Publications on the methods and applications:

Prediction of functional sites in DNA sequences

by Variable Memory Markov models (context tree):


Orlov Yu.L., Potapov V.N., Filippov V.P. (2002)
Recognizing functional DNA sites and segmenting genomes using the program "Complexity"
// Proceedings of the Third International Conference on Bioinformatics of
Genome Regulation and Structure (BGRS'2002), Novosibirsk, Institute of Cytology&Genetics Press, Vol.3, p.244-247.

Orlov Yu.L., Filippov V.P., Potapov V.N., Kolchanov N.A. (2002) Construction of stochastic context trees for genetic texts. In Silico Biology, (IOS Press) 2(3), 233-247.

 

Nucleosome formation site analysis:

Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. (2001) Nucleosome formation potential of exons, introns, and Alu repeats. Bioinformatics 17(11): 1062-4.

Orlov Yu.L., Levitsky V.G. (2004) Nucleosome positioning signal analysis. // Proceedings of BGRS'2004, Novosibirsk, Inst. of Cytology&Genetics Press, Vol.1, p.149-152.

Levitsky V.G., Proscura A.P., Podkolodnaya O.A., Ignatieva E.V., Ananko E.A. (2004) Nucleosome formation potential of the gene regulatory regions. Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004), IC&G Press, Novosibirsk, Vol.1, p.130-133.

 

Programs:

Levitsky V.G., Podkolodnaya O.A., Kolchanov N.A., Podkolodny N.L. (2001) Nucleosome formation potential of eukaryotic DNA: tools for calculation and promoters analysis. Bioinformatics, 17(11), 998–1010.

Levitsky V.G. (2004) RECON: a program for prediction of nucleosome formation potential. Nucleic Acids Res. 32(Web Server issue):W346-9.

 

Database:

Levitsky VG, Ponomarenko MP, Ponomarenko JV, Frolov AS, Kolchanov NA. (1999) Nucleosomal DNA property database. Bioinformatics 15(7-8):582-92.

Levitsky V.G., Katokhin A.V., Podkolodnaya O.A., Furman D.P., Kolchanov N.A. (2005) NPRD: Nucleosome Positioning Region Database. Nucleic Acids Res. 33 Database Issue:D67-70.

 

Additional materials including complete Proceedings of the BGRS conferences (2000, 2002 and 2004) in PDF format are accessible at the official Internet-site of the series of International Conferences on Bioinformatics of Genome Regulation and Structure.

 


Main page

The Institute of Cytology and Genetics (Russia)

This resource has been developed in Institute of Cytology and Genetics, Novosibirsk, Russia
Authors: Yu.L.Orlov, V.G.Levitsky
Leader: N.A.Kolchanov

Version -  2005.