Publications

Articles

Frygelius J., Arvestad L., Wedell A. and Töhönen V. (2010)

Evolution and human tissue expression of the Cres/Testatin subgroup genes, a reproductive tissue-specific subgroup of the type 2 cystatins.

Evolution and Development: 12, 329-342

Stranneheim H., Käller M., Allander T., Andersson B., Arvestad L. and Lundeberg J. (2010)

Classification of DNA sequences using Bloom filters.

Bioinformatics: 26, 1595-1600

Fugelstad J., Bouzenzana J., Djerbi S., Guerriero G., Ezcurra I., Teeri T. T., Arvestad L. and Bulone V. (2009)

Identification of the cellulose synthase genes from the Oomycete Saprolegnia monoica and effect of cellulose synthesis inhibitors on gene expression and enzyme activity.

Fungal Genetics and Biology: 46, 759-767

Arvestad L., Lagergren J. and Sennblad B. (2009)

The gene evolution model and computing its associated probabilities.

Journal of the ACM: 56, 1-44

Åkerborg Ö., Sennblad B., Arvestad L. and Lagergren J. (2009)

Simultaneous bayesian gene tree reconstruction and reconciliation analysis.

Proc. Nat. Acad. Sci. USA: 106, 5714-5719

Rajangam A. S., Yang H., Teeri T. T. and Arvestad L. (2008)

Evolution of a domain conserved in microtubule-associated proteins of eukaryotes.

Computational Biology and Chemistry: Advances and Applications: 1, 51-69

Rajangam A. S., Kumar M., Aspeborg H., Guerriero G., Arvestad L., Pansri P., Brown C. J.-L., Hober S., Blomqvist K., Divne C., Ezcurra I., Mellerowicz E., Sundberg B., Bulone V. and Teeri T. T. (2008)

MAP20, a microtubule-associated protein in the secondary cell walls of Populus tremula L. x tremuloides Michx is a target of the cellulose synthesis inhibitor, 2,6-dichlorobenzonitrile.

Plant Physiology: 148, 1283-1294

Sennblad B., Schreil E., Sonnhammer A.-C. B., Lagergren J. and Arvestad L. (2007)

primetv: A viewer for reconciled trees.

BMC Bioinformatics: 8

Roth C., Rastogi S., Arvestad L., Dittmar K., Light S., Ekman D. and Liberles D. (2007)

Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms.

J Exp Zoolog B Mol Dev Evol

Arvestad L. (2006)

Efficient methods for estimating amino acid replacement rates.

J Mol Evol: 62, 663-673

Svensson Ö., Arvestad L. and Lagergren J. (2006)

Genome-wide survey for biologically functional pseudogenes.

PLoS Comput Biol: 2, e46

Arvestad L., Visa N., Lundeberg J., Wieslander L. and Savolainen P. (2005)

Expressed sequence tags from the midgut and an epithelial cell line of Chironomus tentans: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels.

Insect Mol Biol: 14, 689-695

Djerbi S., Lindskog M., Arvestad L., Sterky F. and Teeri T. (2005)

The genome sequence of black cottonwood (Populus trichocarpa) reveals 18 conserved cellulose synthase (CesA) genes.

Planta: 221, 739-746

Savolainen P., Fitzsimmons C., Arvestad L., Andersson L. and Lundeberg J. (2005)

ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels.

Cytogenet Genome Res: 111, 79-87

Hollich V., Milchert L., Arvestad L. and Sonnhammer E. (2005)

Assessment of protein distance measures and tree-building methods for phylogenetic tree reconstruction.

Mol Biol Evol: 22, 2257-2264

Arvestad L., Berglund A., Lagergren J. and Sennblad B. (2003)

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

Bioinformatics: 19 Suppl 1, i7-15

Savolainen P., Arvestad L. and Lundeberg J. (2000)

mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats..

Mol Biol Evol: 17, 474-488

Savolainen P., Arvestad L. and Lundeberg J. (2000)

A novel method for forensic DNA investigations: repeat-type sequence analysis of tandemly repeated mtDNA in domestic dogs..

J Forensic Sci: 45, 990-999

Arvestad L. and Bruno W. (1997)

Estimation of reversible substitution matrices from multiple pairs of sequences..

J Mol Evol: 45, 696-703

Conferences

Arvestad L., Berglund A., Lagergren J. and Sennblad B. (2004):

Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution.

Proceedings of 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB). ACM Press New York, NY, USA , pages 326-335.

Arvestad L. (1997):

Aligning coding DNA in the presence of frame-shift errors.

8th annual symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science, Springer.