Akberdin IR

Date of Birth: 22.03.1984.

Work Address: Biosoft.ru Company, 6 Akademika Rzhanova street, Novosibirsk, 630090, Russia

Phone: +7 383 363-68-29

Email: [email protected]

Language: English – full professional proficiency

Scholar google, Researchgate, ORCID, Researcher ID, Scopus ID

Work Experience and Current Position:

2024 (January) - present – Leading Research Fellow, Scientific Center for Genetics and Life Sciences; Head of Masters Graduate Program, Department of Computational Biology, Sirius University
2021 (April) - 2023 – Senior Research Fellow, Department of Bioinformatics and Math Biology, Sirius University
2020 (October) - present – Senior Lecturer, Department of Natural Science, Novosibirsk State University
2018 (July) – present – Research Fellow, Biosoft.ru Company, Novosibirsk, Russia.
2015 (July) – 2018 – Postdoctoral Research Fellow, C1-biocatalysis lab, Department of Biology, San Diego State University, San Diego, USA.
2012 – present – Research scientist, Lab of Molecular-Genetic Systems, Institute of Cytology and Genetics, Novosibirsk, Russia.
2011 (May-August) – Part-time researcher, Sobolev Institute of Mathematics, Novosibirsk, Russia.
2011 (June) – present – Editorial Board member of the “In Silico Biology” journal.
2010 (June) – Chairperson of the BGRSSB_2010 Organizing Committee, Novosibirsk, Russia.
2010 – 2012 – Staff scientist, Lab of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia.
2008 – 2010 – Junior scientist, Lab of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia.
2008 (June) – Chairperson of the BGRS’2008 Organizing Committee, Novosibirsk, Russia.
2007 (October-November) – Visiting scientist in UCI, Irvine, USA.
2005 – 2008 – PhD student, Lab of Theoretical Genetics, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia.
2004 (August-September) – Visiting scientist, Erasmus University Medical Center, Rotterdam, Netherland.
2000 – 2005 - Lab assistant, Lab of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Novosibirsk, 630090 Russia.

Research interests:

Systems biology, kinetic modeling of gene, protein, metabolic, signaling networks, structural and parametric inverse problem for dynamical systems, E-cell, E.coli or bacterial metabolism, methanotrophs, C1 utilization.

Degrees:

2010: PhD, IC&G SB RAS, Novosibirsk, Russia

2005: M. Sc. in Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia

Thesis

Degree: PhD in bioinformatics, IC&G SB RAS, Novosibirsk, Russia, 2010

Title: "Modelling of shoot apical meristem development’s regulation in embryogenesis of the Arabidopsis thaliana L "

IC&G SB RAS, Novosibirsk, Russia

PhD advisor: Vitaly A. Likhoshvai, Prof., Dr.Sci.

Degree: M. Sc. in Cytology and Genetics, 2005

Title: "The genetic regulation of litter size in farmed arctic foxes (Alopex lagopus) and Kerry Blue Terrier dogs (Canis familiaris)"

Novosibirsk State University, Novosibirsk, Russia

Thesis advisors: Tatiana I. Axenovich, Prof., Dr.Sci. Irina V. Zorkoltseva, Ph.D.

Education:

Secondary school, Petropavlovsk, Kazakhstan 1990 – 1994.
Secondary school, Kemerovo, Russia 1994 – 1995.
Selective school of physics and mathematics, Novosibirsk, Russia 1999 – 2000.
Novosibirsk State University, Faculty of Natural Sciences, 2000 – 2005.
IC&G SB RAS, post-graduate students, 2005-2008.

Participation in Conferences and Workshops:

2024:

VIII Congress of the Vavilov Society of Genetics and Breeders, Saratov, Russia, June 14-19, 2024, oral and poster presentations.
The 14th International Conference on Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2024), Novosibirsk, Russia, August 05–10, 2024, member of the Program Committee, oral and poster presentations.

2023:

International seminar "Perspectives of Genome Editing and Metabolic Modelling of Methanotrophic Bacteria", Moscow, Russia, March 22, 2023, oral presentation.
Young Scientists’ School in Molecular Pharmacology, Sirius, Russia, May 10-12, 2023, oral presentation.
International Congress “Systems Theory, Algebraic Biology, Artificial Intelligence: Mathematical Foundations And Applications”, Moscow-Novosibirsk, Russia, June 26-29, 2023, oral presentation.
4th Russian Congress of Microbiologists, Tomsk, Russia, September 24-29, 2023, oral presentation.

2022:

XIII International Multiconference on “Bioinformatics of Genome Regulation and Structure/Systems Biology” – BGRS/SB-2022, Novosibirsk, Russia, July 04–08, 2022, member of the Program Committee, oral and poster presentations.
International Conference "Mathematics applied to immunology and virology", Sirius, Russia, November 14-18, 2022, oral presentation.

2021:

XIII international scientific conference and young scientist school "Inverse and Ill-Posed Problems: Theory and Numerics", Novosibirsk, Russia, April 12-22, 2021, oral presentation.
X All-Russian with international participation conference and young scientist school on muscle physiology and activity "New approaches to the study the physiology of extreme states", Moscow, Russia, June 28- July 1, 2021, oral presentation.
V All-Russian with international participation conference "Day of sport informatics", Moscow, Russia, December 3-4, 2021, oral presentation.

2020:

12th International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology” — BGRS\SB-2020, Novosibirsk, Russia, July 6-10, 2020, oral and poster presentations.

2019:

VII Congress and Associate Symposiums of Vavilov Society of Geneticists and Breeders on the 100th Anniversary of the Department of Genetics of Saint Petersburg State University, Saint Petersburg, Russia, June 18-22, 2019, oral presentation.
XVII Russian conference "Distributed Information and Computing Resources" DICR-2019, Novosibirsk, Russia, December 3-6, 2019, oral presentation.

2018:

11th International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology” — BGRS\SB-2018, Novosibirsk, Russia, August 20-25, 2018, poster presentation.

2017:

2017 Multi-omics for Microbiomes - EMSL Integration Conference, Pasco, WA, USA, August 1-3, 2017, contributed talk.
Annual Asilomar Conference, West Coast Bacterial Physiologists, Asilomar, CA, USA, December 15-17, 2017, oral presentation.

2016:

38th Symposium on Biotechnology for Fuels and Chemicals, Baltimore, MD, USA, April 25-28, 2016, oral presentation.
GRC Conference "Molecular Basis of Microbial One-Carbon Metabolism", Waterville Valley, NH, USA, July 31- August 5, 2016, poster presentation.

2015:

VIII Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia, March 17-20, 2015, oral presentation.

2014:

VI VOGiS Congress, Rostov-on-Don, Russia, June 15-20, 2014, oral presentation, II best presentation.
9th International Conference on the Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2014), Novosibirsk, Russia, June 23-28, 2014, oral and poster presentations.
The 4th International Conference on science and applied research "Post-Genome Methods of Analysis in Biology and Laboratory and Clinical Medicine", Kazan, Russia, October 29 - November 1, 2014, oral presentation.

2013:

BREW 2013: Bioinformatics Research and Education Workshop, Berlin, Germany, May 3-4, 2013, oral presentation
38th FEBS Congress 2013 "Mechanisms in Biology", St. Petersburg, Russia, July 6- 11, 2013, poster presentation.

