Research

 Research Projects and Grants

Our main research interests include analysis of biological and health data, omics data integration using machine learning, as well as the application of deep learning in the analysis of medical imaging. We specialize in developing software for biomedical research databases and e-health data management and analysis. We have dealt with various biological questions over the years, including cancer, stem cells, immunology, etc.

Current Research Grants and Projects

• ELIXIR – Estonian representative and node representative
• ConnectedHealth – member
• PerkinElmer – Deep Learning for microscopy images
• BioEndoCar – EU project that aims to develop a non-invasive diagnostic test for endometrium carcinoma (1.05.2018−01.04.2021), Main PI: Jaak Vilo
• CINECA – EU project that develops Common Infrastructure for National Cohorts in Europe, Canada, and Africa, Main PI: Kaur Alasoo
• EHDEN (IMI2) “European Health Data and Evidence Network”
• CONVERGE – EU project with the goal to standardise life science data management across Europe, Main PI: Hedi Peterson
• HealthyCloud – EU project developing strategic agenda including a ready-to-implement roadmap for the Health Research and Innovation Cloud ecosystem, Main PI: Hedi PEterson

• RITA projekt: Masinõppe ja AI toega teenused (Machine learning and AI powered public services)
• GenMed “Implementing Personalised Medicine IT in Estonia” (ERF-TAT; 07.2019-31.12.2022), Main PI: Jaak Vilo
• PSG59 “Computational analysis and learning from biological data (OmicNet) (1.01.2018−31.12.2020)”, Main PI: Hedi Peterson
• EXCITE TK148 “Estonian Centre of Excellence in ICT Research (1.09.2016−1.03.2023)”, Main PI: Jaak Vilo
• Biological Image Analysis: We develop and apply Deep Learning models for various image classification and segmentation tasks. People: Dmytro Fishman, Mikhail Papkov
  Collaborators: PerkinElmer, Leopold Parts

Other ongoing collaborations:

Our main collaborations are based on those around the joint projects. These projects are also providing the main basis of the funding of the group.

Additionally, we collaborate with friends and colleagues in the closely related interest areas – in genomics, omics integration, analysis of medical images, bioinformatics data warehousing, and mining.

Our major local collaborators are Prof. Pärt Peterson, dr. Kai Kisand, prof. Ursel Soomets and Prof. Andres Salumets from the Institute of Biomedicine and Translational Medicine, dr. Lili Milani and Andres Metspalu from EGCUT,  prof. Külli Kingo from the University Hospital. We have also ongoing collaborations with local industry.

Internationally we collaborate mostly with ELIXIR nodes on the infrastructure development and maintenance projects and enjoy research collaborations with many great researchers and institutions thanks to joint EU projects.

PhD thesis defended

• Sulev Reisberg  Developing Computational Solutions for Personalized Medicine
• Tõnis Tasa Bioinformatics approaches in personalised pharmacotherapy
• Elena Sügis Integration methods for heterogeneous biological data
• Vijayachitra Modhukur Profiling of DNA methylation patterns as biomarkers of human diseases
• Anna Leontjeva Using Generative Models to Combine Static and Sequential Features for Classification 
• Tauno Metsalu Statistical analysis of multivariate data in bioinformatics

• Priit Adler Analysis and visualisation of large scale microarray data
• Sten Ilmjärv Estimating differential expression from multiple indicators
• Hedi Peterson Exploiting high-throughput data for establishing relationships between genes
• Raivo Kolde Methods for re-using public gene expression data

• Meelis Kull Statistical enrichment analysis in algorithms for studying gene regulation
• Jüri Reimand Functional analysis of gene lists, networks and regulatory systems

MSc thesis defended

Sten-Oliver Salumaa, ‘Convolutional Neural Networks for Cellular Segmentation‘, MSc thesis, 2018

Nurlan Kerimov, ‘Designing a Robust and Portable Workflow for Detecting Genetic Variants Associated with Molecular Phenotypes Across Multiple Studies‘, MSc thesis, 2019

Finished Grants and Projects

• MLTAT18343 “Comprehensive cis-regulatory resources with uniformly processed gene expression and splicing QTLs (1.07.2018−30.06.2020)”,Main PI: Kaur Alasoo
• IUT34-4 “Data Science Methods and Applications (DSMA) (1.01.2015−31.12.2020)”, Main PI: Jaak Vilo
• ELIXIR-EXCELERATE – H2020 project supporting ELIXIR implementation
• AgedBrainSYSBIO  – FP7 2012-2017
• IMI-EMIF-Platform (Project info)
• IMI-PREDECT – New Models for Preclinical Evaluation of Drug Efficacy in Common Solid Tumours
• CIESCI – Complexity of Interdependent Epigenetic Signals in Cancer Initiation (Complexity-Net, 2010-2012)
• ESNATS, Embryonic Stem Cell-Based Alternative Testing Strategies. Duration of Project: HEALTH-F5-2008-201619, 5y (2008-2013).
• HEXANord – HEalth teXt Analysis network in the Nordic and Baltic countries [intranet]
• DETECTIVE –  Detection of endpoints and biomarkers for repeated dose toxicity using in vitro systems (FP7+Cosmetics Europe) (2011-2016)
• ENFIN, Enabling Systems Biology. EU FP6 Network of Excellence (2005-2010) LSHG-CT-2005-518254
• SIROCCO – Silencing RNAs: organisers and coordinators of complexity in eukaryotic organisms (2010-2011)
• COBRED — Colon and Breast cancer Diagnostics (2007-2010) EU FP6 STREP, LSHB-CT-2007-037730
• FunGenES, Functional genomics of Embryonic Stem Cells, EU FP6 Integrated Project, subcontractor (2006-2007). LSHG-CT-2003-503494
• ATD, Alternative Transcript Diversity, EU FP6 STREP (2004-2007) LSHG-CT-2003-503329
• COST Action IC0702 – SoftStat –– Combining Soft Computing Techniques and Statistical Methods to Improve Data Analysis Solutions.
• Baltic GRID non-funded partner

• MOBJD67 “Predicting the consequences of rare noncoding genetic variation (1.06.2017−31.05.2019)”,Main PI: Kaur Alasoo
• BIIT was a partner in Center of Translational Genomics   (Supported by the University of Tartu (SP1GVARENG)).
• EXCS – Centre of Excellence in Computer Science — 2008-2015.
• Modern scientific computing methods, platforms and applications. (SF0180008s12) (abstract) (target funding)
• BioMedIT  Project on bioinformatics, medical informatics and computational informatics – Archimedes; European Regional Development Fund. (funding link)
• BIIT-chair  — Estonian Information Technology Foundation grant for developing BIIT group and teaching of related subjects.
• ERMOS – Estonian Research Mobility Scheme for Postdoctoral Research Grant (2010-2013)
• Target funding (2006-2011), The methods, environments, and applications for solving large and complex computational problems. (2006-2011), grant no. SF0182712s06. (Abstract)
• “Base funding” (start-up grant for a new research group) from University of Tartu (2005-2006)
• BiGeR Estonian Science Foundation (ETF), no. 5724 (BiGeR) (2004-2007)
• MEM – ETF7437 (2008-2011) Multi-experiment gene expression data matrix analysis (MEM) (Abstract)
• DMMA Estonian Science Foundation (ETF), no. 5722 (DMMA) (2004-2006)
• Tiigriülikool – 2006 – support for ICT in Higher Education. Partial support for computer server emu (4xdual core CPU, 16GB RAM) and hard disk (4TB).Estonian Language Technology Research Programme: Dictionary informatics (information retrieval) (2005-2008)