Geir Kjetil Ferkingstad Sandve

Bilde av Geir Kjetil Ferkingstad Sandve
English version of this page
Telefon +47 22840861
Rom 4420
Brukernavn
Besøksadresse Department of Informatics Ole-Johan Dahls hus Gaustadalléen 23B 0373 Oslo
Postadresse Postboks 1080 Blindern 0316 Oslo

Jeg er professor ved gruppe for Biomedisinsk Informatikk (BMI) ved Institutt for informatikk (IFI), Universitetet i Oslo (UiO).

Min forskning er fokusert på maskinlæring, mer spesifikt på aspekter knyttet til generalisering av modeller, håndtering og utnytting av underliggende kausale mekanismer, samt på en type problemstilling som heter Multiple instance learning. Tidligere fokuserte jeg på statistisk og algoritmisk metodikk for stor-skala analyse av genomiske data, hvor jeg var sentral utvikler av The Genomic HyperBrowser.

Både min nåværende og tidligere forskning er mer utførlig beskrevet i den engelske versjonen av sida, samt websiden for min forskningsgruppe. I tillegg til forskning har jeg også gjennom årene vært mye engasjert i undervisning og veiledning, blant annet i faget IN1000.

Emneord: Genomanalyse, bioinformatikk, algoritmer, programmering, python, masteroppgave

Publikasjoner

  • Kanduri, Chakravarthi; Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Chernigovskaya, Maria & Greiff, Victor [Vis alle 7 forfattere av denne artikkelen] (2022). Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification. GigaScience. ISSN 2047-217X. 11(05). doi: 10.1093/gigascience/giac046. Fulltekst i vitenarkiv
  • Akbar, Rahmad; Robert, Philippe Paul Auguste; Weber, Cédric R.; Widrich, Michael; Frank, Robert & Pavlovic, Milena [Vis alle 19 forfattere av denne artikkelen] (2022). In silico proof of principle of machine learning-based antibody design at unconstrained scale. mAbs. ISSN 1942-0862. 14:e2031482(1), s. 1–18. doi: 10.1080/19420862.2022.2031482.
  • Dahal-Koirala, Shiva; Balaban, Gabriel; Neumann, Ralf Stefan; Scheffer, Lonneke; Lundin, Knut & Greiff, Victor [Vis alle 9 forfattere av denne artikkelen] (2022). TCRpower: quantifying the detection power of T-cell receptor sequencing with a novel computational pipeline calibrated by spike-in sequences. Briefings in Bioinformatics. ISSN 1467-5463. doi: 10.1093/bib/bbab566.
  • Yao, Ying; Wyrozemski, Lukasz Adam; Lundin, Knut; Sandve, Geir Kjetil Ferkingstad & Qiao, Shuo Wang (2021). Differential expression profile of gluten-specific T cells identified by single-cell RNA-seq. PLOS ONE. ISSN 1932-6203. 16:e0258029(10), s. 1–17. doi: 10.1371/journal.pone.0258029. Fulltekst i vitenarkiv
  • Slabodkin, Andrei; Chernigovskaia, Maria; Mikocziova, Ivana; Akbar, Rahmad; Scheffer, Lonneke & Pavlović, Milena [Vis alle 16 forfattere av denne artikkelen] (2021). Individualized VDJ recombination predisposes the available Ig sequence space. Genome Research. ISSN 1088-9051. s. 2209–2224. doi: 10.1101/gr.275373.121. Fulltekst i vitenarkiv
  • Pavlović, Milena; Scheffer, Lonneke; Motwani, Keshav; Kanduri, Chakravarthi; Kompova, Radmila & Vazov, Nikolay Aleksandrov [Vis alle 41 forfattere av denne artikkelen] (2021). The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. Nature Machine Intelligence. 3(11), s. 936–944. doi: 10.1038/s42256-021-00413-z.
