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Bioinformatics benefits from Siberia: on the anniversary of Nikolay Aleksandrovich Kolchanov, Academician of the Russian Academy of Sciences (RAS)

https://doi.org/10.30901/2658-6266-2022-1-o4

Abstract

January 9, 2022 marks the 75th anniversary of Nikolai Aleksandrovich Kolchanov, Doctor of Biological Sciences, Professor, Academician of the Russian Academy of Sciences, Scientific Leader of the Federal Research Center the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, First Vice-President of the Vavilov Society of Geneticists and Breeders. Acad. N.A. Kolchanov is a prominent specialist in the field of bioinformatics and systems computational biology, under whose guidance the largest domestic scientific school in this area has formed and received global development. He is the author and co-author of about 700 publications in domestic and foreign press, holder of 18 copyright certificates and 8 patents. For almost 20 years, Acad. Kolchanov is the Head and Professor of the Department of Information Biology with the Faculty of Natural Sciences of Novosibirsk State University. He supervised the work of 12 doctoral and 2 senior doctorate students. His students, who work in leading domestic and foreign scientific centers, are the pride of Russian science and make a significant contribution to the world level of development of modern bioinformatics at the global level.

About the Authors

E. K. Khlestkina
https://www.vir.nw.ru/direktsiya/
N.I. Vavilov All-Russian Institute of Plant Genetic Resources,
Russian Federation

Elena K. Khlestkina

Dr. Sci. (Biology), Professor of the RAS, Director, VIR, 42, 44 Bolshaya Morskaya Street, St. Petersburg 190000, Russia; member of the Presidium, VOGiS, 3, Podbelsky highway, Pushkin, Saint-Petersburg 196608, Russia



A. A. Nizhnikov
https://bio.spbu.ru/staff/id196_aan.php
All-Russia Research Institute for Agricultural Microbiology, St. Petersburg State University, Vavilov Society of Geneticists and Breeders
Russian Federation

Anton A. Nizhnikov

Dr. Sci. (Biology), Head of Laboratory for Proteomics of Supra-Organismal Systems, ARRIAM, 3, Podbelsky highway, Pushkin, Saint-Petersburg 196608, Russia; Associate Professor, SPbU, 7/9, Universitetskaya embankment, Saint-Petersburg 199034, Russia; Scientific Secretary, VOGiS, 3, Podbelsky highway, Pushkin, Saint-Petersburg 196608, Russia



I. A. Tikhonovich
http://www.arriam.spb.ru/rus/LIST/TikhonovichIA.html
St. Petersburg State University, All-Russia Research Institute for Agricultural Microbiology, Vavilov Society of Geneticists and Breeders
Russian Federation

Igor A. Tikhonovich

Dr. Sci. (Biology), Academician of the Russian Academy of Sciences, Professor, Dean of the Faculty of Biology, SPbU, 7/9, Universitetskaya embankment, Saint-Petersburg 199034, Russia; Scientific Director, ARRIAM, 3, Podbelsky highway, Pushkin, Saint-Petersburg 196608, Russia; President of VOGiS, 3, Podbelsky highway, Pushkin, Saint-Petersburg 196608, Russia



References

1. Ananko E.A., Podkolodny N.L., Stepanenko I.L., Ignatieva E.V., Podkolodnaya O.A., Kolchanov N.A. GeneNet: a database on structure and functional organisation of gene networks. Nucleic Acids Research. 2002;30(1):398-401. DOI: 10.1093/nar/30.1.398

2. Bragina E.Yu., Tiys E.S., Freidin M.B., Koneva L.A., Demenkov P.S., Ivanisenko V.A., Kolchanov N.A., Puzyrev V.P. Insights into pathophysiology of dystropy through the analysis of gene networks: an example of bronchial asthma and tuberculosis. Immunogenetics. 2014;66(7-8):457-465. DOI: 10.1007/s00251-014-0786-1

3. Department of Information Biology, Novosibirsk State University (Kafedra Informatsionnoy Biologii. Novosibirskii Gosudarstvennyi Universitet) [website]. [in Russian]. URL: https://kib.nsu.ru/ [дата обращения: 28.11.2021].

4. Heinemeyer T., Wingender E., Reuter I., Hermjakob H., Kel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Kolpakov F.A., Podkolodny N.L., Kolchanov N.A. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Research. 1998;26(1):362-367. DOI: 10.1093/nar/26.1.362

5. Ivanisenko V.A., Pintus S.S., Grigorovich D.A., Kolchanov N.A. PDBSite: a database of the 3D structure of protein functional sites. Nucleic Acids Research. 2005;33 Suppl 1:D183-D187. DOI: 10.1093/nar/gki105

6. Ivanisenko V.A., Pintus S.S., Grigorovich D.A., Kolchanov N.A. PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Research. 2004;32 Suppl 2:W549-W554. DOI: 10.1093/nar/gkh439

