Preprints

Ø. Monsen, L. Grønvold, A. Datsomor, T. N. Harvey, J. Kijas, A. Sang-Jae Suh, T. R. Hvidsten and S. R. Sandve. The role of transposon activity in shaping cis-regulatory element evolution after whole genome duplication. [bioRxiv]

P. Bhattacharjee, D. Blagojevic, Y. K. Lee, G. B. Gillard, L. Grønvold, T. R. Hvidsten, S. R. Sandve, O. C. Lind, B. Salbu, D. A. Brede and J. E. Olsen. High radiosensitivity in Norway spruce (Picea abies) is rendered by less comprehensive mobilisation of protection, repair and stress responses compared to the radiotolerant A. thaliana. [bioRxiv]

Peer-reviewed articles

For citation statistics see Google scholar.

[77] W. Lai, Y. Song, K. E. Tollefsen and T. R. Hvidsten. SOLA: Dissecting dose-response patterns in multi-omics data using a semi-supervised workflow. Frontiers Genetics - Toxicogenomics 15, 2024. [html]

[76] S. Gupta, A. Vera-Poncede León, M. Kodama, M. Hoetzinger, C. G. Clausen, L. Pless, A. R. A. Verissimo, B. Stengel, V. Calabuig, R. Kvingedal, S. Skugor, B. Westereng, T. N. Harvey, A. Nordborg, S. Bertilsson, M. T. Limborg, T. Mørkøre, S. R. Sandve, P. B. Pope, T. R. Hvidsten and S. Leanti La Rosa. The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production. Communications Biology 7: 1391, 2024. [html | bioRxiv]

[75] A. V. P. de Leon, T. Hensen, M. Hoetzinger, S. Gupta, B. Weston, S. M. Johnsen, J. A. Rasmussen, C. G. Clausen, L. Pless, A. R. A. Verissimo, K. Rudi, L. G. Snipen, C. R. Karlsen, M. T. Limborg, S. Bertilsson, I. Thiele, T. R. Hvidsten, S. R. Sandve, P. B. Pope, S. L. La Rosa. Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health, Nature Microbiology 9: 3059–3074, 2024. [html | bioRxiv]

[74] REVIEW: C. M. Kobel, J. Merkesvik, I. M. T. Burgos, W. Lai, O. Øyås, P. B. Pope, T. R. Hvidsten and V. T. E. Aho. Integrating host and microbiome biology using holo-omics. Molecular Omics 20: 438-452, 2024. [html]

[73] T. Harvey, G. B. Gillard, L. L. Røsæg, F. Grammes, Ø. Monsen, J. O. Vik, T. R. Hvidsten and S. R. Sandve.

The genome regulatory landscape of Atlantic salmon liver through smoltification. PloS ONE e0302388, 2024. [html | bioRxiv]

[72] T. N. Harvey, H. Dvergedal, L. Grønvold, Y. Jin, J. Ødegård, S. A. Korsvoll, T. M. Knutsen, T. R. Hvidsten, S. R. Sandve. Linking genomic prediction for muscle fat content in Atlantic salmon to underlying changes in lipid metabolism regulation. Aquaculture 584: 740678, 2024. [html | bioRxiv]

[71] V. Demko, T. Belova, M. Messerer, T. R. Hvidsten, P-F. Perroud, A. E. Ako, W. Johansen, K. F. X. Mayer, O-A. Olsen and D. Lang. Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens. Communications Biology 7: 261, 2024. [html | bioRxiv]

[70] T. O. Andersen, I. Altshuler, A. V. P. de Leon, J. Walter, E. McGovern, K. Keogh, C. Martin, L. Bernard, H. Fougère, D. P. Morgavi, T. Park, J. L. Firkins, Z. Yu, T. R. Hvidsten, S. M. Waters, M. Popova, M. Ø.Arntzen, L. H. Hagen and P. B. Pope. Metabolic influence of core ciliates within the rumen microbiome. The ISME Journal 17: 1128–1140, 2023. [html | bioRxiv]

[69] H. M. Sahlstrom, A. K. Datsomor, Ø. Monsen, T. R. Hvidsten and S. R. Sandve. Functional validation of transposable element derived cis-regulatory elements in Atlantic salmon. G3: Genes|Genomes|Genetics 13: 4, 2023. [html | bioRxiv]

[68] BOOK CHAPTER: K. Arzumanova, R. V. Rohlfs, L. Grønvold, M. A. Strand, T. R. Hvidsten and S. R. Sandve.

Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model. Chapter 11 in Polyploidy (editor: Yves Van de Peer), Methods in Molecular Biology Series 2545: 209-225, 2023. [html]

[67] P. L. Curci, Jie Zhang, N. Mähler, C. Seyfferth, C. Mannapperuma, T. Diels, T. Van Hautegem, D. Jonsen, N. Street, T. R. Hvidsten, M. Hertzberg, O. Nilsson, D. Inze, H. Nelissen and K. Vandepoele. Identification of new leaf intrinsic yield genes using cross-species network analysis in plants. Plant Physiology 190 (4):  2350–2365, 2022. [html | bioRxiv]

[66] S. Birkeland, T. Slotte, A. K. Brysting, A. L. S. Gustafsson, T. R. Hvidsten, C. Brochmann and M. D. Nowak. What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance? Molecular Ecology 31 (16): 4271-4285, 2022. [html | bioRxiv]

[65] K. R. Jonassen, I. Ormaasen, C. Duffner, T. R. Hvidsten, Å. Frostegård, L. R. Bakken, S. H. W. Vick. A dual enrichment strategy provides soil and digestate competent nitrous oxide-respiring bacteria for mitigating climate forcing in agriculture. mBio 28;13 (3): e0078822, 2022. [html | bioRxiv]

[64] C. Seyfferth, B. A. Wessels, J. Vahala, J. Kangasjärvi, N. Delhomme, T. R. Hvidsten, H. Tuominen and J. Lundberg-Felten. Populus ERF85 balances xylem cell expansion and secondary cell wall formation in hybrid aspen. Cells 10 (8): 1971, 2021. [html | bioRxiv]

[63] K. Kajala, L. Shaar-Moshe, G. A. Mason, M. Gouran, J. Medina, D. Kawa, G. Pauluzzi, M. Reynoso, A. Canto-Pastor, V. Lau, M. A. S. Artur, D. A. West, C. Manzano, S. B. Gray, A. I. Yao, M. Bajic, E. Formentin, N. Nirmal, A. Rodriguez, A. Pasha, A. T. Borowsky, R. B. Deal, D. Kliebenstein, T. R. Hvidsten, N. J. Provart, N. Sinha, D. E. Runcie, J. Bailey-Serres and Siobhan M. Brady. Innovation, conservation, and repurposing of gene function in root cell type development. Cell 184 (12): 3333-3348.e19, 2021. [html | bioRxiv]

[62] G. B. Gillard, L. Grønvold, L. L. Røsæg, M. M. Holen, Ø. Monsen, B. F. Koop, E. B. Rondeau, M. Kumar Gundappa, J. Mendoza, D. J. Macqueen, R. V. Rohlfs, S. R. Sandve and T. R. Hvidsten. Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication. Genome Biology 22: 103, 2021. [html | bioRxiv].

[61] M. L. Gandla, N. Mähler, S. Escamez, T. Skotare, O. Obudulu, L. Möller, I. N. Abreu, J. Bygdell, M. Hertzberg, T. R. Hvidsten, T. Moritz, G. Wingsle, J. Trygg, H. Tuominen and L. J. Jönsson. Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees. Biotechnology for Biofuels 14 (1): 43, 2021. [html]

[60] M. A. Strand, Y. Jin, S. R. Sandvea, P. B. Pope and T. R. Hvidsten. Transkingdom network analysis provides insight into host-microbiome interactions in Atlantic salmon. Computational and Structural Biotechnology Journal 19: 1028-1034, 2021. [html]