  • Arnaout, Ramy A.; Luning Prak, Eline T.; Schwab, Nicholas; Rubelt, Florian; Greiff, Victor & Pavlović, Milena [Vis alle 32 forfattere av denne artikkelen] (2021). The Future of Blood Testing Is the Immunome. Frontiers in Immunology. ISSN 1664-3224. 12:626793, s. 1–6. doi: 10.3389/fimmu.2021.626793. Fulltekst i vitenarkiv
  • Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification . BioRxiv. ISSN 0362-4331.
  • Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). immuneML: an ecosystem for machine learning analysis of adaptive immune receptor repertoires. BioRxiv. ISSN 0362-4331.
  • Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). In silico proof of principle of machine learning-based antibody design at unconstrained scale . BioRxiv. ISSN 0362-4331.
  • Greiff, Victor & Sandve, Geir Kjetil Ferkingstad (2021). One billion synthetic 3D-antibody-antigen complexes enable unconstrained machine-learning formalized investigation of antibody specificity prediction . BioRxiv. ISSN 0362-4331. doi: 10.1101/2021.07.06.451258.
  • Akbar, Rahmad; Robert, Philippe Paul Auguste; Pavlović, Milena; Jeliazkov, Jeliazko R.; Snapkov, Igor & Slabodkin, Andrei [Vis alle 15 forfattere av denne artikkelen] (2021). A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell reports. ISSN 2211-1247. 34:108856(11), s. 1–21. doi: 10.1016/j.celrep.2021.108856. Fulltekst i vitenarkiv
  • Yao, Ying; Zia, Asima; Neumann, Ralf Stefan; Pavlović, Milena; Balaban, Gabriel & Lundin, Knut Erik Aslaksen [Vis alle 8 forfattere av denne artikkelen] (2021). T cell receptor repertoire as a potential diagnostic marker for celiac disease. Clinical Immunology. ISSN 1521-6616. 222:108621, s. 1–7. doi: 10.1016/j.clim.2020.108621. Fulltekst i vitenarkiv
  • Dahal-Koirala, Shiva; Risnes, Louise Fremgaard; Neumann, Ralf Stefan; Christophersen, Asbjørn; Lundin, Knut E. A. & Sandve, Geir Kjetil [Vis alle 8 forfattere av denne artikkelen] (2021). Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs. Frontiers in Immunology. ISSN 1664-3224. 12:639672, s. 1–13. doi: 10.3389/fimmu.2021.639672. Fulltekst i vitenarkiv
  • Lemma, Roza Berhanu; Ledsaak, Marit; Fuglerud, Bettina Maria; Sandve, Geir Kjetil; Eskeland, Ragnhild & Gabrielsen, Odd Stokke (2021). Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB. Scientific Reports. ISSN 2045-2322. 11(9008). doi: 10.1038/s41598-021-88516-w. Fulltekst i vitenarkiv
  • Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan & Sandve, Geir Kjetil (2020). Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methods. BMC Genomics. ISSN 1471-2164. 21. doi: 10.1186/s12864-020-6685-y. Fulltekst i vitenarkiv
  • Khelik, Ksenia; Sandve, Geir Kjetil; Nederbragt, Alexander Johan & Rognes, Torbjørn (2020). NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics. ISSN 1471-2105. 21(1). doi: 10.1186/s12859-020-3414-0. Fulltekst i vitenarkiv
  • Weber, Cédric R.; Akbar, Rahmad; Yermanos, Alexander; Pavlovic, Milena; Snapkov, Igor & Sandve, Geir Kjetil [Vis alle 8 forfattere av denne artikkelen] (2020). immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking. Bioinformatics. ISSN 1367-4803. 36(11), s. 3594–3596. doi: 10.1093/bioinformatics/btaa158. Fulltekst i vitenarkiv
  • du Pré, Fleur; Blazevski, Jana; Dewan, Alisa Elinsdatter; Stamnæs, Jorunn; Kanduri, Srinivasa Kalyana Chakravarthi & Sandve, Geir Kjetil [Vis alle 13 forfattere av denne artikkelen] (2020). B cell tolerance and antibody production to the celiac disease autoantigen transglutaminase 2. Journal of Experimental Medicine (JEM). ISSN 0022-1007. 217:e20190860.(2), s. 1–14. doi: 10.1084/jem.20190860. Fulltekst i vitenarkiv
  • Salvatore, Stefania; Rand, Knut Dagestad; Grytten, Ivar; Ferkingstad, Egil; Domanska, Diana & Holden, Lars [Vis alle 10 forfattere av denne artikkelen] (2019). Beware the Jaccard: the choice of similarity measure is important and non-trivial in genomic colocalisation analysis. Briefings in Bioinformatics. ISSN 1467-5463. s. 1–8. doi: 10.1093/bib/bbz083.
