K. Gorbunov - Publications

2016

Lyubetsky V., Gershgorin R., Seliverstov A., Gorbunov K., Algorithms for reconstruction of chromosomal structures. BMC Bioinformatics, 2016, 17:40, 23 p. DOI: 10.1186/s12859-016-0878-z http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0878-z

2015

Gorbunov K., Gershgorin R., Lyubetsky V., “Rearrangement and Inference of Chromosome Structures” Molecular Biology, 2015, Vol. 49, No. 3, P. 327–338.

2014

Rusin L., Lyubetskaya E., Gorbunov K., Lyubetsky V., “Reconciliation of Gene and Species Trees” BioMed Research International, 2014, Vol. 2014, Article ID 642089, 22 pages. http://dx.doi.org/10.1155/2014/642089

2012

Lyubetsky V., Rubanov L., Rusin L., Gorbunov K., "Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios" Biology Direct, 2012, 7:48. PMID: 24513779 http://www.biologydirect.com/content/7/1/48
Gorbunov K., Lyubetsky V., “The problems of reconciling gene and species trees, mapping a gene tree into a species tree, and gene tree inference” Abstracts of the First RECOMB Satellite Conference on Open Problems in Algorithmic Biology (RECOMB-AB), St. Petersburg, Russia, August 27–29 2012.
Gorbunov K., Seliverstov A., Lyubetsky V., "Geometric Relationship between Parallel Hyperplanes, Quadrics, and Vertices of a Hypercube" Problems of Information Transmission , 2012, 48:2, 185–192 http://dx.doi.org/10.1134%2FS0032946012020081
Gorbunov K., Lyubetsky V., “Fast Algorithm to Reconstruct a Species Supertree from a Set of Protein Trees” Molecular Biology, 2012, Vol. 46, No. 1, P. 161–167.

2011

Zverkóv O., Gorbunov K., Seliverstov A., Lyubetsky V., “Protein clustering with accounting for domen architecture” Proceedings of the 54th conference of Moscow Institute of Physics and Technology “Basic and applied research in life sciences and engineering in modern information environment”, Moscow, Russia, November 25–26 2011, Section of Management and applied mathematics, Vol. 2, P. 88–89.
Gorbunov K., Rubanov L., Rusin L., Lyubetsky V., “An accurate algorithm of cubic complexity to build supertrees” Zitteliana. An International Journal of Palaeontology and Geobiology. Series B, Vol. 30, Abstracts of the international conference “Deep Metazoan Phylogeny 2011 – new data, new challenges", Munchen, Germany, October 11–14 2011, P. 20.
Gorbunov K., Lyubetsky V., “The tree nearest in average to a given set of trees” Information transmission problems, Vol. 47, Iss. 3, 2011

2010

Lopatovskaya K., Gorbunov K., Seliverstov A., Lyubetsky V., “The evolution of proline synthesis transcription regulation in gamma proteobacteria” Molecular Phylogenetics: Contributions to the 2nd Moscow International Conference “Molecular Phylogenetics” (Moscow, Russia, May 18-21, 2010), Moscow, Torus Press, 2010, pp. 132–133.
Gorbunov K., Lyubetsky V., “A Fast Algorithm of Building Species Supertrees with a Set of Gene Trees” Proceedings of the Seventh International Conference on Bioinformatics of Genome Regulation and StructureSystems Biology (BGRSSB’2010), Novosibirsk, Russia, 20-27 June 2010, p. 92.
Lopatovskaya K., Gorbunov K., Rusin L., Seliverstov A., Lyubetsky V., “The Evolution of Proline Synthesis Transcriptional Regulation in Gammaproteobacteria” Moscow University Biological Sciences Bulletin, 2010, V. 65, No. 4, pp. 211–212.
Gorbunov K., Laikova O.N., Rodionov D., Gelfand M., Lyubetsky V., “Evolution of regulatory motifs of bacterial transcription factors” In Silico Biology, 2010, 10, 0012. http://www.bioinfo.de/isb/2010/10/0012/

2009

Gorbunov K., Lyubetsky V., “Inferring gene evolution along a species tree” International Moscow Conference on Computational Molecular Biology: MCCMB’09, pp. 120–121.
Gorbunov K., Lyubetsky V., “Reconstructing the evolution of genes along the species tree” Molecular Biology, 2009, V. 43, No. 5, pp. 881–893.
Gorbunov K., Lyubetskaya E., Asarin E., Lyubetsky V., “Modeling evolution of the bacterial regulatory signals involving secondary structure” Molecular Biology, 2009, V. 43, No. 3, pp. 485–499.

2008

Gorbunov K., Kanovei V., Lyubetsky V., “Inferring optimal scenario of gene evolution along a species tree” Abstracts of The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2008), Novosibirsk, June 22–28, p. 90. http://www.bionet.nsc.ru/meeting/bgrs2008/BGRS2008_Proceedings.pdf

2007

Lyubetsky V., Seliverstov A., Gorbunov K., “Models of gene expression regulation and evolution of regulatory elements” Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, November 16–19 2007, KMK Scientific Press, Moscow, pp. 158–165.
Gorbunov K., Lyubetsky V., “Modeling evolution of the nucleotide sequence with secondary structure” Proceedings of the international scientific conference “Computational Phylogenetics and Molecular Systematics, CPMS’2007”, November 16–19 2007, KMK Scientific Press, Moscow, pp. 68–75.
Gorbunov K., Radionov D., Laikova O., Gelfand M., Lyubetsky V., “Reconstruction of ancestral regulatory signal along a phylogeny” Proceedings of International Moscow Conference on Computational Molecular Biology: ÌÑÑÌÂ’07, 2007, pp. 111–113.
Gorbunov K., Lyubetsky V., “Reconstruction of ancestral regulatory signals along a transcription factor tree” Molecular Biology, 2007, V. 41, No. 5, pp. 836–842.PMID 18240574

