Biomodels Group

Kazantsev FV

Date of Birth: 24.01.1985

Work Address: Institute of Cytology and Genetics, Novosibirsk, 630090, Russia (http://www.bionet.nsc.ru/)

Phone: +7 383 363-49-22 *1320

Fax: +7 383 333-12-78

Email: [email protected]

Language: English-well

Work Experience and Current Position:

  • 2010 – present – junior researcher, Laboratory of high performance calculation in bioinformatics, Institute of Cytology and Genetics, Novosibirsk, Russia.
  • 2007 – 2010 – PhD student, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia.
  • 2003 – 2007 – student, Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia.

Skills:

Software engineering; high performance calculations; systems biology; mathematical and computer dynamic modeling of gene, protein, metabolic, signaling networks (continuous models).

Java, Enterprise Java Beans, Eclipse Rich Client Application, C++, Relational Databases theory, SQL, Oracle XML database, XML.

Degrees:

2007: M. Sc. in Computer Science, Novosibirsk State University, Novosibirsk, Russia

2004: Technician in Computer Science, High College of Informatics affiliated with Novosibirsk State University, Novosibirsk, Russia

Thesis:

Degree: M. Sc. in Computer Science, 2007.

Title: “Development of the software tool for molecular-genetic systems modeling”

Novosibirsk State University, Novosibirsk, Russia

Thesis advisors: PhD Ratushny A.V., Dr. Likhoshvai V.A.

Degree: Technician in Computer Science, 2004.

Title: “The software tool for analysis of systems of the reversible biochemical reactions”

High College of Informatics affiliated with Novosibirsk State University, Novosibirsk, Russia

Thesis advisors: PhD Ratushny A.V.

Education Background:

  • High College of Informatics affiliated with Novosibirsk State University, Computer science, student, 2000 – 2004.
  • Novosibirsk State University, сomputer science, student, 2004-2007.
  • IC&G SB RAS, Bioinformatics, post-graduate student, 2007-2010.

Participation in Conferences and Workshops:

2011:

  • VI Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia, March 21-25, 2011, poster presentation.

2010:

  • International Conference Plantgen, Novosibirsk, Russia, June 7-10, 2010, oral presentation.
  • The Seventh International Conference on Bioinformatics of Genome Regulation and Structure and Systems Biology (BGRS\SB_2010), Novosibirsk, Russia, June 20- 27, 2010, poster presentations, computer demonstration.
  • All-Russian Conference “Mathematical Models and informational technologies in the agricultural biology: results and perspectives”, Saint-Petersburg, October 14-15, 2010, oral presentation.

2009:

  • German-Russian Forum Biotechnology, Novosibirsk, June 15-19, 2009, oral presentation.
  • The fifth Congress of geneticists and selectionists of the Russia, Moscow, June 21 – 27 2009, oral presentation.
  • The All-Russian Conference on computational mathematics КВМ-2009, Novosibirsk, June 23-25, 2009, oral presentation.
  • 7th ISAAC Congress, London, July 13 – July 18, 2009 (http://www.isaac2009.org/Congress/Schedule.html), oral presentation.
  • The 3 rd Annual World Congress of Gene-2009, Foshan, China, December 1-7, 2009 (http://www.bitlifesciences.com/wcg2009/default.asp), oral presentation.

2008:

  • The International Young Scientists Conference “Lomonosov-2008”, Moscow, Russia, April 8-12, 2008, oral presentation.
  • The Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2008), Novosibirsk, Russia, June 22- 28, 2008, oral presentation, poster presentation, computer demonstration.

