Peer-reviewed research articles

Reviews, book chapters and theses

Abstracts and posters

• N. Street, T. R. Hvidsten, B. Sundberg, Y-C. Lin, S. Netotea and Stefan Jansson. Large-‐scale RNA-‐Seq transcriptomics studies exploring wood development and natural variation in aspen (P. tremula): projects and resource development. Plant and Animal Genome XX Conference. January 14-18, 2012, San Diego, USA.
  
• V. Srivastava, O. Obudulu, J. Bygdell, P. Ryden, R. Nilsson, P. Jonsson, E. Freyhult, J. Quarnström, J. Karlsson,  T. Moritz, T. R. Hvidsten, J. Trygg and G. Wingsle. A systems biology approach to studying global response to oxidative stress in Populus. Metabomeeting 2011, September 25-28, Helsinki, Finland.
• S. Netotea, F. Richard and T. R. Hvidsten. Modeling adaptive changes in Populus metabolic and transcriptional networks. 1st Conference on Constraint-based Reconstruction and Analysis (COBRA), June 24-26, 2011, Reykjavik, Iceland.
• F. Lysholm, P. Björkholm, T. R. Hvidsten, B. Persson. Residue-residue contact prediction through matching of known motifs. Critical Assessment of Techniques for Protein Structure Prediction (CASP9), December 5-9, 2010, Asilomar Conference Center, Pacific Grove, CA, USA.
• P. Björkholm, F. Lysholm, A. Kryshtafovych, K. Fidelis, and T. R. Hvidsten. FragHMMent – Contact prediction using hidden Markov models trained on alignments of local descriptors of protein structure. Critical Assessment of Techniques for Protein Structure Prediction (CASP9), December 5-9, 2010, Asilomar Conference Center, Pacific Grove, CA, USA.
• S. Netotea and T. R. Hvidsten. Inferring gene regulatory networks to identify conserved regulation between Arabidopsis and Populus. ECCB, Sep 26 - Sep 29, 2010, Ghent, Belgium.
• P. Björkholm, P. Daniluk, A. Kryshtafovych, K. Fidelis, R. Andersson and T. R. Hvidsten. FragHMMent: Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. ISMB and ECCB, June 27-July 2, 2009, Stockholm, Sweden.
• B. Dedicova, T. R. Hvidsten, O. Nilsson, U.  Egertsdotter. Cryopreservation and survival ability of different Elite embryogenic lines of Norway spruce. 1st International Symposium on Cryopreservation in Horticultural Species, April 5-8, 2009, Leuven, Belgium.
• N. Street, S. Jansson and T. R. Hvidsten. A systems biology approach to model the transcriptional network in trees. UPSC meeting: Future directions in plant research, March 16-18, 2009, Gålsjö bruk, Sweden.
• P. Björkholm, P. Daniluk, A. Kryshtafovych, K. Fidelis, R. Andersson and T. R. Hvidsten. Predicting residue-residue contacts using hidden Markov models trained on local neighborhoods of protein structure. Critical Assessment of Techniques for Protein Structure Prediction (CASP8), December 3-7, 2008, Cagliari, Sardinia, Italy.
• J. E. S. Wikberg, M. Eklund, O. Spjuth, H. Strömbergsson, T. R. Hvidsten and M. Lapins. Proteochemometrics. 17th European Symposium on QSAR in ”omics” and Systems biology, September 21-26, 2008, Uppsala, Sweden.
• P. Björkholm og T. R. Hvidsten. Method for recognizing local descriptors of protein structure using Hidden Markov Models. 8th Swedish Bioinformatics Workshop for Ph.D. Students and Postdocs, February 28-29th, 2008, Uppsala, Sweden.
