Publications after 2013, see: Marit Holden, Clara-Cecilie Günther and Lars Holden

Günther, Clara-Cecilie; Holden, Marit; Holden, Lars; Preprocessing of gene-expression data related to breast cancer diagnosis. NR note SAMBA/35/14 October 2014.

Myhrstad, Mari; Ulven, Stine Marie; Günther, Clara-Cecilie; Ottestad, Inger; Holden, Marit; Ryeng, Einar; Borge, Grethe Iren Andersen; Kohler, Achim; Brønner, Kirsti Wettre; Thoresen, Magne; Holven, Kirsten Bjørklund. Fish oil supplementation induces expression of genes related to cell cycle, ER stress and apoptosis in PBMC-a transcriptomic approach. Journal of Internal Medicine (ISSN 1365-2796) 2014. doi:10.1111/joim.12217

Wollen, Embjørg Julianne; Sejersted, Ynge; Wright, Marianne S.; Bik-Multanowski, Miroslaw; Madetko-Talowska, Anna; Günther, Clara-Cecilie; Nygård, Ståle; Kwinta, Przemko; Pietrzyk, Jacek J.; and Saugstad, Ola D. Transcriptome profiling of the newborn mouse lung after hypoxia and reoxygenation: hyperoxic reoxygenation affects mTOR signaling pathway, DNA repair, and JNK-pathway regulation. Pediatric Research (ISSN 0047-2506) 2013. 74 pp 536-544. doi:10.1038/pr.2013.140

Pietrzyk, Jacek J.; Kwinta, Przemko; Wollen, Embjørg Julianne; Bik-Multanowski, Miroslaw; Madetko-Talowska, Anna; Günther, Clara-Cecilie; Tomasik, Tomasz; Jagla, Mateusz; and Saugstad, Ola D. Gene expression profiling in preterm infants: New aspects of bronchopulmonary dysplasia development. PLOS ONE 2013 8(10) doi: 10.1371/journal.pone.0078585

Lillenes, Meryl S.; Støen, Mari; Gómez-Muñoza, Marta; Torp, Reidun; Günther, Clara-Cecilie; Nilsson, Lars N. G.; Tønjum, Tone. Transient OGG1, APE1, PARP1 and Polβ expression in an Alzheimer's disease mouse model Mechanisms of Ageing and Development (ISSN 0047-6374) 2013. 134(10) pp 467-477. doi: 10.1016/j.mad.2013.09.002

Schee, Kristina; Lorenz, Susanne; Worren, Merete Molton; Günther, Clara-Cecilie; Holden, Marit; Hovig, Johannes Eivind; Fodstad, Øystein; Meza, Leonardo Zepeda; Flatmark, Kjersti. Deep Sequencing the MicroRNA Transcriptome in Colorectal Cancer. PLoS ONE (ISSN 1932-6203) 2013. 8(6). doi: 10.1371/journal.pone.0066165

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. DNase hypersensitive sites and association with multiple sclerosis. Human Molecular Genetics (ISSN 0964-6906) 2013. 23(4) doi: 10.1093/hmg/ddt489.

Paulsen, Jonas; Lien, Tonje Gulbrandsen; Sandve, Geir Kjetil; Holden, Lars; Borgan, Ørnulf; Glad, Ingrid Kristine; Hovig, Johannes Eivind. Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Research (ISSN 0305-1048) 2013. 41(10):5164-5174. doi: 10.1093/nar/gkt227.

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. The Genomic HyperBrowser: an analysis web server for genome-scale data. Nucleic Acids Research (ISSN 0305-1048) 2013. 41(W1) pp W133. doi: 10.1093/nar/gkt342.

Lando, Malin; Wilting, Saskia M.; Snipstad, Kristin; Clancy, Trevor; Bierkens, Mariska; Aarnes, Eva-Katrine; Holden, Marit; Stokke, Trond; Sundfør, Kolbein; Holm, Ruth; Kristensen, Gunnar S Balle; Steenbergen, Renske D.M.; Lyng, Heidi. Identification of eight candidate target genes of the recurrent 3p12p14 loss in cervical cancer by integrative genomic profiling. Journal of Pathology 2013. 230(1):59-69. doi: 10.1002/path.4168.

Omair, Ahmad; Holden, Marit; Lie, Benedicte Alexandra; Reikerås, Olav; Brox, Jens Ivar. Treatment outcome of chronic low back pain and radiographic lumbar disc degeneration are associated with inflammatory and matrix degrading gene variants: a prospective genetic association study. BMC Musculoskeletal Disorders 2013. 14 doi: 10.1186/1471-2474-14-105.

Bøhn, Siv Kjølsrud; Russnes, Kjell Magne; Sakhi, Amrit Kaur; Thoresen, Magne; Holden, Marit; Moskaug, Jan Øivind; Myhrstad, Mari Charlotte; Olstad, Ole Kristoffer; Smeland, Sigbjørn; Blomhoff, Rune. Stress associated gene expression in blood cells is related to outcome in radiotherapy treated head and neck cancer patients. BMC Cancer 2012. 12 doi: 10.1186/1471-2407-12-426.

