2024
248. Automated cell type annotation and exploration of single-cell signaling dynamics using mass cytometry.
Kleftogiannnis D, Gavasso S, Tislevoll BS, van der Meer N, Motzfeldt IKF, Hellesøy M, Gullaksen SE, Griessinger E, Fagerholt O, Lenartova A, Fløisand Y, Schuringa JJ, Gjertsen BT, Jonassen I. iScience. 2024 12;27(7):110261. 10.1016/j.isci.2024.110261
2023
247. Integrative omics-analysis of lipid metabolism regulation by peroxisome proliferator-activated receptor a and b agonists in male Atlantic cod.
Eide M, Goksøyr A, Yadetie F, Gilabert A, Bartosova Z, Frøysa HG, Fallahi S, Zhang X, Blaser N, Jonassen I, Bruheim P, Alendal G, Brun M, Porte C, Karlsen OA. Front Physiol. 2023 22;14:1129089. 10.3389/fphys.2023.1129089
246. Early response evaluation by single cell signaling profiling in acute myeloid leukemia.
Tislevoll BS, Hellesøy M, Fagerholt OHE, Gullaksen SE, Srivastava A, Birkeland E, Kleftogiannis D, Ayuda-Durán P, Piechaczyk L, Tadele DS, Skavland J, Baliakas P, Hovland R, Andresen V, Seternes OM, Tvedt THA, Aghaeepour N, Gavasso S, Porkka K, Jonassen I, Fløisand Y, Enserink J, Blaser N, Gjertsen BT. Nat Commun. 2023 7;14(1):115. 10.1038/s41467-022-35624-4
245. LOCATOR: feature extraction and spatial analysis of the cancer tissue microenvironment using mass cytometry imaging technologies.
Ehsani R, Jonassen I, Akslen LA, Kleftogiannis D. Bioinform Adv. 2023 11;3(1):vbad146. 10.1093/bioadv/vbad146
2021
244. A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis).
Zhou Z, Eichner C, Nilsen F, Jonassen I, Dondrup M. BMC Genomics. 2021 18;22(1):832. 10.1186/s12864-021-08054-7
243. Comprehensive characterization of copy number variation (CNV) called from array, long- and short-read data.
Lavrichenko K, Johansson S, Jonassen I. BMC Genomics. 2021 17;22(1):826. 10.1186/s12864-021-08082-3
242. Repeated bronchoscopy in health and obstructive lung disease: is the airway microbiome stable?
Nielsen R, Xue Y, Jonassen I, Haaland I, Kommedal Ø, Wiker HG, Drengenes C, Bakke PS, Eagan TML. BMC Pulm Med. 2021 21(1):342. 10.1186/s12890-021-01687-0
241. The salmon louse genome: Copepod features and parasitic adaptations.
Skern-Mauritzen R, Malde K, Eichner C, Dondrup M, Furmanek T, Besnier F, Komisarczuk AZ, Nuhn M, Dalvin S, Edvardsen RB, Klages S, Huettel B, Stueber K, Grotmol S, Karlsbakk E, Kersey P, Leong JS, Glover KA, Reinhardt R, Lien S, Jonassen I, Koop BF, Nilsen F. Genomics. 2021 113(6):3666-3680. 10.1016/j.ygeno.2021.08.002
240. SeeCiTe: a method to assess CNV calls from SNP arrays using trio data.
Lavrichenko K, Helgeland Ø, Njølstad PR, Jonassen I, Johansson S. Bioinformatics. 2021 27;37(13):1876-1883. 10.1093/bioinformatics/btab028
239. The chemical defensome of five model teleost fish.
Sci Rep. 2021 11, 10546. 10.21203/rs.3.rs-175531/v1
238. Gene co-expression networks identify novel candidate genes for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis).
237. Application of quantitative transcriptomics in evaluating the ex vivo effects of per- and polyfluoroalkyl substances on Atlantic cod (Gadus morhua) ovarian physiology.
Khan EA, Zhang X, Hanna EM, Yadetie F, Jonassen I, Goksøyr A, Arukwe A. Sci Total Environ. 2021 10;755(Pt 1):142904. 10.1016/j.scitotenv.2020.142904
236. Machine learning approaches for biomarker discovery using gene expression data.
Zhang X, Jonassen I, Goksøyr A. Bioinformatics [Internet]. Brisbane (AU): Exon Publications; 2021 Mar 20. Chapter 4. 10.36255/exonpublications.bioinformatics.2021.ch4
2020
235. RASflow: an RNA-Seq analysis workflow with Snakemake.
Zhang X, Jonassen I. BMC Bioinformatics. 2020 18;21(1):110. 10.1186/s12859-020-3433-x
234. Common gene expression signatures in Parkinson’s disease are driven by changes in cell composition.
Nido GS, Dick F, Toker L, Petersen K, Alves G, Tysnes OB, Jonassen I, Haugarvoll K, Tzoulis C. Acta Neuropathol Commun. 2020 21;8(1):55. 10.1186/s40478-020-00932-7
