Sampsa Hautaniemi (CV)

Professor of Systems Biology
Systems Biology of Drug Resistance in Cancer Lab
Genome-Scale Biology Research Program
Faculty of Medicine
Biomedicum Helsinki
University of Helsinki

Contact information


Postdoctoral Associate, Douglas A. Lauffenburger Laboratory, Biological Engineering & Computational and Systems Biology Initiative (CSBi), Massachusetts Institute of Technology, 2004-2006
Doctor of Technology, Computer Science, Tampere University of Technology, 2003
Master of Science (Eng.), Signal Processing, Tampere University of Technology, 2000

Research interests

Teaching 2017-2018

LSI36002 Systems Medicine Seminar
30277 Introduction to Bioinformatics (Starts in January 2018)
30277 Introduction to Systems Biology (Starts in April 2018)
Clinical Data Mining (NEW! Starts in November 2018)

Selected publications

Citation metrics & all publications in ResearchID

Liu C, Lehtonen R, Hautaniemi S
PerPAS: Topology-based single sample pathway analysis method
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017 Mar 8. doi: 10.1109/TCBB.2017.2679745
[link to pdf]

Icay K, Chen P, Cervera A, Rantanen V, Lehtonen R, Hautaniemi S
SePIA: RNA and small RNA sequence processing, integration, and analysis
BioData Mining, 2016, 9:20
[link to pdf]

Chen P, Huhtinen K, Kaipio K, Mikkonen P, Aittomäki V, Lindell R, Hynninen J, Auranen A, Grénman S, Lehtonen R, Carpén O, Hautaniemi S
Identification of prognostic groups in high-grade serous ovarian cancer treated with platinum-taxane chemotherapy
Cancer Research, 2015, 75(15):2987-98
[link to pdf]

Rantanen V, Valori M, Hautaniemi S
Anima: Modular workflow system for comprehensive image data analysis
Frontiers in Bioengineering and Biotechnology, 2014, 2:25
[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

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

Chen P, Lepikhova T, Hu YZ, Monni O, Hautaniemi S
Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants
Nucleic Acids Research, 2011 Oct;39(18):e123
[pdf] [website]

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 Sep 7;2(9):65
[pdf] [website] [results website] [commentary]

Wu J, Vallenius T, Ovaska K, Westermarck J, Mäkelä TP, Hautaniemi S
Integrated network analysis platform for protein-protein interactions
Nature Methods 2009 Jan;6(1):75-7
[pdf] [web site]

Ovaska K, Laakso M, Hautaniemi S
Fast Gene Ontology based clustering for microarray experiments
BioData Mining 2008 Nov 21;1(1):11
[pdf] [download]

Laakso M, Tuupanen S, Karhu A, Lehtonen R, Aaltonen LA, Hautaniemi S
Computational identification of candidate loci for recessively inherited mutation using high throughput SNP arrays
Bioinformatics 2007 Aug 1;23(15):1952-61
[pdf] [download]

Hua F, Hautaniemi S, Yokoo R, Lauffenburger DA
Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways
Journal of the Royal Society Interface 2006 Aug 22;3(9):515-26

Hautaniemi S, Kharait S, Iwabu A, Wells A, Lauffenburger DA
Modeling of signal-response cascades using decision tree analysis
Bioinformatics 2005 May;21(9):2027-2035

Kauraniemi P, Hautaniemi S, Autio R, Astola J, Monni O, Elkahloun A, Kallioniemi A
Effects of Herceptin treatment on global gene expression patterns in HER2 amplified and non-amplified breast cancer cell lines
Oncogene 2004 Jan;23(4):1010-1013

Hautaniemi S, Edgren H, Vesanen P, Wolf M, Järvinen AK, Yli-Harja O, Astola J, Kallioniemi O, Monni O
A novel strategy for microarray quality control using Bayesian networks
Bioinformatics 2003 Nov;19(16):2031-2038
[pdf] [supplementary page]

Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringnér M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A
Impact of DNA amplification on gene expression patterns in breast cancer
Cancer Research 2002 Nov;62(21):6240-6245

All Systems Biology of Drug Resistance in Cancer Laboratory publications

Sampsa Hautaniemi 07.01.2018