Kel A., Konovalova T., Valeev, T., Cheremushkin, E., Kel-Margoulis, O., Wingender, E.
Composite Module Analyst: a fitness-based tool for identifica-tion of transcription factor binding site combinations.
Bioinformatics. 2006 Vol. 22(10). P. 1190.1197.

Valeev, T., Shtokalo, D., Konovalova, T., Voss, N., Cheremushkin, E., Stegmaier, P., Kel-Margoulis, O., Wingender, E., Kel, A.
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm.
Nucleic Acids Research. 2006. Vol. 34(Web Server issue). P. 541.545

Cheremushkin, E., Konovalova T., Valeev T., Shtokalo D., Taraskina A.
CisSearch: Software Package For Complex Analysis Of Gene Regulatory Sequences.
The 3rd Annual RECOMB Satellite Workshop on Regulatory Genomics, Singapore . July 17th-18th, 2006. P. 100-108.

Cheremushkin, E., Konovalova T., Valeev T., Shtokalo D., Taraskina A.
Software Package For Complex Analysis Of Gene Regulatory.
3rd International Conference .Genomics, Proteomics, Bioinformatics and Nanotechnologies for Medicine., Novosibirsk, Russia. July 12-16, 2006 P. 97.

Golosov K., Cheremushkin, E., Konovalova T., Jeff Holmes.
Recognition of Mutations in Sequences of DNA of the Certain Genetic Lines of Organism C. Elegans.
3rd International Conference .Genomics, Proteomics, Bioinformatics and Nanotechnologies for Medicine., Novosibirsk, Russia July 12-16, 2006 P. 104.

Taraskina A., Cheremushkin, E.
Clustering of Microarray Data with the Modified Fuzzy C-means Method.
3rd International Conference .Genomics, Proteomics, Bioinformatics and Nanotechnologies for Medicine., Novosibirsk, Russia . July 12-16, 2006 . P. 121.

Cheremushkin E.S., Murzin F. A.
Analysis of DNA sequences using Golay Code.
Workshop on Science Intensive Applied Software “PSI’06”, the 26-27 of June, 2006, Novosibirsk, Academgorodok, p.115-119.

Cheremushkin E.S., Konovalova T.G., Valeev T. F., Shtokalo D.N., Taraskina A.S.
CisSearch software package for analysis of regulatory sequences in DNA.
Workshop on Science Intensive Applied Software “PSI’06”, the 26-27 of June, 2006, Novosibirsk, Academgorodok, p.111-114.

Cheremushkin E.S., Valeev T. F., Konovalova T.G., Shtokalo D.N., Golosov K.B., Kel A.
ExPlain: Software system for microarray and analyzing key molecules search.
Workshop on Science Intensive Applied Software “PSI’06”, the 26-27 of June, 2006, Novosibirsk, Academgorodok, p.106-110.

Taraskina A.S., Cheremushkin E.S., Murzin F. A.
Wavelet-analysis and genetic sequences clusterization.
Workshop on Science Intensive Applied Software “PSI’06”, the 26-27 of June, 2006, Novosibirsk, Academgorodok, p.91-94.

Murzin F. A., Valeev T. F.
Studying the advantages of video coding using interpolational method.
Workshop on Science Intensive Applied Software “PSI’06”, the 26-27 of June, 2006, Novosibirsk, Academgorodok, p.86-88.

Taraskina A.S., Cheremushkin E.S.
Microarray data processing with fuzzy Clustering algorithm.
Computational methods and programming, Vol.7, 2006

Taraskina A.S., Konovalova T.G., Valeev T.F., Shtokalo D.N., Cheremushkin E.S.
Graphical results of analysis in software package for analysis of regulatory fragments in DNA.
Proceedings of the conference-and-contest of young scientists "Microsoft
Technologies in Informatics and Programming" Feb 22-24, 2006, Novosibirsk; p.223-224

Taraskina A.S., Konovalova T.G., Valeev T.F., Shtokalo D.N., Cheremushkin E.S.
Software package CisSearch for analysis of regulatory fragments in DNA.
Proceedings of the conference "Lomonosov-2006", April 12-15, 2006, Moscow; Vol.3, p.48-49

Taraskina A.S., Konovalova T.G., Valeev T.F., Shtokalo D.N., Cheremushkin E.S.
Software package CisSearch for analysis of gene regulatory fragments.
Proceedings of the conference "Intellectual potential of Siberia", May 17-18, 2006, Novosibirsk; p.38

Valeev T.F.
GraphCut: Graph minimal cut problem in texture generation.
Proceedings of the conference-and-contest of young scientists "Microsoft
Technologies in Informatics and Programming" Feb 22-24, 2006, Novosibirsk; p.51-52.

