Bioinformatics
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.
MutBase
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.
Recent Publications
- Aging and non-native speech perception: A phonetic training study (2021)
Tamminen H., Kujala T., Näätänen R., Peltola M. S. - Using early assessment performance as early warning signs to identify at-risk students in programming courses (2020)
Ashok Kumar Veerasamy, Daryl D’Souza, Mikko-Ville Apiola, Mikko-Jussi Laakso, Tapio Salakoski - Mapping out the philosophical questions of AI and clinical practice in diagnosing and treating mental disorders (2020)
Susanne Uusitalo, Jarno Tuominen, Valtteri Arstila - Elokuvakokemus kuurosokean osallistujan näkökulmasta (2020)
Riitta Lahtinen, Stina Ojala - Elina Tergujeff & Maria Kautonen (Eds.). Suullinen kielitaito – Opi, opeta, arvioi (Book Review) (2020)
Katja Haapanen - Limits and Virtues of Educational Technology in Elementary School Mathematics (2020)
Athanasios Christopoulos, Henri Kajasilta, Tapio Salakoski, Mikko-Jussi Laakso - Turku Enhanced Parser Pipeline: From Raw Text to Enhanced Graphs in the IWPT 2020 Shared Task (2020)
Jenna Kanerva, Filip Ginter, Sampo Pyysalo - Unsupervised hierarchical clustering identifies a metabolically challenged subgroup of hypertensive individuals (2020)
Felix C. Vaura, Veikko V. Salomaa, Ilkka M. Kantola, Risto Kaaja, Leo Lahti, Teemu J. Niiranen - Integrating Theological Aspects to Engineering Education (2020)
Samuli Laato, Erkki Sutinen - Children in 2077: Designing children's technologies in the age of transhumanism (2020)
Raftopoulos M., Ramchurn R., Mota C., Papangelis K., Wolff A., Yildiz M., Sádaba J., Thibault M., Buruk O., Baykal G.E., Özcan O., Acar S., Göksun T., Baytaş M.A., Akduman G., Best J., Beşevli C., Genç H.U., Coşkun A., Laato S., Kocaballi A.B. - Propagating AI Knowledge Across University Disciplines- The Design of A Multidisciplinary AI Study Module (2020)
Samuli Laato, Henna Vilppu, Juho Heimonen, Antti Hakkala, Jari Björne, Ali Farooq, Tapio Salakoski, Antti Airola - Prebiotic Xylo-Oligosaccharides Ameliorate High-Fat-Diet-Induced Hepatic Steatosis in Rats (2020)
Sanna Lensu, Raghunath Pariyani, Elina Mäkinen, Baoru Yang, Wisam Saleem, Eveliina Munukka, Maarit Lehti, Anastasiia Driuchina, Jere Linden, Marja Tiirola, Leo Lahti, Satu Pekkala - Retention of University Teachers and Doctoral Students in UNIPS Pedagogical Online Courses (2020)
Samuli Laato, Heidi Salmento, Emilia Lipponen, Henna Vilppu, Mari Murtonen, Erno Lehtinen - Potential Benefits of Playing Location-based Games: An Analysis of Game Mechanics (2020)
Samuli Laato, Tarja Pietarinen, Sampsa Rauti, Erkki Sutinen - Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals (2020)
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 (2020)
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 (2020)
Nylund L, Hakkola S, Lahti L, Salminen S, Yang BR, Kalliomäki M, Linderborg K - Assisting nurses in care documentation: from automated sentence classification to coherent document structures with subject headings (2020)
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 (2020)
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 (2020)
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 (2020)
Lauri Koivunen, Samuli Laato, Sampsa Rauti, Juhani Naskali, Petri Nissilä, Pauliina Ojansivu, Tuomas Mäkilä, Mari Norrdal - Evaluation of the Pedagogical Quality of Mobile Math Games in App Marketplaces (2020)
Samuli Laato, Renny Lindberg, Teemu H Laine, Phuong Bui, Boglarka Brezovszky, Lauri Koivunen, Olga De Troyer, Erno Lehtinen - Universal Lemmatizer: A sequence-to-sequence model for lemmatizing Universal Dependencies treebanks (2020)
