HVIDSTEN RESEARCH GROUP

For citation statistics see Google scholar or ISI Web of Science.

 

Preprints

 

  1. M. Schubert, L. Groenvold, S. R. Sandve, T. R. Hvidsten and S. Fjellheim. Evolution of cold acclimation in temperate grasses (Pooideae). bioRxiv doi:10.1101/210021, 2017. [bioRxiv]

 

  1. 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. bioRxiv doi:10.1101/204602, 2017. [bioRxiv]

 

  1. S. R. Sandve, R. V. Rohlfs and T. R. Hvidsten. Subfunctionalization versus neofunctionalization after whole-genome duplication. bioRxiv doi:10.1101/190090, 2017. [bioRxiv]

 

  1. L. Groenvold, M. Schubert, S. R. Sandve, S. Fjellheim and T. R. Hvidsten. Comparative transcriptomics provides insight into the evolution of cold response in Pooideae. bioRxiv doi:10.1101/151431, 2017. [bioRxiv]

 

  1. 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. Diet And Life Stage Associated Remodeling Of Lipid Metabolism Regulation In The Duplicated Atlantic Salmon Genome. bioRxiv doi:10.1101/140442, 2017. [bioRxiv]

 

Peer-reviewed research articles

 

  1. 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. [pdfhtmlbioRxiv]

 

  1. 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. [pdf | html | bioRxiv]

 

  1. 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. [pdf | html | bioRxiv]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdf html]

 

  1. 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. [pdfhtml]

 

  1. 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 [pdfhtml]

 

  1. 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. [pdf | html]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdf | html]

 

  1. 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. [pdf | html]

 

  1. 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. [pdf | html]

 

  1. 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. [pdf | html]

 

  1. 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. [pdf | html]

 

  1. 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. [pdf | html]

 

  1. 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). [pdf | html]

 

  1. 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. [pdfhtml]

 

  1. 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. Proceedings of the National Academy of Sciences 108 (8): 3418-3423, 2011. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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]

 

  1. 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]

 

  1. 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. [pdfhtml]

 

  1. 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]

 

  1. 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]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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]

 

  1. 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. [pdfhtml]

 

  1. 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. [pdfhtml]

 

  1. 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]

 

  1. 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. [pdfhtml]

 

  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. [pdfpdf complete report]

 

 

* Contributed equally.

 

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