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.
- Improving Synchrony in Small Group Asynchronous Online Discussions
Laato S, Murtonen M
- Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin
Virinder Sarhadi, Leo Lahti, Farideh Saberi, Omar Youssef, Arto Kokkola, Tiina Karla, Milja Tikkanen, Hilpi Rautelin, Pauli Puolakkainen, Rasoul Salehi, Sakari Knuutila
- A new approach to solving multiorder time-fractional advection-diffusion-reaction equations using BEM and Chebyshev matrix
Khalighi M, Amirianmatlob M, Malek A
- Understanding students’ game experiences throughout the developmental process of the Number Navigation Game
Phuong Bui, Gabriela Rodríguez-Aflecht, Boglárka Brezovszky, Minna M. Hannula-Sormunen, Samuli Laato, Erno Lehtinen
- Motoric Training Alters Speech Sound Perception and Production — Active Listening Training Does Not Lead into Learning Outcomes
Kimmo U. Peltola, Henna Tamminen, Paavo Alku, Teija Kujala, Maija S. Peltola
- Long term effects on technology enhanced learning: The use of weekly digital lessons in mathematics
Einari Kurvinen, Erkki Kaila, Mikko-Jussi Laakso, Tapio Salakoski
- Supporting the use of standardized nursing terminologies with automatic subject heading prediction: a comparison of sentence-level text classification methods
Hans Moen, Kai Hakala, Laura-Maria Peltonen, Henry Suhonen, Filip Ginter, Tapio Salakoski, Sanna Salanterä
- Listen-and-repeat training improves perception of second language vowel duration: Evidence from mismatch negativity (MMN) and N1 responses and behavioral discrimination
Antti Saloranta, Paavo Alku, Maija S.Peltola
- Carbonic anhydrases from pathogens: Protozoan CAs and related inhibitors as potential antiprotozoal agents (2019)
Ashok Aspatwar, Harlan Barker, Martti Tolvanen, Reza Zolfaghari Emameh, Seppo Parkkila
- Accessibility of TV media for the dual-sensory impaired in Finland and in the UK (2019)
Stina Ojala, Russ Palmer, Riitta Lahtinen