Valeev T.F.
Bitlines encoding and interpolation methods in videocompression.
Proceedings of the conference-and-contest of young scientists "Microsoft
Technologies in Informatics and Programming" Feb 22-24, 2006, Novosibirsk; p.53-55.

Valeev T.F., Dunaev A.A.
Biocontrol visual and audio feedback.
Proceedings of the conference-and-contest of young scientists "Microsoft
Technologies in Informatics and Programming" Feb 22-24, 2006, Novosibirsk; p.165-166.

Golosov K.B., Valeev T.F., Konovalova T.G., Cheremushkin E.S., Shtokalo D.N., Levitskiy-Potapov B., Chekmenev D., Voss N., Kel A.V.
ExPlain: Complex system of genetic information analysis.
Proceedings of the conference-and-contest of young scientists "Microsoft
Technologies in Informatics and Programming" Feb 22-24, 2006, Novosibirsk; p.171-172.

Valeev T.F.
Texture synthesis using graph cuts.
XLIV International Scientific Student Conference, Informatics technologies section.

Valeev T.F.
Studying of interpolation approaches in videocompression algorithms.
XLIV International Scientific Student Conference, Informatics technologies section.

Dunaev A.A., Valeev T.F.
Visual feedback in program hardware-based complex “BOSLAB”
XLIV International Scientific Student Conference, Informatics technologies section.

Taraskina A.S., Konovalova T.G., Valeev T.F., Shtokalo D.N., Cheremushkin E.S.
Software package CisSearch for analysis of gene regulatory fragments.
XLIV International Scientific Student Conference, Informatics technologies section.

Golosov K.B., Konovalova T.G., Cheremushkin E.S.
Visualization system of mutation fragments in nematode genome.
XLIV International Scientific Student Conference, Informatics technologies section.

Golosov K.B., Konovalova T.G., Cheremushkin E.S., Holmes J.
Mutation recognition in DNA sequences of specific genetic lines of C. Elegans.
Proceedings of the conference "Lomonosov-2006", April 12-15, 2006, Moscow; Vol.4, p.43-44.

Shtokalo D.N.
The "PromExtra" program for gene promotor simbols extracting.
Proceedings of the conference "Lomonosov-2006", April 12-15, 2006, Moscow; Vol.4, p.55.

Shtokalo D.N.
Promotor sequences extraction from gene data base.
XLIV International Scientific Student Conference, Informatics technologies section.

Shtokalo D.N.
Software package for promoter extraction.
Proceedings of the conference-and-contest of young scientists "Microsoft
Technologies in Informatics and Programming" Feb 22-24, 2006, Novosibirsk.

2005

Cheremushkin E., Konovalova T., Valeev T., Kel A.
Methods for search of gene regulatory elements binding sites.
Analytical Tools for DNA, Genes and Genomes: Nuts & Bolts. – DNA Press, October 2005; Chapter 9, pp.185-214

Kel A., Konovalova T., Valeev T., Cheremushkin E., Kel-Margoulis O., Wingender E.
Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation.
Proceedings of the German Conference on Bioinformatics (GCB'05), Hamburg, Germany, Oct 5-7, 2005; 8 pp

Konovalova T., Valeev T., Cheremushkin E., Kel A.
Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data.
Advances in Natural Computation, part 2, Springer, Germany, 2005 (LNCS 3611); pp.1202-1205
Proceedings of the First International Conference on Natural Computations (ICNC'05), Changsha, China, Aug 27-29, 2005

Valeev T.
Comparative analysis of the search techniques using microarray data for regulation modules in the DNA sequences.
Tools and Techniques of Program Construction and Optimization, Novosibirsk, 2005; pp.21-28

Konovalova T., Komashko V.
Processing of data of microarray experiments with the use of the R language.
Tools and Techniques of Program Construction and Optimization, Novosibirsk, 2005; pp.117-136

Cheremushkin E.
Analysis of different types of DNA structure with autocorrelation function.
Tools and Techniques of Program Construction and Optimization, Novosibirsk, 2005; pp.247-252

