Publications 2017
Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T (2017)
Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination
Adv Exp Med Biol, 944, 53-62
PubMed 27826891
Expression of Nestin associates with BRCA1 mutations, a basal-like phenotype and aggressive breast cancer
Sci Rep, 7 (1), 1089
PubMed 28439082
Haugarvoll K, Johansson S, Rodriguez CE, Boman H, Haukanes BI, Bruland O, Roque F, Jonassen I, Blomqvist M, Telstad W, Månsson JE, Knappskog PM, Bindoff LA (2017)
GBA2 Mutations Cause a Marinesco-Sjögren-Like Syndrome: Genetic and Biochemical Studies
PLoS One, 12 (1), e0169309
PubMed 28052128
Leiss L, Mutlu E, Øyan A, Yan T, Tsinkalovsky O, Sleire L, Petersen K, Rahman MA, Johannessen M, Mitra SS, Jacobsen HK, Talasila KM, Miletic H, Jonassen I, Li X, Brons NH, Kalland KH, Wang J, Enger PØ (2017)
Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts
BMC Cancer, 17 (1), 108
PubMed 28173797
Malde K, Seliussen BB, Quintela M, Dahle G, Besnier F, Skaug HJ, Øien N, Solvang HK, Haug T, Skern-Mauritzen R, Kanda N, Pastene LA, Jonassen I, Glover KA (2017)
Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species
BMC Genomics, 18 (1), 76
PubMed 28086785
Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families
Am J Hum Genet, 100 (5), 737-750
PubMed 28457472
Oczko-Wojciechowska M, Swierniak M, Krajewska J, Kowalska M, Kowal M, Stokowy T, Wojtas B, Rusinek D, Pawlaczek A, Czarniecka A, Szpak-Ulczok S, Gawlik T, Chmielik E, Tyszkiewicz T, Nikiel B, Lange D, Jarzab M, Wiench M, Jarzab B (2017)
Differences in the transcriptome of medullary thyroid cancer regarding the status and type of RET gene mutations
Sci Rep, 7, 42074
PubMed 28181547
In vitro characterization of six STUB1 variants in spinocerebellar ataxia 16 reveals altered structural properties for the encoded CHIP proteins
Biosci Rep, 37 (2)
PubMed 28396517
Tzoulis C, Sztromwasser P, Johansson S, Gjerde IO, Knappskog P, Bindoff LA (2017)
PNKP Mutations Identified by Whole-Exome Sequencing in a Norwegian Patient with Sporadic Ataxia and Edema
Cerebellum, 16 (1), 272-275
PubMed 27165045
Publications 2016
Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T (2016)
Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination
Adv Exp Med Biol (in press)
PubMed 27405447
Bukowska-Ośko I, Perlejewski K, Nakamura S, Motooka D, Stokowy T, Kosińska J, Popiel M, Płoski R, Horban A, Lipowski D, Caraballo Cortés K, Pawełczyk A, Demkow U, Stępień A, Radkowski M, Laskus T (2016)
Sensitivity of Next-Generation Sequencing Metagenomic Analysis for Detection of RNA and DNA Viruses in Cerebrospinal Fluid: The Confounding Effect of Background Contamination
Adv Exp Med Biol (in press)
PubMed 27645539
Steine IM, Zayats T, Stansberg C, Pallesen S, Mrdalj J, Håvik B, Soulé J, Haavik J, Milde AM, Skrede S, Murison R, Krystal J, Grønli J. (2016)
Implication of NOTCH1 gene in susceptibility to anxiety and depression among sexual abuse victims.
Transl Psychiatry, 13; 6 (12):e977
PubMed 27959334
Flønes I, Sztromwasser P, Haugarvoll K, Dölle C, Lykouri M, Schwarzlmüller T, Jonassen I, Miletic H, Johansson S, Knappskog PM, Bindoff LA, Tzoulis C (2016)
Novel SLC19A3 Promoter Deletion and Allelic Silencing in Biotin-Thiamine-Responsive Basal Ganglia Encephalopathy
PLoS One, 11 (2), e0149055
PubMed 26863430
Ghorbani S, Fossbakk A, Jorge-Finnigan A, Flydal MI, Haavik J, Kleppe R (2016)
Regulation of tyrosine hydroxylase is preserved across different homo- and heterodimeric 14-3-3 proteins
Amino Acids, 48 (5), 1221-9
PubMed 26825549
Gjuvsland AB, Zörgö E, Samy JK, Stenberg S, Demirsoy IH, Roque F, Maciaszczyk-Dziubinska E, Migocka M, Alonso-Perez E, Zackrisson M, Wysocki R, Tamás MJ, Jonassen I, Omholt SW, Warringer J(2016)
Disentangling genetic and epigenetic determinants of ultrafast adaptation
Mol Syst Biol, 12 (12), 892
PubMed 27979908
Johansson BB, Irgens HU, Molnes J, Sztromwasser P, Aukrust I, Juliusson PB, Søvik O, Levy S, Skrivarhaug T, Joner G, Molven A, Johansson S, Njølstad PR (2016)
Targeted next-generation sequencing reveals MODY in up to 6.5% of antibody-negative diabetes cases listed in the Norwegian Childhood Diabetes Registry
Diabetologia (in press)
PubMed 27913849
Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C (2016)
High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities
Mol Ecol, 25 (17), 4392-406
PubMed 27454455
Lien S, Koop BF, Sandve SR, Miller JR, Kent MP, Nome T, Hvidsten TR, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, von Schalburg K, Rondeau EB, Di Genova A, Samy JK, Olav Vik J, Vigeland MD, Caler L, Grimholt U, Jentoft S, Våge DI et al. (2016)
The Atlantic salmon genome provides insights into rediploidization
Nature, 533 (7602), 200-5
PubMed 27088604
Menager H, Kalas M, Rapacki K, Ison J (2016)
Using registries to integrate bioinformatics tools and services into workbench environments
Int. J. Softw. Tools Technol. Transf., 18 (6), 581-586
Neveling K, Mensenkamp AR, Derks R, Kwint M, Ouchene H, Steehouwer M, van Lier B, Bosgoed E, Rikken A, Tychon M, Zafeiropoulou D, Castelein S, Hehir-Kwa J, Tjwan Thung D, Hofste T, Lelieveld SH, Bertens SM, Adan IB, Eijkelenboom A, Tops BB, Yntema H, Stokowy T, Knappskog PM, Høberg-Vetti H, Steen VM et al. (2016)
BRCA Testing by Single-Molecule Molecular Inversion Probes
Clin Chem, 63 (2), 503-512
PubMed 27974384
Ou Y, Xia R, Kong F, Zhang X, Yu S, Jiang L, Zheng L, Lin L (2016)
Overexpression of DEK is an indicator of poor prognosis in patients with gastric adenocarcinoma
Oncol Lett, 11 (3), 1823-1828
PubMed 26998084
Perlejewski K, Bukowska-Ośko I, Nakamura S, Motooka D, Stokowy T, Płoski R, Rydzanicz M, Zakrzewska-Pniewska B, Podlecka-Piętowska A, Nojszewska M, Gogol A, Caraballo Cortés K, Demkow U, Stępień A, Laskus T, Radkowski M (2016)
Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis
Adv Exp Med Biol, 935, 89-98
PubMed 27311319
Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM (2016)
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data
Bioinformatics, 32 (19), 3018-20
PubMed 27288501
Stokowy T, Gawel D, Wojtas B (2016)
Differences in miRNA and mRNA Profile of Papillary Thyroid Cancer Variants
Int J Endocrinol, 2016, 1427042
PubMed 27656207
Stokowy T, Wojtas B, Jarzab B, Krohn K, Fredman D, Dralle H, Musholt T, Hauptmann S, Lange D, Hegedüs L, Paschke R, Eszlinger M (2016)
Two-miRNA classifiers differentiate mutation-negative follicular thyroid carcinomas and follicular thyroid adenomas in fine needle aspirations with high specificity
Endocrine, 54 (2), 440-447
PubMed 27473101
Swierniak M, Pfeifer A, Stokowy T, Rusinek D, Chekan M, Lange D, Krajewska J, Oczko-Wojciechowska M, Czarniecka A, Jarzab M, Jarzab B, Wojtas B (2016)
Somatic mutation profiling of follicular thyroid cancer by next generation sequencing
Mol Cell Endocrinol, 433, 130-7
PubMed 27283500
Waløen K, Kleppe R, Martinez A, Haavik J (2016)
Tyrosine and tryptophan hydroxylases as therapeutic targets in human disease
Expert Opin Ther Targets, 21 (2), 167-180
PubMed 27973928
Zhang X, Peng Q, Li L, Li X (2016)
Recognition of alternatively spliced cassette exons based on a hybrid model
Biochem Biophys Res Commun, 471 (3), 368-72
PubMed 26869516
Publications 2015
Blomberg N, Oliveira A, Mons B, Persson B, Jonassen I (2015)
The ELIXIR channel in F1000Research
F1000Res, 4
PubMed 26913192
Bredholt G, Mannelqvist M, Stefansson IM, Birkeland E, Bø TH, Øyan AM, Trovik J, Kalland KH, Jonassen I, Salvesen HB, Wik E, Akslen LA (2015)
Tumor necrosis is an important hallmark of aggressive endometrial cancer and associates with hypoxia, angiogenesis and inflammation responses
Oncotarget, 6 (37), 39676-91
PubMed 26485755
Bredrup C, Johansson S, Bindoff LA, Sztromwasser P, Kråkenes J, Mellgren AE, Brurås KR, Lind O, Boman H, Knappskog PM, Rødahl E (2015)
High myopia-excavated optic disc anomaly associated with a frameshift mutation in the MYC-binding protein 2 gene (MYCBP2)
Am J Ophthalmol, 159 (5), 973-9.e2
PubMed 25634536
Brunetti D, Torsvik J, Dallabona C, Teixeira P, Sztromwasser P, Fernandez-Vizarra E, Cerutti R, Reyes A, Preziuso C, D’Amati G, Baruffini E, Goffrini P, Viscomi C, Ferrero I, Boman H, Telstad W, Johansson S, Glaser E, Knappskog PM, Zeviani M, Bindoff LA (2015)
Defective PITRM1 mitochondrial peptidase is associated with Aβ amyloidotic neurodegeneration
EMBO Mol Med, 8 (3), 176-90
PubMed 26697887
Dimitrakopoulou K, Vrahatis AG, Bezerianos A (2015)
Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism
BMC Genomics, 16, 147
PubMed 25887273
Farag Y, Berven FS, Jonassen I, Petersen K, Barsnes H (2015)
Distributed and interactive visual analysis of omics data
J Proteomics, 129, 78-82
PubMed 26047716
Fjeld K, Weiss FU, Lasher D, Rosendahl J, Chen JM, Johansson BB, Kirsten H, Ruffert C, Masson E, Steine SJ, Bugert P, Cnop M, Grützmann R, Mayerle J, Mössner J, Ringdal M, Schulz HU, Sendler M, Simon P, Sztromwasser P, Torsvik J, Scholz M, Tjora E, Férec C, Witt H et al. (2015)
A recombined allele of the lipase gene CEL and its pseudogene CELP confers susceptibility to chronic pancreatitis
Nat Genet, 47 (5), 518-22
PubMed 25774637
Ghavidel FZ, Claesen J, Burzykowski T (2015)
A nonhomogeneous hidden markov model for gene mapping based on next-generation sequencing data
J Comput Biol, 22 (2), 178-88
PubMed 25611462
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T et al. (2015)
Tools and data services registry: a community effort to document bioinformatics resources
Nucleic Acids Res, 44 (D1), D38-47
PubMed 26538599
Jacobsen KK, Kleppe R, Johansson S, Zayats T, Haavik J (2015)
Epistatic and gene wide effects in YWHA and aromatic amino hydroxylase genes across ADHD and other common neuropsychiatric disorders: Association with YWHAE
Am J Med Genet B Neuropsychiatr Genet, 168 (6), 423-432
PubMed 26172220
Janus P, Stokowy T, Jaksik R, Szoltysek K, Handschuh L, Podkowinski J, Widlak W, Kimmel M, Widlak P (2015)
Cross talk between cytokine and hyperthermia-induced pathways: identification of different subsets of NF-κB-dependent genes regulated by TNFα and heat shock
Mol Genet Genomics, 290 (5), 1979-90
PubMed 25944781
Kleppe R, Herfindal L, Døskeland SO (2015)
Cell Death Inducing Microbial Protein Phosphatase Inhibitors–Mechanisms of Action
Mar Drugs, 13 (10), 6505-20
PubMed 26506362
Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC (2015)
SDA 7: A modular and parallel implementation of the simulation of diffusional association software
J Comput Chem, 36 (21), 1631-45
PubMed 26123630
Perlejewski K, Popiel M, Laskus T, Nakamura S, Motooka D, Stokowy T, Lipowski D, Pollak A, Lechowicz U, Caraballo Cortés K, Stępień A, Radkowski M, Bukowska-Ośko I (2015)
Next-generation sequencing (NGS) in the identification of encephalitis-causing viruses: Unexpected detection of human herpesvirus 1 while searching for RNA pathogens
J Virol Methods, 226, 1-6
PubMed 26424618
Tröße C, Kongshaug H, Dondrup M, Nilsen F (2015)
Characterisation of iron regulatory protein 1A and 1B in the blood-feeding copepod Lepeophtheirus salmonis
Exp Parasitol, 157, 1-11
PubMed 26115940
Tønne E, Holdhus R, Stansberg C, Stray-Pedersen A, Petersen K, Brunner HG, Gilissen C, Hoischen A, Prescott T, Steen VM, Fiskerstrand T (2015)
Syndromic X-linked intellectual disability segregating with a missense variant in RLIM
Eur J Hum Genet, 23 (12), 1652-6
PubMed 25735484
Vrahatis AG, Dimitrakopoulou K, Balomenos P, Tsakalidis AK, Bezerianos A (2015)
CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis
Bioinformatics, 32 (6), 884-92