[59] L. Michalak,  J. C. Gaby, L. Lagos,  S. L. La Rosa,  T. R. Hvidsten, C. Tétard-Jones, W. G. T. Willats,  N. Terrapon,  V. Lombard,  B. Henrissat, J. Dröge,  M. Ø. Arntzen, L. Heldal Hagen, M. Øverland,  P. B. Pope and  B. Westereng. Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut. Nature Communications 11: 5773, 2020. [html | bioRxiv]

[58] F. Delogu, B. J. Kunath,  M. O. Arntzen,  T. R. Hvidsten and P. B. Pope. Integration of absolute multi-omics reveals translational and metabolic interplay in mixed-kingdom microbiomes. Nature Communications 11: 4708, 2020. [html | bioRxiv]

[57] I. N. Abreu, A. I. Johansson, K. Sokołowska, T. Niittylä, B. Sundberg, T. R. Hvidsten, N. R. Street and Thomas Moritz. A metabolite roadmap of the wood‐forming tissue in Populus tremula. New Phytologist 228 (5): 1559-1572, 2020. [html]

[56] N. Mähler, B. Schiffthaler, K. Robinson, B. Terebieniec, M. Vucak, M. Bailey, C. Mannapperume, S. Jansson, T.R. Hvidsten and N. Street. Leaf shape in Populus tremula is a complex, omnigenic trait. Ecology and Evolution 10 (21):

11922-11940, 2020. [html | Authorea].

[55]  T. D. Mulugeta, T. Nome, T.-H. To, M. K. Gundappa, D. J. Macqueen, D. I. Våge, S. R. Sandve, T. R. Hvidsten.

SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes. BMC Genomics 20: 694, 2019. [html]

[54]  M. Schubert, L. Groenvold, S. R. Sandve, T. R. Hvidsten* and S. Fjellheim*. Evolution of cold acclimation and its role in niche transition in the temperate grass subfamily Pooideae. Plant Physiology 180: 404–419, 2019. [html | bioRxiv1 | bioRxiv2]

[53]  Y.-C. Lin, J. Wang, N. Delhomme, B. Schiffthaler, G. Sundström, A. Zuccolo, B. Nystedt, T. R. Hvidsten, A. de la Torre, R. M. Cossu, M. P. Hoeppner, H. Lantz, D. G. Scofield, N. Zamani, A. Johansson, C. Mannapperuma, K. M. Robinson, N. Mähler, I. J. Leitch, J. Pellicer, E.-J. Park, M. Van Montagu, Y. Van de Peer, M. Grabherr, S. Jansson, P. K. Ingvarsson, and N. R. Street. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. PNAS 115 (46): E10970-E10978, 2018. [html]

[52]  B. Kunath, F. Delogu, M. Arntzen, V. G.H. Eijsink,  T. R. Hvidsten,  P. B. Pope. From proteins to polysaccharides: lifestyle and genetic evolution of Coprothermobacter proteolyticus. The ISME journal 13: 603–617, 2018. [html | bioRxiv]

[51]  S. Varadharajan*,  S. R. Sandve*, G. Gillard, O. K. Tørresen, T. Mulugeta, T. R. Hvidsten, S. Lien, L. Asbjørn Vollestad, S. Jentoft,  A. J. Nederbragt and  K. S. Jakobsen. The grayling genome reveals selection on gene expression regulation after whole genome duplication. Genome Biology and Evolution 10 (10): 2785-2800, 2018.  [html | bioRxiv]

[50]  S. R. Sandve, R. V. Rohlfs and  T. R. Hvidsten. Subfunctionalization versus neofunctionalization after whole-genome duplication. Nature Genetics 50: 908–909, 2018. [html | bioRxiv]

[49]  S. Tylewicz, A. Petterle, S. Marttila, P. Miskolczi, A. Azeez, R. K. Singh, J. Immanen, N. Mähler, T. R. Hvidsten, D. M. Eklund, J. L. Bowman, Y. Helariutta and R. P. Bhalerao. Photoperiodic control of seasonal growth is mediated by ABA acting on cell-cell communication. Science 360 (6385): 212-215, 2018. [html]

