Married, one child

Leningrad State University, Faculty of Biology, Department of Biological Chemistry and

Institute of Experimental Medicine, Department of Biochemical Genetics, Leningrad

1972 - 1978

Diploma: "Analysis of molecular structure of mitochondrial DNA from rat liver by methods of electron microscopy", Department of Biochemical Genetics, Institute of Experimental Medicine, (Advisor Prof. Salamon A.Neifakh)

PostGraduate studentship:

Irkutsk State University, (Irkutsk), Dept. Physico-Chemical Biology

1979 - 1983

Candidate of Science (=PhD) - 1987. Irkutsk State University, Dept. Physico-Chemical Biology, Irkutsk, Russia

EXPERIENCE IN COMPUTATIONAL BIOLOGY & BIOINFORMATICS:

• Development of hypermedia molecular-biological information systems: hypertexts, Java applets, and scientific animation (JavaScript). Web page design and maintenance.
• Computational analysis of networks of genes-controllers of morphogenesis (Drosophila segmentation network, vertebrate Hox networks); reverse engineering of genetic networks.
• Boolean models of genetic networks (analysis by DDLab and original software).
• Dynamical models of genetic networks (connectionist's approach).
• Inferring of genetic network structure via artificial neural networks modeling.
• Computer simulation of patterns of expression of genes-controllers of morphogenesis.
• Application and development of Evolutionary Computations for the tasks of image processing and pattern recognition.
• Working out of software for molecular-biological image processing (Genetic Algorithms-, Genetic Programming-based software for image segmentation, registration, deformations).
• Working out of software for DNA sequences analysis (Genetic Algorithms-based approach for search of gene regulatory regions).
• Analysis of DNA and protein sequences via on-line analytical servers and DOS, UNIX specialized software.

HARDWARE & OPERATING SYSTEMS

* DEC workstations running LINUX, UNIX, X Windows .

LANGUAGES

Moderate: Fortran, Java, C, Khoros package, Perl.

1. "Ecological Monitoring of St.Petersburg City and Suburbs" (Ministry of Science and Technologies, 1989-1992)
2. "Data Bank of Conserved Regions of Mitochondrial Proteins and Investigation of Evolution of Mitochondrial Proteins" (Human Genome, RAS, 1992 - 1993)
3. "Data bank of regulatory regions of human/mammalian homeo box-containing genes and computer analysis of the regulatory regions" (Human Genome, RAS, 1994)
4. "Simulations of the processes in evolutionary and ecological physiology" (RFBR, 1994-1997)
5. "Phylogenetic analysis of the functional organisation of homeobox-genes networks as one of elements of the body plan of Animalia kingdom" (RFBR, 1996-1997)
6. "Evolutionary conservatism of cascades of genes-controllers in regulation of ontogenesis: computer analysis of images of expression patterns and simulation of dynamics of genetic networks/cascades" (RFBR, 1998-1999)
7. Hypermedia information system "HAZARD": chemical mutagens, teratogens, carcinogens" (RFBR, 1998-1999)
8. "SegNet, the database on mechanisms of regulation of genes controlling embryogenesis in Drosophila" (Ministry of Science and Technologies, 1998)
9. "Physiological Model of Gene Regulation in Drosophila" (National Institutes of Health, 1996-2001)
10. "Application of new evolutionary computation techniques - the Mobile Genetic Elements (MGE) in cognitive approaches to registration, classification and segmentation of series of biological and medical images" (INTAS, 1999-2001)
11. "Molecular-Physiological aspects of evolution of the genetic network controlling embryonic segmentation of species of Drosophilidae" (RFBR, 2000-2002)

• Homeobox Genes Promoter Regions DataBase "HOX-Pro DB"
• http://www.iephb.nw.ru/hoxpro or
• http://www.mssm.edu/molbio/hoxpro
• Genetic Networks DataBase "GeNet"
• http://www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm or
• http://academic.mssm.edu/molbio/genet/genet.htm
• Hypermedia information system "HAZARD": chemical mutagens, teratogens, carcinogens
• http://iephb.nw.ru/labs/lab38/spirov/hazard/hazard.html or
• http://academic.mssm.edu/molbio/hoxpro/hazard/hazard.html

• Genes, Morphogenesis and Evolution
• http://www.geocities.com/ResearchTriangle/Thinktank/1765/monogr/monograph.html
• Evolutionary Biology and Evolutionary Computations
• http://www.geocities.com/ResearchTriangle/Thinktank/1765/alife/selfish.html

• "Reconstruction of the Genetic Networks..."
• http://academic.mssm.edu/molbio/tmp/index.htm
• "The Inverse Problem for ODE' Models of the Genetic Networks..."
• http://academic.mssm.edu/molbio/tmp/circuits/hox1circ.html
• "Atlas of Drosophila Genes Expression..."
• http://academic.mssm.edu/molbio/hoxpro/atlas/atlas.html

I.M.Sechenov Institute of Evolutionary Physiology and Biochemistry,

Russian Academy of Sciences

1989-Present

Position: Senior Scientific Researcher, the Head of the Group.