Halle, Cathinka Lønning; Andersen, Erlend K F; Lando, Malin; Aarnes, Eva-Katrine; Hasvold, Grete; Holden, Marit; Syljuåsen, Randi G.; Sundfør, Kolbein; Kristensen, Gunnar S Balle; Holm, Ruth; Malinen, Eirik; Lyng, Heidi. Hypoxia-induced gene expression in chemoradioresistant cervical cancer revealed by dynamic contrast enhanced MRI. Cancer Research 2012. 72(20) :5285-5295. doi: 10.1158/0008-5472.CAN-12-1085.

Omair, Ahmad; Lie, Benedicte Alexandra; Reikerås, Olav; Holden, Marit; Brox, Jens Ivar. Genetic contribution of catechol-O-methyltransferase variants in treatment outcome of low back pain: a prospective genetic association study. BMC Musculoskeletal
Disorders 2012. 13 doi: 10.1186/1471-2474-13-76.

Marit Holden, Ingrid Glad, Håvard Hauge, Evind Hovig, Knut Liestøl. Image restoration and analysis of biomolecular radioactivity images II NR Note SAMBA/11/2012. March 2012.

Reikvam, Håkon; Mosevoll, Knut Anders; Melve, Guro Kristin; Günther, Clara-Cecilie; Sjo, Malvin; Bentsen, Pål-Tore; Bruserud, Øystein The Pretransplantation Serum Cytokine Profile in Allogeneic Stem Cell Recipients Differs from Healthy Individuals, and Various Profiles are Associated with Different Risks of Posttransplantation Complications Biology of Blood and Marrow Transplantation 2012 18(2):190-199.

Sandve, Geir K.; Gundersen, Sveinung; Rydbeck, Halfdan; Glad, Ingrid; Holden, Lars; Holden, Marit; Liestøl, Knut; Clancy, Trevor; Drabløs, Finn;Ferkingstad, Egil; Johansen, Morten; Nygaard, Vegard; Tøstesen, Eivind; Frigessi, Arnoldo; Hovig, Eivind The differential disease regulome BMC Genomics 2011 12(1):353.

Halle, Cathinka; Lando, Malin; Svendsrud, Debbie H.; Clancy, Trevor; Holden, Marit; Sundfør, Kolbein; Kristensen, Gunnar B.; Holm, Ruth; Lyng, Heidi Membranous Expression of Ectodomain Isoforms of the Epidermal Growth Factor Receptor (EGFR) Predicts Outcome after Chemoradiotherapy of Lymph Node Negative Cervical Cancer Clinical Cancer Research 2011 17(16):5501-5512.

Jemtland, Rune; Holden, Marit; Reppe, Sjur; Olstad, Ole K,; Reinholt Finn P,; Gautvik, Vigdis T,; Refvem, Hilde; Frigessi, Arnoldo; Houston Brian; Gautvik, Kaare M Molecular disease map of bone characterizing the postmenopausal osteoporosis phenotype Journal of Bone and Mineral Research 2011 26(8):1793-801

Sandve, Geir K.; Gundersen, Sveinung; Rydbeck, Halfdan; Glad, Ingrid; Holden, Lars; Holden, Marit; Liestøl, Knut; Clancy, Trevor; Ferkingstad, Egil; Johansen, Morten; Nygaard, Vegard; Tøstesen, Eivind; Frigessi, Arnoldo; Hovig, Eivind The Genomic HyperBrowser: inferential genomics at the sequence level Genome biology 2010 11:R121, Issue 12.

Bøhn Siv K.; Myhrstad, Mari C.; Thoresen, Magne; Holden, Marit; Karlsen, Anette; Tunheim, Siv H.; Erlund, Iris; Svendsen, Mette; Seljeflot, Ingebjørg; Moskaug, Jan Ø.; Duttaroy, Asim K.; Laake, Petter; Arnesen, Harald; Tonstad, Serena; Collins, Andrew; Drevon, Christian A.; Blomhoff, Rune Blood cell gene expression associated with cellular stress defense is modulated by antioxidant-rich food in a randomised controlled clinical trial of male smokers BMC Medicine 2010 8:54.

Sjur Reppe, Hilde Refvem; Vigdis T. Gautvik, Ole K. Olstad, Per I. Høvring, Finn P. Reinholt, Marit Holden, Arnoldo Frigessi, Rune Jemtland, Kaare M. Gautvik. Eight genes are highly associated with BMD variation in postmenopausal Caucasian women. Bone March 2010 46(3):604-612, Epub 2009 Nov 14.

Malin Lando, Marit Holden, Linn C. Bergersen, Debbie H. Svendsrud, Trond Stokke, Kolbein Sundfør, Ingrid K. Glad, Gunnar B. Kristensen, Heidi Lyng Gene Dosage, Expression, and Ontology Analysis Identifies Driver Genes in the Carcinogenesis and Chemoradioresistance of Cervical Cancer. PLoS Genetics Nov 2009 5(11): e1000719.

