genomic intervals associated with multiple sclerosis and overlaps with vitamin D receptor occupancy. PLoS ONE.  ISSN 1932-6203.  10(4) . doi: 10.1371/journal.pone.0119605
  • 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 (2014). DNase hypersensitive sites and association with multiple sclerosisxs . Human Molecular Genetics.  ISSN 0964-6906.  23(4), s 942- 948 . doi: 10.1093/hmg/ddt489
  • 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 (2014). Human somatic cell mutagenesis creates genetically tractable sarcomas. Nature Genetics.  ISSN 1061-4036.  46(9), s 964- 972 . doi: 10.1038/ng.3065
  • Paulsen, Jonas; Sandve, Geir Kjetil F.; Gundersen, Sveinung; Lien, Tonje Gulbrandsen; Trengereid, Kai & Hovig, Johannes Eivind (2014). HiBrowse: Multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics.  ISSN 1367-4803.  30(11), s 1620- 1622 . doi: 10.1093/bioinformatics/btu082
  • Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, H; Carninci, P; Forrest, A & Drabløs, Finn (2014). Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC Genomics.  ISSN 1471-2164.  15(1) . doi: 10.1186/1471-2164-15-120
  • 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 (2013). The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research.  ISSN 0305-1048.  41(W1), s W133- W141 . doi: 10.1093/nar/gkt342 Full text in Research Archive
  • 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 (2013). Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. BMC Medicine.  ISSN 1741-7015.  11(163) . doi: 10.1186/1741-7015-11-163
  • Handel, Adam E; Sandve, Geir Kjetil; Disanto, Giulio; Handunnetthi, Lahiru; Giovannoni, Gavin & Ramagopalan, Sreeram V (2013). Integrating multiple oestrogen receptor alpha ChIP studies: overlap with disease susceptibility regions, DNase I hypersensitivity peaks and gene expression. BMC Medical Genomics.  ISSN 1755-8794.  6:45 . doi: 10.1186/1755-8794-6-45
  • Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf; Glad, Ingrid Kristine & Hovig, Johannes Eivind (2013). Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements . Nucleic Acids Research.  ISSN 0305-1048.  41(10), s 5164- 5174 . doi: 10.1093/nar/gkt227
  • 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 (2012). Increased expression of IRF4 and ETS1 in CD4(+) cells from patients with intermittent allergic rhinitis. Allergy. European Journal of Allergy and Clinical Immunology.  ISSN 0105-4538.  67(1), s 33- 40 . doi: 10.1111/j.1398-9995.2011.02707.x
  • Disanto, Giulio; Sandve, Geir Kjetil; Berlanga-Taylor, Antonio; Morahan, Julia; Dobson, Ruth; Giovannoni, Gavin & Ramagopalan, Sreeram V (2012). Genomic Regions Associated with Multiple Sclerosis Are Active in B Cells. PLoS ONE.  ISSN 1932-6203.  7(3) . doi: 10.1371/journal.pone.0032281
  • Disanto, Giulio; Sandve, Geir Kjetil; Berlanga-Taylor, Antonio; Ragnedda, Giammario; Morahan, Julia; Watson, Corey T; Giovannoni, Gavin; Ebers, Georg C & Ramagopalan, Sreeram V (2012). Vitamin D receptor binding, chromatin states and association with multiple sclerosis. Human Molecular Genetics.  ISSN 0964-6906.  21(16), s 3575- 3586 . doi: 10.1093/hmg/dds189
  • Watson, Corey T; Disanto, Giulio; Sandve, Geir Kjetil; Breden, Felix; Giovannoni, Gavin & Ramagopalan, Sreeram V (2012). Age-Associated Hyper-Methylated Regions in the Human Brain Overlap with Bivalent Chromatin Domains. PLoS ONE.  ISSN 1932-6203.  7(9) . doi: 10.1371/journal.pone.0043840
  • 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 (2011). The differential disease regulome . BMC Genomics.  ISSN 1471-2164.  12, s 353 . doi: 10.1186/1471-2164-12-353
  • Gundersen, Sveinung; Kalaš, Matúš; Abul, Osman; Frigessi, Arnoldo; Hovig, Eivind & Sandve, Geir Kjetil (2011). Identifying elemental genomic track types and representing them uniformly . BMC Bioinformatics.  ISSN 1471-2105.  12 . doi: 10.1186/1471-2105-12-494
  • Sandve, Geir Kjetil Ferkingstad; Ferkingstad, Egil & Nygård, Ståle (2011). Sequential Monte Carlo multiple testing. Bioinformatics.  ISSN 1367-4803.  27(23), s 3235- 3241 . doi: 10.1093/bioinformatics/btr568
  • 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 (2010). The Genomic HyperBrowser: inferential genomics at the sequence level . Genome Biology.  ISSN 1465-6906.  11(12) . doi: 10.1186/gb-2010-11-12-r121 Full text in Research Archive
  • Tøstesen, Eivind; Sandve, Geir Kjetil; Liu, Fang & Hovig, Eivind (2009). Segmentation of DNA sequences into twostate regions and melting fork regions . Journal of Physics: Condensed Matter.  ISSN 0953-8984.  21(3) . doi: 10.1088/0953-8984/21/3/034109
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2008). TScan: A two-step de novo motif discovery method. Series on Advances in Bioinformatics and Computational Biology.  ISSN 1751-6404.  8, s 19
  • Klepper, Kjetil; Sandve, Geir Kjetil; Abul, Osman; Johansen, Jostein & Drabløs, Finn (2008). Assessment of composite motif discovery methods. BMC Bioinformatics.  ISSN 1471-2105.  9(123) . doi: 10.1186/1471-2105-9-123 Full text in Research Archive