233. Gene-methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk.
Romanowska J, Haaland ØA, Jugessur A, Gjerdevik M, Xu Z, Taylor J, Wilcox AJ, Jonassen I, Lie RT, Gjessing HK. Clin Epigenetics. 2020 16;12(1):109. 10.1186/s13148-020-00881-x
232. ReCodLiver0.9: overcoming challenges in genome-scale metabolic reconstruction of a non-model species.
Hanna EM, Zhang X, Eide M, Fallahi S, Furmanek T, Yadetie F, Zielinski DC, Goksøyr A, Jonassen I. Front Mol Biosci. 2020 7:591406. 10.3389/fmolb.2020.591406
231. Using deep learning to extrapolate protein expression measurements.
Barzine MP, Freivalds K, Wright JC, Opmanis M, Rituma D, Ghavidel FZ, Jarnuczak AF, Celms E, Čerāns K, Jonassen I, Lace L, Vizcaíno JA, Choudhary JS, Brazma A, Viksna J. Proteomics. 2020 20(21-22):e2000009. 10.1002/pmic.202000009
230. Quantitative transcriptomics, and lipidomics in evaluating ovarian developmental effects in Atlantic cod (Gadus morhua) caged at a capped marine waste disposal site.
Khan EA, Zhang X, Hanna EM, Bartosova Z, Yadetie F, Jonassen I, Goksøyr A, Arukwe A. Environ Res. 2020 189:109906. 10.1016/j.envres.2020.109906
229. Proteogenomics of non-smoking lung cancer in East Asia delineates molecular signatures of pathogenesis and progression.
Chen YJ, Roumeliotis TI, Chang YH, Chen CT, Han CL, Lin MH, Chen HW, Chang GC, Chang YL, Wu CT, Lin MW, Hsieh MS, Wang YT, Chen YR, Jonassen I, Ghavidel FZ, Lin ZS, Lin KT, Chen CW, Sheu PY, Hung CT, Huang KC, Yang HC, Lin PY, Yen TC, Lin YW, Wang JH, Raghav L, Lin CY, Chen YS, Wu PS, Lai CT, Weng SH, Su KY, Chang WH, Tsai PY, Robles AI, Rodriguez H, Hsiao YJ, Chang WH, Sung TY, Chen JS, Yu SL, Choudhary JS, Chen HY, Yang PC, Chen YJ. Cell. 2020 182(1):226-244.e17. 10.1016/j.cell.2020.06.012
228. Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data.
Xue Y, Lanzén A, Jonassen I. Bioinformatics. 2020 36(11):3365-3371. 10.1093/bioinformatics/btaa177
227. Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost.
Xue Y, Jonassen I, Øvreås L, Taş N. FEMS Microbiol Ecol. 2020 96(5):fiaa057. 10.1093/femsec/fiaa057
226. Evaluation of a eukaryote phylogenetic microarray for environmental monitoring of marine sediments.
Lekang K, Lanzén A, Jonassen I, Thompson E, Troedsson C. Mar Pollut Bull. 2020 154:111102. 10.1016/j.marpolbul.2020.111102
2019
225. Common gene expression signatures in Parkinson’s disease are driven by changes in cell composition.
Nido GS, Dick F, Toker L, Petersen K, Alves G, Tysnes OB, Jonassen I, Haugarvoll K, Tzoulis C. Acta Neuropathol Commun. 2020 8(1):55. 10.1186/s40478-020-00932-7
224. The bio.tools registry of software tools and data resources for the life sciences. Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S. Genome Biol. 2019 20(1):164. 10.1186/s13059-019-1772-6
223. An ensemble feature selection framework integrating stability.
Zhang X, Jonassen I. IEEE BIBM. 2019. 10.1109/BIBM47256.2019.8983310
222. Repeated bronchoscopy examination of the airway microbiome.
Nielsen R, Xue Y, Jonassen I, Haaland I, Kommedal Ø, Wiker HG, Drengenes C, Bakke PS, Eagan TML. Eur Respir J. 2019 54(suppl 63): PA2344. 10.1183/13993003.congress-2019.PA2344
221. Bacterial and Archaeal metagenome-assembled genome sequences from Svalbard permafrost.
Xue Y, Jonassen I, Øvreås L, Taş N. Microbiol Resour Announc. 2019 8(27):e00516-19. 10.1128/MRA.00516-19
220. A comparative analysis of feature selection methods for biomarker discovery in study of toxicant-treated Atlantic cod (Gadus Morhua) liver.
Zhang X, Jonassen I. NAIS. 2019. 10.1007/978-3-030-35664-4_11
2018
219. Deblender: a semi-/unsupervised multi-operational computational method for complete deconvolution of expression data from heterogeneous samples.
Dimitrakopoulou K, Wik E, Akslen LA, Jonassen I. BMC Bioinformatics. 2018 19(1):408. 10.1186/s12859-018-2442-5
218. Incorporating genome-wide methylation and genotype data to elucidate how region-wise methylation level might influence allele-defined relative risks.