PubMed 26568631
Winge I, Teigen K, Fossbakk A, Mahootchi E, Kleppe R, Sköldberg F, Kämpe O, Haavik J (2015)
Mammalian CSAD and GADL1 have distinct biochemical properties and patterns of brain expression
Neurochem Int, 90, 173-84
PubMed 26327310
Publications 2014
Dimitrakopoulos GN, Dimitrakopoulou K, Maraziotis IA, Sgarbas K, Bezerianos A (2014)
Supervised method for construction of microRNA-mRNA networks: application in cardiac tissue aging dataset
Conf Proc IEEE Eng Med Biol Soc, 2014, 318-21
PubMed 25569961
Dimitrakopoulou K, Dimitrakopoulos GN, Wilk E, Tsimpouris C, Sgarbas KN, Schughart K, Bezerianos A (2014)
Influenza A immunomics and public health omics: the dynamic pathway interplay in host response to H1N1 infection
OMICS, 18 (3), 167-83
PubMed 24512282
Dudek M, Romanowska J, Wituła T, Trylska J (2014)
Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies
Biochimie, 102, 188-202
PubMed 24769038
Fossbakk A, Kleppe R, Knappskog PM, Martinez A, Haavik J (2014)
Functional studies of tyrosine hydroxylase missense variants reveal distinct patterns of molecular defects in Dopa-responsive dystonia
Hum Mutat, 35 (7), 880-90
PubMed 24753243
Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C (2014)
Characterization of the 18S rRNA gene for designing universal eukaryote specific primers
PLoS One, 9 (2), e87624
PubMed 24516555
Herfindal L, Krakstad C, Myhren L, Hagland H, Kopperud R, Teigen K, Schwede F, Kleppe R, Døskeland SO (2014)
Introduction of aromatic ring-containing substituents in cyclic nucleotides is associated with inhibition of toxin uptake by the hepatocyte transporters OATP 1B1 and 1B3
PLoS One, 9 (4), e94926
PubMed 24740327
Kaján L, Hopf TA, Kalaš M, Marks DS, Rost B (2014)
FreeContact: fast and free software for protein contact prediction from residue co-evolution
BMC Bioinformatics, 15, 85
PubMed 24669753
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP et al. (2014)
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
J Biomed Semantics, 5 (1), 5
PubMed 24495517
Kleppe R, Rosati S, Jorge-Finnigan A, Alvira S, Ghorbani S, Haavik J, Valpuesta JM, Heck AJ, Martinez A (2014)
Phosphorylation dependence and stoichiometry of the complex formed by tyrosine hydroxylase and 14-3-3γ
Mol Cell Proteomics, 13 (8), 2017-30
PubMed 24947669
Korfanty J, Stokowy T, Widlak P, Gogler-Piglowska A, Handschuh L, Podkowiński J, Vydra N, Naumowicz A, Toma-Jonik A, Widlak W (2014)
Crosstalk between HSF1 and HSF2 during the heat shock response in mouse testes
Int J Biochem Cell Biol, 57, 76-83
PubMed 25450459
Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ et al. (2014)
Community-driven development for computational biology at Sprints, Hackathons and Codefests
BMC Bioinformatics, 15 Suppl 14, S7
PubMed 25472764
Nygaard G, Herfindal L, Kopperud R, Aragay AM, Holmsen H, Døskeland SO, Kleppe R, Selheim F (2014)
Time-dependent inhibitory effects of cGMP-analogues on thrombin-induced platelet-derived microparticles formation, platelet aggregation, and P-selectin expression
Biochem Biophys Res Commun, 449 (3), 357-63
PubMed 24845383
Stokowy T, Eszlinger M, Świerniak M, Fujarewicz K, Jarząb B, Paschke R, Krohn K (2014)
Analysis options for high-throughput sequencing in miRNA expression profiling
BMC Res Notes, 7, 144
PubMed 24625073
Stokowy T, Wojtaś B, Krajewska J, Stobiecka E, Dralle H, Musholt T, Hauptmann S, Lange D, Hegedüs L, Jarząb B, Krohn K, Paschke R, Eszlinger M (2014)
A two miRNA classifier differentiates follicular thyroid carcinomas from follicular thyroid adenomas
Mol Cell Endocrinol, 399, 43-9
PubMed 25258301
Wojtas B, Ferraz C, Stokowy T, Hauptmann S, Lange D, Dralle H, Musholt T, Jarzab B, Paschke R, Eszlinger M (2014)
Differential miRNA expression defines migration and reduced apoptosis in follicular thyroid carcinomas
Mol Cell Endocrinol, 388 (1-2), 1-9
PubMed 24631480
Publications 2013
Balzer S, Malde K, Grohme MA, Jonassen I (2013)
Filtering duplicate reads from 454 pyrosequencing data
Bioinformatics, 29 (7), 830-6
PubMed 23376350
Dimitrakopoulou K, Dimitrakopoulos GN, Sgarbas KN, Bezerianos A (2013)
Tamoxifen integromics and personalized medicine: dynamic modular transformations underpinning response to tamoxifen in breast cancer treatment
OMICS, 18 (1), 15-33
PubMed 24299457
Dimitrakopoulou K, Vrahatis AG, Wilk E, Tsakalidis AK, Bezerianos A (2013)
OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection
Comput Methods Programs Biomed, 111 (3), 650-61
PubMed 23796450
Ersland KM, Håvik B, Rinholm JE, Gundersen V, Stansberg C, Steen VM (2013)
LOC689986, a unique gene showing specific expression in restricted areas of the rodent neocortex
BMC Neurosci, 14, 68
PubMed 23844656
Ghavidel FZ, Mertens I, Baggerman G, Laukens K, Burzykowski T, Valkenborg D (2013)
The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results
J Proteomics, 98, 150-8
PubMed 24384257
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P (2013)
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
Bioinformatics, 29 (10), 1325-32
PubMed 23479348
Kleppe R, Ghorbani S, Martinez A, Haavik J (2013)
Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins
FEBS Lett, 588 (1), 92-8
PubMed 24269229
Lanzén A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, Øvreås L (2013)
Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes
PLoS One, 8 (8), e72577
PubMed 24023625
Malcher A, Rozwadowska N, Stokowy T, Jedrzejczak P, Zietkowiak W, Kurpisz M (2013)
The gene expression analysis of paracrine/autocrine factors in patients with spermatogenetic failure compared with normal spermatogenesis
Am J Reprod Immunol, 70 (6), 522-8
PubMed 23869807
Malcher A, Rozwadowska N, Stokowy T, Kolanowski T, Jedrzejczak P, Zietkowiak W, Kurpisz M (2013)