  • Lin, Tien-ho; Ray, Pradipta; Sandve, Geir Kjetil; Uguroglu, Selen & Xing, Eric P. (2008). BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. Lecture Notes in Computer Science.  ISSN 0302-9743.  4955, s 66- 81 . doi: 10.1007/978-3-540-78839-3_7
  • Sandve, Geir Kjetil; Abul, Osman & Drabløs, Finn (2008). Compo: composite motif discovery using discrete models . BMC Bioinformatics.  ISSN 1471-2105.  9(527) . doi: 10.1186/1471-2105-9-527 Full text in Research Archive
  • Sandve, Geir Kjetil; Abul, Osman & Drabløs, Finn (2008). Compo: composite motif discovery using discrete models. BMC Bioinformatics.  ISSN 1471-2105.  9, s 527 . doi: 10.1186/1471-2105-9-527
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2007). False Discovery Rates in Identifying Functional DNA Motifs, In Jack Y. Yang (ed.),  Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering.  IEEE.  ISBN 978-1-4244-1509-0.  False Discovery Rates in Identifying Functional DNA Motifs.  s 387 - 394
  • Sandve, Geir Kjetil; Abul, Osman; Walseng, Vegard & Drabløs, Finn (2007). Improved benchmarks for computational motif discovery. BMC Bioinformatics.  ISSN 1471-2105.  8(193) . doi: 10.1186/1471-2105-8-193 Full text in Research Archive
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2006). A Methodology for Motif Discovery Employing Iterated Cluster Re-assignment. Series on Advances in Bioinformatics and Computational Biology.  ISSN 1751-6404.  4, s 257- 268
  • Sandve, Geir Kjetil & Drabløs, Finn (2006). A survey of motif discovery methods in an integrated framework. Biology Direct.  ISSN 1745-6150.  1 . doi: 10.1186/1745-6150-1-11
  • Sandve, Geir Kjetil; Nedland, Magnar; Bø Syrstad, Øyvind; Eidsheim, Lars Andreas; Abul, Osman & Drabløs, Finn (2006). Accelerating Motif Discovery: Motif Matching on Parallel Hardware. Lecture Notes in Computer Science.  ISSN 0302-9743.  4175, s 197- 206
  • Sandve, Geir Kjetil & Drabløs, Finn (2005). Generalized Composite Motif Discovery. Lecture Notes in Computer Science.  ISSN 0302-9743.  3683, s 763 . doi: 10.1007/11553939

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  • Holden, Lars; Jullum, Martin & Sandve, Geir Kjetil (2017). Statistical modeling of repertoire overlap in entire sampling spaces .
  • Simovski, Boris; Drabløs, Finn Sverre; Gundersen, Sveinung; Johansen, Morten; Domanska, Diana Ewa; Azab, Abdulrahman; Sandve, Geir Kjetil & Hovig, Johannes Eivind (2016). The Genomic HyperBrowser.
  • Ferkingstad, Egil; Sandve, Geir Kjetil F. & Holden, Lars (2015). Monte Carlo null models for genomic data.
  • Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair & Drabløs, Finn (2014). Chromatin data integrated with a human reference atlas of experimentally defined promoters reveal repressed promoters located in active chromatin.
  • Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero; Forrest, Alistair & Drabløs, Finn (2014). Repressed promoters in active chromatin.
  • 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 (2014). A new, high quality reference genome assembly for Atlantic cod.
  • 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 (2014). A new, high quality reference genome assembly for Atlantic cod.
  • Ferkingstad, Egil; Holden, Lars & Sandve, Geir Kjetil (2013). Monte Carlo null models for genomic data.
  • Ferkingstad, Egil; Holden, Lars & Sandve, Geir Kjetil (2013). Monte Carlo null models in ecology .
  • Sandve, Geir Kjetil; Nekrutenko, Anton; Taylor, James & Hovig, Johannes Eivind (2013). Ten Simple Rules for Reproducible Computational Research. PloS Computational Biology.  ISSN 1553-734X.  9(10) . doi: 10.1371/journal.pcbi.1003285
  • Sandve, Geir Kjetil (2008). Potentials and limitations of motif-based binding site prediction in DNA.
  • Sandve, Geir Kjetil; Abul, Osman; Walseng, Vegard & Drabløs, Finn (2007). Improved benchmarks for computational motif discovery.
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2006). A Methodology for Motif Discovery Employing Iterated Cluster Re-assignment.
  • Sandve, Geir Kjetil (2006). Accelerating Motif Discovery: Motif Matching on Parallel Hardware.
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2006). False discovery rates in identifying functional DNA motifs.
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2006). TScan: A two-step de novo motif discovery method.
  • Sandve, Geir Kjetil; Nedland, Magnar; Bø Syrstad, Øyvind; Eidsheim, Lars Andreas; Abul, Osman & Drabløs, Finn (2006). Accelerating motif discovery: motif matching on parallel hardware.
  • Sandve, Geir Kjetil; Stenersen, Kristoffer; Walseng, Vegard; Lekang, Øystein; Klepper, Kjetil; Abul, Osman; Hveem, Tarjei S; Bratlie, Marit Skyrud & Drabløs, Finn (2006). An integrated approach to motif discovery in DNA sequences.
  • Sandve, Geir Kjetil & Drabløs, Finn (2005). Generalized Composite Motif Discovery.

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Published Nov. 4, 2010 2:16 PM - Last modified Aug. 1, 2017 10:46 PM