Publications

(2011) High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface
Kotlar,HK; Lewin,A; Johansen,J; Trone-Holst,M; Haverkamp,T; Markussen,S; Winnberg,A; Ringrose,P; Aakvik,T; Ryeng,E; Jakobsen,K; Drablos,F; Valla,S
Environmental Microbiology Reports 3(6):674-681 [http]

(2011) thermo-msf-parser: An Open Source Java Library to Parse and Visualize Thermo Proteome Discoverer msf Files.
Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L.
J Proteome Res. 2011 Aug 5;10(8):3840-3. Epub 2011 Jul 11. [http]

(2011) Removing noise from pyrosequenced amplicons.
Quince, C.; Lanzen, A.; Davenport, R. J. & Turnbaugh, P. J.
BMC Bioinformatics 12, 38.[http]

(2011) Effects of short-term starvation on ghrelin, GH-IGF system, and IGF-binding proteins in Atlantic salmon.
Hevrøy, E. M.; Azpeleta, C.; Shimizu, M.; Lanzén, A.; Kaiya, H.; Espe, M. & Olsvik, P. A.
Fish Physiol Biochem 37(1), 217--232.[http]

(2011) Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA.
Lanzén, A.; Jørgensen, S. L.; Bengtsson, M. M.; Jonassen, I.; Ovreås, L. & Urich, T.
FEMS Microbiol Ecol 77, 577-589.[http]

(2011) Characterisation of the coccolithovirus intein
Allen, M. J.; Lanzén, A. & Bratbak, G.
Marine Genomics 4, 1-7.[http]

(2011) Histone variant innovation in a rapidly evolving chordate lineage
Alexandra Moosmann, Coen Campsteijn, Pascal WTC Jansen, Carole Nasrallah, Martina Raasholm, Henk G Stunnenberg and Eric M Thompson
BMC Evolutionary Biology 2011, 11:208 [http]

(2011) Compomics-utilities: an open-source Java library for computational proteomics
Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, et al
BMC Bioinformatics. 2011 Mar 8;12(1):70. [http]

(2011) IsobariQ: software for isobaric quantitative proteomics using IPTL, iTRAQ and TMT.
Arntzen MØ, Koehler CJ, Barsnes H, Berven FS, Treumann A,  et al.
J Proteome Res 2011 Feb 4; 10(2):913-20. (DOI:  10.1021/pr1009977, PMID: 21067241) [http]

(2011) SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
Vaudel M, Barsnes H, Berven FS, Sickmann A, Martens L
Proteomics 2011, 11(5):996-9. (DOI:  10.1002/pmic.201000595, PMID: 21337703) [http]

(2011) A global analysis of peptide fragmentation variability
Barsnes H, Eidhammer I, Martens L
Proteomics. 2011 Mar;11(6):1181-8. [http]

(2010) Characteristics of 454 pyrosequencing data–enabling realistic simulation with flowsim. Balzer, S.; Malde, K.; Lanzén, A.; Sharma, A. & Jonassen, I. Bioinformatics 26(18), i420--i425.[http]

(2010) Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context.
Bartossek, R.; Nicol, G. W.; Lanzen, A.; Klenk, H.-P. & Schleper, C.
Environ Microbiol 12(4), 1075--1088.[http]

(2010) The Genomic HyperBrowser: inferential genomics at the sequence level.
Geir K Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid Glad, Lars Holden, Marit Holden, Knut Liestol, Trevor Clancy, Egil Ferkingstad, Morten Johansen, Vegard Nygaard, Eivind Tostesen, Arnoldo Frigessi and Eivind Hovig.
Genome Biology 2010, 11:R121. 2010 Dec 23. [http]

(2010) Identification of nuclear phosphatidylinositol 4,5-bisphosphate-interacting proteins by neomycin extraction.
Lewis AE, Sommer L, Arntzen MO, Strahm Y, Morrice NA, Divecha N, D'Santos CS.
Mol Cell Proteomics. 2010 Nov 3. [http]

(2010) Gene duplications in prokaryotes can be associated with environmental adaptation
Bratlie MS, Johansen J, Sherman BT, Huang DW, Lempicki RA, Drablos F.
BMC genomics 11(1):588 view article

(2010) A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
Rye M.B.; Saetrom P.; Drablos F.
Nucleic acids research (): view article tool

(2010) Genetic and molecular functional characterization of variants within TNFSF13B, a positional candidate preeclampsia susceptibility gene on 13q

Fenstad, M.H.; Johnson, M.P.; Roten, L.T.; Aas, P.A.; Forsmo, S.; Klepper, K.; East, C.E.; Abraham, L.J.; Blangero, J.; Brennecke, S.P.; Austgulen, R.; Moses, E.K.
PloS one 5(9): view article

(2010) PriorsEditor: a tool for the creation and use of positional priors in motif discovery
Klepper, K.; Drablos, F.
Bioinformatics (Oxford, England) 26(17):2195-2197 view article tool

Ma BG, Berezovsky IN. (2010) The MBLOSUM: a server for deriving mutation targets and position-specific substitution rates. Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 28, Issue Number 3, (2010) [ http ]

Aamodt, R. M. (2009) Age-and caste-dependent decrease in expression of genes maintaining dna and rna quality and mitochondrial integrity in the honeybee wing muscle. Exp Gerontol 44, 586-593. [ http ]

van Beijnum, J. R., Petersen, K., and Griffioen, A. W. (2009) Tumor endothelium is characterized by a matrix remodeling signature. Front Biosci (Schol Ed) 1, 216-225.

