K. Gorbunov - Publications

2024

Gorbunov K., Lyubetsky V., Algorithms for the reconstruction of genomic structures with proofs of their low polynomial complexity and high exactness. Mathematics, March 11 2024, Vol. 12, No. 6, Art. 817. DOI: 10.3390/math12060817 (WoS Q1) http://iitp.ru/https://doi.org/10.3390/math12060817

2023

Gorbunov K., Lyubetsky V., Constructing an evolutionary tree and path–cycle graph evolution along it. Mathematics, Apr 24 2023, Vol. 11, No. 9, Art. 2024. DOI: 10.3390/math11092024 (WoS Q1) http://iitp.ru/https://doi.org/10.3390/math11092024

2021

Gorbunov K., Lyubetsky V., Multiplicatively exact algorithms for transformation and reconstruction of directed path-cycle graphs with repeated edges. Mathematics, Oct 14 2021, Vol. 9, No. 20, Art. 2576. DOI: 10.3390/math9202576 (WoS Q1) http://iitp.ru/https://doi.org/10.3390/math9202576

2020

Gorbunov K., Lyubetsky V., Linear time additively exact algorithm for transformation of chain-cycle graphs for arbitrary costs of deletions and insertions. Mathematics, Vol. 8, No. 11, Art. 2001. DOI: 10.3390/math8112001 (WoS Q1) http://iitp.ru/https://doi.org/10.3390/math8112001
Gorbunov K., Lyubetsky V., Evolution of mitochondrial genomic structures in metazoans: algorithm and software. The proceedings of International forum «Biotechnology: state of the art and perspectives», Moscow, Russia, October 28–30 2020, Iss. 18, P. 261–262. DOI: 10.37747/2312-640X-2020-18-260-262 http://iitp.ru/https://doi.org/10.37747/2312-640X-2020-18-260-262
Gorbunov K., Lyubetsky V., An almost exact linear algorithm for transformation of chain-cycle graphs with optimization of the sum of operation costs. Doklady Mathematics, 2020, Vol. 102, No. 2, P. 376–379. DOI: 10.1134/S1064562420050324 http://iitp.ru/https://doi.org/10.1134/S1064562420050324
Gorbunov K., Lyubetsky V., An almost exact linear complexity algorithm of the shortest transformation of chain-cycle graphs. arXiv:2004.14351 [math.CO], Apr 29 2020. http://iitp.ru/https://arxiv.org/abs/2004.14351

2019

Gorbunov K., Lyubetsky V., Linear algorithm for reconstruction of chromosome structures. The proceedings of International congress «Biotechnology: state of the art and perspectives», Moscow, Russia, February 25–27 2019, Iss. 17, P. 350–351. http://iitp.ru/https://elibrary.ru/item.asp?id=37590378

2018

Gorbunov K., Lyubetsky V., A linear algorithm for restructuring a graph. Automation and Remote Control, 2018, Vol. 79, Iss. 12, P. 2203–2216. DOI: 10.1134/S0005117918120093 http://iitp.ru/https://doi.org/10.1134/S0005117918120093
Lyubetsky V., Lyubetskaya E., Gorbunov K., Linear algorithm for a cyclic graph transformation. Lobachevskii Journal of Mathematics, 2018, Vol. 39, No. 9, P. 1217–1227. DOI: 10.1134/S1995080218090147 http://iitp.ru/https://doi.org/10.1134/S1995080218090147

2017

Lyubetsky V., Rubanov L., Gorbunov K., Zverkóv O., Seliverstov A., Highly conserved elements in mitochondrial genomes of ciliates and monocots. Materials of the IX International Congress “Biotechnology: State of the Art and Prospects of Development”, Moscow, Russia, February 20–22 2017, Part 1, P. 393. http://iitp.ru/https://elibrary.ru/item.asp?id=29220438
Lyubetsky V., Gershgorin R., Gorbunov K., Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming. BMC Bioinformatics, 2017, Vol. 18, No. 537. doi:10.1186/s12859-017-1944-x, PMID: 29212445 (WoS Q1) http://dx.doi.org/10.1186/s12859-017-1944-x
Gorbunov K., Lyubetsky V., Transformation of large chromosome structures: an algorithm of equalization of gene contents. CEUR Workshop Proceedings, Feb 23 2018, Vol. 2064, Convergent Cognitive Information Technologies 2017, P. 395–401, in Russian. http://ceur-ws.org/Vol-2064/paper46.pdf
Gorbunov K., Lyubetsky V., The Minimum-Cost Transformation of Graphs. Doklady Mathematics, 2017, Vol. 96, No. 2, P. 503–505. doi:10.1134/S1064562417050313 http://iitp.ru/https://doi.org/10.1134/S1064562417050313
Gorbunov K., Lyubetsky V., A linear algorithm for the shortest transformation of graphs with different operation costs. Journal of Communications Technology and Electronics, 2017, Vol. 62, No. 6, P. 653–662. doi:10.1134/S1064226917060092 http://iitp.ru/https://doi.org/10.1134/S1064226917060092
Gorbunov K., Lyubetsky V., Algorithm of transformation of a graph into another one with minimal cost. Informatics and it"s applications, 2017, Vol. 11, Iss. 1, P. 79–89 (in Russian). doi:10.14357/19922264170107
Gorbunov K., Lyubetsky V., Linear algorithm for minimal rearrangement of structures. Problems of Information Transmission, 2017, Vol. 53, Iss. 1, P. 55–72. doi:10.1134/S0032946017010057
Gershgorin R., Gorbunov K., Zverkóv O., Rubanov L., Seliverstov A., Lyubetsky V., Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates. Life, 2017, Vol. 7, No. 9. doi:10.3390/life7010009, PMID: 28264444 http://www.mdpi.com/2075-1729/7/1/9/htm

2016

Korolev S., Gorbunov K., Zverkóv O., Seliverstov A., Lyubetsky V., Degenerate inverted repeats in the genomes of mycobacterium. CEUR Workshop Proceedings (CEUR-WS.org), Selected Papers of the First International Scientific Conference Convergent Cognitive Information Technologies (Convergent 2016), Moscow, Russia, November 25–26 2016, vol. 1763, p. 182–187, in Russian.
Gorbunov K., Lyubetsky V., A modified algorithm for transformation of chromosomal structures: a condition of absolute exactness. CEUR Workshop Proceedings (CEUR-WS.org), Selected Papers of the First International Scientific Conference Convergent Cognitive Information Technologies (Convergent 2016), Moscow, Russia, November 25–26 2016, vol. 1763, p. 162–172, in Russian.
Lyubetsky V., Gershgorin R., Seliverstov A., Gorbunov K., Algorithms for Reconstruction of Chromosomal Structures. BMC Bioinformatics, 2016, vol. 17, art. 40, 23 pp. DOI: 10.1186/s12859-016-0878-z, PMID: 26780836 http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-0878-z

2015

Gershgorin R., Gorbunov K., Seliverstov A., Lyubetsky V., Evolution of chromosome structures. Proceedings of the 39th IITP RAS Interdisciplinary Conference & School “Information Technology and Systems 2015” (ITaS’15), Sochi, Russia, Sep 7–11 2005, Moscow: IITP, 2015, P. 105–120. http://iitp.ru/https://elibrary.ru/item.asp?id=24378278
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

154, 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.
154, 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]