2012:

The Eighth International Conference on Bioinformatics of Genome Regulation and Structure and Systems Biology (BGRS\SB_2012), Novosibirsk, Russia, June 25- 29, 2012, oral and poster presentations, computer demonstration.
Molecular Phylogenetics, Contributions to the 3rd Moscow International Conference “Molecular Phylogenetics” (MolPhy-3), Moscow, Russia, 31 July – 4 August, 2012, oral presentation.
The International SysPatho Workshop "Systems Biology and Medicine", St. Petersburg-Tsarskoe Selo, September 11-14, 2012, oral and poster presentations.
The 4th International Conference "Mathematical Biology and Bioinformatics", Pushchino, Russia, October 14 – 19, 2012, oral presentation.

2011:

Scientific work visit of Siberian Federal University, Krasnoyarsk, Russia, February 7-8, 2011, oral presentations.
VI Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia, March 21-25, 2011, poster presentation.
Opening «Russian – German Сenter for integrative biology and computation» (RCIBC), Novosibirsk, Russia, April 19 – 20, 2011, oral presentations.
European Conference on Mathematical and Theoretical Biology (ECMTB 2011), Krakow, Poland, June 28-July 3, oral presentation.
International Conference on Systems Biology (ICSB 2011), Heidelberg, Germany, August 28-September 1, poster presentation.
Saint-Petersburg's scientific forum "Science and society. Physiology and medicine of 21 century. VI Saint-Petersburg meeting of Nobel Prizers", Saint-Petersburg, Russia, September, 19-23, oral presentation.
International Conference "Modern challenges of mathematics, informatics and bioinformatics", Novosibirsk, Russia, October, 11 – 14, poster presentation.
II International Conference “Postgenome 2011”, Novosibirsk, Russia, November, 14-17, 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 breeders 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, oral presentation.
The 7th Conference on Computational Methods in Systems Biology (CMSB 2009), Bologna, Italy, August 31st – September 1st, 2009, poster presentation.
Scientific work visit of INRA, Versalle, Toulouse, Lyon, Paris, Sept. 29- Oct. 6, 2009, oral presentations.
The 3rd Annual World Congress of Gene-2009, Foshan, China, December 1-7, 2009, 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.

International conference "Modern problems of Mathematical Modelling and Computational Technologies – 2008", Krasnoyarsk, Russia, August 18-24, 2008, oral presentation.

The 2nd International Conference “Mathematical Biology and Bioinformatics”, Pushchino Moscow region, September 7 – 13, 2008, oral presentation.
The Russian-French Conference "Problems and Prospects in Plant Biotechnology", Institute of Cytology and Genetics, SB RAS, October 21-24, 2008, oral presentation.
The First Annual Russian Innovation Convent, Moscow, Russia, December 9-10, 2008, presentation.

2007:

The International Young Scientists Conference “Challenges of molecular and cell biology”, Tomsk, Russia, May 9-12, 2007, oral presentation – prize-winner.
The 7^th Young Scientist Forum “Molecular Networks”, Vienna, Austria (July 5-7), oral presentation.
The 32^nd FEBS Congress “Molecular Machines”, Vienna, Austria (July 7-12), poster presentation.
The 3-rd Moscow conference on computational molecular biology. Moscow, Russia, July 27-31, 2007, oral presentation.
The 3-rd International conference "Basic Science for Medicine". Novosibirsk, Russia, September 2-8, 2007, poster presentation.
The All-Russian Conference of physics student ВНКСФ-13, 2007, oral presentation.

2006:

The 2d All-Russian Conference “Infocommunication and Computing Technologies and Systems”, Ulan-Ude, Russia (July 1-4), report.
The 3rd International Conference “Genomics, Proteomics, Bioinformatics and Nanotechnologies for Medicine” (GPBM, 2006), Novosibirsk, Russia (July 12-16), poster presentations
The 5th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2006), Novosibirsk, Russia (July 14-22), report and poster presentations.
The 7th All-Russian Conference on Mathematical Modeling and Informational Technologies, Krasnoyarsk, Russia (October 20-23), report.

2005:

The 43th International Conference of Students, Novosibirsk, Russia (April 12-14), report – prize-winner.

2004:

The 42th International Conference of Students, Novosibirsk, Russia (April 13-15), report.
The 3rd Congress of VSGaS “Genetics in XXI century: modern state and perspectives of development”, Moscow, Russia (June 6-12), poster presentation.

2003:

The 41th International Conference of Students, Novosibirsk, Russia (April 15-17), report.
The 3rd International Conference of Students and Junior Scientists “Actual Problems of Modern Biology and Biotechnology”, Alma-Ata, Kazakhstan (April 23-25), report- prize-winner.

Teaching:

2023 – present Lectures and hands-on training in a course "Molecular Biology", Department of Bioinformatics, Sirius University, Sochi

2022 – present Lectures and hands-on training in a course "Systems Biology", Department of Bioinformatics, Sirius University, Sochi

2020 Lecture/training in the course “Modelling COVID-19 epidemics” organized by ISBE.NL / VU University Amsterdam and ELIXIR-Luxembourg / Luxembourg University, Nov 30th- Dec 6th, 2020

2012 Lecture “Automatical generation and analysis of gene network models”, the Virtual Training Workshop on Bioinformatics organized by Asian Bioinformatics Research and Education Network (ABREN) .

2006 – present Lectures and practical training in a course “Mathematical modeling of molecular genetic systems” on the Faculty of Information Biology at the Novosibirsk State University.

Trainees:

2024 Sokolova Tatyana, M.Sc. in Bioinformatics, Sirius University. Thesis: "Reconstruction of regulons for Methylotuvimicrobium alcaliphilum 20ZR based on an analysis of a bunch of transcriptomic data ".

2023 Obrezanenko Valentina, M.Sc. in Bioinformatics, Sirius University. Thesis: "Mathematical modeling of the recruitment of human skeletal muscles during physical exercise".

2023 Miroshnichenko Maxim, M.Sc. in Bioinformatics, Novosibirsk State University. Thesis: "Mathematical modeling of the SARS-CoV-2 infection process and virus spreading in the human body considering B- and T-cell-mediated immune responses".

2022 Son Alisa, Bachelor of Biophysics, Novosibirsk State University. Thesis: "Modelling of the muscle metabolic adaptation to physical exercise considering its fatigue".

2020 Kulyashov Michael, M.Sc. in Bioinformatics, Novosibirsk State University. Thesis: "Genome-scale metabolic modeling of 2,3 – butanediol production by Geobacillus icigianus".

2018 Kulyashov Michael, Bachelor of Bioinformatics, Novosibirsk State University. Thesis: "The study of whole-cell metabolism in Geobacillus icigianus based on genome-scale modeling approach".

2017 Leskova Natalya, M.Sc. in Mathematics, Novosibirsk State University. Thesis: "An investigation of the model of functional state of mouse embryonic stem cells based on a method of solution continuation with respect to parameter ", magna cum laude.

2017 Babich Michael, M.Sc. in Bioinformatics, Novosibirsk State University. Thesis: "Mathematical modeling of transition states in ESC pluripotency utilizing single cell RNAseq data".