Romanowska J, Haaland ØA, Gjerdevik M, Jonassen I, Lie RT, Jugessur A, Gjessing HK. Nor Epidemiol. 2018. 28 1, 42. Abstract
217. Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer.
Kusonmano K, Halle MK, Wik E, Hoivik EA, Krakstad C, Mauland KK, Tangen IL, Berg A, Werner HMJ, Trovik J, Øyan AM, Kalland KH, Jonassen I, Salvesen HB, Petersen K. PLoS One. 2018 13(11):e0206665. 10.1371/journal.pone.0206665
216. Development and testing of an 18S rRNA phylogenetic microarray for marine sediments.
Lekang K, Hadziavdic K, Sandnes Skaar K, Jonassen I, Thompson EM, Troedsson C. J Microbiol Methods. 2018 154:95-106. 10.1016/j.mimet.2018.10.007
215. FAIR Bioinformatics computation and data management: FAIRDOM and the Norwegian Digital Life initiative.
Stanford N, Bacall F, Ghavidel FZ, Golebiewski M, Jonassen I, Kleppe R, Krebs O, Leonov H, Owen S, Peterson K, Rey M, Soiland-Reyes S, Tekle K, Weiderman A, Williams A, Wittig U, Wolstencroft K, Goksøyr A, Snoep J, Vik JO, NETTAB. 2018. PDF
214. RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo [a] pyrene and 17α-ethynylestradiol.
Yadetie F, Zhang X, Hanna EM, Aranguren-Abadía L, Eide M, Blaser N, Brun M, Jonassen I, Goksøyr A, Karlsen OA. Aquat Toxicol. 2018 201:174-186. 10.1016/j.aquatox.2018.06.003
213. Mathematical Modelling of Nitric Oxide/Cyclic GMP/Cyclic AMP Signalling in Platelets.
Kleppe R, Jonassen I, Døskeland SO, Selheim F. Int J Mol Sci. 2018 19(2):612. 10.3390/ijms19020612
212. A novel approach to identify highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer.
Kusonmano K, Halle MK, Wik E, Hoivik EA, Krakstad C, Mauland KK, Tangen IL, Berg A, Werner HMJ, Trovik J, Øyan AM, Kalland K-H, Jonassen I, Salvesen HB, Petersen K. BGRSSB-2018. 2018. 10.18699/BGRSSB-2018-034
211. Norwegian e-Infrastructure for Life Sciences (NeLS).
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2017
210. Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts.
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 K-H, Wang J, Enger PØ. BMC Cancer. 2017 17, 108. 10.1186/s12885-017-3109-8
209. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species.
Dahle G, Besnier F, Skaug HJ, Øien N, Solvang HK, Haug T, Skern-Mauritzen R, Kanda N, Pastene LA, Jonassen I, Glover KA. BMC Genomics. 2017 18, 76. 10.1186/s12864-016-3416-5
208. Protected sampling is preferable in bronchoscopic studies of the airway microbiome.
207. DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments.
Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C. PLoS One. 2017 12 (6), e0179443. 10.1371/journal.pone.0179443
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205. GBA2 mutations cause a marinesco-Sjögren-like syndrome: genetic and biochemical studies.
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204. Tumour-associated glial host cells display a stem-like phenotype with a distinct gene expression profile and promote growth of GBM xenografts.
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203. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species.
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201. Differences in the transcriptome of medullary thyroid cancer regarding the status and type of RET gene mutations.
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199. PNKP mutations identified by whole-exome sequencing in a Norwegian patient with sporadic ataxia and edema.
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198. Sensitivity of next-generation sequencing metagenomic analysis for detection of RNA and DNA viruses in cerebrospinal fluid: the confounding effect of background contamination.
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. Adv Exp Med Biol. 2016 vol 944. 10.1007/5584_2016_42
197. Implication of NOTCH1 gene in susceptibility to anxiety and depression among sexual abuse victims.
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. Transl Psychiatry. 2016 13; 6 (12):e977. 10.1038/tp.2016.248
196. Novel SLC19A3 promoter deletion and allelic silencing in biotin-thiamine-responsive basal ganglia encephalopathy.
Flønes I, Sztromwasser P, Haugarvoll K, Dölle C, Lykouri M, Schwarzlmüller T, Jonassen I, Miletic H, Johansson S, Knappskog PM, Bindoff LA, Tzoulis C. PLoS One. 2016 11 (2), e0149055. 10.1371/journal.pone.0149055
195. Regulation of tyrosine hydroxylase is preserved across different homo- and heterodimeric 14-3-3 proteins.
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194. Disentangling genetic and epigenetic determinants of ultrafast adaptation.
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193. Targeted next-generation sequencing reveals MODY in up to 6.5% of antibody-negative diabetes cases listed in the Norwegian Childhood Diabetes Registry.
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192. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities.
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191. The Atlantic salmon genome provides insights into rediploidization.
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190. Using registries to integrate bioinformatics tools and services into workbench environments.
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188. Overexpression of DEK is an indicator of poor prognosis in patients with gastric adenocarcinoma.
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187. Metagenomic analysis of cerebrospinal fluid from patients with multiple sclerosis.