7. Kel-Margoulis O.V., Romashchenko A.G., Kolchanov N.A., Wingender E., Kel A.E. COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Research. 2000;28(1):311-315. DOI: 10.1093/nar/28.1.311

8. Kolchanov N.A., Ananko E.A., Podkolodnaya O.A., Ignatieva E.V., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Goryachkovskaya T.N., Busygina T.V., Kolpakov F.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G. Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Research. 1999;27(1):303-306. DOI: 10.1093/nar/27.1.303

9. Kolchanov N.A., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Stepanenko I.L., Merkulova T.I., Pozdnyakov M.A., Podkolodny N.L., Naumochkin A.N., Romashchenko A.G. Transcription Regulatory Regions Database (TRRD): its status in 2002. Nucleic Acids Research. 2002;30(1):312-317. DOI: 10.1093/nar/30.1.312

10. Kolchanov N.A., Nedosekina E.A., Ananko E.A., Likhoshvai V.A., Podkolodny N.L., Ratushny A.V., Stepanenko I.L., Podkolodnaya O.A., Ignatieva E.V., Matushkin Y.G. GeneNet database: description and modeling of gene networks. Silico Biology. 2002a;2(2):97-110.

11. KolchanovN.A., Podkolodnaya O.A., Ananko E.A., Ignatieva E.V., Stepanenko I.L., Kel-Margoulis O.V., Kel A.E., Merkulova T.I., Goryachkovskaya T.N., Busygina T.V., Kolpakov F.A., Podkolodny N.L., Naumochkin A.N., Korostishevskaya I.M., Romashchenko A.G., Overton G.C. Transcription Regulatory Regions Database (TRRD): its status in 2000. Nucleic Acids Research. 2000;28(1):298-301. DOI: 10.1093/nar/28.1.298

12. Kolpakov F.A., Ananko E.A., Kolesov G.B., Kolchanov N.A. GeneNet: a gene network database and its automated visualization. Bioinformatics. 1998;14(6):529-537. DOI: 10.1093/bioinformatics/14.6.529

13. Mironova V.V., Omelyanchuk N.A., Novoselova E.S., Doroshkov A.V., Kazantsev F.V., Kochetov A.V., Kolchanov N.A., Mjolsness E., Likhoshvai V.A. Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance. Annals of Botany. 2012;110(2):349-360. DOI: 10.1093/aob/mcs069

14. Mironova V.V., Omelyanchuk N.A., Yosiphon G., Fadeev S.I., Kolchanov N.A., Mjolsness E., Likhoshvai V.A. A plausible mechanism for auxin patterning along the developing root. BMC Systems Biology. 2010;4 Suppl 1:98. DOI: 10.1186/1752-0509-4-98

15. Omelyanchuk N.A., Wiebe D.S., Novikova D.D., Levitsky V.G., Klimova N., Gorelova V., Weinholdt C., Vasiliev G.V., Zemlyanskaya E.V., Kolchanov N.A., Kochetov A.V., Grosse I., Mironova V.V. Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots. Scientific Reports. 2017;7(1):2489. DOI: 10.1038/s41598-017-02476-8

16. Podkolodnaya O.A., Yarkova E.E., Demenkov P.S., Konovalova O.S., Ivanisenko V.A., Kolchanov N.A. Application of the ANDCell computer system to reconstruction and analysis of associative networks describing potential relationships between myopia and glaucoma. Russian Journal of Genetics: Applied Research. 2011;1(1):21-28. DOI: 10.1134/S2079059711010059

17. Rogozin I.B., Kolchanov N.A. Somatic hypermutagenesis in immunoglobulin genes: II. Influence of neighbouring base sequences on mutagenesis. Biochimica et Biophysica Acta (BBA) – Gene Structure and Expression. 1992;1171(1):11-18. DOI: 10.1016/0167-4781(92)90134-L

18. Russian Academy of Sciences (Rossiiskaya Akademiya Nauk) [official portal]. [in Russian]. URL: http://www.ras.ru [дата обращения: 29.11.2021].

19. Shindyalov I.N., Kolchanov N.A., Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?. Protein Engineering, Design and Selection. 1994;7(3):349-358. DOI: 10.1093/protein/7.3.349

20. The Federal Research Center Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences: [website]. [in Russian]. URL: http://www.bionet.nsc.ru [дата обращения: 28.11.2021].

21. Wingender E., Kel A.E., Kel O.V., Karas H., Heinemeyer T., Dietze P., Knüppel R., Romaschenko A.G., Kolchanov N.A. TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Research. 1997;25(1):265-268. DOI: 10.1093/nar/25.1.265


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1. Колчанов Николай Александрович
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2. Колчанов Николай Александрович
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Khlestkina E.K., Nizhnikov A.A., Tikhonovich I.A. Bioinformatics benefits from Siberia: on the anniversary of Nikolay Aleksandrovich Kolchanov, Academician of the Russian Academy of Sciences (RAS). Plant Biotechnology and Breeding. 2022;5(1):47-51. (In Russ.) https://doi.org/10.30901/2658-6266-2022-1-o4

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