Potential biomarkers of nonobstructive azoospermia identified in microarray gene expression analysis
Fertil Steril, 100 (6), 1686-94.e1-7
PubMed 24012201
Petersen K, Rajcevic U, Abdul Rahim SA, Jonassen I, Kalland KH, Jimenez CR, Bjerkvig R, Niclou SP (2013)
Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model
PLoS One, 8 (7), e68288
PubMed 23874576
Pfeifer A, Wojtas B, Oczko-Wojciechowska M, Kukulska A, Czarniecka A, Eszlinger M, Musholt T, Stokowy T, Swierniak M, Stobiecka E, Rusinek D, Tyszkiewicz T, Kowal M, Jarzab M, Hauptmann S, Lange D, Paschke R, Jarzab B (2013)
Molecular differential diagnosis of follicular thyroid carcinoma and adenoma based on gene expression profiling by using formalin-fixed paraffin-embedded tissues
BMC Med Genomics, 6, 38
PubMed 24099521
Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E (2013)
The Genomic HyperBrowser: an analysis web server for genome-scale data
Nucleic Acids Res, 41 (Web Server issue), W133-41
PubMed 23632163
Wojtaś B, Pfeifer A, Jarząb M, Czarniecka A, Krajewska J, Swierniak M, Stokowy T, Rusinek D, Kowal M, Zebracka-Gala J, Tyszkiewicz T, Oczko-Wojciechowska M, Stobiecka E, Lange D, Paschke R, Jarząb B (2013)
Unsupervised analysis of follicular thyroid tumours transcriptome by oligonucleotide microarray gene expression profiling
Endokrynol Pol, 64 (5), 328-34
PubMed 24186587
Xiao Y, Jin J, Chang M, Chang JH, Hu H, Zhou X, Brittain GC, Stansberg C, Torkildsen Ø, Wang X, Brink R, Cheng X, Sun SC (2013)
Peli1 promotes microglia-mediated CNS inflammation by regulating Traf3 degradation
Nat Med, 19 (5), 595-602
PubMed 23603814
Publications 2012
Christoforou A, Dondrup M, Mattingsdal M, Mattheisen M, Giddaluru S, Nöthen MM, Rietschel M, Cichon S, Djurovic S, Andreassen OA, Jonassen I, Steen VM, Puntervoll P, Le Hellard S (2012)
Linkage-disequilibrium-based binning affects the interpretation of GWASs
Am J Hum Genet, 90 (4), 727-33
PubMed 22444669
Dimitrakopoulos G, Sgarbas K, Dimitrakopoulou K, Dragomir A, Bezerianos A, Maraziotis IA (2012)
Multi-scale modeling of gene regulatory networks via integration of temporal and topological biological data
Conf Proc IEEE Eng Med Biol Soc, 2012, 1242-5
PubMed 23366123
Dimitrakopoulou K, Dimitrakopoulos G, Zacharaki EI, Maraziotis IA, Sgarbas K, Bezerianos A (2012)
Revealing the dynamic modularity of composite biological networks in breast cancer treatment
Conf Proc IEEE Eng Med Biol Soc, 2012, 5432-6
PubMed 23367158
Ersland KM, Christoforou A, Stansberg C, Espeseth T, Mattheisen M, Mattingsdal M, Hardarson GA, Hansen T, Fernandes CP, Giddaluru S, Breuer R, Strohmaier J, Djurovic S, Nöthen MM, Rietschel M, Lundervold AJ, Werge T, Cichon S, Andreassen OA, Reinvang I, Steen VM, Le Hellard S (2012)
Gene-based analysis of regionally enriched cortical genes in GWAS data sets of cognitive traits and psychiatric disorders
PLoS One, 7 (2), e31687
PubMed 22384057
Johansson S, Irgens H, Chudasama KK, Molnes J, Aerts J, Roque FS, Jonassen I, Levy S, Lima K, Knappskog PM, Bell GI, Molven A, Njølstad PR (2012)
Exome sequencing and genetic testing for MODY
PLoS One, 7 (5), e38050
PubMed 22662265
Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, Kalaš M, Lambrix P, Taussig MJ, Litton JE, Landegren U, Bongcam-Rudloff E (2012)
Workshop on laboratory protocol standards for the Molecular Methods Database
N Biotechnol, 30 (2), 109-13
PubMed 22687389
Lanzén A, Jørgensen SL, Huson DH, Gorfer M, Grindhaug SH, Jonassen I, Øvreås L, Urich T (2012)
CREST–classification resources for environmental sequence tags
PLoS One, 7 (11), e49334
PubMed 23145153
Ray J, Dondrup M, Modha S, Steen IH, Sandaa RA, Clokie M (2012)
Finding a needle in the virus metagenome haystack–micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire
PLoS One, 7 (4), e34238
PubMed 22509283
Romanowska J, Nowiński KS, Trylska J (2012)
Determining Geometrically Stable Domains in Molecular Conformation Sets
J Chem Theory Comput, 8 (8), 2588-99
PubMed 26592104
Sridhar S, Sharma A, Kongshaug H, Nilsen F, Jonassen I (2012)
Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity
BMC Genomics, 13, 598
PubMed 23131096
Stavrum R, Valvatne H, Stavrum AK, Riley LW, Ulvestad E, Jonassen I, Doherty TM, Grewal HM (2012)
Mycobacterium tuberculosis Mce1 protein complex initiates rapid induction of transcription of genes involved in substrate trafficking
Genes Immun, 13 (6), 496-502
PubMed 22695749
Publications 2011
Balzer S, Malde K, Jonassen I (2011)
Systematic exploration of error sources in pyrosequencing flowgram data
Bioinformatics, 27 (13), i304-9
PubMed 21685085
Dimitrakopoulou K, Tsimpouris C, Papadopoulos G, Pommerenke C, Wilk E, Sgarbas KN, Schughart K, Bezerianos A (2011)
Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection
J Clin Bioinforma, 1, 27
PubMed 22017961
Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK (2011)
Identifying elemental genomic track types and representing them uniformly
BMC Bioinformatics, 12, 494
PubMed 22208806
Herfindal L, Myhren L, Kleppe R, Krakstad C, Selheim F, Jokela J, Sivonen K, Døskeland SO (2011)
Nostocyclopeptide-M1: a potent, nontoxic inhibitor of the hepatocyte drug transporters OATP1B3 and OATP1B1
Mol Pharm, 8 (2), 360-7
PubMed 21214185
Hollup SM, Sadowski MI, Jonassen I, Taylor WR (2011)
Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold
Comput Biol Chem, 35 (3), 174-88
PubMed 21704264
Kleppe R, Krakstad C, Selheim F, Kopperud R, Døskeland SO (2011)
The cAMP-dependent protein kinase pathway as therapeutic target: possibilities and pitfalls
Curr Top Med Chem, 11 (11), 1393-405
PubMed 21513494
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011)
The 14-3-3 proteins in regulation of cellular metabolism
Semin Cell Dev Biol, 22 (7), 713-9
PubMed 21888985