2016 Petrova Kristina, Bachelor of Bioinformatics, Novosibirsk State University. Thesis: "Mathematical modelling of underlying mechanisms on pluripotency maintenance and differentiation of mouse embryonic stem cells".

2015 Babich Michael, Bachelor of Genetics, Novosibirsk State University. Thesis: "The study of mechanism for pluripotency maintenance and differentiation of embryonic stem cells by mathematical modeling approach".

2015 Kotenko Anastasia, M.Sc. in Bioinformatics, Novosibirsk State University. Thesis: "Optimization of bioethanol production in yeast cell".

2015 Leskova Natalya, Bachelor of Mathematics, Novosibirsk State University. Thesis: "Modeling of the regulation of stem cells development".

2014 Cyganova Antonina, Bachelor of Mathematics, Novosibirsk State University. Thesis: "Mathematical modeling of aromatic acids biosynthesis in E.coli cell".

2013 Ermak Timofey, M.Sc. in Computer Sciences, Siberian State University of Telecommunication and Informatics. Thesis: "KiNET – a new web database on kinetics data and parameters for E.coli".

2012 Nasonov Vladimir, M.Sc. in Computer Sciences, Siberian State University of Telecommunication and Informatics. Thesis: "The tool for data visualization is a subsystem of MGSmodelsDB".

2011 Potechin Michael, M.Sc. in Mathematics, Omsk State University. Thesis: "Mathematical modeling of nitrite utilization in E.coli cell".

Grants:

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)".
US National Science Foundation (FIBR EF-0330786 Development Modeling and Bioinformatics).
Siberian Branch of Russian Academy of Sciences (Integration Projects No. 34, 115)
Russian Foundation for Basic Research No. 01-04-49518-а “Genetic analysis of fitness traits in little animals”.
Russian Foundation for Basic Research No. 04-04-48074-а “Changes of genetic structure of complex traits in mammalian during selection”.
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”.
Russian Foundation for Basic Research No. № 05-07-98012-р_обь_в “The development of computing portal for bioinformatics on basis of GRID technology”.
Russian Foundation for Basic Research No. 05-07-98011 “The development of program informational modeling tools of ecosystem on basis of GIS technology and data of distance sounding”.
Travel grant from Netherlands Organization for Scientific Research (for participation at the Summer school “Principles of Genetic Epidemiology, Searching Genes of Complex Disorders, Genetic Epidemiology of Complex Diseases”).
Travel grant from FEBS (for participation at the YSF’2007 and FEBS Congress)
Travel grant from US National Science Foundation (FIBR EF-0330786 Development Modeling and Bioinformatics)
Russian Foundation for Basic Research (RFBR) No. 08-04-01008-а “Computer reconstruction of the E.coli potential regulatory regions and mechanisms of them functioning. Experimental confirmation of the developed models”.
Travel grant from Russian Foundation for Basic Research No. 08-04-16038-моб_з_рос.
Grant from president of Russian Federation SS-2447.2008.4.
Travel grant from Russian Foundation for Basic Research No.09-04-09511-моб_з.
Interdisciplinary integration project of SB RAS №107.
Interdisciplinary integration project of SB RAS №119.
RAS project 21. 26.
RAS project 22. 8.
RAS project 23. 29.
RFBR 10-01-00717-а «Symmetry and chaos in gene networks».
RFBR 11-04-01748-а «Computational analysis and modeling of shoot apical meristem development».
Travel grant from Russian Foundation for Basic Research No. 11-04-09357-моб_з_рос.
Landahl travel grant of the SMB.
EU-FP7 Research Project SysPatho.
Scientific school № 5278.2012.4 "Bioinformatics and systems biology" (2012-2013).
State contract №П857 «Development of software for high-performance computing in bioinformatics».
State contract № 07.514.11.4023 «Design and Development of RESTfull web-services to create a distributed infrastructure oriented to solve the challenges of gene networks reconstruction and analysis".
NSF Microbial Conversion of Greenhouse Gases into Fermentation-Ready Sugars, №1605031.
RFBR Creation of modular mathematical model linking metabolic processes with regulation of gene expression in skeletal muscle during functional shifts associated with changes in the level of motor activity, №17-00-00296.
RFBR Development of a multi-scale immuno-epidemiological mathematical model COVID-19, taking into account the impact on the economy of the region and the scenarios of authority actions, №20-04-60355.
RSF Investigation and modelling of the metabolic and homeostatic variables in nanoparticle onco-transport and drug delivery, №21-75-30020.
Ministry of Science and Higher Education of the Russian Federation grant, Regulatory transcriptomic to estimate a potential of genome modifications and study regeneration processes in livestock, №075-15-2021-1344.
RSF Genome-scale modeling of the metabolism of aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum 20ZR taking into account molecular-genetic mechanisms of its regulation, №23-24-00606.

Patents:

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
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 reconstruction/ Calculation and analysis mathematical models of molecular genetic system (MGSmodeller), License №2008612820, June 2008.
Likhoshvai V.A., Akberdin I.R., Kazantsev F.V., Nasonov V.V., Timonov V.S. Software tool for gene networks mathematical models view and compile (MGSmodelsDB), License №2011616329, August 2011.
Likhoshvai V.A., Akberdin I.R., Kazantsev F.V., Ree M.T., Ree N.A., Khlebodarova T.M., Lashin S.A., Oshepkova E.A., Ratushny A.V. Database "Elementary subsystems: E.coli metabolism" (ElSy: E.coli), License №2012620064, January 2012.
Likhoshvai V.A., Akberdin I.R., Ermak T.V., Timonov V.S., Khlebodarova T.M. Software tool for access and representation of kinetics data and parameters for biochemical reactions (Web-KiNET), License №2013615675, June 2013.
Akberdin I.R., Nuriddinov M.A., Kazantsev F.V., Peltek S.E. The kinetic model of lactate biosynthesis in the thermophile Geobacillus cell (ElSy: Geobac). License №2014610722, January 2014.

Awards:

First-degree diploma of the Government of Novosibirsk region, Akberdin I.R. and Mironova V.V., December 2011.
TerraGenome travel award to participate in the 2017 Multi-omics for Microbiomes meeting held in Pasco, WA.

Peer-Reviewed Articles:

2024:

Kulyashov M.A., Hamilton R., Afshin Y., Kolmykov S.K., Sokolova T.S., Khlebodarova T.M., Kalyuzhnaya M.G., Akberdin I.R. Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study. mSystems. 2024; e01105-24. doi:10.1128/msystems.01105-24.
Esembaeva M. A., Kulyashov M. A., Kolpakov F. A. and Akberdin I. R. A Study of the Community Relationships Between Methanotrophs and Their Satellites Using Constraint-Based Modeling Approach. International Journal of Molecular Sciences. 2024; 25(22):12469. doi:10.3390/ijms252212469.
Esembaeva M. A., Kulyashov M. A., Kolpakov F. A. and Akberdin I. R. A Study of the Community Relationships Between Methanotrophs and Their Satellites Using Constraint-Based Modeling Approach. International Journal of Molecular Sciences. 2024; 25(22):12469. doi:10.3390/ijms252212469.
Arbatskiy M., Balandin D., Akberdin I., and Churov A.. A systems biology approach towards a comprehensive understanding of ferroptosis. International Journal of Molecular Sciences. 2024; 25(21): 11782. doi: 10.3390/ijms252111782.
Kutumova E.O., Akberdin I.R., Egorova V.S., Kolesova E.P., Parodi A., Pokrovsky V.S., Zamyatnin, Jr A.A., Kolpakov F.A. Physiologically based pharmacokinetic model for predicting the biodistribution of albumin nanoparticles after induction and recovery from acute lung injury. Heliyon. 2024; doi: 10.1016/j.heliyon.2024.e30962.
Volyanskaya A.R., Akberdin I.R., Kulyashov M.A., Yevshin I.S., Romanov M.N., Shagimardanova E.I., Gusev O.A., Kolpakov F.A. A bird’s-eye overview of molecular mechanisms regulating feed intake in chickens—with mammalian comparisons. Animal Nutrition Journal. 2024; doi: 10.1016/j.aninu.2024.01.008.