Johannessen, T.-C. A., Wang, J., Skaftnesmo, K.-O., Sakariassen, P. Ø., Enger, P. Ø., Petersen, K., Øyan, A. M., Kalland, K.-H., Bjerkvig, R., and Tysnes, B. B. (2009) Highly infiltrative brain tumours show reduced chemosensitivity associated with a stem cell-like phenotype. Neuropathol Appl Neurobiol 35, 380-393. [ http ]

Ke, X.-S., Qu, Y., Rostad, K., Li, W.-C., Lin, B., Halvorsen, O. J., Haukaas, S. A., Jonassen, I., Petersen, K., Goldfinger, N., Rotter, V., Akslen, L. A., Oyan, A. M., and Kalland, K.-H. (2009) Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis. PLoS One 4, e4687. [ http ]

Leversen, N. A., de Souza, G. A., Målen, H., Prasad, S., Jonassen, I., and Wiker, H. G. (2009) Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods. Microbiology 155, 2375-2383. [ http ]

Lie, K. K., Lanzen, A., Breilid, H., and Olsvik, P. A. (2009) Gene expression profiling in atlantic cod (gadus morhua l.) from two contaminated sites using a custom-made cdna microarray. Environ Toxicol Chem 28, 1711-1721. [ http ]

Pendino, F., Nguyen, E., Jonassen, I., Dysvik, B., Azouz, A., Lanotte, M., Ségal-Bendirdjian, E., and Lillehaug, J. R. (2009) Functional involvement of rinf, retinoid-inducible nuclear factor (cxxc5), in normal and tumoral human myelopoiesis. Blood 113, 3172-3181. [ http ]

Rajcevic, U., Petersen, K., Knol, J. C., Loos, M., Bougnaud, S., Klychnikov, O., Li, K. W., Pham, T. V., Wang, J., Miletic, H., Peng, Z., Bjerkvig, R., Jimenez, C. R., and Niclou, S. P. (2009) itraq-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype. Mol Cell Proteomics 8, 2595-2612. [ http ]

Trösse, C., Waagbø, R., Breck, O., Stavrum, A.-K., Petersen, K., and Olsvik, P. A. (2009) Genome-wide transcription analysis of histidine-related cataract in atlantic salmon (salmo salar l). Mol Vis 15, 1332-1350.

Øyan, A. M., Anensen, N., Bø, T. H., Stordrange, L., Jonassen, I., Øystein Bruserud, Kalland, K.-H., and Gjertsen, B. T. (2009) Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia. BMC Cancer 9, 77. [ http ]

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 ]

Olsvik, P. A., Lie, K. K., Mykkeltvedt, E., Samuelsen, O. B., Petersen, K., Stavrum, A.-K., and Lunestad, B. T. (2008) Pharmacokinetics and transcriptional effects of the anti-salmon lice drug emamectin benzoate in atlantic salmon (salmo salar l.). BMC Pharmacol 8, 16. [ 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 ]

Petersen, K., Oyan, A. M., Rostad, K., Olsen, S., Bø, T. H., Salvesen, H. B., Gjertsen, B. T., Bruserud, O., Halvorsen, O. J., Akslen, L. A., Steen, V. M., Jonassen, I., and Kalland, K.-H. (2007) Comparison of nucleic acid targets prepared from total rna or poly(a) rna for dna oligonucleotide microarray hybridization. Anal Biochem 366, 46-58. [ 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 ]

Stansberg, C., Vik-Mo, A. O., Holdhus, R., Breilid, H., Srebro, B., Petersen, K., Jørgensen, H. A., Jonassen, I., and Steen, V. M. (2007) Gene expression profiles in rat brain disclose cns signature genes and regional patterns of functional specialisation. BMC Genomics 8, 94. [ http ]

Stuhr, L. E. B., Raa, A., Oyan, A. M., Kalland, K. H., Sakariassen, P. O., Petersen, K., Bjerkvig, R., and Reed, R. K. (2007) Hyperoxia retards growth and induces apoptosis, changes in vascular density and gene expression in transplanted gliomas in nude rats. J Neurooncol 85, 191-202. [ 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 ]