I develop computational techniques to solve data-rich applications in human microbial ecology, functional genomics, and digital humanities. There is a great demand for targeted computational tools to extract information from poorly characterized data collections with minimal human intervention. By combining information across multiple, complementary measurement sources it is possible to overcome some of the limitations and statistical uncertainties associated with individual data sets. Open source implementations turn the new models into accessible tools that can guide further modeling and experimentation.
Human gut microbiota constitutes one of the most densely populated ecosystem on our planet. The known pan-genome carries 500-fold more unique genes than our own genome, it is highly dynamic in space and time, and a key contributor to immune system, digestion of food, and various health complications. Characterizing the overall structure, variability, and health associations of this virtual metabolic organ forms a major challenge for contemporary human biology.
Mapping of the three billion base-pair human genome sequence in 2001 was the first step towards uncovering the dynamic and contextual functional properties of the genome. Understanding functional organization of genetic information and its regulation through transcriptional, epigenetic, and other mechanisms remains a key challenge for human biology.
Digital humanities and computational social science
I develop reproducible research tools for high-impact applications in digital humanities. Open data and open source have a central role in this research. During 2016-2019 we are specifically studying Computational History and the Transformation of Public Discourse in Finland 1640–1910, funded by Academy of Finland. See the code page for more info.
Scientific Advisor (AI & Machine Learning) for Blueprint Genetics
Active in Open Knowledge Foundation Finland - Open Science Work Group. Supporting member of Public Library of Science (PLoS); International Society for Microbial Ecology (ISME); Society for Bioinformatics in Northern Europe (SocBIN); Electronic Frontier Finland (EFFI); Amnesty International (founding member and president 2001-2004 for student group at Helsinki University of Technology); Friends of the Earth; Service Civil International (SCI); Association for Online Democrary in Finland; Kansan Muisti; The Association for Investigative Journalism in Finland; Open Knowledge Foundation Finland.
I am grateful to the funding bodies for supporting this research: