Bioinformatics of carbonic anhydrases
The focus of this research consists of bioinformatic studies of carbonic anhydrases (CA), ubiquitous enzymes which are found in all kingdoms of life, focusing on CAs in animals. The ultimate goal is to increase our understanding of how and why various CA isoforms and CAs in different species are different from each other. This would be useful in understanding drug specificity, and in the design of novel, improved forms of CAs. An intermediate goal in this process is the discovery of most likely evolutionary histories of CAs.
The project is run by Martti Tolvanen in collaboration with the group of Seppo Parkkila (University of Tampere).
Conserved domain and evolution of secreted phospholipases A(2)
Secreted phospholipases A(2) (sPLA(2) s) are lipolytic enzymes present in organisms ranging from prokaryotes to eukaryotes but their origin and emergence are poorly understood. We study conserved domains of sPLA(2)
and proposed a model for their evolution.
Protein hydropathy predictions
We investigated the prediction accuracy of 56 hydropathy scales by correlating predicted values with the accessible surface area in known protein structures. Results for different amino acids vary greatly within each scale. We also investigated prediction accuracies of amino acids separately in secondary structural elements and in protein fold families.
Gene expression on the theory of phase synchronization
Using phase synchronization it is possible to detect biological
associations for gene pairs with cell cycle-specific expression profiles. Phase-synchronization clustering is able to detect biologically associated gene pairs that have linearly correlated (simultaneous and inverted) as well as time-delayed expression profiles.
Tools for the submission of mutations to databases and maintenance of locus-specific mutation databases. Advanced, integrated computer systems are needed to store and organize the increasing mutation information.
Turku BioNLP Group
The main focus of the BioNLP group is the development of text mining algorithms and their utilization in knowledge discovery in biology and medicine. The flagship resources developed by the group are the TEES text mining system which won several text mining competitions, and the EVEX resource comprising detailed information about genes, proteins, and their mutual relationships mined from the entire publicly available biomedical literature. The BioNLP group has a number of collaborative projects with universities worldwide.
More information about the group’s projects and publications can be found on its homepage.
Research utilizing the Auria biobank data
The Auria biobank is a project to centralize the storage of patient samples and related information from Turku area hospitals and to provide the means for scientists to utilize this large dataset for research purposes. The IT-department is involved in the Auria-project and we will utilize our expertise in machine learning and large scale data mining to apply the biobank data to different research questions.
- Retention of University Teachers and Doctoral Students in UNIPS Pedagogical Online Courses
Samuli Laato, Heidi Salmento, Emilia Lipponen, Henna Vilppu, Mari Murtonen, Erno Lehtinen
- Potential Benefits of Playing Location-based Games: An Analysis of Game Mechanics
Samuli Laato, Tarja Pietarinen, Sampsa Rauti, Erkki Sutinen
- Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals
Joonatan Palmu, Aaro Salosensaari, Aki S. Havulinna, Susan Cheng, Michael Inouye, Mohit Jain, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Erkki Vartiainen, Tiina Laatikainen, Pekka Jousilahti, Veikko Salomaa, Rob Knight, Leo Lahti, Teemu J. Niiranen
- Diet, perceived intestinal well-being and compositions of fecal microbiota and short chain fatty acids in oat-using subjects with celiac disease or gluten sensitivity
Nylund L., Hakkola S., Lahti L., Salminen S., Kalliomäki M., Yang B., Linderborg K.M.
- Intestinal microbiota analysis supports inclusion of gluten-free oats to diet of subjects with celiac disease or gluten sensitivity
Nylund L, Hakkola S, Lahti L, Salminen S, Yang BR, Kalliomäki M, Linderborg K
- Aging and non-native speech perception: A phonetic training study (2021)
Tamminen H., Kujala T., Näätänen R., Peltola M. S.
- Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings
Moen Hans, Hakala Kai, Peltonen Laura-Maria, Matinolli Hanna-Maria, Suhonen Henry, Terho Kirsi, Danielsson-Ojala Riitta, Valta Maija, Ginter Filip, Salakoski Tapio, Salanterä Sanna.
- The reuse of texts in Finnish newspapers and journals, 1771–1920: A digital humanities perspective
Salmi Hannu, Paju Petri, Rantala Heli, Nivala Asko, Vesanto Aleksi, Ginter Filip
- Exploring unsupervised query paraphrasing to identify relevant search phrases for a literature review
Laura-Maria Peltonen, Miretta Tommila, Hans Moen
- Increasing Customer Awareness on Food Waste at University Cafeteria with a Sensor-Based Intelligent Self-Serve Lunch Line
Lauri Koivunen, Samuli Laato, Sampsa Rauti, Juhani Naskali, Petri Nissilä, Pauliina Ojansivu, Tuomas Mäkilä, Mari Norrdal