CSC - IT CENTER FOR SCIENCE Finland

www.csc.fi

CSC - IT Center for Science is a non-profit company administered by the Ministry of Education, Science and Culture. It provides academia, research institutes and companies with IT support and Finland's widest selection of scientific software and databases and a powerful supercomputing environment. CSC also actively participates in European research infrastructure projects such as ELIXIR (European Life Sciences Infrastructure for Biological Information) and PRACE (The Partnership for Advanced Computing in Europe). In terms of bioinformatics services CSC provides software, databases, user support and training at a national level. The bioinformatics courses cover different areas such as next generation sequencing data analysis, microarray data analysis,R programming and protein modeling.

Dr Eija Korpelainen

studied biochemistry at the University of Turku, Finland and received her PhD from University of Adelaide, Australia in 1996. After working as an EMBO post doctoral fellow at the University of Helsinki, she joined CSC in 2001. In her role as bioinformatics specialist Dr Korpelainen has provided nation-wide bioinformatics services including training, user support and software development. As an example of the latter, she has directed the development of Chipster. Chipster enables biologists to access a comprehensive collection of up-to-date analysis tools, combine them to automatic, sharable workflows, and visualise results interactively. Chipster is open source and it is used in many institutes around the world for analysing and visualising next generation sequencing, microarray and proteomics data. In addition to her current position as Chipster product manager, Dr Korpelainen runs data analysis courses in Finland and abroad, and participates in international bioinformatics projects such as the COST Action SeqAhead, a network for NGS data analysis, where she chairs the Software working group.

Publications

Niemenmaa M, Kallio A, Schumacher A, Klemelä P, Korpelainen E, Heljanko K.
Hadoop-BAM: Directly manipulating next generation sequencing data in the cloud
Bioinformatics. 2012 Feb 2.

Elo LL, Kallio A, Laajala TD, Hawkins RD, Korpelainen E, Aittokallio T.
Optimized detection of transcription factor-binding sites in ChIP-seq experiments
Nucleic Acids Res. 2012 Jan;40(1):e1.

Kallio MA, Tuimala JT, Hupponen T, Klemelä P, Gentile M, Scheinin I, Koski M, Käki J, Korpelainen EI.
Chipster: user-friendly analysis software for microarray and other high-throughput data
BMC Genomics. 2011 Oct 14;12:507.

Juhila J, Sipilä T, Icay K, Nicorici D, Ellonen P, Kallio A, Korpelainen E, Greco D, Hovatta I.
MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus
PLoS One. 2011;6(6):e21495.

Elo LL, Hiissa J, Tuimala J, Kallio A, Korpelainen E, Aittokallio T.
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets
Brief Bioinform. 2009 Sep;10(5):547-55.

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