Martti T. Tammi Ph.D. Uppsala University, Sweden Assistant Professor Joint Appointment DBS / Biochemistry Room: DBS, S2-04-05 Phone : 6516 4255 E-mail: dbstmt@nus.edu.sg Research Associate, Karolinska Institutet, Sweden

Research Areas

Bioinformatics methods development: Large-scale genome sequencing methods, sequence alignment, clustering and database search algorithms, pattern recognition, and comparative genomics.

Research Interests

In the wake of large genome sequencing projects, the rapid development of laboratory techniques have resulted in a huge scaling up of data production. The amount of sequence data is growing rapidly and so is the need to include more data into biological analysis processes. Large scale research is carried out in many different levels including genome, proteome, transcriptome, and metabolome levels, rapidly increasing the wealth of data. Therefore, the most important challenge facing the molecular biology today is to make sense of this mass of data. My interest is in developing computer tools and algorithms that allow extraction of useful biological information - in particular finding biologically meaningful solutions to NP-complete problems with a reasonable amount of computation.

1. A large number of human diseases have unknown etiology, and in many cases, infection by an unrecognized virus is a possibility. Now and then, we are faced with severe outbreaks of new and unknown virus infections. A general method for rapid identification of the agent is crucial. My lab is collaborating with Karolinska Hospital and Karolinska Institutet to develop a large-scale screening method of virus sequences in clinical samples.

2. It is important to develop algorithms that are able to cope with the challenge of continuously increasing amounts of data. We are developing an analysis tool, which is able to analyze very large data sets. Analyzes can be rapidly performed in computer clusters alternatively small mammalian genomes in an ordinary desktop. The software is based on smart cache methods, approximate matching of q-grams and the previously developed DNP method. The basic engine can be coupled with different analysis algorithms. The software is used for genome wide comparative analyses of four chicken strains and analysis of repeats in an extremely repetitive parasite genome.

3. A large number of genomes have been sequenced. However, complicated parts of these genomes tend to be left unfinished to a large extent. This is due to a lack of tools to resolve complex regions, including repeated regions and cases where homologous chromosomes show a high degree of polymorphism. To gain better understanding of the sequenced organisms, repeated regions should be resolved. We are developing a graphical assembly editing and visualization tool, specifically designed for finishing and analysis of complex genomes. Analysis can be performed in semi-automatic fashion. The software uses a combination of mate pair and DNP information, making it a powerful tool for resolving nearly identical repeats.

4. Development of novel sequence classification method to solve two seemingly different problems: A molecular replacement method for solving protein structures and prediction of allergens.

Collaboration with Karolinska Institutet, Karolinska Hospital, and Uppsala University.

Selected Publications

• Tobias Allander, Martti T. Tammi, Margareta Eriksson, Annelie Bjerkner, Annika Tiveljung Lindell and Bjorn Andersson. Cloning of a Human Parvovirus by Molecular Screening of Respiratory Samples. Proc. Nat. Acad. Sci. 2005 Accepted.

• The Trypanosoma cruzi Genome Sequencing Consortium. The genome sequence of Trypanosoma cruzi, etiological agent of Chagas' disease. Science. 2005 July 15; 309(5733): 409-15.

• International Chicken Polymorphism Map Consortium. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature. 2004 Dec 9; 432(7018): 717-22.

• Porcel BM, Tran AN, Tammi M, Nyarady Z, Rydaker M, Urmenyi TP, Rondinelli E, Pettersson U, Andersson B, Aslund L Gene survey of the pathogenic protozoan Trypanosoma cruzi. Genome Res. 2000 Aug;10(8):1103-7.

• Tammi MT, Arner E, Britton T, Andersson B.Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs. Bioinformatics. 2002 Mar;18(3):379-88.

• Tammi MT, Arner E, Andersson B. TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences. Comput Methods Programs Biomed. 2003 Jan;70(1):47-59.

• Tammi MT, Arner E, Kindlund E, Andersson B. Correcting errors in shotgun sequences. Nucleic Acids Res. 2003 Aug 1;31(15):4663-72.

• Tammi MT, Arner E, Kindlund E, Andersson B. ReDiT: Repeat Discrepancy Tagger - a shotgun assembly finishing aid. Bioinformatics. 2004 Mar 22;20(5):803-4. Epub 2004 Jan 29.