Jenna Kanerva, Filip Ginter, Tapio Salakoski - Misinformation sharing and social media fatigue during COVID-19: An affordance and cognitive load perspective (2020)
Islam A.K.M.N., Laato S., Talukder S., Sutinen E. - Did location-based games motivate players to socialize during COVID-19? (2020)
Laato S., Islam A.K.M.N., Laine T.H. - Location-based games and the COVID-19 pandemic: An analysis of responses from game developers and players (2020)
Laato S., Laine T.H., Islam A.K.M.N. - What drives unverified information sharing and cyberchondria during the COVID-19 pandemic? (2020)
Samuli Laato, A.K.M. Najmul Islam, Muhammad Nazrul Islam, Eoin Whelan - Do primal instincts explain engagement in location-based games? A hypothesis-forming focus group study on territorial behavior (2020)
Samuli Laato, Bastian Kordyaka, Sampsa Rauti, Sonja M. Hyrynsalmi, Marianna Hoikkala, Tarja Pietarinen, Teemu D. Laajala, Mauri Paloheimo, Nobufumi Inaba, Sami Hyrynsalmi - AI in Cybersecurity Education- A Systematic Literature Review of Studies on Cybersecurity MOOCs (2020)
Samuli Laato, Ali Farooq, Henri Tenhunen, Tinja Pitkämäki, Antti Hakkala, Antti Airola - Unusual purchasing behavior during the early stages of the COVID-19 pandemic: The stimulus-organism-response approach (2020)
Samuli Laato, A.K.M. Najmul Islam, Ali Farooq, Amandeep Dhir - Towards automated detection of psychosocial risk factors with text mining (2020)
Uronen L, Moen H, Teperi S, Martimo KP, Hartiala J, Salantera S - Changing Role of EMS -Analyses of Non-Conveyed and Conveyed Patients in Finland (2020)
Paulin J, Kurola J, Salanterä S, Moen H, Guragain N, Koivisto M, Käyhkö N, Aaltonen V, Iirola T - Augmented Reality to Enhance Visitors’ Experience at Archaeological Sites (2020)
Samuli Laato, Antti Laato - Maternal prenatal psychological distress and hair cortisol levels associate with infant fecal microbiota composition at 2.5 months of age (2020)
Aatsinki A, Keskitalo A, Laitinen V, Munukka E, Uusitupa H, Lahti L, Kortesluoma S, Mustonen P, Rodrigues AJ, Coimbra B, Huovinen P, Karlsson H, Karlsson L - Improving Synchrony in Small Group Asynchronous Online Discussions (2020)
Laato S, Murtonen M - Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin (2020)
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 (2020)
Khalighi M, Amirianmatlob M, Malek A - Understanding students’ game experiences throughout the developmental process of the Number Navigation Game (2020)
Phuong Bui, Gabriela Rodríguez-Aflecht, Boglárka Brezovszky, Minna M. Hannula-Sormunen, Samuli Laato, Erno Lehtinen - Location-based Games as Interfaces for Collecting User Data (2020)
Sampsa Rauti, Samuli Laato - Motoric Training Alters Speech Sound Perception and Production — Active Listening Training Does Not Lead into Learning Outcomes (2020)
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 (2020)
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 (2020)
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 (2020)
Antti Saloranta, Paavo Alku, Maija S.Peltola - Classifying online corporate reputation with machine learning: a study in the banking domain (2020)
Anette Rantanen, Joni Salminen, Filip Ginter, Bernard J. Jansen - 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 - Proceedings of the First NLPL Workshop on Deep Learning for Natural Language Processing (2019)
Joakim Nivre, Filip Ginter, Stephan Oepen, Jörg Tiedemann - Biomedical Named Entity Recognition with Multilingual BERT (2019)
Hakala K, Pyysalo S - CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics,and Coreference (2019)
William A Baumgartner Jr., Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy Hailu, Harrison Pielke-Lombardo, Michael Regan, Lawrence Hunter - Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task (2019)
Thang Minh Ngo, Jenna Kanerva, Filip Ginter, Sampo Pyysalo