2023:

Kulyashov M.A., Kolmykov S.K., Khlebodarova T.M., Akberdin I.R. State-of the-Art Constraint-Based Modeling of Microbial Metabolism: From Basics to Context-Specific Models with a Focus on Methanotrophs. Microorganisms. 2023; 11(12):2987. doi:10.3390/microorganisms11122987.
Kiselev I.N., Akberdin I.R., Kolpakov F.A. (2023) Delay-differential SEIR modeling for improved modelling of infection dynamics. Scientific Reports, 13: 13439. doi:10.1038/s41598-023-40008-9.
Vertyshev A.Yu., Akberdin I.R., Kolpakov F.A. (2023) Numerous Trigger-like Interactions of Kinases/Protein Phosphatases in Human Skeletal Muscles Can Underlie Transient Processes in Activation of Signaling Pathways during Exercise. International Journal of Molecular Sciences, 24(13):11223. doi:10.3390/ijms241311223.
Akberdin I.R., Kozlov K.N., Kazantsev F.V., Fadeev S.I., Likhoshvai V.A., Khlebodarova T.M. (2023) Impact of Negative Feedbacks on De Novo Pyrimidines Biosynthesis in Escherichia coli. International Journal of Molecular Sciences, 24(5): 4806. doi:10.3390/ijms24054806.

2022:

Kutumova E.O., Akberdin I.R., Kiselev I.N., Sharipov R.N., Egorova V.S., Syrocheva A.O., Parodi A., Zamyatnin A.A. Jr., Kolpakov F.A. (2022) Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools. International Journal of Molecular Sciences, 23(20):12560. doi:10.3390/ijms232012560.
Afonyushkin V.N., Akberdin I.R., Kozlova Y.N., Schukin I.A., Mironova T.E., Bobikova A.S., Cherepushkina V.S., Donchenko N.A., Poletaeva Y.E., Kolpakov F.A. (2022) Multicompartmental Mathematical Model of SARS-CoV-2 Distribution in Human Organs and Their Treatment. Mathematics, 10(11),1925. doi:10.3390/math10111925.
Kutumova E., Akberdin I., Kiselev I., Sharipov R., Kolpakov F. (2022). Modular Representation of Physiologically Based Pharmacokinetic Models: Nanoparticle Delivery to Solid Tumors in Mice as an Example. Mathematics., 10(7), 1176. doi:10.3390/math10071176.
Kolpakov F., Akberdin I., Kiselev I., Kolmykov S., Kondrakhin Yu., Kulyashov M., Kutumova E., Pintus S., Ryabova A., Sharipov R., Yevshin I., Zhatchenko S., Kel A. (2022). BioUML-towards a universal research platform. Nucleic Acids Research, gkac286. doi:10.1093/nar/gkac286.

2021:

Akberdin I.R., Kiselev I.N., Pintus S.S., Sharipov R.N., Vertyshev A.Y., Vinogradova O.L.; Popov D.V., Kolpakov F.A. (2021). A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle. Int. J. Mol. Sci., 22(19), 10353. doi: 10.3390/ijms221910353.
Kiselev I.N., Akberdin I.R., Kolpakov F.A. (2021). A Delay Differential Equation approach to model the COVID-19 pandemic. bioRxiv. doi: 10.1101/2021.09.01.21263002.
Pintus S.S., Akberdin I.R., Yevshin I., Makhnovskii P., Tyapkina O., Nigmetzyanov I., Nurullin L., Devyatiyarov R., Shagimardanova E., Popov D., Kolpakov F. A., Gusev O., Gazizova G.R. (2021). Genome-wide atlas of promoter expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy of skeletal muscle. Biology, 10(6), 557. doi: 10.3390/biology10060557.

2020:

Savina M.S., Kazantsev F.V., Bezmaternykh K.D., Shtokalo D.N., Mironova V.V., Akberdin I.R. (2020). In memory of Vitaly A. Likhoshvai: lessons, conversations and memories. Letters to Vavilov Journal of Genetics and Breeding, 6(4): pp. 193-198. doi: 10.18699/Letters2020-6-25 (in Russian).
Turnaev I.I., Gunbin K.V., Suslov V.V., Akberdin I.R., Kolchanov N.A., Afonnikov D.A. The Phylogeny of Class B Flavoprotein Monooxygenases and the Origin of the YUCCA Protein Family. Plants, 9: 1092, doi: 10.3390/plants9091092.
Kulyashov M., Peltek S.E., Akberdin I.R. (2020). A Genome-Scale Metabolic Model of 2,3-Butanediol Production by Thermophilic Bacteria Geobacillus icigianus. Microorganisms, 8: pp. 1002, doi: 10.3390/microorganisms8071002.
Akberdin I.R., Vertyshev A., Pintus S.S., Popov D.V. and Kolpakov F.A. (2020). A mathematical model linking Ca2+-dependent signaling pathway and gene expression regulation in human skeletal muscle. Mathematical Biology and Bioinformatics, 15(1): pp. 20-39, doi: 10.17537/2020.15.20.
Akberdin I.R., Kiselev I.N., Pintus S.S., Vertyshev A., Makhnovskii P.A., Popov D.V. and Kolpakov F.A. (2020). Integrated Modular Model Linking Metabolism, Signaling Transduction and Gene Expression Regulation in Human Skeletal Muscle. Selected Proceedings of the XVII International Conference Distributed Information-Computational Resources (DICR-2019), Novosibirsk, Russia, December 03-06, 2019, pp. 1-5.

2019:

Kolpakov F., Akberdin I., Kashapov T., Kiselev I., Kolmykov S., Kondrakhin Yu., Kutumova E., Mandrik N., Pintus S., Ryabova A., Sharipov R., Yevshin I. and Kel A. (2019). BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Research, 47(W1): W225-W233, doi: 10.1093/nar/gkz440.
Kiselev I.N., Akberdin I.R., Vertyshev A., Popov D.V. and Kolpakov F.A. (2019). A modular visual model of energy metabolism in human skeletal muscle. Mathematical Biology and Bioinformatics, 14(2): pp. 373-392, doi: 10.17537/2019.14.373.
Henard C.A., Akberdin I.R., Kalyuzhnaya M.G. and Guarnieri M.T. (2019). Muconic Acid Production from Methane using Rationally-engineered Methanotrophic Biocatalysts. Green Chemistry, doi: 10.1039/c9gc03722e.