Major Accomplishments:

• Leading executor of the "HUMAN GENOME" (Russian Academy of Sciences) projects entitled:
• "Data Bank of Conserved Regions of Mitochondrial Proteins and Investigation of Evolution of Mitochondrial Proteins" (1992 - 1993)
• "Data bank of regulatory regions of human/mammalian homeo box-containing genes and computer analysis of the regulatory regions" (1994)
• Executor of the "Russian Foundation for Basic Research" project entitled: "Simulations of the processes in evolutionary and ecological physiology" (1994-1997)
• The Head of the "Russian Foundation for Basic Research" project entitled: "Phylogenetic analysis of the functional organisation of homeobox-genes networks as one of elements of the body plan of Animalia kingdom" (1996-1997)
• The Head of the "Russian Foundation for Basic Research" project entitled: "Evolutionary conservatism of cascades of genes-controllers in regulation of ontogenesis: computer analysis of images of expression patterns and simulation of dynamics of genetic networks/cascades" (1998-1999)
• The Head of the "Russian Foundation for Basic Research" project entitled: Hypermedia information system "HAZARD : chemical mutagens, teratogens, carcinogens" (1998-1999)
• The Head of the "Russian Foundation for Basic Research" project entitled: "Molecular-Physiological aspects of evolution of the genetic network controlling embryonic segmentation of species of Drosophillidae" (2000-2002)
• Participant of the INTAS project "Application of new evolutionary computation techniques - the Mobile Genetic Elements (MGE) in cognitive approaches to registration, classification and segmentation of series of biological and medical images" (1999-2001)
• Collaborator of the NIH project "Physiological Model of Gene Regulation in Drosophila" (NIH, MtSinai School of Medicine, J.Reinitz - the head of the project, 1998-2001)
• Supervisor of the Homeobox Genes Promoter Regions DataBase "HOX-Pro DB" hypermedia information system

Other activities:

• In frame of Russian HUMAN GENOME Project I participate in development of Encyclopedia Hypertext (Chapter about human/mammalian homeobox genes) via FLEXIS Hypertext Encyclopedia software (E.Golovanov, 1992).
• In outlook of collaborative biodiversity project I become acquainted with ETI Biodiversity Information System Linnaeus II.

Institute of High-Performance Computing and DataBases,

Ministry of Science

1996- 1998

Position: Leading Scientific Researcher, the Head of the group

Major Accomplishments:

Executor of the program of Ministry of Science and Technologies entitled "SegNet, the database on mechanisms of regulation of genes controlling embryogenesis in Drosophila"

Collaborator of the NIH project "Physiological Model of Gene Regulation in Drosophila" (NIH, MtSinai School of Medicine, J.Reinitz - the head of the project, 1996-1998)

Second Leningrad Medical Institute, Academy of Medical Sciences 1983-1989

Major Accomplishments:

Computer Center of the Institute, researcher

Major Accomplishments:

Irkutsk State University, Irkutsk (East Siberia)

1979-1983

Computer Center of the University, technician-programmer.

Major Accomplishments:

EMPLOYMENT DURING SCHOOL

Institute of Experimental Medicine (Leningrad) 1974-1978

Can read German.

The 8th Prague Symposium on Computer Simulation in Biology, Ecology, & Medicine, Prague, October, 1992.

International Conference "Mechanisms of Development: Ontogenetic and Phylogenetic Aspects", Moscow, Russia, July 1994.

International Conference and School on Evolutionary Physiology, St.Petersburg, Russia, April 1996.

The First International Conference on Evolutionary Computations and Its Applications, Moscow, Russia, June 1996.

The International Conference on Nonlinear Dynamics and Chaos: Applications in Physics, Biology and Medicine, Saratov, Russia, July, 1996.

The Fourth International Conference on Parallel Problem Solving from Nature, Berlin, September, 1996.

The XXIV International Conference and Scientific Discussion Club "New Information Technologies in Science, Education, Telecommunications and Business", Ukraine, Crimea, Gurzuf, May, 1997.

The XXV International Conference and Scientific Discussion Club "New Information Technologies in Science, Education, Telecommunications and Business", Ukraine, Crimea, Gurzuf, May, 1998.

High-Performance Computing and Networking: International Conference and Exhibition, Amsterdam, The Netherlands, April 21-23, 1998.