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186. RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data.
Stokowy T, Garbulowski M, Fiskerstrand T, Holdhus R, Labun K, Sztromwasser P, Gilissen C, Hoischen A, Houge G, Petersen K, Jonassen I, Steen VM. Bioinformatics. 2016 32 (19), 3018-20. 10.1093/bioinformatics/btw359
185. Differences in miRNA and mRNA profile of papillary thyroid cancer variants.
Stokowy T, Gawel D, Wojtas B. Int J Endocrinol. 2016 1427042. 10.1155/2016/1427042
184. Two-miRNA classifiers differentiate mutation-negative follicular thyroid carcinomas and follicular thyroid adenomas in fine needle aspirations with high specificity.
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183. Somatic mutation profiling of follicular thyroid cancer by next generation sequencing.
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182. Tyrosine and tryptophan hydroxylases as therapeutic targets in human disease.
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2015
180. The ELIXIR channel in F1000Research.
Blomberg N, Oliveira A, Mons B, Persson B, Jonassen I. F1000Res. 2015 4. 10.12688/f1000research.7587.2
179. Tumor necrosis is an important hallmark of aggressive endometrial cancer and associates with hypoxia, angiogenesis and inflammation responses.
Bredholt G, Mannelqvist M, Stefansson IM, Birkeland E, Bø TH, Øyan AM, Trovik J, Kalland KH, Jonassen I, Salvesen HB, Wik E, Akslen LA. Oncotarget. 2015 6 (37), 39676-91. 10.18632/oncotarget.5344
178. High myopia-excavated optic disc anomaly associated with a frameshift mutation in the MYC-binding protein 2 gene (MYCBP2).
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177. Defective PITRM1 mitochondrial peptidase is associated with Aβ amyloidotic neurodegeneration.
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176. Integromics network meta-analysis on cardiac aging offers robust multi-layer modular signatures and reveals micronome synergism.
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175. Distributed and interactive visual analysis of omics data.
Farag Y, Berven FS, Jonassen I, Petersen K, Barsnes H. J Proteomics. 2015 129:78-82. 10.1016/j.jprot.2015.05.029
174. A recombined allele of the lipase gene CEL and its pseudogene CELP confers susceptibility to chronic pancreatitis.
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95. Three-way interaction between 14-3-3 proteins, the N-terminal region of tyrosine hydroxylase, and negatively charged membranes.
Halskau Ø, Ying M, Baumann A, Kleppe R, Rodriguez-Larrea D, Almås B, Haavik J, Martinez A. J Biol Chem. 2009 284 (47), 32758-69. 10.1074/jbc.M109.027706
94. TRUNCATULIX–a data warehouse for the legume community.
Henckel K, Runte KJ, Bekel T, Dondrup M, Jakobi T, Küster H, Goesmann A. BMC Plant Biol. 2009 9, 19. 10.1186/1471-2229-9-19
93. Genome-wide profiling of histone h3 lysine 4 and lysine 27 trimethylation reveals an epigenetic signature in prostate carcinogenesis.
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. PLoS One. 2009 4 (3), e4687. 10.1371/journal.pone.0004687
92. Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods.
Leversen NA, de Souza GA, Målen H, Prasad S, Jonassen I, Wiker HG. Microbiology. 2009 155 (Pt 7), 2375-83. 10.1099/mic.0.025270-0
91. 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.
Lybaek H, Ørstavik KH, Prescott T, Hovland R, Breilid H, Stansberg C, Steen VM, Houge G. Eur J Hum Genet. 2009 17 (7), 904-10. 10.1038/ejhg.2008.261
90. Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Hüser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A. BMC Syst Biol. 2009 3, 82. 10.1186/1752-0509-3-82
89. Functional involvement of RINF, retinoid-inducible nuclear factor (CXXC5), in normal and tumoral human myelopoiesis.
Pendino F, Nguyen E, Jonassen I, Dysvik B, Azouz A, Lanotte M, Ségal-Bendirdjian E, Lillehaug JR (2009)
Blood. 2009 113 (14), 3172-81. 10.1182/blood-2008-07-170035
88. Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation.
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. PNAS. 2009 106 (12), 4834-9. 10.1073/pnas.0806514106
87. Probing the “dark matter” of protein fold space.
Taylor WR, Chelliah V, Hollup SM, MacDonald JT, Jonassen I. Structure. 2009 17 (9), 1244-52. 10.1016/j.str.2009.07.012
86. Upregulation of immunoglobulin-related genes in cortical sections from multiple sclerosis patients.
Torkildsen Ø, Stansberg C, Angelskår SM, Kooi EJ, Geurts JJ, van der Valk P, Myhr KM, Steen VM, Bø L. Brain Pathol. 2009 20 (4), 720-9. 10.1111/j.1750-3639.2009.00343.x
85. Genes of cell-cell interactions, chemotherapy detoxification and apoptosis are induced during chemotherapy of acute myeloid leukemia.