Lanzén A, Jørgensen SL, Bengtsson MM, Jonassen I, Øvreås L, Urich T (2011)
Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA
FEMS Microbiol Ecol, 77 (3), 577-89
PubMed 21627670
Mannelqvist M, Stefansson IM, Bredholt G, Hellem Bø T, Oyan AM, Jonassen I, Kalland KH, Salvesen HB, Akslen LA (2011)
Gene expression patterns related to vascular invasion and aggressive features in endometrial cancer
Am J Pathol, 178 (2), 861-71
PubMed 21281818
Romanowska J, McCammon JA, Trylska J (2011)
Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site
PLoS Comput Biol, 7 (7), e1002099
PubMed 21814503
Skavland J, Jørgensen KM, Hadziavdic K, Hovland R, Jonassen I, Bruserud O, Gjertsen BT (2011)
Specific cellular signal-transduction responses to in vivo combination therapy with ATRA, valproic acid and theophylline in acute myeloid leukemia
Blood Cancer J, 1 (2), e4
PubMed 22829110
Stansberg C, Ersland KM, van der Valk P, Steen VM (2011)
Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex
BMC Neurosci, 12, 15
PubMed 21269499
Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO et al. (2011)
The genome sequence of Atlantic cod reveals a unique immune system
Nature, 477 (7363), 207-10
PubMed 21832995
Stavrum R, Stavrum AK, Valvatne H, Riley LW, Ulvestad E, Jonassen I, Assmus J, Doherty TM, Grewal HM (2011)
Modulation of transcriptional and inflammatory responses in murine macrophages by the Mycobacterium tuberculosis mammalian cell entry (Mce) 1 complex
PLoS One, 6 (10), e26295
PubMed 22039457
Sztromwasser P, Puntervoll P, Petersen K (2011)
Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows
J Integr Bioinform, 8 (2), 163
PubMed 21788681
Publications 2010
Balzer S, Malde K, Lanzén A, Sharma A, Jonassen I (2010)
Characteristics of 454 pyrosequencing data–enabling realistic simulation with flowsim
Bioinformatics, 26 (18), i420-5
PubMed 20823302
Dankel SN, Fadnes DJ, Stavrum AK, Stansberg C, Holdhus R, Hoang T, Veum VL, Christensen BJ, Våge V, Sagen JV, Steen VM, Mellgren G (2010)
Switch from stress response to homeobox transcription factors in adipose tissue after profound fat loss
PLoS One, 5 (6), e11033
PubMed 20543949
Davidson WS, Koop BF, Jones SJ, Iturra P, Vidal R, Maass A, Jonassen I, Lien S, Omholt SW (2010)
Sequencing the genome of the Atlantic salmon (Salmo salar)
Genome Biol, 11 (9), 403
PubMed 20887641
Jensen BO, Kleppe R, Kopperud R, Nygaard G, Døskeland SO, Holmsen H, Selheim F (2010)
Dipyridamole synergizes with nitric oxide to prolong inhibition of thrombin-induced platelet shape change
Platelets, 22 (1), 8-19
PubMed 20958117
Kalas M, Puntervoll P, Joseph A, Bartaseviciūte E, Töpfer A, Venkataraman P, Pettifer S, Bryne JC, Ison J, Blanchet C, Rapacki K, Jonassen I (2010)
BioXSD: the common data-exchange format for everyday bioinformatics web services
Bioinformatics, 26 (18), i540-6
PubMed 20823319
Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, INB-Partners, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G et al. (2010)
The EMBRACE web service collection
Nucleic Acids Res, 38 (Web Server issue), W683-8
PubMed 20462862
Romanowska J, Larsson G, Eriksson M, Wikström BM, Westerlund H, Theorell T (2010)
Health effects on leaders and co-workers of an art-based leadership development program
Psychother Psychosom, 80 (2), 78-87
PubMed 21196805
Sørensen AR, Stidsen CE, Ribel U, Nishimura E, Sturis J, Jonassen I, Bouman SD, Kurtzhals P, Brand CL (2010)
Insulin detemir is a fully efficacious, low affinity agonist at the insulin receptor
Diabetes Obes Metab, 12 (8), 665-73
PubMed 20590743
Publications 2009
Dittami SM, Scornet D, Petit JL, Ségurens B, Da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, Van de Peer Y, Cock JM, Boyen C, Tonon T (2009)
Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress
Genome Biol, 10 (6), R66
PubMed 19531237
Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A (2009)
EMMA 2–a MAGE-compliant system for the collaborative analysis and integration of microarray data
BMC Bioinformatics, 10, 50
PubMed 19200358
Dondrup M, Hüser AT, Mertens D, Goesmann A (2009)
An evaluation framework for statistical tests on microarray data
J Biotechnol, 140 (1-2), 18-26
PubMed 19297690
Halskau Ø, Ying M, Baumann A, Kleppe R, Rodriguez-Larrea D, Almås B, Haavik J, Martinez A (2009)
Three-way interaction between 14-3-3 proteins, the N-terminal region of tyrosine hydroxylase, and negatively charged membranes
J Biol Chem, 284 (47), 32758-69
PubMed 19801645
Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A (2009)
TRUNCATULIX–a data warehouse for the legume community
BMC Plant Biol, 9, 19
PubMed 19210766
Ke XS, Qu Y, Rostad K, Li WC, Lin B, Halvorsen OJ, Haukaas SA, Jonassen I, Petersen K, Goldfinger N, Rotter V, Akslen LA, Oyan AM, Kalland KH (2009)
Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis
PLoS One, 4 (3), e4687
PubMed 19262738
Leversen NA, de Souza GA, Målen H, Prasad S, Jonassen I, Wiker HG (2009)
Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods
Microbiology, 155 (Pt 7), 2375-83
PubMed 19389770
Lybaek H, Ørstavik KH, Prescott T, Hovland R, Breilid H, Stansberg C, Steen VM, Houge G (2009)
An 8.9 Mb 19p13 duplication associated with precocious puberty and a sporadic 3.9 Mb 2q23.3q24.1 deletion containing NR4A2 in mentally retarded members of a family with an intrachromosomal 19p-into-19q between-arm insertion
Eur J Hum Genet, 17 (7), 904-10
PubMed 19156171
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A (2009)
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
BMC Syst Biol, 3, 82
PubMed 19698148
Pendino F, Nguyen E, Jonassen I, Dysvik B, Azouz A, Lanotte M, Ségal-Bendirdjian E, Lillehaug JR (2009)
Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis
Blood, 113 (14), 3172-81
PubMed 19182210