2018:

Akberdin I.R., Thompson M., Hamilton R., Desai N., Alexander D., Henard C.A., Guarnieri M.T., Kalyuzhnaya M.G. (2018). Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. Scientific reports, 8(1):2512, doi:10.1038/s41598-018-20574-z.
Akberdin I.R., Omelyanchuk N.A., Fadeev S.I., Leskova N.E., Oschepkova E.A., Kazantsev F.V., Matushkin Yu.G., Afonnikov D.A., Kolchanov N.A. (2018). Pluripotency gene network dynamics: system views from parametric analysis. PLOS One, doi: 10.1371/journal.pone.0194464.
Akberdin I.R., Thompson M., & Kalyuzhnaya M.G. (2018). Book Chapter 7: “Systems Biology and Metabolic Modeling of C1-Metabolism.” in Methane Biocatalysis: Paving the Way to Sustainability, Editors: Kalyuzhnaya, Marina G., Xing, Xin-Hui, Springer Publishing, doi: 10.1007/978-3-319-74866-5.
Khmelenina V.N., Rozova O.N., Akberdin I.R., Kalyuzhnaya M.G. & Trotsenko Y. A. (2018). Book Chapter 6: “Pyrophosphate-Dependent Enzymes in Methanotrophs: New Findings and Views.” in Methane Biocatalysis: Paving the Way to Sustainability, Editors: Kalyuzhnaya, Marina G., Xing, Xin-Hui, Springer Publishing, doi: 10.1007/978-3-319-74866-5.
Akberdin I. R., Collins D.A., Hamilton R., Oshchepkov D.Y., Shukla A.K., Nicora C.D., Nakayasu E.S., Adkins J.N., Kalyuzhnaya M.G. (2018). Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR. Frontiers in Microbiology. 9:2735. doi: 10.3389/fmicb.2018.02735.
Kazantsev F., Akberdin I., Lashin S. , Ree N., Timonov V., Ratushny A., Khlebodarova T., Likhoshvai V. (2018). MAMMOTH: a new database for curated mathematical models of biomolecular systems. J. Bioinform. Comput. Biol., doi.org/10.1142/S0219720017400108.

2017:

Demidenko A., Akberdin I.R., Allemann M., Allen E.E., & Kalyuzhanaya M.G. (2017). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G (B1). Frontiers in Microbiology, 7, 2167, doi:10.3389/fmicb.2016.02167.

2016:

Collins D.A., Akberdin I.R., Kalyuzhnaya M.G. (2016). Methylobacter. Bergey’s Manual of Systematics of Archaea and Bacteria, 1-11, doi: 10.1002/9781118960608.gbm01179.pub2.
Zakhrtsev M., Medvedeva I., Orlov Y., Akberdin I., Krebs O., & Schulze W. X. (2016). Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. BMC Plant Biology, 16(1), 262, doi:10.1186/s12870-016-0868-3.

2015:

Rozanov A.S., Kotenko A.V., Akberdin I.R., Peltek S.E. (2015). Recombinant strains of Saccharomyces cerevisiae for ethanol production from plant biomass. Russian Journal of Genetics: Applied Research, 5(4), pp. 375–382, doi: 10.1134/S2079059715040139.
Turnaev I.I., Akberdin I.R., Suslov V.V., Afonnikov D.A. (2015). The number of homologs of some enzymes involved in tryptophan biosynthesis is correlated to the proportion of proteins associated with transcription in plants. Russian Journal of Genetics: Applied Research, 5(3), pp. 308-312, doi:10.1134/S2079059715030193.

2014:

Ivanisenko N. V., Mishchenko E. L., Akberdin I.R., Demenkov P. S., Likhoshvai V. A., Kozlov K. N., Todorov D.I., Gursky V.V., Samsonova M.G., Samsonov A.M., Clausznitzer D., Kaderali L., Kolchanov N.A., Ivanisenko V. A. (2014). A New Stochastic Model for Subgenomic Hepatitis C Virus Replication Considers Drug Resistant Mutants. PlOS One, 9(3), e91502. doi: 10.1371/journal.pone.0091502.
Akberdin I.R., Ivanisenko N. V., Kazantsev F.V., Oschepkova E.A., Omelyanchuk N.A., Matushkin Yu.G., Afonnikov D.A. (2014). Modeling of regulatory mechanisms for mESC self-renewal: kinetic and stochastic approaches. Mathematical Biology and Bioinformatics, 9(2), pp.504-517.

2013:

Akberdin I.R., Kazantsev F.V., Ermak T.V., Timonov V.S., Khlebodarova T.M., Likhoshvai V.A. (2013). In silico cell: challenges and perspectives. Mathematical Biology and Bioinformatics, 8(1), pp. 295-315.
Khlebodarova T.M., Kogai V.V., Akberdin I.R., Ri N.A., Fadeev S.I., Likhoshvai V.A. (2013). Modeling of Nitrite Utilization in E. coli Cells: Flux Analysis. Mathematical Biology and Bioinformatics, 8(1), pp. 276-294.
N.V. Ivanisenko, E.L. Mishchenko, I.R. Akberdin, P.S. Demenkov, V.A. Likhoshvai, K.N. Kozlov, D.I. Todorov, M.G. Samsonova, A.M. Samsonov, N.A. Kolchanov, V.A. Ivanisenko (2013). Replication of the subgenomic HCV replicon in the presence of the NS3 protease inhibitors: a stochastic model. Biophysics (Russian), 58(5), pp. 758–774.
Nuriddinov M.A., Kazantsev F.V., Rozanov A.S., Kozlov K.N., Peltek S.E., Kolchanov N.A.& Akberdin I.R. Мathematical modeling of ethanol and lactic acid biosynthesis by thermophilic Geobacillus bacteria. Russian Journal of Genetics: Applied Research, 17 (4/1), pp. 686-704.

2012:

E.L. Mishchenko, N.V. Ivanisenko, I.R. Akberdin, P.S. Demenkov, V.A. Likhoshvai, N.A. Kolchanov, V.A. Ivanisenko. (2012). Suppression of subgenomic Hepatitis C Virus RNA replicon replication in huh-7 cells by the NS3 protease inhibitor sch5030334: a stochastic mathematical model. Russian Journal of Genetics: Applied Research, 16(2), pp. 339-347.
F.V. Kazantsev, I.R. Akberdin, N.L. Podkolodnyy, V.A. Likhoshvai. (2012). New facilities of the MGSmodeller. Russian Journal of Genetics: Applied Research, 16(4/1), pp. 799-804.

2010:

I.R. Akberdin, S.I. Fadeev, I.A. Gainova, F.V. Kazantsev, V.K. Korolev, V.A. Likhoshvai and A.E. Medvedev. (2010). New computer technologies for construction and numerical analysis of mathematical models of molecular genetic systems. "Progress in Analysis and its Applications", Proc.of the 7th ISAAC Congress, World Scientific Publ., Singapore, pp. 563-569.