Marit Holden, Shiwei Deng, Leszek Wojnowski, Bettina Kulle GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies Bioinformatics 2008 24(23):2784-2785.

Marit Holden, Ingrid Glad, Håvard Hauge, Knut Liestøl. Image restoration and analysis of biomolecular radioactivity images NR Note SAMBA/27/08. June 2008.

Vigdis Nygaard, Fang Liu, Marit Holden, Winston P Kuo, Jeff Trimarchi, Lucila Ohno-Machado, Connie L Cepko, Arnoldo Frigessi, Ingrid K Glad, Mark A van de Wiel, Eivind Hovig, Heidi Lyng. Validation of oligoarrays for quantitative exploration of the transcriptome BMC Genomics 2008 9:258.

Hege Bøvelstad, Ståle Nygård, Hege Størvold, Magne Aldrin, Ørnulf Borgan, Arnoldo Frigessi, Ole Christian Lingjærde. Predicting survival from microarray data - a comparative study Bioinformatics 2007 23(16):2080-2087.

Hans-Olav Fjærli, Geir Bukholm, Camilla Skjæret, Marit Holden, Britt Nakstad. Cord blood gene expression in infants hospitalized with respiratory syncytial virus bronchiolitis Journal of Infectious Diseases 2007 196:394-404.

Hans-Olav Fjærli, Geir Bukholm, Anne Krog, Camilla Skjæret, Marit Holden, Britt Nakstad. Whole blood gene expression in infants with respiratory syncytial virus bronchiolitis BMC Infectious Diseases 2006 6:175.

Mark A. van de Wiel, Marit Holden, Ingrid K. Glad, Heidi Lyng, Arnoldo Frigessi. Bayesian Process-Based Modeling of Two-Channel Microarray Experiments: Estimating Absolute mRNA Concentrations, in Bayesian Inference for Gene Expression and Proteomics, edited by Kim-Anh Do, Peter Müller and Marina Vannucci, 2006, pages: 75-96.

Jeanne-Marie Berner, Christophe Müller, Marit Holden; Junbai Wang, Eivind Hovig, Ola Myklebost. Sampling Effects on Gene Expression Data from a Human Tumour Xenograft Scandinavian Journal of Laboratory Animal Science 2006 33(1):17-30.

Vigdis Nygaard, Marit Holden, Anders Løland, Mette Langaas, Ola Myklebost, Eivind Hovig. Limitations of mRNA amplification from small-size cell samples BMC Genomics 2005 6:147.

Arnoldo Frigessi, Mark A. van de Wiel, Marit Holden, Debbie H. Svendsrud, Ingrid K. Glad and Heidi Lyng. Genome-wide estimation of transcript concentrations from spotted cDNA microarray data Nucleic Acids Research - Methods Online 2005;33(17):e143.

Lina Cekaite, Ola Haug, Ola Myklebost, Magne Aldrin, Bjørn Østenstad, Marit Holden, Arnoldo Frigessi, Eivind Hovig and Mouldy Sioud. Analysis of the humoral immune response to immunoselected phage-displayed peptides by a microarray-based method. Proteomics 2004 Sep;4(9):2572-2582.

Arnoldo Frigessi, Mark A. van de Wiel, Marit Holden, Ingrid K. Glad and Heidi Lyng. Model-based estimation of transcript concentrations from spotted microarray data. NR Report 999, ISBN 82-539-0507-6. May 2004. A web page with a program for estimating the model parameters is found here.

Turid Follestad, Mette Langaas, Håvard Rue, Marit Holden and Anders Løland. glme: a C-program for parameter estimation using Gibbs-sampling in large linear mixed-effects models, with applications to DNA microarray data NR Note SAMBA/10/04. March 2004.

Marit Holden and Ola Haug. Experimental design and statistical analysis of SNP data obtained in genetic association studies NR Note SAMBA/28/03. December 2003. The corresponding web pages are found here.

Marit Holden og Anders Løland. Introduksjon til analyse av cDNA mikromatrisedata. Norsk Epidemiologi 2003 13 (2):291-296.

Vigdis Nygaard, Anders Løland , Marit Holden, Mette Langaas, Håvard Rue, Fang Liu, Ola Myklebost, Øystein Fodstad, Eivind Hovig and Birgitte Smith-Sørensen. Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance. BMC Genomics 2003 4:11.

Tor-Kristian Jenssen, Mette Langaas, Winston P. Kuo, Birgitte Smith-Sørensen, Ola Myklebost, Eivind Hovig. Analysis of repeatability in spotted cDNA microarrays Nucleic Acids Res. 2002 30:3235-3244. See Remarks to paper.

M. Langaas. Bioinformatikk - et interessant forskningsfelt for statistikere? Artikkel skrevet til Norsk Statistisk Forenings tidsskrift Tilfeldig Gang [pdf]

K. Aas. Microarray Data Mining: A Survey NR Note SAMBA/02/01. February 2001.

Statistical Methods in Bioinformatics. NR Information sheet.