Øyan AM, Anensen N, Bø TH, Stordrange L, Jonassen I, Bruserud Ø, Kalland KH, Gjertsen BT. BMC Cancer. 2009 9, 77. 10.1186/1471-2407-9-77
2008
84. A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
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. J Biotechnol. 2008 140 (1-2), 45-50. 10.1016/j.jbiotec.2008.11.006
83. High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.
de Souza GA, Målen H, Søfteland T, Saelensminde G, Prasad S, Jonassen I, Wiker HG. BMC Genomics. 2008 9, 316. 10.1186/1471-2164-9-316
82. Salmon louse (Lepeophtheirus salmonis) transcriptomes during post molting maturation and egg production, revealed using EST-sequencing and microarray analysis.
Eichner C, Frost P, Dysvik B, Jonassen I, Kristiansen B, Nilsen F. BMC Genomics. 2008 9, 126. 10.1186/1471-2164-9-126
81. The BREW workshop series: a stimulating experience in PhD education.
Giegerich R, Brazma A, Jonassen I, Ukkonen E, Vingron M. Brief Bioinform. 2008 9 (3), 250-3. 10.1093/bib/bbn002
80. Structural fragments in protein model refinement.
Hollup SM, Taylor WR, Jonassen I. Protein Pept Lett. 2008 15 (9), 964-71. 10.2174/092986608785849263
79. Repeats and EST analysis for new organisms.
Malde K, Jonassen I. BMC Genomics. 2008 9, 23. 10.1186/1471-2164-9-23
78. An in silico method for detecting overlapping functional modules from composite biological networks.
Maraziotis IA, Dimitrakopoulou K, Bezerianos A. BMC Syst Biol. 2008 2, 93. 10.1186/1752-0509-2-93
77. MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A. Bioinformatics. 2008 24 (23), 2726-32. 10.1093/bioinformatics/btn452
76. Molecular dynamics study of the ribosomal A-site.
Romanowska J, Setny P, Trylska J. J Phys Chem B. 2008 112 (47), 15227-43. 10.1021/jp806814s
75. Amino acid contacts in proteins adapted to different temperatures: hydrophobic interactions and surface charges play a key role.
Saelensminde G, Halskau Ø, Jonassen I. Extremophiles. 2008 13 (1), 11-20. 10.1007/s00792-008-0192-4
74. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
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. J Biotechnol. 2008 136 (1-2), 77-90. 10.1016/j.jbiotec.2008.05.008
73. Analysis of gene-expression data using J-Express.
Stavrum AK, Petersen K, Jonassen I, Dysvik B. Curr Protoc Bioinformatics. 2008 Chapter 7, Unit 7.3. 10.1002/0471250953.bi0703s21
72. Genomic diversity among Beijing and non-Beijing Mycobacterium tuberculosis isolates from Myanmar.
Stavrum R, Valvatne H, Bø TH, Jonassen I, Hinds J, Butcher PD, Grewal HM. PLoS One. 2008 3 (4), e1973. 10.1371/journal.pone.0001973
71. Prediction of protein structure from ideal forms.
Taylor WR, Bartlett GJ, Chelliah V, Klose D, Lin K, Sheldon T, Jonassen I. Proteins. 2008 70 (4), 1610-9. 10.1002/prot.21913
70. Activation and stabilization of human tryptophan hydroxylase 2 by phosphorylation and 14-3-3 binding.
Winge I, McKinney JA, Ying M, D’Santos CS, Kleppe R, Knappskog PM, Haavik J. Biochem J. 2008 410 (1), 195-204. 10.1042/BJ20071033
2007
69. Increased expression of SIM2-s protein is a novel marker of aggressive prostate cancer.
Halvorsen OJ, Rostad K, Øyan AM, Puntervoll H, Bø TH, Stordrange L, Olsen S, Haukaas SA, Hood L, Jonassen I, Kalland KH, Akslen LA. Clin Cancer Res. 2007 13 (3), 892-7. 10.1158/1078-0432.CCR-06-1207
PubMed 17289882
68. Characterization of early stages of human B cell development by gene expression profiling.
Hystad ME, Myklebust JH, Bø TH, Sivertsen EA, Rian E, Forfang L, Munthe E, Rosenwald A, Chiorazzi M, Jonassen I, Staudt LM, Smeland EB. J Immunol. 2007 179 (6), 3662-71. 10.4049/jimmunol.179.6.3662
67. Growing functional modules from a seed protein via integration of protein interaction and gene expression data.
Maraziotis IA, Dimitrakopoulou K, Bezerianos A. BMC Bioinformatics. 2007 8, 408. 10.1186/1471-2105-8-408
66. CoryneCenter – an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A. BMC Syst Biol. 2007 1, 55. 10.1186/1752-0509-1-55
65. Global gene expression in classification, pathogenetic understanding and identification of therapeutic targets in acute myeloid leukemia.
Oyan AM, Bø TH, Jonassen I, Ulvestad E, Tore Gjertsen B, Bruserud O, Kalland KH. Curr Pharm Biotechnol. 2007 8 (6), 344-54. 10.2174/138920107783018435
64. Comparison of nucleic acid targets prepared from total RNA or poly(A) RNA for DNA oligonucleotide microarray hybridization.
