Contact information

Sampsa Hautaniemi, Prof.

Biomedicum Helsinki, B524b
P.O.Box 63 (Haartmaninkatu 8)
phone +358 2941 25419



Systems biology of drug resistance in cancer

The focus of the Hautaniemi lab is to understand and find effective means to overcome drug resistance in cancers. Our approach is to use systems biology, i.e., integration of large and complex molecular & clinical data (big data) from cancer patients with computational methods and wet lab experiments, to identify efficient patient-specific therapeutic targets.

We are particularly interested in developing and applying machine learning based methods that enable integration of various types of molecular data (DNA, RNA, proteomics, etc.) to clinical information.

All our research is done in a cross-disciplinary and collaborative setting with oncologists, pathologists, biochemists and geneticians.

Five representative publications (all publications):

  • Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grenman S, Lehtonen R, Carpén O, Hautaniemi S.
    Identification of prognostic groups in high-grade serous ovarian cancer treated with platinum-taxane chemotherapy
    Cancer Research, 75(15):2987-98, 2015.
    [link to pdf]
  • Ovaska K, Matarese F, Grote K, Charapitsa I, Cervera A, Liu C, Reid G, Seifert M, Stunnenberg HG, Hautaniemi S.
    Integrative analysis of deep sequencing data identifies estrogen receptor early response genes and links ATAD3B to poor survival in breast cancer
    PLoS Computational Biology, 2013, 9(6): e1003100.
    [link to pdf]
  • Ovaska K, Lyly L, Sahu B, Jänne O, Hautaniemi S.
    Genomic region operation kit for flexible processing of deep sequencing data
    IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, Jan-Feb;10(1):200-6.
    [link to pdf]
  • Louhimo R, Lepikhova T, Monni O, Hautaniemi S.
    Comparative analysis of algorithms for integration of copy number and expression data
    Nature Methods, 2012 Feb; 9(4):351-5.
    [link to pdf]
  • Ovaska K, Laakso M, Haapa-Paananen S, Louhimo R, Chen P, Aittomäki V, Valo E, Nunez-Fontarnau J, Rantanen V, Karinen S, Nousiainen K, Lahesmaa-Korpinen A-M, Miettinen M, Saarinen L, Kohonen P, Wu J, Westermarck J, Hautaniemi S.
    Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
    Genome Medicine, 2010, 2:65.
    [link to pdf]


Hautaniemi lab also coordinates the HERCULES EU-project.

For any Bioinformatics related issues, see also the Bioinformatics helpdesk website.