[48]  J. Felten, J. Vahala, J. Love, A. Gorzsas, M. Rueggeberg, N. Delhomme, J. Lesniewska, J. Kangasjarvi, T. R. Hvidsten, E. J. Mellerowicz and B. Sundberg. Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen. New Phytologist 218 (3): 999-1014, 2018. [html | bioRxiv]

[47]  G. Gillard, T. N. Harvey, A. Gjuvsland, Y. Jin, M. Thomassen, S. Lien, M. Leaver, J. S. Torgersen, T. R. Hvidsten, J. O. Vik and S. R. Sandve. Life-stage-associated remodelling of lipid metabolism regulation in Atlantic salmon. Molecular Ecology 27 (5): 1200-1213, 2018. [html | bioRxiv] 

[46]  O. Obudulu, N. Mähler, T. Skotare, J. Bygdell, I. N. Abreu, M. Ahnlund, M. L. Gandla, A. Petterle, T. Moritz, T. R. Hvidsten, L. Jönsson, G. Wingsle, J. Trygg and H. Tuominen. A multi-omics approach reveals function of Secretory  Carrier-Associated Membrane Proteins in wood formation of Populus trees. BMC Genomics 19: 11, 2018. [html]

[45]  D. Sundell*, N. R. Street*, M. Kumar*, E. J. Mellerowicz, M. Kucukoglu, C. Johnsson, V. Kumar, C. Mannapperuma, N. Delhomme, O. Nilsson, H. Tuominen, E. Pesquet, U. Fischer, T. Niittyla, B. Sundberg, T. R. Hvidsten. AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula. Plant Cell 29 (7): 1585-1604, 2017. [html | bioRxiv]

[44]  F. Robertson, M. Kumar Gundappa, F. Grammes, T. R. Hvidsten, A. Redmond, S. Lien, S. Martin, P. Holland, S. Sandve, D. Macqueen. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biology 18:111, 2017. [html | bioRxiv]

[43]  N. Mähler, J. Wang, B. K. Terebieniec, P. K. Ingvarsson, N. R. Street, T. R. Hvidsten. Gene co-expression network connectivity is an important determinant of selective constraint. PLoS Genetics 13 (4): e1006402, 2017. [html | bioRxiv]

[42]  S. Jokipii-Lukkari*, D. Sundell*, O. Nilsson, T. R. Hvidsten, N. R. Street, H. Tuominen. NorWood: A gene expression resource for evo-devo studies of conifer wood development. New Phytologist 216: 482–494, 2017. [html]

[41]  S. Lien, B. F. Koop, S. R. Sandve, J. R. Miller, M. P. Kent, T. Nome, T. R. Hvidsten, J. S. Leong, D. R. Minkley, A. Zimin, F. Grammes, H. Grove, A. Gjuvsland, B. Walenz, R. A. Hermansen, K. von Schalburg, E. B. Rondeau, A. Di Genova, J. K. A. Samy, J. O. Vik, M. D. Vigeland, L. Caler, U. Grimholt, S. Jentoft, D. I. Våge, P. de Jong, T. Moen, M. Baranski, Y. Palti, D. R. Smith, J. A. Yorke, A. J. Nederbragt, A. Tooming-Klunderud, K. S. Jakobsen, X. Jiang, D. Fan, Y. Hu, D. A. Liberles, R. Vidal, P. Iturra, S. J. M. Jones, I. Jonassen, A. Maass, S. W. Omholt and W. S. Davidson. The Atlantic salmon genome provides insights into rediploidization. Nature 533: 200–205, 2016. [html]

[40]  O.  Obudulu, J. Bygdell , B. Sundberg,  T. Moritz, T. R. Hvidsten, J. Trygg  and G. Wingsle. Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. BMC Genomics 17:119, 2016. [html]

[39]  REVIEW: R. A. Hermansen, T. R. Hvidsten, S. R. Sandve and D. A. Liberles. Extracting functional trends from whole genome duplication events using comparative genomics. Biological Procedures Online 18: 11, 2016. [html]

[38]  REVIEW: P. K. Ingvarsson, T. R. Hvidsten and N. R. Street. Towards integration of population and comparative genomics in forest trees. New Phytologist 212 (2): 338–344, 2016. [html]