  • Snir, Omri; Kanduri, Srinivasa Kalyana Chakravarthi; Lundin, Knut Erik Aslaksen; Sandve, Geir Kjetil & Sollid, Ludvig Magne (2019). Transcriptional profiling of human intestinal plasma cells reveals effector functions beyond antibody production. United European Gastroenterology journal. ISSN 2050-6406. 0(0), s. 1–9. doi: 10.1177/2050640619862461.
  • Brown, Alex; Snapkov, Igor; Akbar, Rahmad; Pavlovic, Milena; Miho, Enkelejda & Sandve, Geir Kjetil [Vis alle 7 forfattere av denne artikkelen] (2019). Augmenting adaptive immunity: progress and challenges in the quantitative engineering and analysis of adaptive immune receptor repertoires. Molecular Systems Design & Engineering. ISSN 2058-9689. 4(4), s. 701–736. doi: 10.1039/c9me00071b.
  • Grytten, Ivar; Rand, Knut Dagestad; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2019). Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes. PLoS Computational Biology. ISSN 1553-734X. 15(2), s. 1–13. doi: 10.1371/journal.pcbi.1006731. Fulltekst i vitenarkiv
  • Gheorghe, Marius; Sandve, Geir Kjetil; Khan, Aziz; Cheneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). A map of direct TF–DNA interactions in the human genome. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(4). doi: 10.1093/nar/gky1210. Fulltekst i vitenarkiv
  • Kanduri, Srinivasa Kalyana Chakravarthi; Bock, Christoph; Gundersen, Sveinung; Hovig, Eivind & Sandve, Geir Kjetil (2019). Colocalization analyses of genomic elements: approaches, recommendations and challenges. Bioinformatics. ISSN 1367-4803. 35(9), s. 1615–1624. doi: 10.1093/bioinformatics/bty835. Fulltekst i vitenarkiv
  • Domanska, Diana Ewa; Kanduri, Srinivasa Kalyana Chakravarthi; Simovski, Boris & Sandve, Geir Kjetil (2018). Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis. BMC Bioinformatics. ISSN 1471-2105. 19(481). doi: 10.1186/s12859-018-2438-1. Fulltekst i vitenarkiv
  • Yao, Ying; Zia, Asima; Wyrozemski, Lukasz Adam; Lindeman, Ida; Sandve, Geir Kjetil & Qiao, Shuo Wang (2018). Exploiting antigen receptor information to quantify index switching in single-cell transcriptome sequencing experiments. PLOS ONE. ISSN 1932-6203. 13(12), s. 1–17. doi: 10.1371/journal.pone.0208484. Fulltekst i vitenarkiv
  • Simovski, Boris; Kanduri, Srinivasa Kalyana Chakravarthi; Gundersen, Sveinung; Titov, Dmytro; Domanska, Diana Ewa & Bock, Christoph [Vis alle 15 forfattere av denne artikkelen] (2018). Coloc-stats: A unified web interface to perform colocalization analysis of genomic features. Nucleic Acids Research (NAR). ISSN 0305-1048. 46(1), s. W186–W193. doi: 10.1093/nar/gky474. Fulltekst i vitenarkiv
  • Risnes, Louise Fremgaard; Christophersen, Asbjørn; Dahal-Koirala, Shiva; Neumann, Ralf Stefan; Sandve, Geir Kjetil & Sarna, Vikas Kumar [Vis alle 9 forfattere av denne artikkelen] (2018). Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease. Journal of Clinical Investigation. ISSN 0021-9738. 128(6), s. 2642–2650. doi: 10.1172/JCI98819. Fulltekst i vitenarkiv
  • Rand, Knut Dagestad; Grytten, Ivar; Nederbragt, Alexander Johan; Storvik, Geir Olve; Glad, Ingrid Kristine & Sandve, Geir Kjetil (2017). Coordinates and intervals in graph-based reference genomes. BMC Bioinformatics. ISSN 1471-2105. 18:263, s. 1–8. doi: 10.1186/s12859-017-1678-9. Fulltekst i vitenarkiv