Salvesen HB, Carter SL, Mannelqvist M, Dutt A, Getz G, Stefansson IM, Raeder MB, Sos ML, Engelsen IB, Trovik J, Wik E, Greulich H, Bø TH, Jonassen I, Thomas RK, Zander T, Garraway LA, Oyan AM, Sellers WR, Kalland KH, Meyerson M, Akslen LA, Beroukhim R (2009)
Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation
Proc Natl Acad Sci U S A, 106 (12), 4834-9
PubMed 19261849
Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I (2009)
Probing the “dark matter” of protein fold space
Structure, 17 (9), 1244-52
PubMed 19748345
Torkildsen Ø, Stansberg C, Angelskår SM, Kooi EJ, Geurts JJ, van der Valk P, Myhr KM, Steen VM, Bø L (2009)
Upregulation of immunoglobulin-related genes in cortical sections from multiple sclerosis patients
Brain Pathol, 20 (4), 720-9
PubMed 19919606
Øyan AM, Anensen N, Bø TH, Stordrange L, Jonassen I, Bruserud Ø, Kalland KH, Gjertsen BT (2009)
Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia
BMC Cancer, 9, 77
PubMed 19265549
Publications 2008
Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A (2008)
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data
J Biotechnol, 140 (1-2), 45-50
PubMed 19103235
de Souza GA, Målen H, Søfteland T, Saelensminde G, Prasad S, Jonassen I, Wiker HG (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
PubMed 18597682
Eichner C, Frost P, Dysvik B, Jonassen I, Kristiansen B, 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
PubMed 18331648
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M (2008)
The BREW workshop series: a stimulating experience in PhD education
Brief Bioinform, 9 (3), 250-3
PubMed 18216087
Hollup SM, Taylor WR, Jonassen I (2008)
Structural fragments in protein model refinement
Protein Pept Lett, 15 (9), 964-71
PubMed 18991773
Malde K, Jonassen I (2008)
Repeats and EST analysis for new organisms
BMC Genomics, 9, 23
PubMed 18205940
Maraziotis IA, Dimitrakopoulou K, Bezerianos A (2008)
An in silico method for detecting overlapping functional modules from composite biological networks
BMC Syst Biol, 2, 93
PubMed 18976494
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008)
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
Bioinformatics, 24 (23), 2726-32
PubMed 18765459
Romanowska J, Setny P, Trylska J (2008)
Molecular dynamics study of the ribosomal A-site
J Phys Chem B, 112 (47), 15227-43
PubMed 18973356
Saelensminde G, Halskau Ø, Jonassen I (2008)
Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role
Extremophiles, 13 (1), 11-20
PubMed 18825305
Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A (2008)
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
J Biotechnol, 136 (1-2), 77-90
PubMed 18597880
Stavrum AK, Petersen K, Jonassen I, Dysvik B (2008)
Analysis of gene-expression data using J-Express
Curr Protoc Bioinformatics, Chapter 7, Unit 7.3
PubMed 18428687
Stavrum R, Valvatne H, Bø TH, Jonassen I, Hinds J, Butcher PD, Grewal HM (2008)
Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar
PLoS One, 3 (4), e1973
PubMed 18398483
Taylor WR, Bartlett GJ, Chelliah V, Klose D, Lin K, Sheldon T, Jonassen I (2008)
Prediction of protein structure from ideal forms
Proteins, 70 (4), 1610-9
PubMed 18175329
Winge I, McKinney JA, Ying M, D’Santos CS, Kleppe R, Knappskog PM, Haavik J (2008)
Activation and stabilization of human tryptophan hydroxylase 2 by phosphorylation and 14-3-3 binding
Biochem J, 410 (1), 195-204
PubMed 17973628
Publications 2007
Halvorsen OJ, Rostad K, Øyan AM, Puntervoll H, Bø TH, Stordrange L, Olsen S, Haukaas SA, Hood L, Jonassen I, Kalland KH, Akslen LA (2007)
Increased expression of SIM2-s protein is a novel marker of aggressive prostate cancer
Clin Cancer Res, 13 (3), 892-7
PubMed 17289882
Hystad ME, Myklebust JH, Bø TH, Sivertsen EA, Rian E, Forfang L, Munthe E, Rosenwald A, Chiorazzi M, Jonassen I, Staudt LM, Smeland EB (2007)
Characterization of early stages of human B cell development by gene expression profiling
J Immunol, 179 (6), 3662-71
PubMed 17785802
Maraziotis IA, Dimitrakopoulou K, Bezerianos A (2007)
Growing functional modules from a seed protein via integration of protein interaction and gene expression data
BMC Bioinformatics, 8, 408
PubMed 17956603
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A (2007)
CoryneCenter – an online resource for the integrated analysis of corynebacterial genome and transcriptome data
BMC Syst Biol, 1, 55
PubMed 18034885
Oyan AM, Bø TH, Jonassen I, Ulvestad E, Tore Gjertsen B, Bruserud O, Kalland KH (2007)
Global gene expression in classification, pathogenetic understanding and identification of therapeutic targets in acute myeloid leukemia
Curr Pharm Biotechnol, 8 (6), 344-54
PubMed 18289043
Petersen K, Oyan AM, Rostad K, Olsen S, Bø TH, Salvesen HB, Gjertsen BT, Bruserud O, Halvorsen OJ, Akslen LA, Steen VM, Jonassen I, Kalland KH (2007)
Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization
Anal Biochem, 366 (1), 46-58
PubMed 17449007
Rostad K, Mannelqvist M, Halvorsen OJ, Oyan AM, Bø TH, Stordrange L, Olsen S, Haukaas SA, Lin B, Hood L, Jonassen I, Akslen LA, Kalland KH (2007)
ERG upregulation and related ETS transcription factors in prostate cancer
Int J Oncol, 30 (1), 19-32
PubMed 17143509
Raa A, Stansberg C, Steen VM, Bjerkvig R, Reed RK, Stuhr LE (2007)
Hyperoxia retards growth and induces apoptosis and loss of glands and blood vessels in DMBA-induced rat mammary tumors
BMC Cancer, 7, 23
PubMed 17263869
Saelensminde G, Halskau Ø, Helland R, Willassen NP, Jonassen I (2007)
Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins
Extremophiles, 11 (4), 585-96
PubMed 17429573
Skjaerven L, Jonassen I, Reuter N (2007)
TMM@: a web application for the analysis of transmembrane helix mobility
BMC Bioinformatics, 8, 232
PubMed 17601351