[37]  N. Delhomme, G. Sundström, N. Zamani, H. Lantz, Y.-C. Lin, T. R. Hvidsten, M. P. Höppner, P. Jern , Y. Van de Peer, J. Lundeberg, M. G. Grabherr and N. R. Street. Serendipitous Meta-Transcriptomics: the fungal community of Norway spruce (Picea abies). PLoS ONE 10(9): e0139080, 2015 [html]

[36]  D. Sundell*, C. Mannapperuma*, S. Netotea, N. Delhomme, Y-C. Lin, A. Sjödin, Y. Van der Peer, S. Jansson, T. R. Hvidsten and N. Street. The Plant Genome Integrative Explorer Resource: PlantGenIE.org. New Phytologist 208 (4): 1149–1156, 2015. [html]

[35]  PROTOCOL: N. Delhomme, N. Mähler, B. Schiffthaler, D. Sundell, C. Mannapperuma, T. R. Hvidsten and N. R. Street. Guidelines for RNA-Seq data analysis. EpiGeneSys Protocol, 2015. [pdf]

[34]  N. Mähler, O. Cheregi, C. Funk, S. Netotea and T. R. Hvidsten. Synergy: A web resource for exploring gene regulation in Synechocystis sp. PCC6803. PLoS ONE 9(11): e113496, 2014. [html]

[33]  K. M. Robinson*, N. Delhomme*, N. Mähler, B. Schiffthaler, J. Onskog, B. R. Albrectsen, P. K Ingvarsson, T. R. Hvidsten, S. Jansson and N. R. Street. Populus tremula (European aspen) shows no evidence of sexual dimorphism. BMC Plant Biology 14: 276, 2014. [html]

[32]  M. Pfeifer*, K. G. Kugler*, S. R. Sandve, B. Zhan, H. Rudi, T. R. Hvidsten, IWGSC, K. F. X. Mayer and O.-A. Olsen. Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345 (6194): 285-287, 2014. [html]

[31]  S. Netotea, D. Sundell, N. R. Street and T. R. Hvidsten. ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. BMC Genomics 15: 106, 2014. [html]

[30]  J. Immanen, K. Nieminen, H. D. Silva, F. R. Rojas, L. A. Meisel, H. Silva, V. A. Albert, T. R. Hvidsten, Y. Helariutta. Characterization of cytokinin signaling and homeostasis gene families in two hardwood tree species: Populus trichocarpa and Prunus persica. BMC Genomics 14: 885, 2013. [html]

[29]  V. Srivastava*, O. Obudulu*, J. Bygdell, T. Löfstedt, P. Rydén, R. Nilsson, M. Ahnlund, A. Johansson, P. Jonsson, E. Freyhult, J. Qvarnström, J. Karlsson, M. Melzer, T. Moritz, J. Trygg, T. R. Hvidsten and G. Wingsle. OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants. BMC Genomics 14: 893, 2013.  [html]

[28]  B. Nystedt*, N. R. Street*, A. Wetterbom, A. Zuccolo, Y-C. Lin, D. G. Scofield, F. Vezzi, N. Delhomme, S. Giacomello, A. Alexeyenko, R. Vicedomini, K. Sahlin, E. Sherwood, M. Elfstand, L. Gramzow, K. Holmberg, J. Hällman, O. Keech, L. Klasson, M. Koriabine, M. Kucukoglu, M. Käller, J. Luthman, F. Lysholm, T. Niittylä, Å. Olson, N. Rilakovic, C. Ritland, J. A. Rosselló, J. Sena, T. Svensson, C. Talavera-López, G. Theißen, H. Tuominen, K. Vanneste, Z-Q. Wu, B. Zhang, P. Zerbe, L. Arvestad, R. Bhalerao, J. Bohlmann, J. Bousquet, R. Garcia-Gil, T. R. Hvidsten, P. de Jong, J. MacKay, M. Morgante, K. Ritland, B. Sundberg, S. L. Thompson, Y. Van de Peer, B. Andersson, O. Nilsson, P. K. Ingvarsson, J. Lundeberg and S. Jansson. The Norway spruce genome sequence and conifer genome evolution. Nature 497: 579-584, 2013.  [html]