2009:

I.R. Akberdin, F.V. Kazantsev, N.A. Omelyanchuk, V.A. Likhoshvai (2009). Mathematical model of auxin metabolism in meristem cells of plant shoots. VOGiS Herald journal, 13(1), pp. 170-176.
F.V. Kazantsev, I.R. Akberdin, K.D. Bezmaternykh, V.A. Likhoshvai (2009). The tool for automatic generation of gene network’s mathematical models. VOGiS Herald journal, 13(1), pp. 163-170.
V.A. Likhoshvai, N.A. Omelyanchuk, V.V. Mironova, F.V. Kazantsev, I.R. Akberdin, V.K. Korolev, S.I. Fadeev, N.A. Kolchanov (2009). Modeling of auxin regulated kateral organ initiation in Arabidopsis thaliana L.. VOGiS Herald journal, 13(1), pp. 176-186.
I.R Akberdin, F.V. Kazantsev, V.A. Likhoshvai, S.I. Fadeev, I.A. Gainova, V.K. Korolev, A.E. Medvedev (2009). Computer system of modules integration for automatic construction and numerical analysis of molecular genetic systems. SEMR, 6, pp. 440-456.

2008:

Omelyanchuk N.A., Mironova V.V., Zalevsky E.M., Podkolodny N.L., Ponomarev D.K., Nikolaev S.V., Akberdin I.R., Ozonov E.A., Likhoshvai V.A., Fadeev S.I., Penenko A.V., Lavrekha V.V., Zubairova U.S., Kolchanov N.A. (2008) Plant Morphogenesis: reconstruction in databases and modelling. Computational systems biology, publishing house of the SB RAS, pp. 539-587.

2007:

Ilya R. Akberdin, Evgeniy A. Ozonov, Victoria V. Mironova, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai, Dmytry N. Gorpinchenko, Nikolai A. Kolchanov (2007). A cellular automaton to model the development of primary shoot meristems of Arabidopsis thaliana. Journal of Bioinformatics and Computational Biology, 5(02B), pp. 641-650. doi: 10.1142/S0219720007002862.
Ilya R. Akberdin, Evgeniy A. Ozonov, Victoria V. Mironova, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai, Dmytry N. Gorpinchenko, Nikolai A. Kolchanov (2007). Mathematical model of the Arabidopsis thaliana L. morphogenesis in a cellular automaton terms. The FEBS Journal, 274(1), pp. 134.
Axenovich T.I., Zorkoltseva I.V., Akberdin I.R., Beketov S.V., Kashtanov S.N., Zakharov I.A., Borodin P.M. Inheritance of litter size at birth in farmed arctic foxes (Alopex lagopus, Canidae, Carnivora). Heredity. 2007 Feb; 98(2):99-105. Epub 2006 Sep 27. PMID: 17006530. doi: 10.1038/sj.hdy.6800908.

2006:

Zorkoltseva I.V., Akberdin I.R., Kulikova A.V, Knyazev S.V, Borodin P.M, Axenovich T.I. (2006) Changes in litter size in Kerry Blue Terrier dogs with abnormal dentition. Russian Journal of Genetics, 42(3), pp. 339-340.
Akberdin I.R., Ozonov E.A., Mironova V.V., Komarov A.V., Omelyanchuk N.A., Likhoshvai V.A. (2006) A cellular automaton to model the development of shoot apical meristem of Arabidopsis thaliana. Bioinformatics of Genome Regulation and Structure II. Springer Science+Business Media, Inc., 2, pp. 185-189.
Akberdin I.R., Kashevarova N.A., Khlebodarova T.M., Bazhan S.I., Likhoshvai V.A. (2006) A mathematical model for the Influenza virus life cycle. Proceedings of the 5^th International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 2, pp.105-109.
Komarov A.V., Akberdin I.R., Ozonov E.A., Evdokimov A.A., Likhoshvai V.A. (2006) On the reconstruction of genetic automaton on the basis of Boolean dynamic data. Proceedings of the 5^th International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, 3, pp. 69-74.
Akberdin I. R., Ozonov E. A., Mironova V.V., Gorpinchenko D. N., Omelyanchuk N. A., Likhoshvai V. A., Kolchanov N. A.. (2006) A Cellular Automaton Model of Morphogenesis in Arabidopsis thaliana. Biophysics (Russian), 51(7), pp. 91-94.

Abstracts

2019:

Akberdin I.R., Kiselev I., Vertyshev A., Popov D., Kolpakov F. Computational modeling of energy metabolism and intracellular signaling in human skeletal muscle // Proceedings of the VII Congress and Associate Symposiums of Vavilov Society of Geneticists and Breeders on the 100th Anniversary of the Department of Genetics of Saint Petersburg State University, Saint Petersburg, Russia.

2018:

Akberdin I.R., Thompson M., Hamilton R., Collins D., Kalyuzhnaya M.G. Methane utilization in Methylomicrobium alcaliphilum 20ZR: new routes of C1-metabolism // Proceedings of the 11th International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”, BGRS\SB-2018, Novosibirsk, Russia, p. 130.

2016:

Akberdin I., But S., Kalyuzhnaya M. Methane valorization: construction and validation of whole genome metabolic model of Methylomicrobium alcaliphilum 20Z // Proceedings of the 38th Symposium on Biotechnology for Fuels and Chemicals. SIMB, Baltimore, MD, USA.

2014:

Akberdin I.R., Kazantsev F.V., Ermak T.V., Khlebodarova T.M., Likhoshvai V.A. Kinetic modeling of metabolic pathways in a bacterial cell // Proceedings of the 6th VOGiS Congress, Rostov-on-Don, Russia, p. 52.
Akberdin I.R., Ermak T.V., Kazantsev F.V., Khlebodarova T.M., Likhoshvai V.A. Kinetic modeling of pyrimidine biosynthesis is a first step to in silico bacterial cell // Proceedings of the 9th BGRS\SB-2014, Novosibirsk, Russia, p. 17.
Akberdin I.R., Ivanisenko N.V., Oshchepkova E.A., Omelyanchuk N.A., Matushkin Yu.G., Afonnikov D.A., Kolchanov N.A. Regulatory mechanisms for mESC self-renewal: kinetic and stochastic modeling // Proceedings of the 9th BGRS\SB-2014, Novosibirsk, Russia, p. 18.
Ermak T.V., Akberdin I.R., Timonov V.S., Mischenko E.L., Oshchepkova E.A., Perfilyeva O.A., Smirnova O.G., Khlebodarova T.M., Likhoshvai V.A. KINET 1.0 - a new web database on kinetics data and parameters for E.coli metabolic pathways // Proceedings of the 9th BGRS\SB-2014, Novosibirsk, Russia, p. 48.
Ivanisenko N., Mishchenko E., Akberdin I., Demenkov P., Kozlov K., Todorov D., Gursky V.V., Samsonova M.G., Samsonov A.M., Clausznitzer D., Kaderali L., Kolchanov N.A., Ivanisenko V.A. Mathematical model for subgenomic Hepatitis C Virus replication: impaсt of drug resistance emergence on long-term kinetics of NS3 protease inhibitors action // Proceedings of the 9th BGRS\SB-2014, Novosibirsk, Russia, p. 71.
Oshchepkova E.A., Omelyanchuk N.A., Akberdin I.R., Ermak T.V., Afonnikov D.A. Database of quantitative characters of processes in embryonic stem cells // Proceedings of the 9th BGRS\SB-2014, Novosibirsk, Russia, p. 120.
Turnaev I.I., Gunbin K.V., Akberdin I.R., Mironova V.V., Omelyanchuk N.A., Afonnikov D.A. Increasing the number of paralogs for enzymes involved in tryptophan biosynthesis during the evolution of land plants // Proceedings of the 9th BGRS\SB-2014, Novosibirsk, Russia, p. 163.
Akberdin I.R., Ivanisenko N.V., Oshchepkova E.A., Omelyanchuk N.A., Matushkin Yu.G., Afonnikov D.A., Kolchanov N.A. The modeling of regulatory mechanisms for mESC self-renewal: kinetic and stochastic approaches // Proceedings of the 4th International Conference on science and applied research "Post-Genome Methods of Analysis in Biology and Laboratory and Clinical Medicine", Kazan, Russia, p. 100.