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. Anal Biochem. 2007 366 (1), 46-58. 10.1016/j.ab.2007.03.013
PubMed 17449007
63. ERG upregulation and related ETS transcription factors in prostate cancer.
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. Int J Oncol. 2007 30 (1), 19-32. 10.3892/ijo.30.1.19
62. Hyperoxia retards growth and induces apoptosis and loss of glands and blood vessels in DMBA-induced rat mammary tumors.
Raa A, Stansberg C, Steen VM, Bjerkvig R, Reed RK, Stuhr LE. BMC Cancer. 2007 7, 23. 10.1186/1471-2407-7-23
61. Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins.
Saelensminde G, Halskau Ø, Helland R, Willassen NP, Jonassen I. Extremophiles. 2007 11 (4), 585-96. 10.1007/s00792-007-0072-3
60. TMM@: a web application for the analysis of transmembrane helix mobility.
Skjærven L, Jonassen I, Reuter N. BMC Bioinformatics. 2007 8, 232. 10.1186/1471-2105-8-232
59. Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation.
Stansberg C, Vik-Mo AO, Holdhus R, Breilid H, Srebro B, Petersen K, Jørgensen HA, Jonassen I, Steen VM. BMC Genomics. 2007 8, 94. 10.1186/1471-2164-8-94
58. Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users.
Suhr ML, Dysvik B, Bruland O, Warnakulasuriya S, Amaratunga AN, Jonassen I, Vasstrand EN, Ibrahim SO. Oncol Rep. 2007 18 (5), 1061-75. 10.3892/or.18.5.1061
2006
57. Gene expression profiles of head and neck carcinomas from Sudanese and Norwegian patients reveal common biological pathways regardless of race and lifestyle.
Dysvik B, Vasstrand EN, Løvlie R, Elgindi OA, Kross KW, Aarstad HJ, Johannessen AC, Jonassen I, Ibrahim SO. Clin Cancer Res. 2006 12 (4), 1109-20. 10.1158/1078-0432.CCR-05-0115
56. Protein model refinement using structural fragment tessellation.
Jonassen I, Klose D, Taylor WR. Comput Biol Chem. 2006 30 (5), 360-6. 10.1016/j.compbiolchem.2006.08.002
55. Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
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. Phytochemistry. 2006 68 (1), 19-32. 10.1016/j.phytochem.2006.09.026
54. RBR: library-less repeat detection for ESTs.
Malde K, Schneeberger K, Coward E, Jonassen I. Bioinformatics. 2006 22 (18), 2232-6. 10.1093/bioinformatics/btl368
53. Angiogenesis-independent tumor growth mediated by stem-like cancer cells.
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. PNAS. 2006 103 (44), 16466-71. 10.1073/pnas.0607668103
52. Dynamic domain threading.
Taylor WR, Lin K, Klose D, Fraternali F, Jonassen I. Proteins. 2006 64 (3), 601-14. 10.1002/prot.20915
51. 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.
Øyan AM, Bø TH, Jonassen I, Gjertsen BT, Bruserud Ø, Kalland KH. Int J Oncol. 2006 28 (5), 1065-80. 10.3892/ijo.28.5.1065
2005
50. Gene expression profiles in prostate cancer: association with patient subgroups and tumour differentiation.
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. Int J Oncol. 2005 26 (2), 329-36. 10.3892/ijo.26.2.329
49. Gene expression profiling of minor salivary glands clearly distinguishes primary Sjögren’s syndrome patients from healthy control subjects.
Hjelmervik TO, Petersen K, Jonassen I, Jonsson R, Bolstad AI. Arthritis Rheum. 2005 52 (5), 1534-44. 10.1002/art.21006
48. Guest editorial: WABI special section part 2.
Kim J, Jonassen I. IEEE-ACM Trans Comput Biol Bioinform. 2005 2 (1), 1-2. 10.1109/TCBB.2005.11
47. CD34 expression in native human acute myelogenous leukemia blasts: differences in CD34 membrane molecule expression are associated with different gene expression profiles.
Oyan AM, Bø TH, Jonassen I, Ulvestad E, Gjertsen BT, Kalland KH, Bruserud O. Cytometry B Clin Cytom. 2005 64 (1), 18-27. 10.1002/cyto.b.20044
46. Antidepressant drugs activate SREBP and up-regulate cholesterol and fatty acid biosynthesis in human glial cells.
Raeder MB, Fernø J, Glambek M, Stansberg C, Steen VM. Neurosci Lett. 2005 395 (3), 185-90. 10.1016/j.neulet.2005.10.096
45. Antipsychotic drugs activate SREBP-regulated expression of lipid biosynthetic genes in cultured human glioma cells: a novel mechanism of action?
Fernø J, Raeder MB, Vik-Mo AO, Skrede S, Glambek M, Tronstad KJ, Breilid H, Løvlie R, Berge RK, Stansberg C, Steen VM.
