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University of Helsinki Institute of Biotechnology
 
Institute of Biotechnology
DNA Sequencing and Genomics

Research Director:
Petri Auvinen
Tel +358 (0) 2941 58902
e-mail petri.auvinen -at- helsinki.fi

Laboratory Engineer:
Lars Paulin
Tel +358 (0) 2941 58887
e-mail lars.paulin -at- helsinki.fi

Viikinkaari 5D
(Biocenter 2, 4th floor)
P.O.Box 56
FIN-00014 University of Helsinki

Tel +358 (0) 2941 58884

Sequencing service e-mail:
bio-alf -at- helsinki.fi

Institute of Biotechnology
Street address: Viikinkaari 5D (P.O.Box 56)
00014 University of Helsinki
Finland
Tel: +358 (0) 294 1911
Tel: +358 (0) 2941 4482624

Business Identity Code:
FI-03134717
(University of Helsinki)

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Research and collaboration

DNA sequencing and Genomics laboratory is located in Cultivator 2 building second floor at Viikki campus in Helsinki. We are a part of the Institute of Biotechnology.

Our own research focuses on genomics and functional genomics. Typical for both of these areas is that they involve large amounts of data to be analyzed and because of that we often collaborate with other groups in order to cover required disciplines. We have several research projects going on in the laboratory. Majority of our projects are funded with grants from various sources. There are several different ways how collaborative projects are handled in our laboratory. One very efficient arrangement has been long time visitors in the laboratory. At the moment we have several graduate students in the laboratory pursuing their projects who obtain their salaries from joint grants.

We have several areas of interest. De novo genome sequencing projects are one of those. We have finished several microbe genomes from which we are at the moment preparing manuscripts. We have been starting with the conventional Sanger/ clone library approach and lately more and more transferred DNA sequencing to the 454-plaform. Following the genome sequencing we are working constantly on the assembly of the genomes as wells as the annotation of the genomes sequenced. In the annotation phase we most often collaborate closely with others groups who are specialist of the genome in hand. We have been working also on several EST library projects starting from sequencing of the clones until annotation of the obtained sequences.

We have been interested about the microbe diversity of some complex environments like compost, moldy houses and human gut flora. These projects have been made in collaboration with several groups in Finland. We have constructed clone libraries of 16S ribosomal genes from several environments. These libraries have been subsequently sequenced utilizing our semiautomatic pipeline. Using this metagenomic approach we have obtained detailed picture of the microbes in various environments. Based on these in house data we have been constructing diagnostic DNA microarrays based on LDR (ligase detection reaction) technique. This method is very good in measuring even one nucleotide differences in targets which is a very important feature in microbe detection. This year we are going to start metagenomic projects with several environments using the short read 454 technology.

We have been working for several years on producing DNA microarrays to other groups but along this we have been working on understanding and developing methods for analyzing results obtained from various microarray platforms. We are interested on meta-analysis of large data set and fusion of data from various technologies. At the moment we are working on the analysis of transcription of tissues specific genes.

If you have possible collaborative projects in mind do not hesitate to contact us.