  • Salvatore, Stefania; Domanska, Diana Ewa; Wood, Mollie; Nordeng, Hedvig Marie Egeland & Sandve, Geir Kjetil (2017). Complex patterns of concomitant medication use: A study among Norwegian women using paracetamol during pregnancy. PLOS ONE. ISSN 1932-6203. 12(12). doi: 10.1371/journal.pone.0190101. Fulltekst i vitenarkiv
  • Khelik, Ksenia; Lagesen, Karin; Sandve, Geir Kjetil; Rognes, Torbjørn & Nederbragt, Alexander Johan (2017). NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinformatics. ISSN 1471-2105. 18(1), s. 1–14. doi: 10.1186/s12859-017-1748-z. Fulltekst i vitenarkiv
  • Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix & Lirussi, Lisa [Vis alle 16 forfattere av denne artikkelen] (2017). Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. Scientific Reports. ISSN 2045-2322. 7(1). doi: 10.1038/s41598-017-07314-5. Fulltekst i vitenarkiv
  • Domanska, Diana Ewa; Vodak, Daniel; Christin, Lund-Andersen; Salvatore, Stefania; Hovig, Eivind & Sandve, Geir Kjetil (2017). The rainfall plot: Its motivation, characteristics and pitfalls. BMC Bioinformatics. ISSN 1471-2105. 18. doi: 10.1186/s12859-017-1679-8.
  • Roy, Bishnudeo; Neumann, Ralf Stefan; Snir, Omri; Iversen, Rasmus; Sandve, Geir Kjetil & Lundin, Knut Erik Aslaksen [Vis alle 7 forfattere av denne artikkelen] (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. 199((2)), s. 782–791. doi: 10.4049/jimmunol.1700169. Fulltekst i vitenarkiv
  • Simovski, Boris; Vodak, Daniel; Gundersen, Sveinung; Domanska, Diana Ewa; Azab, Abdulrahman & Holden, Lars [Vis alle 25 forfattere av denne artikkelen] (2017). GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome. GigaScience. ISSN 2047-217X. 6(7), s. 1–12. doi: 10.1093/gigascience/gix032. Fulltekst i vitenarkiv
  • 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.
  • 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.
  • Bengtsen, Mads; Klepper, Kjetil; Gundersen, Sveinung; Cuervo Torre, Ignacio; Drabløs, Finn & Hovig, Johannes Eivind [Vis alle 9 forfattere av denne artikkelen] (2015). c-Myb Binding Sites in Haematopoietic Chromatin Landscapes. PLOS ONE. ISSN 1932-6203. 10(7). doi: 10.1371/journal.pone.0133280. Fulltekst i vitenarkiv
  • 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.
  • Ricigliano, Vito A. G.; Handel, Adam E; Sandve, Geir Kjetil F.; Annibali, Viviana; Ristori, Giovanni & Mechelli, Rosella [Vis alle 8 forfattere av denne artikkelen] (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.
  • 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. Fulltekst i vitenarkiv
  • 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.
  • 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. Fulltekst i vitenarkiv
  • Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, H; Carninci, P & Forrest, A [Vis alle 7 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
  • Molyneux, Sam; Waterhouse, PD; Shelton, Dawne; Shao, Yang W; Watling, Christopher M & Tang, Qing-Lian [Vis alle 18 forfattere av denne artikkelen] (2014). Human somatic cell mutagenesis creates genetically tractable sarcomas. Nature Genetics. ISSN 1061-4036. 46(9), s. 964–972. doi: 10.1038/ng.3065.
  • Disanto, Giulio; Sandve, Geir Kjetil; Ricigliano, Vito AG; Pakpoor, Julia; Berlanga-Taylor, Antonio & Handel, Adam E [Vis alle 12 forfattere av denne artikkelen] (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.
