Laboratoř bioinformatiky

2012

  • Vohradsky J, (2012) Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes. Nucleic Acids Res 40: 7096-103. 

2011

  • Vohradska EVohradsky J, (2011) Virtual mutagenesis of the yeast cyclins genetic network reveals complex dynamics of transcriptional control networks. PLoS One 6: e18827.
  • Panek J., Krasny L., Bobek J., Jezkova E., Korelusova J., Vohradsky J, (2011) The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures. Nucleic Acids Res 39: 3418-26.
  • Munzarova V.,Panek J., Gunisova Ss., Danyi I., Szamecz B., Valasek L., (2011) Translation reinitiation relies on the interaction between eIF3a/TIF32 and progressively folded cis-acting mRNA elements preceding short uORFs. PLoS Genet 7: e1002137.
  • Mikulik K.,Bobek J.Zikova A., Smetakova M., Bezouskova S., (2011) Phosphorylation of ribosomal proteins influences subunit association and translation of poly (U) in Streptomyces coelicolor. Mol Biosyst 7: 817-23. 

2010

  • Vohradsky JPanek J, Vomastek T (2010) Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation. Nucleic Acids Res 38: 4579-4585.
  • To CC, Vohradsky J (2010) Measurement variation determines the gene network topology reconstructed from experimental data: a case study of the yeast cyclin network. FASEB J 24: 3468-3478.

2009

  • Vu TT, Vohradsky J (2009) Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data. Genomics 93: 426-433.
  • Palečková P, Bobek J, Mikulik K (2009) tmRNA of Streptomyces collinus and Streptomyces griseus during the growth and in the presence of antibiotics. Microbial Biotechnology 2: 114-122. 

2008

  • P. Palečková, J. Bobek, and K. Mikulik, (2008) tmRNA of Streptomyces collinus and Streptomyces griseus during the growth and in the presence of antibiotics. Microbial Biotechnology 1.
  • J.P. Swiercz, Hindra, J. Bobek, H.J. Haiser, C. Di Berardo, B. Tjaden, and M.A. Elliot, (2008) Small non-coding RNAs in Streptomyces coelicolor. Nucleic Acids Res 36, 7240-51.
  • Panek, J. (2008) A comparative computational analysis of protein sequences and literature mining classify 'orphan' neurotransmitter transporters. J Theor Biol.
  • Vohradsky, J., Branny, P., Li, X.M. and Thompson, C.J. (2008) Effect of protein degradation on spot M(r) distribution in 2-D gels-a case study of proteolysis during development of Streptomyces coelicolor cultures. Proteomics8, 2371-2375.
  • Mikulik, K., Paleckova, P., Felsberg, J.,Bobek, J., Zidkova, J. and Halada, P. (2008) SsrA genes of streptomycetes and association of proteins to the tmRNA during development and cellular differentiation. Proteomics.
  • Panek, J., Bobek, J., Mikulik, K., Basler, M. and Vohradsky, J. (2008) Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics9, 217.
  • To, C.C. and Vohradsky, J. (2008) Supervised inference of gene-regulatory networks. BMC Bioinformatics9, 2.
  • Valis, K., Neubauerova, J., Man, P., Pompach, P., Vohradsky, J. and Kovar, J. (2008) VDAC2 and aldolase A identified as membrane proteins of K562 cells with increased expression under iron deprivation. Mol Cell Biochem311, 225-231. 

2007

  • Vohradsky, J., Branny, P. and Thompson, C.J. (2007) Comparative analysis of gene expression on mRNA and protein level during development of Streptomyces cultures by using singular value decomposition, Proteomics, 7, 3853-3866.
  • To, C.C. and Vohradsky, J. (2007) A parallel genetic algorithm for single class pattern classification and its application for gene expression profiling in Streptomyces coelicolor. BMC Genomics8, 49.
  • Vu, T.T. and Vohradsky, J. (2007) Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae, Nucleic Acids Res35, 279-287.
  • Panek, J.,Eidhammer, I., Aasland, R.(2007)Using hydropathy features for function prediction of membrane proteins, Mol Membr Biol24, 304-312.
  • Paleckova, P., Kontrova, F., Kofronova, O., Bobek, J., Benada, O., Mikulik, K.(2007) Effect of protein kinase inhibitors on protein phosphorylation and germination of aerial spores from Streptomyces coelicolor, Folia Microbiol (Praha)52, 215-222.
  • Paleckova, P., Felsberg, J., Bobek, J., Mikulik, K.(2007) tmRNA abundance in Streptomyces aureofaciens, S. griseus and S. colinus under stress-inducing conditions, Folia Microbiol (Praha)52, 463-470. 