Stansberg C, Vik-Mo AO, Holdhus R, Breilid H, Srebro B, Petersen K, Jørgensen HA, Jonassen I, Steen VM (2007)
Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation
BMC Genomics, 8, 94
PubMed 17408481
Suhr ML, Dysvik B, Bruland O, Warnakulasuriya S, Amaratunga AN, Jonassen I, Vasstrand EN, Ibrahim SO (2007)
Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users
Oncol Rep, 18 (5), 1061-75
PubMed 17914555
Publications 2006
Dysvik B, Vasstrand EN, Løvlie R, Elgindi OA, Kross KW, Aarstad HJ, Johannessen AC, Jonassen I, Ibrahim SO (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 (4), 1109-20
PubMed 16489063
Jonassen I, Klose D, Taylor WR (2006)
Protein model refinement using structural fragment tessellation
Comput Biol Chem, 30 (5), 360-6
PubMed 16982212
Küster H, Becker A, Firnhaber C, Hohnjec N, Manthey K, Perlick AM, Bekel T, Dondrup M, Henckel K, Goesmann A, Meyer F, Wipf D, Requena N, Hildebrandt U, Hampp R, Nehls U, Krajinski F, Franken P, Pühler A (2006)
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses
Phytochemistry, 68 (1), 19-32
PubMed 17081576
Malde K, Schneeberger K, Coward E, Jonassen I (2006)
RBR: library-less repeat detection for ESTs
Bioinformatics, 22 (18), 2232-6
PubMed 16837527
Sakariassen PØ, Prestegarden L, Wang J, Skaftnesmo KO, Mahesparan R, Molthoff C, Sminia P, Sundlisaeter E, Misra A, Tysnes BB, Chekenya M, Peters H, Lende G, Kalland KH, Øyan AM, Petersen K, Jonassen I, van der Kogel A, Feuerstein BG, Terzis AJ, Bjerkvig R, Enger PØ (2006)
Angiogenesis-independent tumor growth mediated by stem-like cancer cells
Proc Natl Acad Sci U S A, 103 (44), 16466-71
PubMed 17056721
Taylor WR, Lin K, Klose D, Fraternali F, Jonassen I (2006)
Dynamic domain threading
Proteins, 64 (3), 601-14
PubMed 16752419
Øyan AM, Bø TH, Jonassen I, Gjertsen BT, Bruserud Ø, Kalland KH (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 (5), 1065-80
PubMed 16596222
Publications 2005
Halvorsen OJ, Oyan AM, Bø TH, Olsen S, Rostad K, Haukaas SA, Bakke AM, Marzolf B, Dimitrov K, Stordrange L, Lin B, Jonassen I, Hood L, Akslen LA, Kalland KH (2005)
Gene expression profiles in prostate cancer: association with patient subgroups and tumour differentiation
Int J Oncol, 26 (2), 329-36
PubMed 15645116
Hjelmervik TO, Petersen K, Jonassen I, Jonsson R, Bolstad AI (2005)
Gene expression profiling of minor salivary glands clearly distinguishes primary Sjögren’s syndrome patients from healthy control subjects
Arthritis Rheum, 52 (5), 1534-44
PubMed 15880807
Kim J, Jonassen I (2005)
Guest editorial: WABI special section part II
IEEE-ACM Trans. Comput. Biol. Bioinform., 2 (1), 1-2
Oyan AM, Bø TH, Jonassen I, Ulvestad E, Gjertsen BT, Kalland KH, Bruserud O (2005)
CD34 expression in native human acute myelogenous leukemia blasts: differences in CD34 membrane molecule expression are associated with different gene expression profiles
Cytometry B Clin Cytom, 64 (1), 18-27
PubMed 15668952
Raeder MB, Fernø J, Glambek M, Stansberg C, Steen VM (2005)
Antidepressant drugs activate SREBP and up-regulate cholesterol and fatty acid biosynthesis in human glial cells
Neurosci Lett, 395 (3), 185-90
PubMed 16324787
Fernø J, Raeder MB, Vik-Mo AO, Skrede S, Glambek M, Tronstad KJ, Breilid H, Løvlie R, Berge RK, Stansberg C, Steen VM (2005)
Antipsychotic drugs activate SREBP-regulated expression of lipid biosynthetic genes in cultured human glioma cells: a novel mechanism of action?
Pharmacogenomics J, 5 (5), 298-304
PubMed 16027736
Schneeberger K, Malde K, Coward E, Jonassen I (2005)
Masking repeats while clustering ESTs
Nucleic Acids Res, 33 (7), 2176-80
PubMed 15831790
Stansberg C, Subramaniam S, Collet B, Secombes CJ, Cunningham C (2005)
Cloning of the Atlantic salmon (Salmo salar) IL-1 receptor associated protein
Fish Shellfish Immunol, 19 (1), 53-65
PubMed 15722231
Publications 2004
Bø TH, Dysvik B, Jonassen I (2004)
LSimpute: accurate estimation of missing values in microarray data with least squares methods
Nucleic Acids Res, 32 (3), e34
PubMed 14978222
Flikka K, Yadetie F, Laegreid A, Jonassen I (2004)
XHM: a system for detection of potential cross hybridizations in DNA microarrays
BMC Bioinformatics, 5, 117
PubMed 15333145
Kim J, Jonassen I (2004)
Guest editorial: WABI special section part 1
IEEE-ACM Trans. Comput. Biol. Bioinform., 1 (4), 137-138
Kleppe R, Haavik J (2004)
Different stabilities and denaturation pathways for structurally related aromatic amino acid hydroxylases
FEBS Lett, 565 (1-3), 155-9
PubMed 15135070
Küster H, Hohnjec N, Krajinski F, El YF, Manthey K, Gouzy J, Dondrup M, Meyer F, Kalinowski J, Brechenmacher L, van Tuinen D, Gianinazzi-Pearson V, Pühler A, Gamas P, Becker A (2004)
Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula
J Biotechnol, 108 (2), 95-113
PubMed 15129719
Malde K, Coward E, Jonassen I (2004)
A graph based algorithm for generating EST consensus sequences
Bioinformatics, 21 (8), 1371-5
PubMed 15572463
Subramaniam S, Stansberg C, Cunningham C (2004)
The interleukin 1 receptor family
Dev Comp Immunol, 28 (5), 415-28
PubMed 15062641
Taylor WR, Jonassen I (2004)
A structural pattern-based method for protein fold recognition
Proteins, 56 (2), 222-34
PubMed 15211507
Publications 2003
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F (2003)
EMMA: a platform for consistent storage and efficient analysis of microarray data
J Biotechnol, 106 (2-3), 135-46
PubMed 14651856
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F (2003)
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology
J Biotechnol, 106 (2-3), 157-67
PubMed 14651858
Hüser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Pühler A, Wiegräbe I, Tauch A (2003)
Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source
J Biotechnol, 106 (2-3), 269-86
PubMed 14651867
Malde K, Coward E, Jonassen I (2003)