International Conference on Soft Computing and Measurements, St.Petersburg, Russia, 22-26 June, 1998.

International Conference on Bioinformatics of Genome Regulation and Structure, (BGRS'98), Novosibirsk, August 24-31, 1998.

The Second International Conference on Soft Computing and Measurements, St.Petersburg, Russia, June, 1999.

The 1st International Workshop on Computer Science and Information Technologies (CSIT'99), Moscow, Russia, January, 1999.

The Third International Conference on Soft Computing and Measurements, St.Petersburg, Russia, June, 2000.

The XXV International Conference and Scientific Discussion Club "New Information Technologies in Medicine and Ecology", Ukraine, Crimea, Gurzuf, 1-15 June, 2000.

The Second International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2000), Novosibirsk, August, 2000.

The 2nd International Workshop on Computer Science and Information Technologies (CSIT'2000), Ufa, Russia, Sept., 2000.
 

Spirov A.V., Mihailovski G.P., Zelikman E.A., Kozlov Y.P., Statistical analysis of spatio-temporal structure of populations of mass species of zooplankton of Barenz Sea. I. Investigation of large-scale space structure of populations, Biologicheskie Nauki, 1982, 61-67 (in Russian).

Spirov A.V., Mihailovski G.P., Zelikman E.A., Kozlov Y.P. Statistical analysis of spatio-temporal structure of populations of mass species of zooplankton of Barenz Sea. II. Dynamics of large-scale spatial structure of populations, Biologicheskie Nauki, 1984,55-63 (in Russian).

Spirov A.V., Boinovich M.M. On diffusion instability of system of reagents, distributed on surface with curvature, RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY, 1985, 59, No9, 2277-2282.

Spirov A.V. and Pushnoi G.V. Chemical teratogens for mammalian as analogs of morphogens, ONTOGENEZ, [Moscow], 1992, No4, 313-314.

Spirov A.V. Synergetic models of interaction of pattern of morphogens and form in models of morphogenesis. ONTOGENEZ, [Moscow], 1992, No5, 612-618.

Spirov A.V. Organization of vertebrate network of HOX genes and limb fate map. In: Proceedings of 8th Prague Symp. Comp. Simulation in Biol., Ecol., & Med., Prague, 1992, 26-30.

Spirov A.V. Pattern of expression of homeobox-containing genes in mesenchyme of a limb bud as coordinate network for following morphogenetic processes, IZV.ROS.ACAD.NAUK: ser.biol., 1992, No5 (translated in English as "AS BIOLOGY BULLETIN").

Spirov A.V. Changes of initial symmetry in the pattern-form interaction model of Sea urchin early development. J.THEOR.BIOLOGY, 1993, 161 (4): 491- 504.

Spirov A.V. Computer modeling of genes expression and morphogenetic movements in embryo development. In: Proceedings of the 1993 Summer Society of Computer Simulation Conference, Joel M.Schoen (ed.). Boston, Massachusetts, 1993. P.185-191.

Spirov A.V. Phylogenetic trees of HOX genes promoters, conservation of regulatory regions and possible mechanism of vertebrate HOX net expression. Ontogenez, [Moscow]. 1994. 25, No4. P.75-76.

Kaimanovich V.A., Krupitsky E.M. & Spirov A.V. Electrical activity of biomembranes and vectorization of intracellular processes. JOURNAL OF ELECTRO & MAGNETOBIOLOGY. 1994, 13, (2), 149-158.

Spirov A.V. Self-organisation of gene nets in evolution via recruiting of new netters. In: Proceedings of the First International Conference on Evolutionary Computations and Its Applications, Moscow, Russia, P.399-405, (1996).

Spirov A.V. The Role Of Some Conservative Sequences In Regulatory Elements Of Antp-Like, Homeobox-Containing Genes Of Vertebrates, JOURNAL OF EVOLUTIONARY BIOCHEMISTRY AND PHYSIOLOGY, [St.-Petersburg], 1996, V.32, No5, P.556-568.

Spirov A.V., Self-Assemblage of Gene Networks in Evolution via Recruiting of New Netters. Lecture Notes in Computer Science, 1996, V.1141, P.91-100.

Spirov A.V. Self-Assemblage of Gene Networks in Evolution via Recruiting of New Netters, CANADIAN SOCIETY OF THEORETICAL BIOLOGY BULLETIN, 1996 http://132.248.34.3/denis_html/cstbspring96/CSTB-Spring9 6-2.html

Spirov A.V. and M.G. Samsonova, Strategy of Co-evolution of Transposons and Host Genome: Application to Evolutionary Computations. In: Proceedings of the Third Nordic Workshop on Genetic Algorithms and their Applications, Helsinki University, P.71-82, 1997.

