Sampsa Hautaniemi (CV)

Professor of Systems Biology
Director of the Systems Oncology (ONCOSYS) research program

Systems Biology of Drug Resistance in Cancer Lab
Research Program in Systems Oncology
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 2020-2021

TMED-915 Introduction to Bioinformatics (January 2021)
TMED-917 Introduction to Systems Biology (April 2021)

Selected publications

Citation metrics & all publications in publons

Häkkinen A, Koiranen J, Casado J, Kaipio K, Lehtonen O, Petrucci E, Hynninen J, Hietanen S, Carpén O, Pasquini L, Biffoni M, Lehtonen R, Hautaniemi S.
qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets
Bioinformatics, 2020 Dec 22;36(20):5086-5092
[Abstract and pdf]

Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, Ojanperä E, Hietanen S, Grénman S, Lehtonen R, Huhtinen K, Carpén O, Hynninen J, Färkkilä A, Hautaniemi S.
Prospective longitudinal ctDNA workflow reveals clinically actionable alterations in ovarian cancer
JCO Precision Oncology, 2019:3,1-12
[Abstract and pdf]

Kozlowska E, Färkkilä A, Vallius T, Carpén O, Kemppainen J, Grénman S, Lehtonen R, Hynninen J, Hietanen S, Hautaniemi S.
Mathematical modeling predicts response to chemotherapy and drug combinations in ovarian cancer
Cancer Research, 2018, 78(14):4036-4044
[Abstract and pdf]

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
[Abstract and 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
[Abstract and 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
[Abstract and pdf]

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

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
[Abstract and 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
[Abstract and 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
[Abstract and pdf]

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

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
[Abstract and pdf]

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
[Abstract and pdf]

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
[Abstract and pdf]

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
[Abstract and pdf]

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
[Abstract and pdf]

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
[Abstract and pdf]

All Systems Biology of Drug Resistance in Cancer Laboratory publications

Sampsa Hautaniemi 12.01.2021