2007:

  • The XLV International Scientific Student’s Conference “The Student and scientific and Technical Progress”, Novosibirsk, Russia, April 10-12, 2007, oral presentation

2006:

  • The XLIV International Scientific Student’s Conference “The Student and scientific and Technical Progress”, Novosibirsk, Russia, April 10-13 , 2006, oral presentation.
  • The 7th All-Russian Conference on Mathematical Modeling and Informational Technologies, Krasnoyarsk, Russia, oral presentation

Teaching:

2006 – 2010: seminarian at High College of Informatics affiliated with Novosibirsk State University. Course “Introduction to the modeling of biological processes”

Grants:

Patents:

  1. Likhoshvai V.A., Kazantsev F.V., Akberdin I.R., Bezmaternykh K.D. Software tool for mathematical models autogeneration on basis of the gene networks structure (MGSgenerator), License №2008611941, April 2008
  2. Likhoshvai V.A., Kazantsev F.V., Akberdin I.R., Bezmaternykh K.D., Lashin S.A., Podkolodnaya N.N., Ratushny A.V. A computer system for reconsnruction/ Calculation and analysis matimatical models of molecular genetic system (MGSmodeller), License №2008612820, June 2008.

Papers:

2012:

2010:

  • I.R. Akberdin, S.I. Fadeev, Gainova I.A., F.V. Kazantsev, V.K. Korolev, V.A. Likhoshvai, A.E. Medvedev. New computer technologies for construction and numerical analysis of mathematical models molecular genetic systems. Progress in Analysis and its Applications, World Scientific Publ., Singapore, pp. 563-569.

2009:

  • I.R. Akberdin, F.V. Kazantsev, V.A. Likhoshvai, S.I. Fadeev, Gainova I.A., V.K. Korolev, A.E. Medvedev. Computer system of modules integration for automatic construction and numerical analysis of molecular genetic systems. Siberian Electronic Mathematical Reports, V.6, pp. 440-456.
  • F.V. Kazantsev, I.R. Akberdin, K.D. Bezmaternykh, V.A. Likhoshvai. THE TOOL FOR AUTOMATIC GENERATION OF GENE NETWORK’S MATHEMATICAL MODELS. VOGiS Herald, V.13(1), pp. 163-169.
  • I.R. Akberdin, F.V. Kazantsev, N. A. Omelyanchuk, V.A. Likhoshvai. Mathematical model of auxin metabolism in meristem cells of plant shoots. VOGiS Herald, V.13(1), pp. 170-175.
  • V.A. Likhoshvai, N. A. Omelyanchuk, V.V. Mironova, F.V. Kazantsev, I.R. Akberdin, V.K. Korolev, S.I. Fadeev, N.A. Kolchanov. Modeling of auxin regulated lateral organ initiation in Arabidopsis thaliana L. VOGiS Herald, V.13(1), pp. 176-185.

Abstracts:

2012:

  • N. L. Podkolodnyy, P.S. Demenkov, K.V. Gunbin, Y.L. Orlov, E.S. Fomin, N.A. Alemasov, F.V. Kazantsev, O.V. Vishnevsky, V.A.Ivanisenko, D.A. Afonnikov, N.V. Kuchin, B.M. Glinsky, N.A. Kolchanov. HIGH PERFORMANCE COMPUTING IN BIOINFORMATICS: CASE STUDIES. Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 243.
  • Novoselova E.S., Mironova V.V., Kazantsev F.V. Omelyanchuk N.A., Likhoshvai V.A. Role of auxin dose-dependent control in specification of root vascular cells. Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 222.
  • Kazantsev F.V., Akberdin I.R., Mironova V.V., Podkolodnyy N.L., Likhoshvai V.A. High performance computing with MGSmodeller. Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 140.
  • Akberdin I.R., Kazantsev F.V., Ree N.A., Timonov V.S., Oshchepkova E.A., Ratushny A.V., Khlebodarova T.M., Fadeev S.I., Kolchanov N.A., Likhoshvai V.A. Modeling and analysis of dynamics of the gene networks: automatic generation and storage in a new database. Abstracts of International Syspatho Workshop “Systems Biology and Medicine”, St. Petersburg, Russia, pp. 67-68.
  • Akberdin I.R., Kazantsev F.V., Ermak T.V., Ree N.A., Timonov V.S., Khlebodarova T.M., Likhoshvai V.A. Computational modeling of gene network dynamics in E.coli. Abstracts of the 4th International Conference “Mathematical Biology and Bioinformatics”, Pushchino, Russia, pp. 108-109.
  • Ф.В. Казанцев , В.В. Миронова, Е.С. Новоселова, Н.Л. Подколодный, В.А. Лихошвай. Язык моделирования молекулярно-генетических систем SiBML. тезисы конференции “Параллельные вычислительные технологии (ПаВТ) 2012″,Новосибирск, Россия, 26-30 марта 2012 г. С. 722
  • Новоселова ЕС, Миронова ВВ, Омельянчук НА, Казанцев ФВ, Лихошвай ВА.
    Математическое моделирование ауксин зависимого контроля дифференцировки сосудистых клеток корня. II(X) Международная Ботаническая Конференция молодых ученых в Санкт-Петербурге,
    2012, Санкт-Петербург