Pharmacogenomics J. 2005 5 (5), 298-304. 10.1038/sj.tpj.6500323
44. Masking repeats while clustering ESTs.
Schneeberger K, Malde K, Coward E, Jonassen I. Nucleic Acids Res. 2005 33 (7), 2176-80. 10.1093/nar/gki511
43. Cloning of the Atlantic salmon (Salmo salar) IL-1 receptor associated protein.
Stansberg C, Subramaniam S, Collet B, Secombes CJ, Cunningham C. Fish Shellfish Immunol. 2005 19 (1), 53-65. 10.1016/j.fsi.2004.11.006
2004
42. LSimpute: accurate estimation of missing values in microarray data with least squares methods.
Bø TH, Dysvik B, Jonassen I. Nucleic Acids Res. 2004 32 (3), e34. 10.1093/nar/gnh026
41. XHM: a system for detection of potential cross hybridizations in DNA microarrays.
Flikka K, Yadetie F, Laegreid A, Jonassen I. BMC Bioinformatics. 2004 5, 117. 10.1186/1471-2105-5-117
40. Guest editorial: WABI special section part 1.
Kim J, Jonassen I. IEEE-ACM Trans Comput Biol Bioinform. 2004 1 (4), 137-138. 10.1109/TCBB.2004.42
39. Different stabilities and denaturation pathways for structurally related aromatic amino acid hydroxylases.
Kleppe R, Haavik J. FEBS Lett. 2004 565 (1-3), 155-9. 10.1016/j.febslet.2004.03.092
38. Construction and validation of cDNA-based Mt6k-RIT macro- and microarrays to explore root endosymbioses in the model legume Medicago truncatula.
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. J Biotechnol. 2004 108 (2), 95-113. 10.1016/j.jbiotec.2003.11.011
37. A graph based algorithm for generating EST consensus sequences.
Malde K, Coward E, Jonassen I. Bioinformatics. 2004 21 (8), 1371-5. 10.1093/bioinformatics/bti184
36. The interleukin 1 receptor family.
Subramaniam S, Stansberg C, Cunningham C. Dev Comp Immunol. 2004 28 (5), 415-28. 10.1016/j.dci.2003.09.016
35. A structural pattern-based method for protein fold recognition.
Taylor WR, Jonassen I. Proteins. 2004 56 (2), 222-34. 10.1002/prot.20073
2003
34. EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F. J Biotechnol. 2003 106 (2-3), 135-46. 10.1016/j.jbiotec.2003.08.010
33. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F. J Biotechnol. 2003 106 (2-3), 157-67. 10.1016/j.jbiotec.2003.08.007
32. Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source.
Hüser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Pühler A, Wiegräbe I, Tauch A. J Biotechnol. 2003 106 (2-3), 269-86. 10.1016/j.jbiotec.2003.08.006
31. Fast sequence clustering using a suffix array algorithm.
Malde K, Coward E, Jonassen I. Bioinformatics. 2003 19 (10), 1221-6. 10.1093/bioinformatics/btg138
30. Cloning and characterisation of a putative ST2L homologue from Atlantic salmon (Salmo salar).
Stansberg C, Subramaniam S, Olsen L, Secombes CJ, Cunningham C. Fish Shellfish Immunol. 2003 15 (3), 211-24. 10.1016/S1050-4648(02)00162-6
29. Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data.
Wang J, Bø TH, Jonassen I, Myklebost O, Hovig E. BMC Bioinformatics. 2003 4, 60. 10.1186/1471-2105-4-60
28. Bioinformatics support for high-throughput proteomics.
Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F. J Biotechnol. 2003 106 (2-3), 147-56. 10.1016/j.jbiotec.2003.08.009
2002
27. New feature subset selection procedures for classification of expression profiles.
Bø T, Jonassen I. Genome Biol. 2002 3 (4), RESEARCH0017. 10.1186/gb-2002-3-4-research0017
26. A fast top-down method for constructing reliable radiation hybrid frameworks.
Bø TH, Jonassen I, Eidhammer I, Helgesen C. Bioinformatics. 2002 18 (1), 11-8. 10.1093/bioinformatics/18.1.11
25. Association of nucleotide patterns with gene function classes: application to human 3′ untranslated sequences.
Conklin D, Jonassen I, Aasland R, Taylor WR. Bioinformatics. 2002 18 (1), 182-9. 10.1093/bioinformatics/18.1.182
24. Structure motif discovery and mining the PDB.
Jonassen I, Eidhammer I, Conklin D, Taylor WR. Bioinformatics. 2002 18 (2), 362-7. 10.1093/bioinformatics/18.2.362
23. Cloning of a Salmo salar interleukin-1 receptor-like cDNA.
Subramaniam S, Stansberg C, Olsen L, Zou J, Secombes CJ, Cunningham C. Dev Comp Immunol. 2002 26 (5), 415-31. 10.1016/S0145-305X(01)00091-X