2013:

Akberdin I.R., Kazantsev F.V., Ermak T., Timonov V.S., Khlebodarova T.M., Likhoshvai V.A. Mathematical modeling of gene network dynamics in E.coli // Proceedings of the 38th FEBS Congress 2013 "Mechanisms in Biology", St. Petersburg, Russia, p. 562.

2012:

Ermak T., Timonov V.S., Akberdin I.R., Khlebodarova T.M., Likhoshvai V.A. KINET – a new web database on kinetics data and parameters for E.coli // Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 91.
Khlebodarova T.M., Akberdin I.R., Fadeev S.I., Likhoshvai V.A. Modeling and analysis of dynamics of the ribopyrimidines de novo biosynthesis in E.coli // Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 143.
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.
Savina M.S., Mironova V.V., Akberdin I.R., Omelyanchuk N.A., Likhoshvai V.A. Mathematical model of auxin responsive reporter DR5 activity in plant cell // Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 279.
Ivanisenko N.V., Mishchenko E.L., Akberdin I.R., Demenkov P.S., Likhoshvai V.A., Kolchanov N.A., Ivanisenko V.A. Suppression of subgenomic HCV RNA by NS3 protease antivirals in cells: a basic stochastic mathematical model // Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 129.
Turnaev I.A., Akberdin I.R., Mironova V.V., Omelyanchuk N.A., Afonnikov D.A. Molecular evolution of proteins belonging to auxin biosynthesis gene network in plants // Proceedings of the 8th International Conference BGRS\SB_2012, Novosibirsk, Russia, p. 320.
Turnaev I.I., Akberdin I.R., Mironova V.V., Omelianchuk N.A., Afonnikov D.A. Molecular evolution of proteins belonging to auxin biosynthesis gene network in plants // Proceedings of the Molecular Phylogenetics, Contributions to the 3rd Moskow International Conference “Molecular Phylogenetics” (MolPhy-3), Moscow, Russia, p. 89.
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.
Ivanisenko N.V., Mishchenko E.L., AkberdinI.R., Demenkov P.S., Likhoshvai V.A., Samsonova M.G., Clausznitzer D., Kaderali L., Kolchanov N.A. and Ivanisenko V.A. A stochastic model for suppression of subgenomic hepatitis C virus replication in Huh-7 cells // Abstracts of International Syspatho Workshop "Systems Biology and Medicine", St. Petersburg, Russia, p. 78.
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.
Akberdin I.R., Trifonova E.A., Gainova I.A., Makasheva V.A., Likhoshvai V.A. Reconstruction and analysis of mTOR signalling's mathematical model // Abstracts of the 4th International Conference "Mathematical Biology and Bioinformatics", Pushchino, Russia, pp. 119-120.

2011:

Akberdin I.R. , Kazantsev F.V., Ree M.T., Ree N.A., Timonov V.S., Oshchepkova E.A., Ratushny A.V., Khlebodarova T.M., Likhoshvai V.A. MGSmodelsDB – a new database of mathematical models of Escherichia coli cell subsystems // Proceedings of the VI Moscow International Congress “Biotechnology: state of the art and prospects of development”, Moscow, Russia,Vol. 2, p. 397.
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.
Mischenko E., Ivanisenko N., Akberdin I., Likhoshvai V., Kozlov K., Gursky V., Samsonova M., Kolchanov N., Ivanisenko V. A mathematical model for the suppression of subgenomic Hepatitis C virus replication in Huh-7 cells in the presence of the NS3 protease inhibitors // Proceedings of the International Conference on Systems Biology 2011, Heidelberg, Germany, August 28 – September 1, p. 269.
Mischenko E., Ivanisenko N., Akberdin I., Likhoshvai V., Kozlov K., Gursky V., Samsonova M., Kolchanov N., IvanisenkoV. A mathematical model for the suppression of subgenomic Hepatitis C virus replication in a cell by the NS3 protease inhibitor SCH503034 // Proceedings of the Saint-Petersburg's scientific forum "Science and society. Physiology and medicine of 21 century. VI Saint-Petersburg meeting of Nobel Prizers", Saint-Petersburg, Russia, September, 19-23, pp. 13-14.
Timonov V.S., Gunbin K.V., Kazantsev F.V., Akberdin I.R., Demenkov P.S., Lashin S.A., Ananko E.A., Ivanisenko V.A., Podkolodny N.L., Kolchanov N.A. Gene networks modeling: GeneNet system in 2011 // Proceedings of the International Conference "Modern challenges of mathematics, informatics and bioinformatics", Novosibirsk, Russia, October, 11 – 14, p. 65.
Akberdin I.R., Kazantsev F.V., Ree M.T., Ree N.A., Nasonov V.V., Timonov V.S., Lashin S.A., Oshchepkova E.A., Ratushny A.V., Khlebodarova T.M., Likhoshvai V.A. A new database of mathematical models describing elementary subsystems of Escherichia coli cell // Proceedings of the II International Conference “Postgenome 2011”, Novosibirsk, Russia, p. 106.

2010:

I.R. Akberdin, F.V. Kazantsev, S.I. Fadeev., I.A. Gainova, V.A. Likhoshvai.Development of shoot apical meristem in silico under phytohormone regulation // Proceedings of the Plantgen, Novosibirsk, Russia, p. 45.
V.M. Efimov, A.S. Novikov, A.A. Tikhonov, I.R. Akberdin, V.A. Likhoshvai. Reduction of gene net dynamic models using proper orthogonal decomposition // Proceedings of the Seventh International Conference on Bioinformatics of Genome Regulation and Structure and Systems Biology (BGRS_SB’10), Novosibirsk, Russia, June 20- 27, 2010, p.67.
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 MGS-generator and STEP+ modules // Proceedings of the Seventh International Conference on Bioinformatics of Genome Regulation and Structure and Systems Biology (BGRS_SB’10), Novosibirsk, Russia, June 20- 27, 2010, p.77.
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 and Systems Biology (BGRS_SB’10), Novosibirsk, Russia, June 20- 27, 2010, p.129.
I.A. Gainova, I.R. Akberdin, F.V. Kazantsev, V.A. Likhoshvai, S.I. Fadeev, V.K. Korolev, A.E. Medvedev. Mathematical modeling of shoot apical meristem’s development on the different hierarchical levels // Proceedings of the All-Russian Conference “Mathematical Models and informational technologies in the agricultural biology: results and perspectives”, Saint-Petersburg, October 14-15, 2010, ISBN 978-5-9900138-4-1, pp. 117-120.

