Publications

Giegerich, R., Brazma, A., Jonassen, I., Ukkonen, E., and Vingron, M. (2008) The brew workshop series: a stimulating experience in phd education. Brief Bioinform 9, 250-253. [ http ]

Boye, K., Grotterød, I., Aasheim, H.-C., Hovig, E., and Maelandsmo, G. M. (2008) Activation of nf-kappab by extracellular s100a4: analysis of signal transduction mechanisms and identification of target genes. Int J Cancer 123, 1301-1310. [ http ]

Eichner, C., Frost, P., Dysvik, B., Jonassen, I., Kristiansen, B., and Nilsen, F. (2008) Salmon louse (lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using est-sequencing and microarray analysis. BMC Genomics 9, 126. [ http ]

Gilfillan, G. D., Selmer, K. K., Roxrud, I., Smith, R., Kyllerman, M., Eiklid, K., Kroken, M., Mattingsdal, M., Egeland, T., Stenmark, H., Sjøholm, H., Server, A., Samuelsson, L., Christianson, A., Tarpey, P., Whibley, A., Stratton, M. R., Futreal, P. A., Teague, J., Edkins, S., Gecz, J., Turner, G., Raymond, F. L., Schwartz, C., Stevenson, R. E., Undlien, D. E., and Strømme, P. (2008) Slc9a6 mutations cause x-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking angelman syndrome. Am J Hum Genet 82, 1003-1010. [ http ]

Hansen, T. E., Puntervoll, P., Seternes, O. M., and Jørgensen, J. B. (2008) Atlantic salmon possess three mitogen activated protein kinase kinase 6 paralogs responding differently to stress. FEBS J 275, 4887-4902. [ http ]

Holden, M., Deng, S., Wojnowski, L., and Kulle, B. (2008) Gsea-snp: applying gene set enrichment analysis to snp data from genome-wide association studies. Bioinformatics 24, 2784-2785. [ http ]

Klepper, K., Sandve, G. K., Abul, O., Johansen, J., and Drablos, F. (2008) Assessment of composite motif discovery methods. BMC Bioinformatics 9, 123. [ http ]

Kraus, I., Driesch, C., Vinokurova, S., Hovig, E., Schneider, A., von Knebel Doeberitz, M., and Dürst, M. (2008) The majority of viral-cellular fusion transcripts in cervical carcinomas cotranscribe cellular sequences of known or predicted genes. Cancer Res 68, 2514-2522. [ http ]

Lanzén, A. and Oinn, T. (2008) The taverna interaction service: enabling manual interaction in workflows. Bioinformatics 24, 1118-1120. [ http ]

Lyng, H., Lando, M., Brøvig, R. S., Svendsrud, D. H., Johansen, M., Galteland, E., Brustugun, O. T., Meza-Zepeda, L. A., Myklebost, O., Kristensen, G. B., Hovig, E., and Stokke, T. (2008) Genecount: genome-wide calculation of absolute tumor dna copy numbers from array comparative genomic hybridization data. Genome Biol 9, R86. [ http ]

Malde, K. and Jonassen, I. (2008) Repeats and est analysis for new organisms. BMC Genomics 9, 23. [ http ]

Nygaard, V., Liu, F., Holden, M., Kuo, W. P., Trimarchi, J., Ohno-Machado, L., Cepko, C. L., Frigessi, A., Glad, I. K., van de Wiel, M. A., Hovig, E., and Lyng, H. (2008) Validation of oligoarrays for quantitative exploration of the transcriptome. BMC Genomics 9, 258. [ http ]

Ranheim, T., Mattingsdal, M., Lindvall, J. M., Holla, O. L., Berge, K. E., Kulseth, M. A., and Leren, T. P. (2008) Genome-wide expression analysis of cells expressing gain of function mutant d374y-pcsk9. J Cell Physiol 217, 459-467. [ http ]

Rødland, E. K., Mattingsdal, M., Olstad, O. K., Ovstebø, R., Kierulf, P., Muller, F., and Frøland, S. S. (2008) Expression of genes in normal human monocytes in response to aspergillus fumigatus. Med Mycol 46, 327-336. [ http ]

Sandve, G. K., Abul, O., and Drabløs, F. (2008) Compo: composite motif discovery using discrete models. BMC Bioinformatics 9, 527. [ http ]

de Souza, G. A., Målen, H., Søfteland, T., Saelensminde, G., Prasad, S., Jonassen, I., and Wiker, H. G. (2008) High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using mycobacterium tuberculosis as an example. BMC Genomics 9, 316. [ http ]

Stavrum, A. K., Petersen, K., Jonassen, I., and Dysvik, B. (2008) Analysis of gene-expression data using j-express. Curr Protoc Bioinformatics Chapter 7, Unit 7.3. [ http ]

Stavrum, R., Valvatne, H., Bø, T. H., Jonassen, I., Hinds, J., Butcher, P. D., and Grewal, H. M. S. (2008) Genomic diversity among beijing and non-beijing mycobacterium tuberculosis isolates from myanmar. PLoS ONE 3, e1973. [ http ]