22. Regulation of tyrosine hydroxylase by stress-activated protein kinases.
Toska K, Kleppe R, Armstrong CG, Morrice NA, Cohen P, Haavik J. J Neurochem. 2002 83 (4), 775-83. 10.1046/j.1471-4159.2002.01172.x
21. Phosphorylation of tyrosine hydroxylase in isolated mice adrenal glands.
Toska K, Kleppe R, Cohen P, Haavik J. Ann N Y Acad Sci. 2002 971, 66-8. 10.1111/j.1749-6632.2002.tb04435.x
2001
20. The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
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. Nucleic Acids Res. 2001 29 (1), 37-40. 10.1093/nar/29.1.37
19. J-Express: exploring gene expression data using Java.
Dysvik B, Jonassen I. Bioinformatics. 2001 17 (4), 369-70. 10.1093/bioinformatics/17.4.369
2000
18. InterPro–an integrated documentation resource for protein families, domains and functional sites.
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, Bioinformatics. 2000 16 (12), 1145-50. 10.1093/bioinformatics/16.12.1145
17. Structure comparison and structure patterns.
Eidhammer I, Jonassen I, Taylor WR. J Comput Biol. 2000 7 (5), 685-716. 10.1089/106652701446152
16. Discovering patterns conserved in sets of unaligned protein sequences.
Jonassen I. Methods Mol Biol. 2000 143, 33-52. 10.1385/1-59259-368-2:33
15. Searching the protein structure databank with weak sequence patterns and structural constraints.
Jonassen I, Eidhammer I, Grindhaug SH, Taylor WR. J Mol Biol. 2000 304 (4), 599-619. 10.1006/jmbi.2000.4211
14. Correlations of receptor binding and metabolic and mitogenic potencies of insulin analogs designed for clinical use.
Kurtzhals P, Schäffer L, Sørensen A, Kristensen C, Jonassen I, Schmid C, Trüb T. Diabetes. 2000 49 (6), 999-1005. 10.2337/diabetes.49.6.999
13. Mining for putative regulatory elements in the yeast genome using gene expression data.
Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E. Proc Int Conf Intell Syst Mol Biol. 2000 8, 384-94. PubMed 10977099
1999
12. Discovery of local packing motifs in protein structures.
Jonassen I, Eidhammer I, Taylor WR. Proteins. 1999 34 (2), 206-19. 10.1002/(SICI)1097-0134(19990201)34:2<206::AID-PROT6>3.0.CO;2-N
1998
11. Approaches to the automatic discovery of patterns in biosequences.
Brazma A, Jonassen I, Eidhammer I, Gilbert D. J Comput Biol. 1998 5 (2), 279-305. 10.1089/cmb.1998.5.279
10. Predicting gene regulatory elements in silico on a genomic scale.
Brazma A, Jonassen I, Vilo J, Ukkonen E. Genome Res. 1998 8 (11), 1202-15. 10.1101/gr.8.11.1202
9. Secretory expression of human albumin domains in Saccharomyces cerevisiae and their binding of myristic acid and an acylated insulin analogue.
Kjeldsen T, Pettersson AF, Drube L, Kurtzhals P, Jonassen I, Havelund S, Hansen PH, Markussen J. Protein Expr Purif. 1998 13 (2), 163-9. 10.1006/prep.1998.0876
1997
8. Efficient discovery of conserved patterns using a pattern graph.
Jonassen I. Comput Appl Biosci. 1997 13 (5), 509-22. 10.1093/bioinformatics/13.5.509
7. Effect of fatty acids and selected drugs on the albumin binding of a long-acting, acylated insulin analogue.
Kurtzhals P, Havelund S, Jonassen I, Markussen J. J Pharm Sci. 1997 86 (12), 1365-8. 10.1021/js9701768
6. Crystal structure of a prolonged-acting insulin with albumin-binding properties.
Whittingham JL, Havelund S, Jonassen I. Biochemistry. 1997 36 (10), 2826-31. 10.1021/bi9625105
1996
5. Discovering patterns and subfamilies in biosequences.
Brazma A, Jonassen I, Ukkonen E, Vilo J. Proc Int Conf Intell Syst Mol Biol. 1996 4, 34-43. PubMed 8877502
4. Albumin binding and time action of acylated insulins in various species.
Kurtzhals P, Havelund S, Jonassen I, Kiehr B, Ribel U, Markussen J. J Pharm Sci. 1996 85 (3), 304-8. 10.1021/js950412j
3. Soluble, fatty acid acylated insulins bind to albumin and show protracted action in pigs.
Markussen J, Havelund S, Kurtzhals P, Andersen AS, Halstrøm J, Hasselager E, Larsen UD, Ribel U, Schäffer L, Vad K, Jonassen I. Diabetologia. 1996 39 (3), 281-8. 10.1007/BF00418343
1995
2. Finding flexible patterns in unaligned protein sequences.
Jonassen I, Collins JF, Higgins DG. Protein Sci. 1995 4 (8), 1587-95. 10.1002/pro.5560040817
1. 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.
Kurtzhals P, Havelund S, Jonassen I, Kiehr B, Larsen UD, Ribel U, Markussen J. Biochem J. 1995 312 ( Pt 3), 725-31. 10.1042/bj3120725