We are using comparative genomics and DNA and protein sequence analysis to examine the structure, function and evolution of genes. We have considered protein genes as well as non-coding RNAs (nc-RNA), i.e RNA that do not code for proteins but have other functions. The evolution of proteins is being studied in a number of projects where we make use of tools such as gene prediction, profile-based searches and methods of phylogenetic analysis. We have developed methods to effectively identify ncRNAs in genomic sequences and have applied these methods on a large number of ncRNA families. We have identified a large number of previously unrecognized homologues and these results have allowed a better understanding of the secondary structure and evolution of these RNAs.

RNA bioinformatics    

•  SRP RNA
  
• SRPDB
• SRPSCAN, prediction of SRP RNA genes
• P and MRP RNA
  
• Identification of P and MRP RNAs
• Iron responsive element
  
• Evolution of the iron responsive element
• Stem-loop motif of histone mRNA
  • 3' end processing of histone mRNA
• Evolution of U12 introns

The evolution of proteins and protein domains.

• Bioinformatic analysis of mucin proteins (with Gunnar C. Hansson, GU)
  
• Proteins of ribonucleases P and MRP
• Eukaryotic Gene Order Browser (eGOB)

Recent publications

• Genomics and Bioinformatics - An Introduction to Programming Tools for Life Scientists Cambridge University Press 2012 (available from May 2012). Web resources to book.

• Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C. RNAcentral: A vision for an international database of RNA sequences. RNA. 2011 Sep 22
• Davila Lopez, M., and Samuelsson, T. eGOB : Eukaryotic Gene Order Browser Bioinformatics 2011 Apr 15;27(8):1150-1.

• Sterky FH, Ruzzenente B, Gustafsson CM, Samuelsson T, Larsson NG LRPPRC is a mitochondrial matrix protein that is conserved in metazoans BBRC 2010
• Spår, H, Samuelsson T, Martin Hällberg B, Gustafsson CM. Structure of Mitochondrial Transcription Termination Factor 3 reveals a novel nucleic acid-binding domain BBRC 2010.
• Davila Lopez, M., Martinez Guerra, J.J., Samuelsson, T. Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes. 2010 PLOS ONE.
• Bartschat S, Samuelsson T. U12 type introns were lost at multiple occasions during evolution . 2010 BMC Genomics.

• Rosenblad MA, Larsen N, Samuelsson T, Zwieb C Kinship in the SRP RNA familyi 2009. RNA biology
• Davila Lopez, M., Alm Rosenblad, M., and Samuelsson, T. Conserved and variable domains of RNase MRP RNA. 2009. RNA Biology.
• Kalen,M, Wallgard E, Asker N, Nasevicius A, Athley E, Billgren E, Larson JD, Wadman SA, Norseng E, Clark KJ, He L, Karlsson-Lindahl L, Häger AK, Weber H, Augustin H, Samuelsson T, Kemmet CK, Utesch CM, Essner JJ, Hackett PB, Hellström Combination of reverse and chemical genetic screens reveals angiogenesis inhibitors and targets. Chem Biol. 2009 Apr 24;16(4):432-41

• Davila Lopez, M., Alm Rosenblad, M., and Samuelsson, T. Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. 2008 May;36(9):3001-10.
• Davila Lopez, M., Samuelsson, T. Early evolution of histone mRNA 3' end processing RNA. 2008 Jan;14(1):1-10.
• He L, Sun Y, Takemoto M, Norlin J, Tryggvason K, Samuelsson T and Betsholtz C: From cataloguing glomerulus-enriched gene transcripts towards systematic understanding of kidney glomeruli. Journal of American S ociety of Nephrology 2008 Feb;19(2):260-8

• Lang, T., Hansson, GC., Samuelsson T. Gel-forming mucins appeared early in metazoan evolution. Proc Natl Acad Sci U S A. 2007 104, 16209-16214
• Piccinelli, P. and Samuelsson, T. Evolution of the iron responsive elementi 2007 RNA 13(7):952-66.
• Häsler, J., Samuelsson, T., Strub, K. Useful junk: Alu RNAs in the human transcriptome. 2007 Cellular and Molecular Life Sciences 64(14):1793-800.
• Isaksson A, Berggren M, Ekeland-Sjoberg K, Samuelsson T, Ricksten A. Cell specific internal translation efficiency of Epstein-Barr virus present in solid organ transplant patients. J Med Virol. 2007 Mar 26;79(5):573-581
• He L, Sun Y, Patrakka J, Mostad P, Norlin J, Xiao Z, Andrae J, Tryggvason K, Samuelsson T, Betsholtz C, Takemoto M. Glomerulus-specific mRNA transcripts and proteins identified through kidney expressed sequence tag database analysis. Kidney Int. 2007 Feb 28

• Rosenblad,MA, López, MD., Piccinelli, P. and Samuelsson, T. Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. Nucleic Acids Res. 2006;34(18):5145-56.
• Lang T, Hansson GC, Samuelsson T. An inventory of mucin genes in the chicken genome shows that the mucin domain of Muc13 is encoded by multiple exons and that ovomucin is part of a locus of related gel-forming mucins. BMC Genomics. 2006 Aug 3;7(1):197
• Takemoto M, He L, Norlin J, Patrakka J, Xiao Z, Petrova T, Bondjers C, Asp J, Wallgard E, Sun Y, Samuelsson T, Mostad P, Lundin S, Miura N, Sado Y, Alitalo K, Quaggin SE, Tryggvason K, Betsholtz C. Large-scale identification of genes implicated in kidney glomerulus development and function. EMBO J. 2006 Mar 8;25(5):1160-74.
• Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C. The tmRDB and SRPDB resources. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D163-8.
• Gariani T, Samuelsson T, Sauer-Eriksson AE. Conformational variability of the GTPase domain of the signal recognition particle receptor FtsY. J Struct Biol. 2006 Jan;153(1):85-96.

PhD students

Teaching

• Introduction to bioinformatics
• Sequence bioinformatics