• H. Strömbergsson, T. R. Hvidsten, J. E. S. Wikberg, A. Kryshtafovych, P. Daniluk, K. Fidelis and G. J. Kelywegt. Enzyme Wide Modeling of Protein-Ligand Interactions. ISMB/ECCB: 3DSIG: The 3rd Structural Bioinformatics and Computational Biophysics Satellite Meeting, pp. 62, 19-20 July, 2007, Vienna, Austria.
• T. R. Hvidsten, A. Kryshtafovych, P. Daniluk, K. Fidelis and J. Komorowski. Prediction of protein function using local descriptors of protein structure. Critical Assessment of Techniques for Protein Structure Prediction (CASP7), November 26-30, 2006, Asilomar Conference Center, Pacific Grove, CA, USA.
• H. Strömbergsson and T. R. Hvidsten. Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures. Tenth Annual Conference of the Swedish Structural Biology Network, 16-19 June, 2006, Tällberg, Sweden.
• T. R. Hvidsten, B. Wilczynski, A. Kryshtafovych, J. Tiuryn, J. Komorowski and K. Fidelis. Learning regulatory binding site modules from sequence and expression data. Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB), April 2-5, 2006, Venice, Italy.
• U. Bergström, J. A. Olsson, T. R. Hvidsten, J. Komorowski, J. Brandt. Altered Gene Expression in the Olfactory Bulb Following Exposure to 2,6-Dichlorophenyl Methylsulfone. Eurotox: The 42nd Congress of the European Societies of Toxicology, September 11-14, 2005, Cracow, Poland.
• J. L. Dennis, T. R. Hvidsten, E. C. Wit, J. Komorowski, A. K. Bell, I. Downie, J. Mooney, C. Verbeke, C. Bellamy, W. N. Keith, K. A. Oien. Markers of adenocarcinoma characteristic of the site of origin - Development of a diagnostic algorithm. 187th Meeting of the Pathological-Society-of-Great-Britain-and-Ireland, January 6-7, 2005, London, England.
• T. R. Hvidsten, A. Kryshtafovych, P. Daniluk, K. Fidelis, J. Komorowski. Predicting function from local substructures of proteins. 5th Swedish Bioinformatics Workshop for Ph.D. Students and Postdocs, November 26-27th, 2004, Lund, Sweden.
• R. Andersson, J. Vesterlund, T. R. Hvidsten and J. Komorowski. Genomic Rosetta: a toolkit for functional genomics. 5th Swedish Bioinformatics Workshop for Ph.D. Students and Postdocs, November 26-27th, 2004, Lund, Sweden.
• A. Johansson, H. Midelfart, T. R. Hvidsten and J. Komorowski. A Rough Set approach to functional classification of genes using a combination of heterogeneous data sources, Bioinformatics 2004, June 3-6, Linköping, Sweden.
• P. Daniluk, A. Kryshtafovych, T. R. Hvidsten, J. Komorowski and K. Fidelis. Identifying structural similarity of proteins using local descriptors of protein structure, Pacific Symposium on Biocomputing 2004, Hawaii, USA.
• B. Wilczynski, T. R. Hvidsten, A. Kryshtafovych, J. Komorowski and K. Fidelis. An iterative approach to gene regulation pathways discovery, Pacific Symposium on Biocomputing 2004, Hawaii, USA.
• A. Kryshtafovych, T.R. Hvidsten, J. Komorowski, K. Fidelis. Fold Recognition Using Sequence Fingerprints of Protein Local Substructures. CSB 2003, 517-518, Stanford, 11-14. August, 2003.
• B. Wilczynski, T.R. Hvidsten, A. Kryshtafovych, L. Stubbs, J. Komorowski, K. Fidelis. A rule-based framework for gene regulation pathways discovery. CSB 2003, 517-518, Stanford, 11-14. August, 2003.
• T. R. Hvidsten, A. Kryshtafovych, K. Fidelis and J. Komorowski. A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins, Bioinformatics 2003, May 22-24, Helsinki, Finland.