Urich, T., Lanzén, A., Qi, J., Huson, D. H., Schleper, C., and Schuster, S. C. (2008) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3, e2527. [ http ]

Korkmaz, B., Hajjar, E., Kalupov, T., Reuter, N., Brillard-Bourdet, M., Moreau, T., Juliano, L., and Gauthier, F. (2007) Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase. A kinetic and molecular modeling analysis. J Biol Chem 282, 1989-1997. [ http ]

Lindqvist, C., Laakkonen, L., and Albert, V. A. (2007) Polyglutamine variation in a flowering time protein correlates with island age in a Hawaiian plant radiation. BMC Evol Biol 7, 105. [ http ]

Skjaerven, L., Jonassen, I., and Reuter, N. (2007) TMM@: a web application for the analysis of transmembrane helix mobility. BMC Bioinformatics 8, 232. [ http ]

Soltis, D. E., Ma, H., Frohlich, M. W., Soltis, P. S., Albert, V. A., Oppenheimer, D. G., Altman, N. S., Depamphilis, C., and Leebens-Mack, J. (2007) The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression. Trends Plant Sci 12, 358-367. [ http ]

Oyan, A. M., Bø, T. H., Jonassen, I., Gjertsen, B. T., Øystein Bruserud, and Kalland, K.-H. (2006) cDNA microarray analysis of non-selected cases of acute myeloid leukemia demonstrates distinct clustering independent of cytogenetic aberrations and consistent with morphological signs of differentiation. Int J Oncol 28, 1065-80.

Andersen, M., Lenhard, B., Whatling, C., Eriksson, P., and Odeberg, J. (2006) Alternative promoter usage of the membrane glycoprotein CD36. BMC Mol Biol 7, 8. [ http ]

Barsnes, H., Mikalsen, S.-O., and Eidhammer, I. (2006) MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences. BMC Bioinformatics 7, 42. [ http ]

Berven, F. S., Karlsen, O. A., Straume, A. H., Flikka, K., Murrell, J. C., Fjellbirkeland, A., Lillehaug, J. R., Eidhammer, I., and Jensen, H. B. (2006) Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Arch Microbiol 184, 362-377. b. [ http ]

Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., Forrest, A. R. R., Alkema, W. B., Tan, S. L., Plessy, C., Kodzius, R., Ravasi, T., Kasukawa, T., Fukuda, S., Kanamori-Katayama, M., Kitazume, Y., Kawaji, H., Kai, C., Nakamura, M., Konno, H., Nakano, K., Mottagui-Tabar, S., Arner, P., Chesi, A., Gustincich, S., Persichetti, F., Suzuki, H., Grimmond, S. M., Wells, C. A., Orlando, V., Wahlestedt, C., Liu, E. T., Harbers, M., Kawai, J., Bajic, V. B., Hume, D. A., and Hayashizaki, Y. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38, 626-635. [ http ]

Cui, L., Wall, P. K., Leebens-Mack, J. H., Lindsay, B. G., Soltis, D. E., Doyle, J. J., Soltis, P. S., Carlson, J. E., Arumuganathan, K., Barakat, A., Albert, V. A., Ma, H., and dePamphilis, C. W. (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16, 738-749. [ http ]

Dysvik, B., Vasstrand, E. N., Løvlie, R., Elgindi, O. A.-A., Kross, K. W., Aarstad, H. J., Johannessen, A. C., Jonassen, I., and Ibrahim, S. O. (2006) Gene expression profiles of head and neck carcinomas from Sudanese and Norwegian patients reveal common biological pathways regardless of race and lifestyle. Clin Cancer Res 12, 1109-1120. [ http ]

Engstrom, P. G., Suzuki, H., Ninomiya, N., Akalin, A., Sessa, L., Lavorgna, G., Brozzi, A., Luzi, L., Tan, S. L., Yang, L., Kunarso, G., Ng, E. L.-C., Batalov, S., Wahlestedt, C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Wells, C., Bajic, V. B., Orlando, V., Reid, J. F., Lenhard, B., and Lipovich, L. (2006) Complex Loci in human and mouse genomes. PLoS Genet 2, e47. [ http ]

Flikka, K., Martens, L., Vandekerckhove, J., Gevaert, K., and Eidhammer, I. (2006) Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 6, 2086-2094. [ http ]

Fredman, D., Sawyer, S. L., Strömqvist, L., Mottagui-Tabar, S., Kidd, K. K., Wahlestedt, C., Chanock, S. J., and Brookes, A. J. (2006) Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection. Hum Mutat 27, 173-186. [ http ]

Frith, M. C., Ponjavic, J., Fredman, D., Kai, C., Kawai, J., Carninci, P., Hayshizaki, Y., and Sandelin, A. (2006) Evolutionary turnover of mammalian transcription start sites. Genome Res 16, 713-722. [ http ]

Gómez-Skarmeta, J. L., Lenhard, B., and Becker, T. S. (2006) New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences. Dev Dyn 235, 870-885. [ http ]

