Research

 Research Projects and Grants

Our main research interests include analysis of biological data and omics integration using data mining and 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 the most experience in analysing cancer and immune system related data but have dealt with various biological questions over the years.

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

Publications
  1. Sten-Oliver Salumaa, ‘Convolutional Neural Networks for Cellular Segmentation‘, MSc thesis, 2018
  2. Jones, William; Alasoo, KaurFishman, DmytroParts, Leopold. Computational Biology – Deep Learning. Emerging Topics in Life Sciences. Nov 14, 2017 doi: 10.1042/ETLS20160025

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

Jüri Reimand Functional analysis of gene lists, networks and regulatory systems
Meelis Kull Statistical enrichment analysis in algorithms for studying gene regulation
Raivo Kolde Methods for re-using public gene expression data
Sten Ilmjärv Estimating differential expression from multiple indicators
Hedi Peterson Exploiting high-throughput data for establishing relationships between genes
Priit Adler Analysis and visualisation of large scale microarray data
Tauno Metsalu Statistical analysis of multivariate data in bioinformatics
Anna Leontjeva Using Generative Models to Combine Static and Sequential Features for Classification 


Current Research Grants and Projects

International:
  • ELIXIR – Estonian representative and node representative
  • ELIXIR-EXCELERATE – H2020 project supporting ELIXIR implementation
  • PerkinElmer – Deep Learning for microscopy images
  • BioEndoCar – EU project that aims to develop a non-invasive diagnostic test for endometrium carcinoma
Estonian funding:
  • IUT34-4 “Data Science Methods and Applications (DSMA) (1.01.2015−31.12.2020)”, Main PI: Jaak Vilo
  • PSG59Computational analysis and learning from biological data (OmicNet) (1.01.2018−31.12.2020)”,Main PI: Hedi Peterson
  • MOBJD67 “Predicting the consequences of rare noncoding genetic variation (1.06.2017−31.05.2019)”,Main PI: Kaur Alasoo
  • MLTAT18343 “Comprehensive cis-regulatory resources with uniformly processed gene expression and splicing QTLs (1.07.2018−30.06.2020)”,Main PI: Kaur Alasoo
  • TAR16013 (EXCITE) “Estonian Centre of Excellence in ICT Research (1.09.2016−1.03.2023)”,Main PI: Maarja Kruusmaa, Tallinn University of Technology

Other ongoing collaborations:

Finished Grants and Projects

EU grants and projects:
  • 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
Estonian funding agencies:
  • 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)