• B. Wilczynski, T.R. Hvidsten, A. Kryshtafovych, L. Stubbs, J. Komorowski and K. Fidelis. Identifying Gene Regulation Mechanisms based on Local Gene Expression Similarities using Rule Based Classifiers, in Currents in Computational Molecular Biology - RECOMB 2003, edited by R. Spang, P. Beziat and M. Vingron, pp. 293, April 10-13, 2003, Berlin, Germany.
• T. R. Hvidsten, A. Kryshtafovych, J. Komorowski and K. Fidelis. Applying sequence-derived features from similar 3-D local structures to protein fold recognition, in Currents in Computational Molecular Biology - RECOMB 2003, edited by R. Spang, P. Beziat and M. Vingron, pp. 191-192, April 10-13, 2003, Berlin, Germany.
• A. Kryshtafovych, T. R. Hvidsten, J. Komorowski, P. Daniluk, M. Wilczynska and K. Fidelis. Automated local structure based classification of protein folds, Pacific Symposium on Biocomputing 2003, Hawaii, USA.
• T. R. Hvidsten, A. Kryshtafovych, J. Komorowski and K. Fidelis. Identifying gene regulation mechanisms using rule based classifiers, Pacific Symposium on Biocomputing 2003, Hawaii, USA.
• T. R. Hvidsten. Protein fold prediction using sequence based features from local structures, 3rd Annual Workshop in Bioinformatics for PhD Students and PostDocs, November 22-23, 2002, Stockholm, Sweden.
• T. R. Hvidsten, A. Kryshtafovych, A. Zemla, R. Vemuri, J. Komorowski and K. Fidelis. Applying sequence derived feature templates based on 3-D local structures to protein fold recognition, Bioinformatics 2002, April 4-7, Bergen, Norway.
• H. Midelfart, W. Kusnierczyk, T. R. Hvidsten, A. Lægreid and J. Komorowski. Learning Yeast Gene Function from Expression Programs and Gene Ontology, in Conference Proceedings of the Norwegian Biochemical Society’s Wintermeeting, pp. 63, January 17-20, 2002, Røros, Norway.
• T. R. Hvidsten, A. K. Sandvik, H. Midelfart, A. Lægreid and J. Komorowski. A method based on rough set supervised learning used to predict the biological function of unknown genes from DNA microarray gene expression data, in Conference Proceedings of the Third International Meeting on Microarray Data Standards, Annotations, Ontologies and Databases, pp. 167, Mars 28-30, 2001, Stanford University, Palo Alto, USA.
• J. Komorowski, A. Lægreid, T. R. Hvidsten, T.-K. Jenssen, A. K. Sandvik and D. Tjeldvoll. A methodology and tools for knowledge discovery from gene expressions, Bioinformatics 2000, Denmark.
• D. Tjeldvoll, A. Lægreid, T. R. Hvidsten, T.-K. Jenssen, A. K. Sandvik and J. Komorowski. Semi-automatic annotation of genes, Bioinformatics 2000, Denmark.
• T. R. Hvidsten, T.-K. Jenssen, J. Komorowski, A. Lægreid, A. K. Sandvik and D. Tjeldvoll. Template-based gene expression analysis, in Currents in Computational Molecular Biology - RECOMB 2000, edited by S. Miyano, R. Shamir and T. Takagi, pp. 10-11, ISBN 4-946443-61-4, Universal Academy Press, Inc, April 8-11, 2000, Tokyo, Japan.
• T. R. Hvidsten, J. Komorowski, A. K. Sandvik and A. Lægreid. A framework for learning gene functions from microarray data, NBS Vintermøte 2001 - 37. Norwegian Biochemical Society’s Wintermeeting, Beitostølen.
• T. R. Hvidsten, T.-K. Jenssen, A. Lægreid, A. Øhrn and J. Komorowski. Boolean reasoning in the clustering of gene expression data, Data Mining for Bioinformatics – Towards In Silico Biology, November 10-12 1999, Hinxton – Cambridge, UK.