Publications

A selected list of key publications by Genome Designs' founders is presented below. These works describe our flagship MPW pathway database, as well as basic principles and the technology we use in genome annotation, functional reconstruction and metabolic engineering, as well as dynamic modeling, which describes cellular metabolism in motion.

Liele, I., Swainston, N., Fleming, R.M.T., Hoppe, A., Sahoo, S., Aurich, M.K., Haraldsdottir, H., Mo, M.L., Rolfsson, O., Stobbe, M.D., Lorleifsson, S.G., Agren, R., Blling, C., Bordel, S., Chavali, A.K., Dobson, P., Dunn, W.B., Endler, L., Hala, D., Hucka, M., Hull, D., Jameson, D., Jamshidi, N., Jonsson, J.J., Juty, N., Keating, S., Nookaew, I., Le Novere, N., Malys, N., Mazein, A., Papin, J.A., Price, N.D., Selkov Sr., E, Sigurdsson, M.I., Simeonidis, E., Sonnenschein, N., Smallbone, K., Sorokin, A., van Beek, J.H.G.M., Weichart, D., Goryanin, I., Nielsen, J., Westerhoff, H.V., Kell, D.B., Mendes, P., Palsson, B.ō., A community-driven global reconstruction of human metabolism, Nature Biotechnology 2013, doi:10.1038/nbt.2488

A. Kaznadzey, N. Alexandrova, V. Novichkov, D. Kaznadzey, PSimScan: Algorithm and Utility for Fast Protein Similarity Search, PLoS ONE 2013, vol. 8, issue 3, p. e58505

Ross Overbeek, Niels Larsen, Natalia Maltsev, Gordon D. Pusch, and Evgeni Selkov, Metabolic Reconstruction Using the WIT/WIT2 Systems in: Databases and Systems 2002, ed: S. Letovsky, pp 37-45

Covert M.W., Schilling C.H., Famili I., Edwards J.S., Goryanin I.I., Selkov E., Palsson B.O. , Metabolic Modeling of Microbial Strains in silico, Trends Biochem Sci. 2001, 26(3):179-86.

Ross Overbeek, Niels Larsen, Gordon D. Pusch, Mark DíSouza, Evgeni Selkov Jr, Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, and Evgeni Selkov, WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction, Nucleic Acids Res. 2000, 28(1):123-5.

Selkov E., Overbeek R., Kogan Y., Chu L., Vonstein V., Holmes D., Silver S., Haselkorn R., Fonstein M., Functional analysis of gapped microbial genomes: amino acid metabolism of Thiobacillus ferrooxidans, PNAS 2000, vol. 97 no. 7:3509-3514

Igor Goryanin, T. Charles Hodgman, Evgeni Selkov, Mathematical simulation and analysis of cellular metabolism and regulation, Bioinformatics 1999, 15 (9): 749-758.

Evgeni Selkov Jr, Yuri Grechkin, Natalia Mikhailova, Evgeni Selkov, MPW: the Metabolic Pathways Database, Nucleic Acids Res. 1998, 26(1):43Ė45.

Evgeni Selkov, Miliusha Galimova, Igor Goryanin, Yuri Gretchkin, Natalia Ivanova, Yuri Komarov, Natalia Maltsev, Natalia Mikhailova, Valeri Nenashev, Ross Overbeek, Elena Panyushkina, Lyudmila Pronevitch and Evgeni Selkov Jr., The metabolic pathway collection: an update, Nucl. Acids Res. 1997, 25 (1): 37-38.

E. Selkov, N. Maltsev, Gary J. Olsen, R. Overbeek, William B. Whitman, A reconstruction of the metabolism of Methanococcus jannaschii from sequence data, Gene 1997, 197:11-26

Evgeni Selkov, Svetlana Basmanova, Terry Gaasterland, Igor Goryanin, Yuri Gretchkin, Natalia Maltsev, Valeri Nenashev, Ross Overbeek, Elena Panyushkina, Lyudmila Pronevitch, Evgeni Selkov, Jr, and Ilya Yunus, The Metabolic Pathway Collection from EMP: The Enzymes and Metabolic Pathways Database, Nucleic Acids Res. 1996, 24(1):26-8.

T. Gaasterland and E. Selkov, Reconstruction of Metabolic Networks Using Incomplete Information, Proc Int Conf Intell Syst Mol Biol. 1995, 3:127-35.

Ye. Ye. Sel'kov, L. Ya. Linichuk and N.V. Avseenko, Homeostasis of the period of auto-oscillations in a model of the circadian cell clock, Biophysics 1989, 34:496-501

Selíkov E. E., Goryanin I.I, Nearly ideal biochemical relaxational generator based on covalent modification of enzyme, Mol. Biol. 1986, 20(6):1550-1561

Boiteux A. & Hess B., Sel'kov E. E., Experimental and theoretical studies of the regulatory hierarchy in glycolysis. in: Selforganization 1984, ed. Krinsky V.I. (Springer Series in Synergetics), Vol. 27:240-254.

Goryanin I.I, Selíkov E. E., and Serdyuk K.I., A refined mathematical model of an almost ideal biochemical relaxation oscillator based on the covalent modification of an enzyme, Mol. Biol. 1982, 26(2): 310-322

Reich J. G., Selíkov E. E., Energy Metabolism of the Cell, A Theoretical Treatise, 1981, Academic Press, London & New York

Selíkov E. E., Instability and Self-Oscillations in the Cell Energy Metabolism, Ber. Bunsenges. Phys. Chem. 1980, 84(4): 399-402

Boiteux A, Hess B, Sel'kov EE., Creative functions of instability and oscillations in metabolic systems. Curr Top Cell Regul. 1980, 17:171Ė203

I.A. Malkova, S. V. Popova and Ye. Ye. Sel'kov, Multiplicity of steady states and auto-oscillations in the open reaction catalyzed by phosphofructokinase of E.coli, Biophysics 1980, 55:520-525

Sel'kov E. E., Oscillatory basis of cell energy metabolism In: Pattern formation by dynamic systems and pattern recognition, ed. H. Haken (Springer Series in Synergetics) 1979, pp. 166-174

S.V. Popova and E. E. Selíkov, Description of the kinetics of two-substrate reactions of the type S1+S2=S3+S4 by a generalized Monod, Wyman, and Changeux model, Mol. Biol. 1979, 13:96-104

S.V. Popova and E. E. Selíkov, Reversible Enzymatic Reactions, a theoretical analysis, Mol. Biol. 1978, 78:878-889

P. M. Gillevet, A. Ally, M. Dolan, E. Hsu, M. S. Purzycki, R. Overbeek, E.E. Selkov, S. Smith, C. Wang, and W. Gilbert, Mycoplasma capricolum Genome Project in: Bacterial Genomes: Physical Structure and Analysis, ed. by: F.J. de Bruijn, J.R. Lupski, G.M. Weinstock, ITP, 1977, pp.526-540

S.V. Popova and E. E. Selíkov, Generalization of the model by Monod, Wyman and Changeux for the case of a reversible monosubstrate reaction SR,TP, FEBS Lett. 1975, 53:269-273

Ye.Ye. Selíkov, Two alternative auto-oscillatory steady states in the metabolism of the thiols Ė two alternative types of cell multiplication: normal and malignant, Biophysics (New York) 1970, 15(6), 1104-1112


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