Biomodels Group

Lashin SA

 

Date of Birth: 24.09.1980.

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

Telephone:+73833634969*1320

FAX: +73833331278

Email: [email protected]

Work Experience and Current Position:

Skills:

Systems biology, bioinformatics, evolution, mathematical and computer modeling, data analysis, genomics, parallel computing, programming, algorithms.

Degrees:

2010: Ph. D in Mathematical biology and bioinformatics, Institute of Cytology and Genetics, Novosibirsk, Russia.

2003: M. Sc. in Applied Mathematics and System Programming, Novosibirsk State University, Novosibirsk, Russia

Thesis:

Degree: Ph. D in Mathematical biology and bioinformatics.

Title: “Mathematical and computer modeling of coevolution in communities of unicellular haploid organisms”.

Institution: Institute of Cytology and Genetics, Novosibirsk, Russia.

Thesis advisor: Yuri G. Matushkin, Doc., Ph.D.

Diploma:

Degree: M. Sc. in Applied Mathematics and System Programming

Title: “Development of the methods for finding optimal solutions of interval systems of equations.”

Institution:Novosibirsk State University, Novosibirsk, Russia

Diploma advisor: Sergey P. Shary, Dr.Sci.

Education Background:

Participation in creating scientific software

Principal investigator:

  • Haploid Evolutionary Constructor (http://evol-constructor.bionet.nsc.ru/) – software package for modeling of evolution of prokaryotic communities.
  • TerMotif predictor – software package for prediction of rho-independent transcription terminators in bacterial genomes.

Co-author:

Participation in Conferences and Workshops:

2011:

  • II International Conference “Postgenome-2011″ , Novosibirsk, Russia, Nov. 14-17, 2011.
  • International Conference “Biosphere origin and evolution”, BOE 2011, Rethymno, Crete, Greece, Oct. 16-20, 2011.
  • International Conference “Modern challenges of mathematics, informatics and bioinformatics”, devoted to the 100th anniversary of professor Alexei A. Lyapunov, Novosibirsk, Russia, Oct. 11–14.
  • International Moscow Conference On Computational Molecular Biology, MCCMB’11 Moscow, Russia, July 21-24, 2011.
  • 3rd School for young scientists “Bioinformatics and systems biology” (invited lecture), Novosibirsk, Russia, Sep. 22-25, 2011.
  • VI Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia, Mar. 21-25, 2011

2010:

  • Joint Indo-Russian Workshop “Predictive Biology Using Systems and Integrative Analysis and Methods”, Chandigar, India (15-19 November, 2010).
  • International conference “Mathematical biology and bioinformatics III”, Puschino, Russia (10-15 October, 2010).
  • Second international school-conference in memory of acad. Lavrentiev M.M. “Theory and numerical methods for inverse and ill-posed problems” (invited speaker), Novosibirsk, Russia (21-29 September, 2010).
  • Problems of ecology: Readings in memory of Professor M. M. Kozhov (international school-conference), Irkutsk, Russia (20-25 September, 2010).
  • ERASysBio Summer School, Tenerife, Spain (27 July 2010).
  • Joint Russian-French Workshop “Genomics, bioinformatics and modeling in life science”, Novosibirsk, Russia (18-21 June 2010).

2009:

  • International Autumn School for Young Scientists on Computational Systems Biology and Bioinformatics, Novosibirsk, Russia (1-2 September, 2009).
  • Fourth International Moscow Conference on Computational Molecular Biology (MCCMB’09), Moscow, Russia (20-23, July, 2009).
  • V Congress of VOGIS, Moscow, Russia (21-27, June, 2009).

2008:

  • (June 22-28) Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS 2008), Novosibirsk, Russia.
  • (June 29-July 2) The BGRS’2008 International Summer School for Young Scientists «Evolution, Systems Biology and High Performance Computing Bioinformatics», Novosibirsk, Russia.
  • (October 28-30) IX Russian Conference of Young Scientists for Mathematical Modeling and Information Technologies (YM2008), Kemerovo, Russia.

2007:

  • (October 28 – November 2) Second International Conference «Biosphere origin and evolution», Loutraki, Greece.
  • (July 27-31) Third International Moscow Conference on Computational Molecular Biology (MCCMB 07), Moscow, Russia.

2006:

  • (July 14-22) The 5th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2006), Novosibirsk, Russia.

2005:

  • (June 26-29) International Workshop Biosphere Origin and Evolution, Novosibirsk, Russia.
  • (September 11-16), The 2005 BGRS International Summer School for young scientists “Evolution, Systems Biology and High Performance Computing Bioinformatics”, Novosibirsk, Russia.

2004:

  • (June 24-29) The 3rd Congress of biophysics, Voronezh, Russia.

  • (July 25-30) The 4th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS’2004), Novosibirsk, Russia.

Teaching:

2005 – present Lectures and practical training in the course “Information technologies – Programming in C” on the Chair of Information Biology at the Novosibirsk State University.

2005 – present Lectures and practical training in the course “Information technologies – Programming in C++” on the Chair of Information Biology at the Novosibirsk State University.