Fast sequence clustering using a suffix array algorithm
Bioinformatics, 19 (10), 1221-6
PubMed 12835265
Stansberg C, Subramaniam S, Olsen L, Secombes CJ, Cunningham C (2003)
Cloning and characterisation of a putative ST2L homologue from Atlantic salmon (Salmo salar)
Fish Shellfish Immunol, 15 (3), 211-24
PubMed 12892743
Wang J, Bø TH, Jonassen I, Myklebost O, Hovig E (2003)
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
BMC Bioinformatics, 4, 60
PubMed 14651757
Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F (2003)
Bioinformatics support for high-throughput proteomics
J Biotechnol, 106 (2-3), 147-56
PubMed 14651857
Publications 2002
Bø T, Jonassen I (2002)
New feature subset selection procedures for classification of expression profiles
Genome Biol, 3 (4), RESEARCH0017
PubMed 11983058
Bø TH, Jonassen I, Eidhammer I, Helgesen C (2002)
A fast top-down method for constructing reliable radiation hybrid frameworks
Bioinformatics, 18 (1), 11-8
PubMed 11836206
Conklin D, Jonassen I, Aasland R, Taylor WR (2002)
Association of nucleotide patterns with gene function classes: application to human 3′ untranslated sequences
Bioinformatics, 18 (1), 182-9
PubMed 11836227
Jonassen I, Eidhammer I, Conklin D, Taylor WR (2002)
Structure motif discovery and mining the PDB
Bioinformatics, 18 (2), 362-7
PubMed 11847094
Subramaniam S, Stansberg C, Olsen L, Zou J, Secombes CJ, Cunningham C (2002)
Cloning of a Salmo salar interleukin-1 receptor-like cDNA
Dev Comp Immunol, 26 (5), 415-31
PubMed 11906722
Toska K, Kleppe R, Armstrong CG, Morrice NA, Cohen P, Haavik J (2002)
Regulation of tyrosine hydroxylase by stress-activated protein kinases
J Neurochem, 83 (4), 775-83
PubMed 12421349
Toska K, Kleppe R, Cohen P, Haavik J (2002)
Phosphorylation of tyrosine hydroxylase in isolated mice adrenal glands
Ann N Y Acad Sci, 971, 66-8
PubMed 12438091
Publications 2001
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M et al. (2001)
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
Nucleic Acids Res, 29 (1), 37-40
PubMed 11125043
Dysvik B, Jonassen I (2001)
J-Express: exploring gene expression data using Java
Bioinformatics, 17 (4), 369-70
PubMed 11301307
Publications 2000
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M et al. (2000)
InterPro–an integrated documentation resource for protein families, domains and functional sites
Bioinformatics, 16 (12), 1145-50
PubMed 11159333
Eidhammer I, Jonassen I, Taylor WR (2000)
Structure comparison and structure patterns
J Comput Biol, 7 (5), 685-716
PubMed 11153094
Jonassen I (2000)
Discovering patterns conserved in sets of unaligned protein sequences
Methods Mol Biol, 143, 33-52
PubMed 11084901
Jonassen I, Eidhammer I, Grindhaug SH, Taylor WR (2000)
Searching the protein structure databank with weak sequence patterns and structural constraints
J Mol Biol, 304 (4), 599-619
PubMed 11099383
Kurtzhals P, Schäffer L, Sørensen A, Kristensen C, Jonassen I, Schmid C, Trüb T (2000)
Correlations of receptor binding and metabolic and mitogenic potencies of insulin analogs designed for clinical use
Diabetes, 49 (6), 999-1005
PubMed 10866053
Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E (2000)
Mining for putative regulatory elements in the yeast genome using gene expression data
Proc Int Conf Intell Syst Mol Biol, 8, 384-94
PubMed 10977099
Publications 1999
Jonassen I, Eidhammer I, Taylor WR (1999)
Discovery of local packing motifs in protein structures
Proteins, 34 (2), 206-19
PubMed 10022356
Publications 1998
Brazma A, Jonassen I, Eidhammer I, Gilbert D (1998)
Approaches to the automatic discovery of patterns in biosequences
J Comput Biol, 5 (2), 279-305
PubMed 9672833
Brazma A, Jonassen I, Vilo J, Ukkonen E (1998)
Predicting gene regulatory elements in silico on a genomic scale
Genome Res, 8 (11), 1202-15
PubMed 9847082
Kjeldsen T, Pettersson AF, Drube L, Kurtzhals P, Jonassen I, Havelund S, Hansen PH, Markussen J (1998)
Secretory expression of human albumin domains in Saccharomyces cerevisiae and their binding of myristic acid and an acylated insulin analogue
Protein Expr Purif, 13 (2), 163-9
PubMed 9675058
Publications 1997
Jonassen I (1997)
Efficient discovery of conserved patterns using a pattern graph
Comput Appl Biosci, 13 (5), 509-22
PubMed 9367124
Kurtzhals P, Havelund S, Jonassen I, Markussen J (1997)
Effect of fatty acids and selected drugs on the albumin binding of a long-acting, acylated insulin analogue
J Pharm Sci, 86 (12), 1365-8
PubMed 9423147
Whittingham JL, Havelund S, Jonassen I (1997)
Crystal structure of a prolonged-acting insulin with albumin-binding properties
Biochemistry, 36 (10), 2826-31
PubMed 9062110
Publications 1996
Brazma A, Jonassen I, Ukkonen E, Vilo J (1996)
Discovering patterns and subfamilies in biosequences
Proc Int Conf Intell Syst Mol Biol, 4, 34-43
PubMed 8877502
Kurtzhals P, Havelund S, Jonassen I, Kiehr B, Ribel U, Markussen J (1996)
Albumin binding and time action of acylated insulins in various species
J Pharm Sci, 85 (3), 304-8
PubMed 8699334
Markussen J, Havelund S, Kurtzhals P, Andersen AS, Halstrøm J, Hasselager E, Larsen UD, Ribel U, Schäffer L, Vad K, Jonassen I (1996)
Soluble, fatty acid acylated insulins bind to albumin and show protracted action in pigs
Diabetologia, 39 (3), 281-8
PubMed 8721773
Publications 1995
Jonassen I, Collins JF, Higgins DG (1995)
Finding flexible patterns in unaligned protein sequences
Protein Sci, 4 (8), 1587-95
PubMed 8520485
Kurtzhals P, Havelund S, Jonassen I, Kiehr B, Larsen UD, Ribel U, Markussen J (1995)
Albumin binding of insulins acylated with fatty acids: characterization of the ligand-protein interaction and correlation between binding affinity and timing of the insulin effect in vivo
Biochem J, 312 ( Pt 3), 725-31
PubMed 8554512