2006

Gorbunov K., Lyubetsky V., “Inferring regulatiory signal profiles and evolutionary events” Proceedings of the Fifth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS"2006), Novosibirsk, Russia, July 16–22 2006, Vol. 3, P. 151–154. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2006/BGRS_2006_V3_031.pdf
Lyubetsky V., Gorbunov K., Rusin L., V'yugin V., “Algorithms to reconstruct evolutionary events at molecular level and infer species phylogeny” An article in the book: “Bioinformatics of Genome Regulation and Structure II”, Springer Science & Business Media, Inc. 2006, pp. 189–204. http://www.springerlink.com/content/q67568k37g687647/

2005

Pirogov S., Gorbunov K., Lyubetsky V., “Macro- and microconditions in a model of attenuator regulation of gene expression in bacteria” Proceedings of the RAS conference “Issues of control and modeling in complex systems, VII International conference”, 27 June – 1 July 2005, Samara, pp. 210–215. [in Russian]
Gorbunov K., Lyubetsky V., “Algorithms to reconstruct ancestral gene evolution events” MCCMB’05, 2005, pp. 128–129.
Lyubetsky V., Gorbunov K., V'yugin V., Rusin L., “Removing noise in protein multiple alignment” Information Processes, 2005, V. 5, No 5, pp. 380–391. [in Russian] http://www.jip.ru/2005/380-391.pdf
Lyubetsky V., Gorbunov K., Pirogov S., Rubanov L., Seliverstov A., “An algorithm and search results for a model of gene expression regulation with RNA secondary structures in bacteria” Information Processes, 2005, V. 5, No 5, pp. 337–366. [in Russian] http://www.jip.ru/2005/337-366.pdf
Gorbunov K., Lyubetsky V., “Identification of Ancestral Genes That Introduce Incongruence between Protein- and Species Trees” Molecular biology, 2005, V. 39, No 5, pp. 741–751. PMID: 16240718

2004

Lyubetsky V., Gorbunov K., V'yugin V., “Inferring evolutionary events, quality of COGs, measuring the dissimilarity between gene and species trees” Presentation abstracts of the EMBO World Phylogenetic Course 2004. November 1–7 2004, Rio de Janeiro, Brazil.
Gorbunov K., Lyubetsky V., “New approach for detecting common secondary structures in a set of RNA sequences” Biophysics (Moscow), 2004, V. 48, Suppl. 1 (2003), pp. 56–67.
Gorbunov K., Lyubetsky V., “A model of biosynthesis regulation” Proceedings of VI International conference “Issues of control and modeling in complex systems”, June 14-17 2004, RAS, pp. 151–153. [in Russian]
Gorbunov K., Lyubetsky V., “A Model of Tryptophan Biosynthesis Regulation” Proceedings of the Fourth International Conference on Bionnformatics of Genome Regulation and Structure (BGRS’2004), Novosibirsk, July 25–30 2004, V. 2, pp. 53–55. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2004/BGRS_2004_V2_011.pdf

2003

Gorbunov K., Lyubetsky V., “Detecting common secondary structures in a set of RNA sequences and its testing” MCCMB’03, 2003, pp. 83–85.
Gorbunov K., Lyubetsky V., Mironov A., “Search for Conserved Secondary Structures of RNA” Molecular biology, V. 37, No 5, 2003, p. 723-732. PMID 14593922
Lyubetsky V., Gorbunov K., Searching for alternative RNA secondary structures. Information processes, V. 3, No 1, 2003, p. 47-60. [in Russian]

2002

Gorbunov K., Lyubetsky V., “An Algorithm for Searching for Common Secondary Structures in a Set of RNA Sequences” Proceedings of The Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2002), Novosibirsk, Russia, July 14–20, 2002, V. 3, pp. 20–22. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/2002/BGRS_2002_3_004.pdf
Gorbunov K., Lyubetsky V., An algorithm to search for conservative RNA secondary structures in a database of RNA fragments. Information processes, 2002, V. 2, No 1, p. 55-58. [in Russian]

2001

Gorbunov K., Lyubetskaya E., Lyubetsky V., On two algorithms of searching for alternative RNA structures. Information processes, V. 1, No 2, 2001, p. 178-187. [in Russian]
Danilova L., Gorbunov K., Gelfand M., Lyubetsky V., “Algorithm of Regulatory Signal Recognition in DNA Sequences” Molecular Biology, V. 35, No 6, 2001, p. 841-848. PMID 11771146
Danilova L., Gorbunov K., Gelfand M., Lyubetsky V., An algorithm to detect regulatory signals in DNA sequence data (1). Information processes, V. 1, No 1, 2001, p. 56-63. [in Russian]

2000

Gorbunov K., Lyubetsky V., On an algorithm of detecting regulatory signal in sequence data. Logic research. Issue 7, Moscow, Nauka, 2000, p. 159-163. [in Russian]
V'yugin V., Gorbunov K., Lyubetsky V., Algorithms of detecting regulatory signal and constructing evolutionary trees. Proceedings of II international conference of the RAS «Issues in control and modeling in complex systems», Samara, 2000, RAS Press, p. 130-137. [in Russian]