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University of Helsinki

Hautaniemi Lab


Laboratory information:

Contact information:

Sampsa Hautaniemi
Biomedicum Helsinki, B524b
P.O.Box 63 (Haartmaninkatu 8)
phone +358 9 191 25419
fax +358 9 191 25610




Photo: Sampsa Hautaniemi

Sampsa Hautaniemi
Professor of Systems Biology


Photo: Marko Laakso

Marko Laakso
PhD, Posdoctoral associate

I am interested in the analysis of microarray data (SNP, expression, ChIP), data annotations and modelling of the gene regulations. Current work concentrates on various cancer types (colorectal, breast and prostate cancers) and their means of inheritance. New methods and tools are needed in order to use computers in comparison of patient and reference samples and to integrate sample measurements into other relevant data sources.

Photo: Javier Nez-Fontarnau

Javier Nez-Fontarnau
PhD (Theoretical Computer Science), Post-doctoral associate

in collaboration with Prof. Lauri Aaltonen (Department of Medical Genetics).

Central in my work is the development of Anduril, a component-based workflow framework for scientific data analysis specialized in high-throughput experiments in biomedical research.

vladimir pic

Vladimir Rogojin
PhD (Theoretical Computer Science), Post-doctoral associate

I am focusing on simulation, visualization and analysis of cellular signaling networks in order to reveal key features responsible for cancerous cellular behavior and to predict drug targets. I am developing various computational methods and algorithms and implementing necessary tools to solve this problem. I am applying discrete mathematics and theoretical computer science.

More information about me and my research here http://www.vrogojin.net.


Alejandra Cervera
MSc (Bioinformatics), PhD student in HBGP

My project focuses on RNA-seq analysis.


Ping Chen
MSc (Bioinformatics), PhD student in FICS

My current work concentrates on transcriptome data analysis, especially alternative splicing using exon arrays and RNA-seq.

Photo: Sirkku Karinen

Sirkku Karinen
MSc (Bioinformatics), PhD student in FICS

My current project aims at finding gene variants that are related to spesific pathways. The search from databases is automated and output is evaluated by bioinformatics methods to determine which SNPs are functionally most important to breast cancer survival.

chengyu photo

Chengyu Liu
MSc (Computer science), PhD student in GPBM

My research interests are machine learning and data mining. My current project is about using machine learning methods to find signature of metastasis in breast cancer, and using these genes to predict survival.

Photo: Riku Louhimo

Riku Louhimo
MSc (Bioinformatics), PhD student in HBGP

My current goal is to comprehensively integrate different types of molecular data and existing knowledge in a diverse set of cancers in order to characterize new cancer genes.
Additionally, I am interested in altered cell signaling and survival analysis.

Photo: Kristian Ovaska

Kristian Ovaska
MSc (Computer Science), PhD student in HBGP

My project is bioinformatics pipeline that allows for systematic and rapid analysis of biological data. My second major project is to model computationally the EGFR pathway.

Photo: Ville Rantanen

Ville Rantanen
MSc (Electrical and Communications Engineering), PhD student

My research interests are in automated image segmentation and analysis. The oncoming project which I am involved in, will be extracting features from multidimensional microscope images on cancer cell; and using these features to predict survival.


Lilli Saarinen
BSc (Engineering in Biotechnology), MSc (Computer Science), PhD student

Currently on maternity leave.

Photo: Viljami Aittomäki

Viljami Aittomäki
BSc (Bioinformation Technology), MSc student

My current project involves machine learning application to mine large-scale genotype data in breast cancer.


Amjad Alkodsi
MSc student (Systems Biology)

My project involves drug sensitivity prediction for cancer samples.


Julia Casado
MSc student (MBI)

My research interest is on epigenomics, specifically the analysis of ChIP-Seq data.

chiara Chiara Facciotto
MSc student (Bioinformatics, MBI)

My project focuses on an analysis of epigenetic changes in ER+ MCF-7 breast cancer cells at different time points after estradiol stimulus.

Rony Lindell
MSc Student (Bioinformation technology), MD student at HU

My current focus is on whole exome data analysis. My goal is to create a pipeline that finds base variants in exome sequences that may explain the cancer phenotype (current focus is on GBM). Reliable cancer-causing variations should be good targets for pharmacological substances. The analysis involves eg. alignment of reads, variant calling and possibly measurement of causality by integrating results from other sources.

Lauri Lauri Lyly
MSc student (Bioinformatics), MD student at HU

I'm immersed in library development to get acquainted with the lab. On the research side I'm going to focus on deep sequencing method development and data analysis but I've yet to determine a more specific interest.
Elmo Elmo Saarentaus
BSc student (Biological technology), MD student at HU

I'm working part-time on my dissertation that I hope to achieve from the lab during my MD study career. The focus of my thesis is (currently) on identifying fusion genes from RNA sequencing data.
Photo: Erkka Valo

Erkka Valo
MSc student (Bioinformatics)

My current research interests include analysis of high-throughput data produced from microarrays, flow cytometry experiments and next generation sequencing platforms, computational prediction of transcription factors regulating a set of genes, and prediction of functional RNA motifs involved in regulation of gene expression.


Miko Valori
MSc student (TRANSMED)

My main interest is in image analysis.

tiia pic

Tiia Pelkonen
MA (English Translation and Interpreting),

Project assistant at the Hautaniemi lab and Program secretary for the GSB research program

In the Hautaniemi lab my tasks include mainly the administrative duties of the research projects.


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