Research

The analysis conducted in recent years shows that a comprehensive study of the genome will determine, in the near future, the further development of such disciplines as medicine, biotechnology and modern agriculture. That is why, the proper functioning of such units as ECBiG will affect many spheres of social and economic life.

ECBiG conducts research recognized by the European Community as a key to the supra-regional and global scale. Since the bio-economy in Poland is only in the initial phase of development, there is a need for direct support of the development of this area to prevent the exclusion of Polish science from the international circuit of knowledge.

ECBiG research conducted on both, genomes (their structure, mechanisms of functioning) and products resulting from expression of information encoded in them (RNA and proteins), can be applied in the socio - economic practice, particularly in medicine and agriculture.

More about research in bioinformatics see Bioserver and RNApolis, in genomics - see IBCH.

Areas of research

  • DNA copy numer variation in plants, animals and humans
  • RNA analysis
  • proteomics
  • metabolomics
  • system biology
  • immunology
  • gene expression profiling
  • molecular mechanisms and markers of acute myeloid leukemia

Results of research

RNApolis is a flagship of RNA bioinformatics group carrying out the research in ECBiG. This portal collects the most important information about computational tools dedicated to RNA analysis developed by the group, and allows to enter them directly from one place.
http://rnapolis.pl/


RNA FRABASE is a database of RNA structures and search engine to locate 3D fragments with a specified sequence and/or secondary structure within all experimentally determined RNAs. It has already attracted 400,000 (400 thousand) returning visitors from 150 countries. By March 2015, it had achieved over 2.8 mln hits, which represents 860 workloads daily (1 session runs every two minutes).
http://rnafrabase.cs.put.poznan.pl/


RNAComposer is one of the first fully automated systems for RNA 3D structure prediction and it is the fastest on the market. It is widely used for scientific as well as educational purposes. It has already gathered 10,000 (10 thousand) returning visitors and hits 56 workloads daily. By March 2015, it had been run 100,000 times.
http://rnacomposer.cs.put.poznan.pl/


RNApdbee is a webserver to annotate secondary structures of knotted and unknotted RNAs. Published in 2014 (NAR), it already has 500 regular users and hit 3500 sessions from the release date.
http://rnapdbee.cs.put.poznan.pl/


RNAlyzer – is standalone application devoted for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models (published in NAR, 2013). Our approach is based on the idea of local neighborhood, defined as a set of atoms included in the sphere centered around a user-defined atom. A unique feature of the RNAlyzer is the simultaneous visualization of the model-reference structure distance at different accuracy levels, from the individual residues to the entire molecules based on RMSD measure.
http://rnalyzer.cs.put.poznan.pl


RNAssess – is a computational server dedicated to evaluation of quality of RNA models. The server provides: (i) ranking of multiple 3D models (ii) visualization of prediction accuracy of atoms (iii) the ability to present results in an interactive way (iv) graphical interpretation of inaccurate predicted regions (v) plots that show structural regions of models predicted correctly below a certain threshold of accuracy. Server integrates a set of measures, namely RMSD, Deformation Index, Interactions Network Fidelity, P-value and Cutoff.
http://rnassess.cs.put.poznan.pl


GeVaDSs - decision support system for novel Genetic Vaccine development process; an intelligent database is described where the results of immunological experiments can be stored and analysed. It was published as a result of an EU grant – Compuvac and was successfully used by immunologists working on genetic vaccines against Hepatitis C and West Nile viruses.
http://gevads.cs.put.poznan.pl/


A new method was proposed to integrate co-expression data obtained through DNA microarray analysis and protein-protein interaction network data; it was applied to Arabidopsis thaliana. The method identifies small subsets of highly interacting proteins and is able to support functional identification of complex genetic traits.


The mechanisms of RNA degradation appear as one of the most important factors influencing RNA activity. The RNA degradation process has been described in terms of bioinformatics and computer science. A formulation of a new problem, called RNA Partial Degradation Problem (RNA PDP), has been proposed and its computational complexity proved to be strongly NP-complete. The proposed algorithm solving the problem is capable of reconstructing an RNA molecule using the results of biochemical analysis of its degradation.


To simplify and speed up the DNA sequencing process, a pipeline of preprocessing raw data was developed; it diminishes influence of low quality reads. Also a method was proposed for preliminary joining overlapping reads, which resulted in significant decreasing the cardinality of initial sets.


GRASShopPER - an algorithm for the de novo assembly was proposed in a parallel version. A hybrid parallel programming strategy resulted in the two-level approach: computations in threads and computations on different nodes in a cluster. Tests carried out on real data of Prochloroccocus marinus coming from Roche sequencer showed, that the algorithm was speeded up 20 times in comparison to the sequential approach, holding high accuracy and beating results of other algorithms.


SphereGrinder - SphereGrinder is platform independent computational tool that allows for comprehensive quality inspection conducted between the set of predicted protein models and the reference structure. SphereGrinder has been successfully used in CASP challenge since 2010. It is implemented as an online application available for free use by all academic users.
http://spheregrinder.cs.put.poznan.pl.


PSQAM server which allows to identify and visualize possible chemical/physical, folding, packing inconsistencies in order to refine analyzed protein model. It is also particularly suited to assess applicability of the target sequence to structural template alignments, a major source of comparative modeling errors. Server combines several types of potential energies such as statistical and physics-based potentials.