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. // Proceedings of the German-Russian Forum Biotechnology, Novosibirsk, Russia, p. 6.
I.R. Akberdin, F.V. Kazantsev, V.A. Likhoshvai. Modelling 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 (2009). 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, Fadeev S.I., Gainova I.A., Likhoshvai V.A. (2009) Mathematical modelling of a plant development on the different levels // Abstracts of 3 rd Annual World Congress of Gene-2009, Foshan, China, December 1-7, 2009, p. 152.

2008:

Akberdin I.R., Ozonov E.A., Mironova V.V., Kazantcev F.V., Omelyanchuk N.A., Likhoshvai V.A. «Mathematical model of the Arabidopsis thaliana L. morphogenesis in a cellular automaton terms». // Proceedings of the International Young Scientists Conference “Lomonosov-2008””, Moscow, Russia, 8 – 12 April 2008, P.1.
Akberdin I.R., Omelyanchuk N.A., Fadeev S.I., Efimov V.M., Gainova I.A., Likhoshvai V.A. Mathematical model of auxin metabolism in shoots of Arabidopsis thaliana L. // Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2008), Novosibirsk, Russia, June 22- 28, 2008, p.23.
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 (BGRS'2008), Novosibirsk, Russia, June 22- 28, 2008, p.113.
Kazantsev F.V., Akberdin I.R., Bezmaternykh K.D., Likhoshvai V.A. MGSgenerator – the tool for automatical generation of molecular genetic system mathematical models on basis of gene network structure // Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2008), Novosibirsk, Russia, June 22- 28, 2008, p.114.
Likhoshvai V.A., Akberdin I.R., Mironova V.V., Omelyanchuk N.A., Fadeev S.I., Mjolsness E. Modeling and comparative analysis of auxin transport mechanisms in shoot and root // Proceedings of the Sixth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2008), Novosibirsk, Russia, June 22- 28, 2008, p.141.
I. R. Akberdin. Modelling of the development regulation of 2d plant tissue // Proceedings of the International Conference "Modern problems of Mathematical Modelling and Computational Technologies – 2008", Krasnoyarsk, Russia, August 18-24, 2008, p. 4.
I. R. Akberdin, F. V. Kazantsev, N. A. Omelyanchuk, V. A. Likhoshvai. Mathematical model of auxin metabolism in shoots of Arabidopsis thaliana L. // Proceedings of the2nd International Conference “Mathematical Biology and Bioinformatics”, Pushchino Moscow region, September 7-13, 2008, p. 49.

2007:

Ilya R. Akberdin, Evgeniy A. Ozonov, Victoria V. Mironova, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai, Dmytry N. Gorpinchenko, Nikolai A. Kolchanov «Mathematical model of the Arabidopsis thaliana L. morphogenesis in a cellular automaton terms» // Proceedings 7th YSF “Molecular Networks”, Vienna, Austria, 5 – 7 July 2007, P.10.
Ilya R. Akberdin, Evgeny A. Ozonov, Victorya V. Mironova, Dmitry N. Gorpinchenko, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai, Denis S. Miginsky, Nikolai A. Kolchanov. 2d modelling and analysis of spatially distributed cells types of primary shoot apical meristem (SAM) of Arabidopsis thaliana // Proceedings of the 3-rd Moscow conference on computional molecular biology. Moscow, Russia, July 27-31, 2007, p. 25-26.
Ilya R. Akberdin, Evgeny A. Ozonov, Victorya V. Mironova, Dmitry N. Gorpinchenko, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai, Nikolai A. Kolchanov. Modelling and analysis of spatially distributed systems regulation in apical meristem of Arabidopsis thaliana // Proceedings of the 3-rd International conference "Basic Science for Medicine", Novosibirsk, Russia, September 2-8, 2007, p.95.
Ilya R. Akberdin, Evgeniy A. Ozonov, Victoria V. Mironova, Dmytry N. Gorpinchenko, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai. Mathematical model of the Arabidopsis thaliana L. morphogenesis in a cellular automaton terms (2007) // Proceedings of the International Young Scientists Conference “Challenges of molecular and cell biology”, Tomsk, Russia, May 9-12, 2007, PP. 5-6.
Evgeniy A. Ozonov, Ilya R. Akberdin, Victoria V. Mironova, Nadezda A. Omelyanchuk, Vitaly A. Likhoshvai // Proceedings of the All-Russian Conference of physics student ВНКСФ-13, 471-472

2006:

Akberdin I. R., Ozonov E. A., Mironova V.V., Komarov A. V., Omelyanchuk N. A., Likhoshvai V. A. Two-dimensional model the development of shoot meristem of Arabidopsis thaliana in cellular automaton terms // Materials of The 3rd International Conference “Genomics, Proteomics, Bioinformatics and Nanotechnologies for Medicine” (GPBM, 2006), Novosibirsk, p. 95.
Akberdin I. R., Ozonov E. A., Mironova V.V., Komarov A. V., Omelyanchuk N. A., Likhoshvai V. A. AGNS database and cellular automaton to model the development of shoot meristems of Arabidopsis thaliana // Materials of the 7th All-Russian School-Seminar of Junior Scientists on Mathematical Modeling and Informational Technologies, Irkutsk, pp.6-10.
Akberdin I. R., Ozonov E. A., Mironova V.V., Komarov A. V., Omelyanchuk N. A., Likhoshvai V. A. Modeling of morphogenesis of Arabidopsis thaliana in cellular automaton terms // Materials of 7th All-Russian Conference on Mathematical Modeling and Informational Technologies, Krasnoyarsk, Vol.1, p. 10.
Kazantcev 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 system // Materials of 7th All-Russian Conference on Mathematical Modeling and Informational Technologies, Krasnoyarsk, Vol.1, p. 14.

2005:

Akberdin I. R. Regulation of litter size in farmed arctic foxes (Alopex lagopus) and Kerry Blue Terrier dogs (Canis familiaris) // Materials of XLIII International Scientific Student's Conference "The Student and scientific and Technical Progress": Biology / Novosibirsk State University, Novosibirsk, p. 3.

2004:

Akberdin I. R. Materials of XLII International Scientific Student's Conference "The Student and scientific and Technical Progress": Biology / Novosibirsk State University, Novosibirsk, p. 41.
Akberdin I. R., Beketov S.V., Kashtanov S.N., Kulikova A.V., Axenovich T.I. Studying of genetic regulation of litter size in polycarpic animals // Materials of the 3rd Congress of VSGaS “Genetics in XXI century: modern state and perspectives of development”, Moscow.

2003:

Akberdin I. R., Zykovich A.S. Development of gene mapping methods of quantitative traits in silico // Materials of XLI International Scientific Student's Conference "The Student and scientific and Technical Progress": Biology / Novosibirsk State University, Novosibirsk, p. 16.
Akberdin I. R., Zykovich A.S. Studying of statistic properties of mapping in silico // Materials of III International Scientific Student's Conference "Actual Problems of Modern Biology and Biotechnology": Genetics / Kazakhstan State University, Alma-Ata, p. 160.

Biomodels Group

Akberdin IR