  • 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.
  • Handel, Adam E; Sandve, Geir Kjetil; Disanto, Giulio; Berlanga-Taylor, Antonio; Gallone, Anna & Hanwell, Heather EC [Vis alle 10 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
  • Sandve, Geir Kjetil; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid Kristine; Gunathasan, Krishanthi & Holden, Lars [Vis alle 21 forfattere av denne artikkelen] (2013). The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research (NAR). ISSN 0305-1048. 41(W1), s. W133–W141. doi: 10.1093/nar/gkt342. Fulltekst i vitenarkiv
  • Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf & Glad, Ingrid Kristine [Vis alle 7 forfattere av denne artikkelen] (2013). Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Research (NAR). ISSN 0305-1048. 41(10), s. 5164–5174. doi: 10.1093/nar/gkt227.
  • 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.
  • Disanto, Giulio; Sandve, Geir Kjetil; Berlanga-Taylor, Antonio; Ragnedda, Giammario; Morahan, Julia & Watson, Corey T [Vis alle 9 forfattere av denne artikkelen] (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.
  • Disanto, Giulio; Sandve, Geir Kjetil; Berlanga-Taylor, Antonio; Morahan, Julia; Dobson, Ruth & Giovannoni, Gavin [Vis alle 7 forfattere av denne artikkelen] (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.
  • Bruhn, Sören; Barrenäs, Fredrik; Mobini, R; Andersson, B; Chavali, S. & Egan, B. S. [Vis alle 12 forfattere av denne artikkelen] (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.
  • Sandve, Geir Kjetil; Gundersen, Sveinung; Rydbeck, Halfdan; Glad, Ingrid Kristine; Holden, Lars & Holden, Marit [Vis alle 15 forfattere av denne artikkelen] (2011). The differential disease regulome. BMC Genomics. ISSN 1471-2164. 12. 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 [Vis alle 14 forfattere av denne artikkelen] (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. Fulltekst i vitenarkiv
  • 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.
  • 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. Fulltekst i vitenarkiv
  • 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 (LNCS). 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. doi: 10.1186/1471-2105-9-527.
  • 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.
  • 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. Fulltekst i vitenarkiv
  • Abul, Osman; Sandve, Geir Kjetil & Drabløs, Finn (2007). False Discovery Rates in Identifying Functional DNA Motifs. I Yang, Jack Y. (Red.), Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering. IEEE. ISSN 978-1-4244-1509-0. 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. Fulltekst i vitenarkiv
  • 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 (LNCS). ISSN 0302-9743. 4175, s. 197–206.
  • 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 (2005). Generalized Composite Motif Discovery. Lecture Notes in Computer Science (LNCS). ISSN 0302-9743. 3683. doi: 10.1007/11553939.

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  • Kanduri, Chakravarthi; Sandve, Geir Kjetil Ferkingstad; Hovig, Eivind; De, Subhajyoti & Layer, Ryan (2021). Editorial: Genomic Colocalization and Enrichment Analyses. Frontiers in Genetics. ISSN 1664-8021. 11. doi: 10.3389/fgene.2020.617876.
  • Sandve, Geir Kjetil Ferkingstad (2021). ImmuneML and the case for domain-tailored machine learning platforms.
  • Balaban, Gabriel; Grytten, Ivar; Rand, Knut Dagestad; Scheffer, Lonneke & Sandve, Geir Kjetil (2021). Ten simple rules for quick and dirty scientific programming. PLoS Computational Biology. ISSN 1553-734X. 17:e1008549(3), s. 1–15. doi: 10.1371/journal.pcbi.1008549.
  • Molyneux, Sam D.; Waterhouse, Paul D.; Shelton, Dawne; Shao, Yang W.; Watling, Christopher M. & Tang, Qing-Lian [Vis alle 18 forfattere av denne artikkelen] (2020). Author Correction: Human somatic cell mutagenesis creates genetically tractable sarcomas (Nature Genetics, (2014), 46, 9, (964-972), 10.1038/ng.3065). Nature Genetics. ISSN 1061-4036. 52(4). doi: 10.1038/s41588-020-0589-2.
