Bioinformatics research projects
Jaak Vilo
vilo@egeen.ee
http://www.egeen.ee/u/vilo/


Director of Informatics, EGeen
Associate Professor, Department of Computer Science, University of Tartu
Scientist, Estonian Biocentre
Consultant, ArrayExpress, European Bioinformatics Institute


Gene regulation and genetic networks bioinformatics

  Gene regulation by transcriptional control is largely based on DNA
  sequence specific control elements like transcription factor binding
  sites, signals for enhancers, silencers, DNA structural elements,
  etc., and combinatorial aspects of those. Our groups aim is to
  capture those signals in a systematic manner, store information in a
  single database, and facilitate users to access and analyse that
  data. Our goal is to reverse-engineer gene regulatory networks.

Alternative Splicing data analysis

  Alternative splicing is a mechanism for a cell for a fine-scale
  control about which forms of proteins are produced (which exons will
  be included in the final product) from each gene at each stage of
  development, external conditions, or in various tissue types. Our
  groups aim is to study these mechanisms of fine-scale control based
  on the analysis of DNA specific signals that carry information for
  such control.


Gene expression data analysis

  Microarray gene expression studies are providing a rich wealth of
  novel data for large-scale bioinformatics analysis. The aim is to
  develop fast data analysis methods for serving the needs of large
  groups of researchers using public databases like ArrayExpress. The
  research builds upon the initial development of the Expression
  Profiler analysis tools (part of ArrayExpress infrastructure).

Functional genomics and data integration studies

  Various functional genomics data from large scale experiments like
  different protein-protein interaction methods, phenotypic data from
  systematic gene knockouts, genome-wide binding localisation studies
  (ChIP on chip), etc., although never perfectly accurate, provide a
  wealth of new information that has to be put into context of other
  data sources. The key is the integration of those data sources in
  order to facilitate data analysis that can help us to gain better
  hypothesis on function and design new experiments.

GPCR receptor bioinformatics

  Based on our previous study for G-protein coupled receptor - GPCR
  coupling specificity predictions our aim is to increase our ability
  to predict GPCR-mediated signalling pathways and mechanims for
  signal transduction.

Data mining methods development for bioinformatics

  Many above mentioned areas of research will need the development of
  underlying computational data analysis and visualization methods.
  The group will focus on developing those computational methods and
  help the bioinformaticians to utilize best computational methods in
  their research.

Pattern discovery and recognition in sequences; sequence algorithms

  Biological studies to discover motifs in DNA, RNA, or protein
  sequences in large extent rely on basic reserarch of algorithmics of
  sequence based methods or combinatorial pattern matching. The task
  is to develop new pattern discovery and pattern matching algorithms
  and tools that can be used for large scale bioinformatics
  studies. One of those tools is SPEXS, an algorithm developed by Jaak
  Vilo and used for the analysis of DNA and protein sequences.

Medical and clinical data handling and storage, population and
statistical genetics, pharmacogenetics.

  Of utmost importance for any biomedical research whose aim is to
  study human health and genetics, is the proper capture of the
  clinical data.  The aim is to develop data management solutions for
  health, clinical, lifestyle, environmental data and the analysis of
  those data. These data together with drug consumption and treatement
  effects information allow to develop predictive methods for drug
  efficacy studies.