[27]  H. Miranda*, O. Cheregi*, S. Netotea, T. R. Hvidsten, T. Moritz and C. Funk. Co-expression analysis, proteomic and metabolomic study on the impact of a Deg/HtrA protease triple mutant in Synechocystis sp. PCC 6803 exposed to temperature and high light stress. Journal of Proteomics 78: 294 – 311, 2013 (online 2012). [html]

[26]  J. Önskog, E. Freyhult, M. Landfors, P. Rydén and T. R. Hvidsten. Classification of microarrays; synergistic effects between normalization, gene selection and machine learning. BMC Bioinformatics 12: 390, 2011. [html]

[25]  K. Baba*, A. Karlberg*, J. Schmidt, J. Schrader, T. R. Hvidsten, L. Bako and R. P. Bhalerao. Activity-dormancy transition in the cambial meristem involves stage specific modulation of auxin response in Hybrid Aspen. PNAS 108 (8): 3418-3423, 2011. [html]

[24]  N. Street, S. Jansson and T. R. Hvidsten. A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. BMC Plant Biology 11: 13, 2011. [html]

[23]  E. Freyhult, M. Landfors, J. Önskog, T. R. Hvidsten and P. Rydén. Challenges in microarray class discovery: a comprehensive examination of normalization, gene selection and clustering, BMC Bioinformatics 11: 503, 2010. [html]

[22]  REVIEW: B. Wilczynski and T. R. Hvidsten. A computer scientist’s guide to the regulatory genome. Fundamenta Informaticae 103: 323-332, 2010. [html]

[21]  T. R. Hvidsten, A. Lægreid, A. Kryshtafovych, G. Andersson, K. Fidelis and J. Komorowski. A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity. PLoS ONE 4(7): e6266, 2009. [pdf | html]

[20]  P. Björkholm, P. Daniluk, A. Kryshtafovych, K. Fidelis, R. Andersson and T. R. Hvidsten. Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics 25: 1264-1270, 2009. [pdf | html]

[19]  T. R. Hvidsten*, A. Kryshtafovych* and K. Fidelis. Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions, Proteins: Structure, Function, and Bioinformatics 75 (4): 870-884, 2009. [pdf | html]

[18]  K. Wabnik, T. R. Hvidsten, A. Kedzierska, J. Van Leene, G. De Jaeger, G. T. S. Beemster, J. Komorowski and M. T. R. Kuiper. Gene expression trends and protein features effectively complement each other in gene function prediction, Bioinformatics 25 (3):322-330, 2009. [pdf | html]

[17]  BOOK CHAPTER: J. Fahlén, M. Landfors, E. Freyhult, J. Trygg, T. R. Hvidsten and P. Rydén. Bioinformatic strategies for cDNA-microarray data processing. Chapter 6 in Batch Effects and Noise in Microarray Experiments: Sources and Solutions, John Wiley & Sons, 2009. [html]

[16]  H. Strömbergsson, P. Daniluk, A. Kryshtafovych, K. Fidelis, J. E. S. Wikberg, G. J. Kleywegt and T. R. Hvidsten. An Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space, Journal of Chemical Information and Modeling 48 (11): 2278–2288, 2008. [pdf | html]

[15]  R. Andersson, C. Bruder, A. Piotrowski, U. Menzel, T. D. de Ståhl, T. R. Hvidsten, J. Dumanski, J. Komorowski. A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling, Bioinformatics 24(6): 751-758, 2008. [pdf | html]

[14]  C. R. Andersson*, T. R. Hvidsten*, A. Isaksson, M. G. Gustafsson, J. Komorowski. Revealing cell cycle control by combining model-based detection of periodic expression with cis-regulatory descriptors, BMC Systems Biology 1: 45, 2007. [pdf | html]