Hajjar, E., Korkmaz, B., Gauthier, F., Brandsdal, B. O., Witko-Sarsat, V., and Reuter, N. (2006) Inspection of the binding sites of proteinase3 for the design of a highly specific substrate. J Med Chem 49, 1248-1260. [ http ]

Jonassen, I., Klose, D., and Taylor, W. R. (2006) Protein model refinement using structural fragment tessellation. Comput Biol Chem 30, 360-366. [ http ]

Laakkonen, L., Jobson, R. W., and Albert, V. A. (2006) A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power. Plant Biol (Stuttg) 8, 758-764. [ http ]

Laitinen, R., Broholm, S., Albert, V., Teeri, T., and Elomaa, P. (2006) Patterns of MADS-box gene expression mark flower-type development in Gerbera hybrida (Asteraceae). BMC Plant Biol 6, 11. [ http ]

Lindqvist, C., Scheen, A.-C., Yoo, M.-J., Grey, P., Oppenheimer, D. G., Leebens-Mack, J. H., Soltis, D. E., Soltis, P. S., and Albert, V. A. (2006) An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers. BMC Plant Biol 6, 16. [ http ]

Maeda, N., Kasukawa, T., Oyama, R., Gough, J., Frith, M., Engström, P. G., Lenhard, B., Aturaliya, R. N., Batalov, S., Beisel, K. W., Bult, C. J., Fletcher, C. F., Forrest, A. R. R., Furuno, M., Hill, D., Itoh, M., Kanamori-Katayama, M., Katayama, S., Katoh, M., Kawashima, T., Quackenbush, J., Ravasi, T., Ring, B. Z., Shibata, K., Sugiura, K., Takenaka, Y., Teasdale, R. D., Wells, C. A., Zhu, Y., Kai, C., Kawai, J., Hume, D. A., Carninci, P., and Hayashizaki, Y. (2006) Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet 2, e62. [ http ]

Malde, K. and Giegerich, R. (2006) Calculating pssm probabilities with lazy dynamic programming. J. Funct. Program. 16, 75-81.

Rastogi, S., Reuter, N., and Liberles, D. A. (2006) Evaluation of models for the evolution of protein sequences and functions under structural constraint. Biophys Chem 124, 134-144. [ http ]

Rayner, T., Rocca-Serra, P., Spellman, P., Causton, H., Farne, A., Holloway, E., Irizarry, R., Liu, J., Maier, D., Miller, M., Petersen, K., Quackenbush, J., Sherlock, G., Stoeckert, C., White, J., Whetzel, P., Wymore, F., Parkinson, H., Sarkans, U., Ball, C., and Brazma, A. (2006) A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 7, 489. b. [ http ]

Saetrom, P., Snøve, O., Nedland, M., Grünfeld, T. B., Lin, Y., Bass, M. B., and Canon, J. R. (2006) Conserved microRNA characteristics in mammals. Oligonucleotides 16, 115-144. [ http ]

Sakariassen, P. O., Prestegarden, L., Wang, J., Skaftnesmo, K.-O., Mahesparan, R., Molthoff, C., Sminia, P., Sundlisæter, E., Misra, A., Tysnes, B. B., Chekenya, M., Peters, H., Lende, G., Kalland, K. H., Oyan, A. M., Petersen, K., Jonassen, I., van der Kogel, A., Feuerstein, B. G., Terzis, A. J. A., Bjerkvig, R., and Enger, P. O. (2006) Angiogenesis-independent tumor growth mediated by stem-like cancer cells. Proc Natl Acad Sci U S A. b. [ http ]

Snove, O. and Rossi, J. (2006) Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi. Genome Biol 7, 231. [ http ]

Snove, O. and Rossi, J. J. (2006) Chemical modifications rescue off-target effects of rnai. JJ. ACS Chem. Biol. 1, 274–276.

Snove, O. and Rossi, J. J. (2006) Expressing short hairpin RNAs in vivo. Nat Methods 3, 689-695. [ http ]

Taylor, W. R., Lin, K., Klose, D., Fraternali, F., and Jonassen, I. (2006) Dynamic domain threading. Proteins. [ http ]

Teeri, T. H., Elomaa, P., Kotilainen, M., and Albert, V. A. (2006) Mining plant diversity: Gerbera as a model system for plant developmental and biosynthetic research. Bioessays 28, 756-767. [ http ]

Teeri, T. H., Kotilainen, M., Uimari, A., Ruokolainen, S., Ng, Y., Malm, U., Pollanen, E., Broholm, S., Laitinen, R., Elomaa, P., and Albert, V. A. (2006) Developmental Genetics of the Flower, Advances in Botanical Research 44., eds. Soltis, D. E., Leebens-Mack, J. H., and Soltis, P. S. (Elsevier, London.). [ http ]

Vlieghe, D., Sandelin, A., Bleser, P. J. D., Vleminckx, K., Wasserman, W. W., van Roy, F., and Lenhard, B. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res 34, D95-D97. [ http ]

Yoo, M.-J., Albert, V., Soltis, P., and Soltis, D. (2006) Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinasegenes in plants. BMC Plant Biol 6, 3. [ http ]