2011:

  • Казанцев Ф.В., Акбердин И.Р., Насонов В.В., Тимонов В.С., Лихошвай В.А. MGSmodelsDB – web-ресурс для накопления математических моделей элементарных подсистем молекулярно-генетических систем. тезисы 3-ей школы молодых ученых «Биоинформатика и системная биология», Новосибирск, Россия, 22-25 сентября 2011. (http://conf.nsc.ru/BSB2011/ru/reportview/88232)
  • Новоселова Е.С., Миронова В.В., Казанцев Ф.В., Омельянчук Н.А., Лихошвай В.А. Математическое моделирование транспорта ауксина в центральном цилиндре корня A. Thaliana. тезисы 3-ей школы молодых ученых «Биоинформатика и системная биология», Новосибирск, Россия, 22-25 сентября 2011. (http://conf.nsc.ru/BSB2011/ru/reportview/81722)
  • Тимонов В.С., Гунбин К.В., Казанцев Ф.В., Акбердин И.Р., Деменков П.С., Подколодный Н.Л. Программный пакет GenenetStudio: визуальное моделирование сетевых моделей биомолекулярных систем. тезисы 3-ей школы молодых ученых «Биоинформатика и системная биология», Новосибирск, Россия, 22-25 сентября 2011.( http://conf.nsc.ru/BSB2011/ru/reportview/81692)
  • Тимонов В.С., Гунбин К.В., Казанцев Ф.В., Акбердин И.Р., Деменков П.С., Лашин С.А., Ананько Е.А., Иванисенко В.А., Подколодный Н.Л., Колчанов Н.А. Моделирование генных сетей: система GeneNet в 2011 году. Международная конференция “Современные проблемы математики, информатики и биоинформатики”, 11 – 14 октября 2011 г., Новосибирск, Россия.
  • Vladimir Timonov, Fedor Kazantsev, Konstantin Gunbin, Ilya Akberdin, Pavel Demenkov, Elena Ananko, Nikolay Podkolodny, Vladimir Ivanisenko, Nikolay Kolchanov. The visual reconstruction and analysis of biomolecular systems: The GeneNet software in 2011. International German/Russian Summer School on Integrative Biological Pathway Analysis and Simulation,4-7 July 2011, Билефельд, ГЕРМАНИЯ.
  • Akberdin I., Kazantsev F., Ree M., Ree N., Timonov V., Khlebodarova T.M., Likhoshvai V.A. Automatic generation of mathematical models of molecular-genetic systems. Proceedings of the European Conference on Mathematical and Theoretical Biology (ECMTB 2011), Krakow, Poland, June 28-July 3, p. 38 (http://www.impan.pl/~ecmtb11/files/SectionTalks.pdf)
  • Акбердин И.Р., Казанцев Ф.В., Ри М.Т., Ри Н.А., Тимонов В.С., Ощепкова Е.А., Ратушный А.В., Хлебодарова Т.М., Лихошвай В.А. MGSmodelsDB – новая база математических моделей элементарных подсистем клетки Escherichia coli. (2011). Сборник материалов VI Московского Международного конгресса «Биотехнология: состояние и перспективы развития», Москва, Россия, т. 2, стр. 397.