[13]  U. Bergström*, J. A. Olsson*, T. R. Hvidsten, J. Komorowski, I. Brandt. Differential gene expression in the olfactory bulb following exposure to the olfactory toxicant 2,6-dichlorophenyl methylsulphone and its 2,5-dichlorinated isomer in mice, NeuroToxicology 28 (6): 1120-1128, 2007. [html]

[12]  REVIEW: T. R. Hvidsten and J. Komorowski. Rough sets in bioinformatics, Transactions on Rough Sets VII edited by E. Orlowska, J. F. Peters and A. Skowron, Lecture notes in computer science 4400, pp. 225-243, Springer-Verlag Berlin Heidelberg New York, 2007. [pdf | html]

[11]  B. Wilczyński, T. R. Hvidsten, A. Kryshtafovych, J. Tiuryn, J. Komorowski, K. Fidelis. Using Local Gene Expression Similarities to Discover Regulatory Binding Site Modules, BMC Bioinformatics 7:505, 2006. [pdf | html]

[10]  H. Strömbergsson, A. Kryshtafovych, P. Prusis, K. Fidelis, J. E. S. Wikberg, J. Komorowski and T. R. Hvidsten. Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures, Proteins: Structure, Function and Bioinformatics 65: 568-579, 2006. [pdf | html]

[9]  T. R. Hvidsten, B. Wilczyński, A. Kryshtafovych, J. Tiuryn, J. Komorowski and K. Fidelis. Discovering regulatory binding site modules using rule-based learning, Genome Research 15: 856-66, 2005. [pdf | html | supplement]

[8]  J. L. Dennis, T. R. Hvidsten, J. Komorowski, E. C. Wit, A. Bell, I. Downie, J. Mooney, C. Verbeke, C. Bellamy, W.N. Keith and K.A. Oien. Markers of Adenocarcinoma Characteristic of the Site of Origin – Development of a Diagnostic Algorithm, Clinical Cancer Research 11(10): 3766-72, 2005. [pdf | html]

[7]  T. R. Hvidsten, A. Lægreid and J. Komorowski. Learning rule-based models of biological process from gene expression time profiles using gene ontology, Bioinformatics 19:1116-23, 2003. [pdf | html | supplement]

[6]  A. Lægreid, T. R. Hvidsten, H. Midelfart, J. Komorowski, and A. K. Sandvik. Predicting Gene Ontology Biological Process from Temporal Gene Expression Patterns, Genome Research 13(5): 965-979, 2003. [pdf | html | supplement]

[5]  T. R. Hvidsten, A. Kryshtafovych, J. Komorowski and K. Fidelis. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins, ECCB2003, Bioinformatics 19 Suppl 2: II81-II91, 2003. [pdf | html]

[4]  REVIEW: J. Komorowski, T. R. Hvidsten, T.-K. Jenssen, D. Tjeldvoll, E. Hovig, A. Lægreid and A. K. Sandvik. New knowledge derived from measurement of gene expression with the DNA microarray method, Tidsskr Nor Lægeforen 121 (10): 1229-1232, 2001. [pdf | html]

[3]  T. R. Hvidsten, J. Komorowski, A. K. Sandvik and A. Lægreid. Predicting Gene Function from Gene Expressions and Ontologies, in Pacific Symposium on Biocomputing 6: 299-310, 2001. [pdf | html]

[2]  J. Komorowski, T. R. Hvidsten, T.-K. Jenssen, D. Tjeldvoll, E. Hovig, A. K. Sandvik and A. Lægreid. Towards Knowledge Discovery from cDNA Microarray Gene Expression Data, in Principles of Data Mining and Knowledge Discovery (PKDD'2000) edited by Djamel A. Zighed, Jan Komorowski and Jan Zytkow, Lecture Notes in Computer Science 1910: 470-475, 2000. [pdf | html]

[1]  T. R. Hvidsten, M. S. Bjanger, J. Komorowski, M. F. White and B. Guanglai.  Fault Diagnosis in Rotating Machinery using Rough Sets and Rosetta, in European Congress on Intelligent Techniques & Soft Computing (EUFIT'99), Aachen, September 1999. [pdf | pdf complete report]

* Contributed equally.

Color map: First author,  Second author, Middle author,  Second last author, Last author.