Spirov A.V. and Samsonova M.G. The GeNet database as a tool for the analysis of regulatory gene networks. In: Proc. of Int. Workshop on Information Processing in Cells and Tissues, Sheffield UK, (1997), P.56-63.

Spirov A.V. Game of Morphogenesis: What Can We Learn from the Pattern-Form Interplay Models? INTERNATIONAL JOURNAL OF BIFURCATIONS AND CHAOS, [Berkeley], 1998, 8, (5), 991-1001.

Spirov A.V., Kadyrov A.S. Transposon Element Technique Applied to GA-based John Muir's Trail Test, In: High-Performance Computing and Networking, 1998, P.925-928.

Serov V.N., Spirov A.V. and Samsonova M.G. Graphical interface to genetic network database GeNet, BIOINFORMATICS, 1998, 14 (6):546-547.

Spirov A.V., Kazansky A.B., Kadyrov A.S. Utilizing of "Parasitic" Mobile Genetic Elements in Genetic Algorithms. In: Int.Conf.on Soft Computing and Measurments, St.Petersburg, (1998), P.266-269.

M.G.Samsonova, K.G.Savostyanova, V.N.Serov, S.Yu.Surkova, A.V.Spirov. // GeNet: a database of genetic networks // CANADIAN SOCIETY OF THEORETICAL BIOLOGY BULLETIN (Spr. 1998)
http://dbm.ulb.ac.be/~denis/cstbspring98/CSTB-Spring98-Samsonova.html

V.N.Serov, E.G.Savostyanova, S.Yu.Surkova, O.V.Kirillova, A.V.Spirov, J.Reinitz, M.G.Samsonova A database of genetic networks controlling embryogenesis.CANADIAN SOCIETY OF THEORETICAL BIOLOGY BULLETIN, Spring 1998.
http://www.mar.dfo-mpo.gc.ca/science/mesd/he/science/cstb/papers/serov/.

M.G.Samsonova, E.G.Savostyanova, V.N.Serov, A.V.Spirov, J.Reinitz // GeNet, a database of genetic networks // Proceedings of BGRS'98, 105-110, Novosibirsk, August 24-31, 1998.

Spirov A.V. Hox-Pro Db: The Ways Of Evolution Of Ensembles Of Homeobox Genes-Controllers Of Development. Proceedings of BGRS'98, Novosibirsk, August 24-31, 1998.

Spirov A.V. Modern Internet technologies for hypermedia information systems describing ensembles of genes-controllers of development, Proceedings of the Workshop on Computer Science and Information Technologies CSIT'99, Moscow, Russia, 1999,
http://msu.JurInfoR.ru/CSIT99/Spirov99.htm

Bowler T., D.Kosman, E.Mjasnikova, M.G.Samsonova, A.V.Spirov and J.Reinitz, Quantitative atlas of segmentation gene expression, Proceedings of the 40th Annual Drosophila Research
Conference DoubleTree Hotel, Meydenbauer Ctr., Bellevue, Washington MARCH 24-28, 1999, P.180B http://www.faseb.org/genetics/gsa/dros/dros-99/d-00.htm

Spirov A.V.,  Bowler T. and Reinitz J.,   HOX-Pro: A Specialized Database for Clusters and Networks of Homeobox Genes, NUCLEIC ACIDS RESEARCH, 2000; 28: 337-340.
http://www3.oup.co.uk/nar/Volume_27/Issue_01/gkd054_gml.html

Spirov,A.V., Timakin,D.L., Reinitz,J. and Kosman,D. Experimental Determination Of Drosophila Embryonic Coordinates By Genetic Algorithms, the Simplex Method, And Their Hybrid. In Proceedings of Second European Workshop On Evolutionary Computation In Image Analysis And Signal Processing, Edinburgh, April 17, 2000.

Spirov A.V. The Problems of The Genetic Networks Inference From Large-Scale Gene Expression Datasets, In: Proceedings of The 2nd International Workshop on Computer Science and Information Technologies, Ufa, Russia, Sept., 2000.

Kirillova O.V. and Spirov A.V. Boolean approach to the reverse engineering problem
on example of early embriogenesis of fruit fly Drosophila melanogaster investigation,
Submitted to BioInformatics.

Alexander V. Spirov, David Hollaway, David Kosman and John Reinitz, Statistical Features of Expression of the Segmentation Genes in Early Drosophila Development at Single-Nucleus Resolution, In preparation.

Spirov,A.V., Ozerski,P.V., Timakin,D.L., Kazansky,A.B. and Kosman,D., 2000, Temporal Ranking, Registration and Classification of the Time-Series of Expression Patterns of Drosophila Segmentation Genes, In preparation.

References are Available Upon Request

Complete list of publications