2010:

  • F.V. Kazantsev, I.R. Akberdin, M.T. Ree, N.A. Ree, K.D. Bezmaternykh, V.A. Likhoshvai. MGSmodelsDB – the database for storing Mathematical Models of Molecular Genetic Systems. Proceedings of the Seventh International Conference on bioinformatics of genome regulation and structure\System Biology (2010) p.129
  • I.R. Akberdin, F.V. Kazantsev, V.A. Likhoshvai, S.I. Fadeev, I.A. Gainova,V.K. Korolev, A.E. Medvedev. Automatic generation and numerical analysis of mathematical models for molecular-genetic objects in an integrated system of MGSgenerator and STEP+ modules. Proceedings of the Seventh International Conference on bioinformatics of genome regulation and structure\System Biology (2010) p.77

2009:

  • I.R. Akberdin, F.V. Kazantsev, S.I. Fadeev., I.A. Gainova, V.A. Likhoshvai. Mathematical model of the auxin metabolism in shoots if Arabidopsis thaliana L. Materials of German-Russian Forum Biotechnology, Novosibirsk, Russia, p. 6.
  • I.R. Akberdin, F.V. Kazantsev, V.A. Likhoshvai. Modeling of the molecular genetics mechanisms of the plant developments regulation. Proceedings of the fifth Congress of geneticists and selectionists of the Russia, Moscow, 2, p. 365.
  • I.A.Gainova, I.R Akberdin, F.V.Kazantsev, V.A.Likhoshvai, S.I.Fadeev, V.K.Korolev, A.E.Medvedev. New computer technologies for the construction and numerical analysis of mathematical models for molecular genetic systems. Abstracts of the 7th ISAAC Congress, July 13-18, 2009, Imperial College London, Department of Mathematics, London, United Kingdom, p.106.
  • Akberdin I.R., Kazantsev F.V., Fadeev S.I., Gainova I.A., Likhoshvai V.A. Mathematical modeling of a plant development on the different levels. Abstracts of 3 rd Annual World Congress of Gene-2009, Foshan, China, December 1-7, p. 152.

2008:

  • Akberdin I. R., Kazantsev F. V., Omelyanchuk N. A., Likhoshvai V. A. Mathematical model of auxin metabolism in shoots of Arabidopsis thaliana L. Abstracts of the 2nd International Conference “Mathematical Biology and Bioinformatics”. Pushchino, Moscow region, September 7-13, p. 49.
  • Akberdin I.R., Ozonov E.A., Mironova V.V., Kazantsev F.V., Omelyanchuk N.A., Likhoshvai V.A. «Mathematical model of the Arabidopsis thaliana L. morphogenesis in a cellular automaton terms». Abstracts of the International Young Scientists Conference “Lomonosov-2008″, Moscow, Russia, 8 – 12 April, p.1.
  • Kazantsev F.V., Akberdin I.R., Bezmaternykh K.D., Likhoshvai V.A. MGSgenerator – the tool for automatically generation of molecular genetic system mathematical models on basis of gene networks structure. Proceedings of the Sixth International Conference on bioinformatics of genome regulation and structure, p.114.
  • Kazantsev F.V., Akberdin I.R., Bezmaternykh K.D., Lashin S.A., Podkolodnaya N.N., Likhoshvai V.A., MGSmodeller – a computer system for reconstruction, calculation and analysis mathematical models of molecular genetic system. Proceedings of the Sixth International Conference on bioinformatics of genome regulation and structure, p.113.

2007:

  • Kazantsev F.V., Set of programs for developing mathematical models of genetic molecular systems. Materials of XLV International Scientific Student’s Conference “The Student and scientific and Technical Progress”: Information technologies / Novosibirsk State University, Novosibirsk, p. 168.

2006:

  • Kazantsev F.V. Computer system for construction, calculation and analysis of model of genetic molecular systems. Materials
    of XLIV International Scientific Student’s Conference “The Student and scientific and Technical Progress”: Information technologies / Novosibirsk State University, Novosibirsk, p. 164.
  • Kazantsev F.V., Podkolodnaya N.N., Akberdin I.R., Bezmaternich K.D., Krokus I.V., Lashin S.A., Ratushny A.V., Likhoshvai V. A. MGSmodeller – the computer system for construction, calculation and analysis of model of genetic molecular systems. Materials of 7th All-Russian Conference on Mathematical Modeling and Informational Technologies, Krasnoyarsk, V.1, p. 14.

 

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