  • Widrich, Michael; Schäfl, Bernhard; Pavlović, Milena; Ramsauer, Hubert; Gruber, Lukas & Holzleitner, Markus [Vis alle 11 forfattere av denne artikkelen] (2020). Modern Hopfield Networks and Attention for Immune Repertoire Classification.
  • Gheorghe, Marius; Sandve, Geir Kjetil Ferkingstad; Khan, Aziz; Chèneby, Jeanne; Ballester, Benoit & Mathelier, Anthony (2019). Erratum: A map of direct TF-DNA interactions in the human genome (Nucleic acids research (2019) 47 4 (e21)). Nucleic Acids Research (NAR). ISSN 0305-1048. 47(14). doi: 10.1093/nar/gkz582.
  • Alsøe, Lene; Sarno, Antonio; Carracedo Huroz, Sergio; Domanska, Diana Ewa; Dingler, Felix & Lirussi, Lisa [Vis alle 16 forfattere av denne artikkelen] (2017). Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1 .
  • Kanduri, Chakravarthi; Domanska, Diana; Hovig, Eivind & Sandve, Geir Kjetil (2017). Genome build information is an essential part of genomic track files. Genome Biology. ISSN 1465-6906. 18(1). doi: 10.1186/s13059-017-1312-1.
  • Simovski, Boris; Drabløs, Finn Sverre; Gundersen, Sveinung; Johansen, Morten; Domanska, Diana Ewa & Azab, Abdulrahman [Vis alle 8 forfattere av denne artikkelen] (2016). The Genomic HyperBrowser.
  • Ferkingstad, Egil; Sandve, Geir Kjetil F. & Holden, Lars (2015). Monte Carlo null models for genomic data.
  • Tørresen, Ole Kristian; Jentoft, Sissel; Star, Bastiaan; Sandve, Geir Kjetil F.; Skage, Morten & Hansen, Marianne Helén Selander [Vis alle 9 forfattere av denne artikkelen] (2014). A new, high quality reference genome assembly for Atlantic cod.
  • Rye, Morten Beck; Sandve, Geir Kjetil F.; Daub, Carsten O; Kawaji, Hideya; Carninci, Piero & Forrest, Alistair [Vis alle 7 forfattere av denne artikkelen] (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 [Vis alle 7 forfattere av denne artikkelen] (2014). Repressed promoters in active chromatin.
  • Tørresen, Ole Kristian; Walenz, Brian; Grove, Harald; Lien, Sigbjørn; Knight, James & Star, Bastiaan [Vis alle 15 forfattere av denne artikkelen] (2014). A new, high quality reference genome assembly for Atlantic cod.
  • 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.
  • Ferkingstad, Egil; Holden, Lars & Sandve, Geir Kjetil (2013). Monte Carlo null models for genomic data.
  • Sandve, Geir Kjetil; Abul, Osman; Walseng, Vegard & Drabløs, Finn (2007). Improved benchmarks for computational motif discovery.
  • Sandve, Geir Kjetil; Stenersen, Kristoffer; Walseng, Vegard; Lekang, Øystein; Klepper, Kjetil & Abul, Osman [Vis alle 9 forfattere av denne artikkelen] (2006). An integrated approach to motif discovery in DNA sequences.
  • 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.
  • 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.
  • Sandve, Geir Kjetil & Drabløs, Finn (2005). Generalized Composite Motif Discovery.
  • Holden, Lars; Jullum, Martin & Sandve, Geir Kjetil (2017). Statistical modeling of repertoire overlap in entire sampling spaces. Norsk Regnesentral.
  • Ferkingstad, Egil; Holden, Lars & Sandve, Geir Kjetil (2013). Monte Carlo null models in ecology. Norsk Regnesentral.
  • Sandve, Geir Kjetil (2008). Potentials and limitations of motif-based binding site prediction in DNA. NTNU-trykk. ISSN 978-82-471-1169-7. 2008(239).

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Publisert 4. nov. 2010 14:16 - Sist endret 7. sep. 2020 11:17