University homepage Suomenkielinen versio puuttuu Inte på svenska In english
University of Helsinki Department of Computer Science
 

Department of Computer Science

Teemu Kivioja

Biomedicum, room B526a
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland
Tel. +358 9 191 25681
Fax. +358 9 191 25554
Email: First_name.Last_name@helsinki.fi

(In Exactum building: room B218, Tel. +358 9 191 51376, usually Mondays and Tuesdays)

I work as a researcher in two research groups: Taipale lab (Genome-Scale Biology Program and Institute of Biomedicine, University of Helsinki, and National Institute for Health and Welfare), and in Professor Esko Ukkonen's group (Department of Computer Science, University of Helsinki).

Teaching

Seminar regulatory networks, autumn 2007

Tieteellinen kirjoittaminen, autumn 2008 (in Finnish)

Publications

Articles in refereed international scientific journals

  • Teemu Kivioja, Janne Ravantti, Anatoly Verkhovsky, Esko Ukkonen, and Dennis Bamford. Local average intensity-based method for identifying spherical particles in electron micrographs. Journal of Structural Biology, 131:126-134, 2000.
  • Teemu Kivioja, Mikko Arvas, Kari Kataja, Merja Penttilä, Hans Söderlund, and Esko Ukkonen. Assigning probes into a small number of pools separable by electrophoresis. Bioinformatics, 18(Suppl. 1, ISMB 2002 special issue):S199-206, 2002.
  • Peddinti V. Gopalacharyulu, Erno Lindfors, Catherine Bounsaythip, Teemu Kivioja, Laxman Yetukuri, Jaakko Hollmen, and Matej Oresic. Data integration and visualization system for enabling conceptual biology. Bioinformatics, 21(Suppl. 1, ISMB 2005 special issue):i177-i185, 2005.
  • Teemu Kivioja, Mikko Arvas, Markku Saloheimo, Merja Penttilä, and Esko Ukkonen. Optimization of cDNA-AFLP experiments using genomic sequence data. Bioinformatics, 21(11):2573-2579, 2005.
  • Jari Rautio, Michael Bailey, Teemu Kivioja, Hans Söderlund, Merja Penttilä, and Markku Saloheimo. Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis. BMC Biotechnology, 7:28, 2007.
  • Mikko Arvas, Teemu Kivioja, Alex Mitchell, Markku Saloheimo, David Ussery, Merja Penttilä, and Stephen Oliver. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics. 8:325, 2007.
  • Markku Varjosalo, Mikael Björklund, Fang Cheng, Heidi Syvänen, Teemu Kivioja, Sami Kilpinen, Zairen Sun, Olli Kallioniemi, Hendrik G. Stunnenberg, Wei-Wu He, Päivi Ojala, and Jussi Taipale. Application of Active and Kinase-Deficient Kinome Collection for Identification of Kinases Regulating Hedgehog Signaling. Cell, 133:537-548, 2008.

Articles in refereed international scientific conference proceedings

  • Shunsuke Inenaga, Teemu Kivioja, and Veli Mäkinen. Finding missing patterns. In Proceedings of Algorithms in Bioinformatics: 4th International Workshop (WABI 2004), LNCS 3240, pages 463-474. Springer-Verlag, 2004.

Other scientific publications

  • Teemu Kivioja. Computational Tools for a Novel Transcriptional Profiling Method. PhD thesis, University of Helsinki, 2004.
  • Mikko Koivisto, Teemu Kivioja, Heikki Mannila, Pasi Rastas, and Esko Ukkonen. Hidden markov modelling techniques for haplotype analysis (invited paper). In Proceedings of Algorithmic Learning Theory: 15th International Conference (ALT 2004), LNAI 3244, pages 37-52. Springer-Verlag, 2004.

Teemu Kivioja