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I am a computer scientist applying and developing efficient computational methods needed in the lab. As the experiments in the lab can generate very large and complex data sets, both the design and analysis of the experiments create many interesting computational challenges, especially when the assay is new and thus standard approaches do not exist. I have worked on many sequencing-based assays but lately I have concentrated on design and analysis of CRISPR-cas9 and STARR-seq experiments.

I am a senior staff scientist working in Taipale and Aaltonen groups at the University of Helsinki. My research is Bioinformatics and Computational Biology from genetics and functional regulatory genomics perspective. I’m involved especially with genetic epidemiology and biobank research related projects and have special interest in functional genomics, gene regulation and functional understanding of non-coding genetic variation.

My long time interest is regulation of the cell cycle and more recently, cellular growth control. The aim is to understand how a normal cell homeostasis differs from a tumorigenic one. I have carried out high throughput siRNA screens of human and Drosophila genes to map cell cycle regulators. Currently I am working with an oncogenic Mediator-12 model to understand how the same mutation can lead to benign uterine leiomyomas (UL) or malignant uterine leiomyosarcomas (ULMS). Our exome sequencing collaboration with Prof L Aaltonen’s group has shown that Mediator-12, which is part of the transcriptional regulator Mediator complex, is mutated in high percentage of ULs. Part of my job is to oversee that our next generation sequencers are working well. I’m also involved in the everyday tasks of running the lab at the University of Cambridge site.

Francis Crick once notably said “If you wish to understand function, study structure”, Roger D. Kornberg took this further by noting “Extension of the structure to atomic resolution will one day reveal the regulatory mechanism”. To understand how DNA sequence controls gene expression, one must first understand the binding specificity of transcription factors (TF) to DNA and/or other TFs/proteins. Therefore, the major aim of my research is to use X-ray crystallography to study the molecular principles underlying the interactions between TF and TF/other proteins or between TF and DNA.