Shtokalo D., Cheremushkin E.
Construction of the programme complex “Regulatory Sequences Analyzer” for recognition of cis-elements in the DNA sequence.
Tools and Techniques of Program Construction and Optimization, Novosibirsk, 2005; pp.253-264

Valeev T., Murzin F.
Some algorithms of videosequences compression and their investigation.
Proceedings of the 15^th International Conference on Computer Graphics and Applications (GraphiCon'05), Jun 20-24, 2005; pp 326-328

Valeev, T.
Analysis of video comperssion algorithms.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 22-24, 2005; p.110-111

Valeev, T.
Genetic algorithm as alternative for solving of some NP-complete tasks.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 22-24, 2005; p.112-113

Konovalova T., Valeev T., Cheremushkin E.
Search of composite promoter modules that regulates eucariotic gene expression.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 22-24, 2005; p.121-122

Cheremushkin, E.
DNA analysis with spread-spectrum signal theory applications.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 22-24, 2005; p.140-142

Cheremushkin E., Konovalova T., Valeev T.
Development of propram package for DNA regulatory regions analysis.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 22-24, 2005; p.142-143

2004

Cheremushkin E.S., Kel A., Lobiv I.V., Murzin F., Polovinko O.
VISUALIZATION OF DNA SEQUENCES BY COLOR CUBE TRANSFORMATION.
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.28

Lobanova M.V., Konovalova T., Cheremushkin E.
WEB-BASED TOOL FOR ANALYSIS OF SNPS IN NONCODING DNA.
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.33

Cheremushkin E.S., Kel A.
PHYLOGENETIC FOOTPRINT: A NEW METHOD FOR PROMOTER ALIGNMENT
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.33

Lobanova M.V., Cheremushkin …., Konovalova ’., Tchekmenev D.,Beschastnov E., Dunaev A., Murzin F.
GRESA DEVELOPMENT TOOLS: THE ENVIRONMENT OF DEVELOPMENT AND TESTING OF APPLICATIONS IN THE FIELD OF THE DNA REGULATION SEQUENCES ANALYSIS
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.35

Cheremushkin E.S.
THE METHOD OF IDENTIFICATION OF NUCLEAR RECEPTOR BINDING SITES
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.35

Konovalova T.G., Ivanov V., Valeev T., Cheremushkin E., Beschastnov, E., Komashko V., Lobanova M., Kel A.
A TOOL FOR REVEALING COMPOSITE MODULES, REGULATING GENE EXPRESSION ACCORDING TO MICRO ARRAY DATA
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.36

Konovalova T.G., Ivanov V., Valeev T., Cheremushkin E., Beschastnov, E., Komashko V., Lobanova M., Kel A.
A TOOL FOR REVEALING COMPOSITE MODULES, REGULATING GENE EXPRESSION ACCORDING TO MICRO ARRAY DATA
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.36

Cheremushkin E.S., Dunaev A., Murzin F.
SYSTEM OF STATISTICAL COMPARISON OF METHODS OF SEARCH OF CIS-ELEMENTS
Proceedings of Computer Applications In Scientific Researches IVTN-2004 p.37

Cheremushkin E. S., Konovalova T. G., Murzin F. A., Kel A. E.
A system of recognition of cis-elements on DNA sequences.
Software tools and mathematical foundations of informatics. - Novosibirsk, 2004. - P. 255-269.

E. S. Cheremushkin
System of statistical comparison of methods of search of cis-elements.
Samsung Young Scientists Day (Novosibirsk)

Cheremushkin E., Polovinko O., Lobiv I., Dunaev A.
Visualization and identification of subsequences in regulatory DNA sequences.
XLII International Scientific Student Conference (Novosibirsk)

Cheremushkin E.S.
Statistical cis-elemtns search methods comparison.
XLII International Scientific Student Conference (Novosibirsk)

Cheremushkin E.S.
Philogenetic footprint and promoter alignment.
XLII International Scientific Student Conference (Novosibirsk)

Cheremushkina E.N., Cheremushkin E.S., Tchekmenev D., Kel O.
Algorithms of identification of nuclear receptors binding sites.
XLII International Scientific Student Conference (Novosibirsk)

Beschastnov, E., Lobanova M., Konovalova (Ivanova), T., Cheremushkin, E.
Program system for revealing Cis-elements.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 21-23, 2004; p 90-91

