Sami Kilpinen

Summary

Affiliation: University of Helsinki
Country: Finland

Publications

  1. ncbi Classification of unknown primary tumors with a data-driven method based on a large microarray reference database
    Kalle A Ojala
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Tukholmankatu 8, 00140 Helsinki, Finland
    Genome Med 3:63. 2011
  2. ncbi Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations
    Reija Autio
    Department of Signal Processing, Tampere University of Technology, Tampere, Finland
    BMC Bioinformatics 10:S24. 2009
  3. ncbi Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data
    Sami K Kilpinen
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Tukholmankatu 8, Helsinki, Finland
    BioData Min 4:5. 2011
  4. ncbi Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome
    Sami Kilpinen
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
    PLoS ONE 5:e15068. 2010
  5. ncbi Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
    Sami Kilpinen
    Medical Biotechnology, VTT Technical Research Centre and University of Turku, Itäinen Pitkäkatu 4C, Turku, Finland
    Genome Biol 9:R139. 2008
  6. ncbi Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication
    Maija Wolf
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
    BMC Cancer 10:181. 2010
  7. ncbi GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets
    John Patrick Mpindi
    FIMM, Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
    PLoS ONE 6:e17259. 2011
  8. ncbi Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2
    Juha K Rantala
    Medical Biotechnology, VTT Technical Research Centre of Finland, Turku, Finland
    Neoplasia 12:877-88. 2010
  9. ncbi High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx
    Anna Kaarina Järvinen
    Institute of Biomedicine and Biomedicum Biochip Center, Genome Scale Biology Research Program, University of Helsinki, Helsinki, Finland
    Genes Chromosomes Cancer 47:500-9. 2008
  10. ncbi TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming
    Kristiina Iljin
    Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku, Turku, Finland
    Cancer Res 66:10242-6. 2006

Collaborators

Detail Information

Publications13

  1. ncbi Classification of unknown primary tumors with a data-driven method based on a large microarray reference database
    Kalle A Ojala
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Tukholmankatu 8, 00140 Helsinki, Finland
    Genome Med 3:63. 2011
    ..It is not tied to any a priori defined gene set as many previous methods, and is adaptable to emerging new information...
  2. ncbi Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations
    Reija Autio
    Department of Signal Processing, Tampere University of Technology, Tampere, Finland
    BMC Bioinformatics 10:S24. 2009
    ..Furthermore, even in the case of the widely-used, industry-standard Affymetrix oligonucleotide microarrays, the various array generations have different probe sets representing different genes, hindering the data integration...
  3. ncbi Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data
    Sami K Kilpinen
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Tukholmankatu 8, Helsinki, Finland
    BioData Min 4:5. 2011
    ..abstract:..
  4. ncbi Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome
    Sami Kilpinen
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
    PLoS ONE 5:e15068. 2010
    ....
  5. ncbi Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
    Sami Kilpinen
    Medical Biotechnology, VTT Technical Research Centre and University of Turku, Itäinen Pitkäkatu 4C, Turku, Finland
    Genome Biol 9:R139. 2008
    ..This database of gene expression patterns in normal human tissues and pathological conditions covers 113 million datapoints and is available from the GeneSapiens website...
  6. ncbi Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication
    Maija Wolf
    Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
    BMC Cancer 10:181. 2010
    ..Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma...
  7. ncbi GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets
    John Patrick Mpindi
    FIMM, Institute of Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
    PLoS ONE 6:e17259. 2011
    ..We developed and validated a new bioinformatic method for the identification of genes upregulated in subsets of samples of a given tumour type ('outlier genes'), a hallmark of potential oncogenes...
  8. ncbi Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2
    Juha K Rantala
    Medical Biotechnology, VTT Technical Research Centre of Finland, Turku, Finland
    Neoplasia 12:877-88. 2010
    ..In addition, nuclear GINS2 protein levels distinguished actively proliferating cancer cells suggesting potential use of GINS2 staining as a biomarker of cell proliferation as well as a potential therapeutic target...
  9. ncbi High-resolution copy number and gene expression microarray analyses of head and neck squamous cell carcinoma cell lines of tongue and larynx
    Anna Kaarina Järvinen
    Institute of Biomedicine and Biomedicum Biochip Center, Genome Scale Biology Research Program, University of Helsinki, Helsinki, Finland
    Genes Chromosomes Cancer 47:500-9. 2008
    ..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat...
  10. ncbi TMPRSS2 fusions with oncogenic ETS factors in prostate cancer involve unbalanced genomic rearrangements and are associated with HDAC1 and epigenetic reprogramming
    Kristiina Iljin
    Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku, Turku, Finland
    Cancer Res 66:10242-6. 2006
    ..Activation of ERG by fusion with TMPRSS2 may lead to epigenetic reprogramming, WNT signaling, and down-regulation of cell death pathways, implicating ERG in several hallmarks of cancer with potential therapeutic importance...
  11. ncbi Fibroblast growth factor receptor 4 regulates tumor invasion by coupling fibroblast growth factor signaling to extracellular matrix degradation
    Nami Sugiyama
    Molecular Cancer Biology Research Program, Departments of Pathology and Virology, Haartman Institute, Helsinki, Finland
    Cancer Res 70:7851-61. 2010
    ..These results will help to explain the reported association of the FGFR4-R388 variant with the progression and poor prognosis of certain types of tumors...
  12. ncbi Role of ErbB4 in breast cancer
    Maria Sundvall
    Department of Medical Biochemistry and Molecular Biology, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
    J Mammary Gland Biol Neoplasia 13:259-68. 2008
    ..This review focuses on recent advances in our understanding about the role of ErbB4 in breast carcinogenesis, as well as in the potential clinical relevance of ErbB4 in breast cancer prognostics and therapy...
  13. ncbi NMD microarray analysis for rapid genome-wide screen of mutated genes in cancer
    Maija Wolf
    Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku, FIN 20520 Turku, Finland
    Cell Oncol 27:169-73. 2005
    ....