2004 – present Lectures and practical training in the course “Mathematical modeling of molecular genetic systems” on the Chair of Information Biology at the Novosibirsk State University.

2003 – 2005 Lectures and practical training in the course “Mathematical and computer modeling of biological processes” on the Chair of Bioinformatics at the High College of Informatics, Novosibirsk, Russia.

Grants:

  1. RAS Program 22. Molecular and cellular biology. Project 8 “Systems biology: computer-experimental approaches”.

  2. RAS Program 23. Biodiversity. Project 29 “Bioinformatics of genetic variability”.

  3. INNOVATION PROJECT of Federal Agency of Science and innovation IT-CP.5/001 “Development of software for computer modeling and design in postgenomic system biology (system biology in silico)”.
  4. Siberian Branch of Russian Academy of Sciences (Integration Projects No. 34, 115)
  5. Russian Foundation for Basic Research No. 10-04-01310-а “Mathematical and computer modeling of coevolution in communities of trophically linked organisms”.
  6. Russian Foundation for Basic Research No. 07-04-01447-а “The development of experimental theoretical platforms for studying of potential regulatory site’s traits of prokaryote”.
  7. Russian Foundation for Basic Research No. 06-04-49556-а “The investigation of gene expression efficiency depending on its nucleotide contents with bioinformatics methods”.
  8. Russian Foundation for Basic Research No. № 05-07-98012-р_обь_в “The development of computing portal for bioinformatics on basis of GRID technology”.
  9. Russian Foundation for Basic Research No. 05-07-98012 “The development of computing portal for bioinformatics on basis of GRID technology”.

Patents:

  1. Ratushny A.V., Nedosekina E.A., Lashin S.A., Turnaev I.I., Vladimirov N.V., Podkolodny N.L., Likhoshvai V.A. Database of mathematical models of molecular-genetic processes (ModelER) // Inventor’s certificate №2006620196, June 2006.
  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:

2010:

  • Lashin S.A., Suslov V.V., Matushkin Yu.G. Comparative modeling of coevolution in communities of unicellular organisms: adaptability and biodiversity // Journal of Bioinformatics and Computational Biology, 2010, V 8, N. 3, p. 627-643.

  • Lashin S.A., Suslov V.V., Matushkin Yu.G. Modeling of coevolution of unicellular haploid organisms using “Evolutionary constructor” software // In book: Ecological, biotechnological, medicine and theoretical microbiology. Eds.: Vlasov V.V., Degermendzhy A.G., Kolchanov N.A., Parmon V.N., Repin V.E. Novosibirsk: SB RAS 2010, p. 347-375.

  • Likhoshvai V.A., Khlebodarova T.M., Ratushny A.V., Lashin S.A., Turnaev I.I. Podkolodnaya O.A., Ananko E.A., Smirnova O.G., Ibragimova S.S., Kolchanov N.A. Computer genetical constructor: mathematical modeling of genetic and metabolic subsystems of E. coli // In book: Ecological, biotechnological, medicine and theoretical microbiology. Eds.: Vlasov V.V., Degermendzhy A.G., Kolchanov N.A., Parmon V.N., Repin V.E. Novosibirsk: SB RAS 2010, p.376-391.

2009:

  • Lashin S.A., Suslov V.V., Matushkin Y.G. Evolution modeling of trophic web-like communities with compensatory and non-compensatory metabolism // VOGIS Herald, 2009, V.13, №1, P.150-158.
  • Lashin S.A., Matushkin Y.G., Khlebodarova T.M., Likhoshvai V.A. Correlation between the operon structure and the genome length in 14 mycoplasm species // VOGIS Herald, 2009, V.13, №1, P.84-89.

2008:

  • Lashin S.A., Kolchanov N.A., Matushkin Y.G. Evolutionary constructor: methodology and software package for modelling of evolution of food web-like related populations of unicellular haploid organisms // Computational technologies. 2008. V. 13. № 6. P. 91-101

  • Lashin S.A., Suslov V.V., Likhoshvai V.A., Matushkin Y.G., Kolchanov N.A. Computer modeling of communities evolution: the program “Evolutionary constructoe” // In book “Systems computer biology”, Novosibirsk: SB RAS, 2008, P. 662-676.

2007:

  • Lashin S.A., Suslov V.V., Kolchanov N.A., Matushkin Yu.G. Simulation of coevolution in community by using the “Evolutionary Constructor” program. In Silico Biology, 2007, V 7, N 3, 261-275

2005:

  • Ratushny A.V., Likhoshvai V.A. Ananko E.A., Vladimirov N.V., Gunbin K.V., Lashin S.A., Nedosekina E.A., Nikolaev S.V., Omelyanchuk L.V., Matushkin Yu.G., Kolchanov N.A. Novosibirsk school of system computer biology: historical excurse and perspectives. Vestnik VOGiS, v. 9, pp. 232-261.

Abstracts:

devoted to the 100th anniversary of professor Alexei A. Lyapunov

 

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