Cheremushkin, E.
Phylogenetic footprint: New method for promoter alignment.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 21-23, 2004; p 133-134

Cheremushkin, E.
System of statistical comparison of methods of searching Cis-elements.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 21-23, 2004; p 134-135

Cheremushkin, E., Polovinko O., Lobiv I., Dunaev A.
Visualization methods of subsequences identification in regulatory sequences of DNA.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 21-23, 2004; p136-137

Cheremushkina E., Cheremushkin, E., Chekmenev D., Kel O
Method of identification of nuclear receptors binding sites.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 21-23, 2004; p137-139

Konovalova (Ivanova), T., Beschastnov, E., Lobanova M., Cheremushkin, E.
GRESA Development Tools: The incorporated environment of development and testing of applications in the field of the DNA regulation sequences analysis.
Proceedings of the conference-and-contest of young scientists "Microsoft Technologies in Informatics and Programming" Feb 21-23, 2004;
P 7-109

2003

Cheremushkin, E. and Kel, A. (2003).
Whole genome human/mouse phylogenetic footprinting of potential transcription regulatory signals.
Proceedings of the Pacific Symposia on Biocomputing, 2003; p.291-302.
PMID: 12603036

Alexander Kel, Klaus Hornischer, Olga Kel-Margoulis, Evgeniy Cheremushkin and Edgar Wingender
Phylogenetic footprints of Composite Regulatory Elements in human, mouse and rat genomes.
Proceedings of the meeting: "Genome Informatics", Cold Spring Harbor Laboratory, May 7-May 11, 2003, p.66

Kel, A.E., Goessling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V., Wingender, E. (2003)
MATCH(TM): a tool for searching transcription factor binding sites in DNA sequences
Nucleic Acids Res. V.31, p.3576-3579.
PMID: 12824369

Konovalova (Ivanova), T., Cheremushkin, E., Beschastnov, E., and Kel, A.
Applicating of the metropolis algorithm to reveal composite modules in promoters of eukaryotic genes
Proceedings of the European Conference on Computational Biology, (ECCB'2003), Paris, France, Sept. 27-30, 447-448 (2003).

Olga Kel-Margoulis, Klaus Hornisher, Eugeny Cheremushkin, Alexander Kel
Revealing of composite regulatory elements by phylogenetic footprint of three genomes
Proceedings of the "Moscow Conference on Computational Molecular Biology (MCCMB'03)" Moscow, Russia, July 22-25, 2003, p.43

Dunaev A. A., Kel A. E., Lobiv I. V., Murzin F. A., Polovinko O. N., Cheremushkin E. S.
Visualization of genetic information
New informational technologies in science and education. - Novosibirsk, 2003. - P. 147-156.

2002

Kel-Margoulis OV, Ivanova TG, Wingender E, Kel AE.
Automatic annotation of genomic regulatory sequences by searching for composite clusters.
Pac Symp Biocomput. 2002;:187-98. PMID: 11928475

2001

Alexander Kel, Michael Zhang, Olga Kel-Margoulis, Tatyana Ivanova, Edgar Wingender,
A decision tree classifier of promoters based on identification of transcription factor binding sites. (2001)
Proceedings of the conference BIOINFORMATICS 2001, Skovde, Sweden, March 29 - April 1, 2001, p. 23

Alexander Kel , Theresa Zhang , Michael Zhang, Olga Kel-Margoulis, Tatyana Ivanova, Edgar Wingender,
A decision tree classifier of promoters based on composite modules of TF binding sites (2001),
In Currents in computational molecular biology (edited by: Nadia El-Mabrouk, Thomas Lengauer & David Sankoff), p.31-32

Alexander Kel , Olga Kel-Margoulis, Tatyana Ivanova, Michael Zhang, Edgar Wingender,
A decision tree classifier of promoters based on TF binding sites (2001),
Proceedings of the conference ISMB2001, 9th International Conference on Intelectual Systems for Molecular Biology, Copenhagen, Denmark, July 21-25, , 2001 , p.48

Alexander Kel, Olga Kel-Margoulis, Tatyana Ivanova, Edgar Wingender, ClusterScan: A Tool for Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters (2001)
Proceedings of the German Conference on Bioinformatics GCB 2001, Braunschweig, Germany, October 7-10, 2001, p.96-101.