2006

  • J. Vohradsky, and C.J. Thompson, Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions. Proteomics 6 (2006) 785-793.
  • Basler, M., Linhartova, I., Halada, P., Novotna, J., Bezouskova, S., Osicka, R., Weiser, J., Vohradsky, J. and Sebo, P. (2006) The iron-regulated transcriptome and proteome of Neisseria meningitidis serogroup C, Proteomics6, 6194-6206.
  • Palečková, P., Bobek, J., Felsberg, J., Mikulík,K. (2006) Activity of translation system and abundance of tmRNA during development of Streptomyces aureofaciens producing tetracyclin, Foila Microbiol. 51 (6), 517-524. 

2005

  • Nováková L, Sasková L, Pallová P, Janecek J, Novotná J, Ulrych A, Echenique J, Trombe MC, Branny P: Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substrates, FEBS Journal 272, 1243-1254 (2005).
  • Nguyen LD, Kalachová L, Novotná J, Holub M, Kofro?ová O, Benada O, Thompson CJ, Weiser J: A cultivation system using glass beads immersed in a liquid medium facilitates studies of Streptomyces differentiation, Applied and Environmental Microbiology 71, 2848-2852 (2005).
  • Panek J, Eidhammer I and Aasland R: A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins. Proteins: Structure, Function, and Bioinformatics. Published online 11 Jan 2005

2004

  • J. Bobek, P. Halada, J. Angelis, J. Vohradsky, and K. Mikulik, Activation and expression of proteins during synchronous germination of aerial spores of Streptomyces granaticolori. Proteomics 4 (2004) 3864-3880

2003

  • Vohradsky J, Janda I, Grünenfelder B, Berndt P, Röder D, Langen H, Weiser J and Jenal U: Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server. Proteomics. 3, 1874-1882, 2003.
  • Novotna JVohradsky J, Berndt P, Gramajo H, Langen H, Li XM, Minas W, Orsaria L, Röder D and Thompson CJ: Proteomic studies of diauxic lag in the differentiating prokaryoteStreptomyces coelicolor reveal a regulatory network of stress-induced proteins and central metabolic enzymes. Molecular Microbiology. 48: 1289-1303, 2003.

2002

  • Vu TT and Vohradsky J: Genexp - a genetic network simulation environment. Bioinformatics. 18: 1400-1401, 2002.
  • Tucková L, Novotná J, Novák P, Flegelová Z, Kveton T, Jelínková L, Zídek Z, Man P, Tlaskalová-Hogenová H: Activation of macrophages by gliadin fragments: isolation and characterization of active peptide, Journal of Leukocyte Biology 71, 625-631(2002).
  • Mikulik K, Bobek J, Bezouskova S, Benada O, Kofronova O. Expression of proteins and protein kinase activity during germination of aerial spores of Streptomyces granaticolor. Biochem Biophys Res Commun. 2002 Nov 29;299(2):335-342.

2001

  • Li XM, Novotna JVohradsky J and Weiser J: Major proteins related to chlortetracycline biosynthesis in a Streptomyces aureofaciens production strain studied by quantitative proteomics.Applied Microbiology and Biotechnology. 57: 717-724, 2001.
  • Vohradsky J: Neural model of the genetic network. Journal of Biological Chemistry. 276: 36168-36173, 2001.
  • Vohradsky J and Ramsden JJ: Genome resource utilization during prokaryotic development. FASEB Journal. 15: 2054-2056, 2001.
  • Grünenfelder B, Rummel G, Vohradsky J, Röder D, Langen H and Jenal U: Proteomic analysis of the bacterial cell cycle. Proceedings of the National Academy of Sciences of the United States of America. 98: 4681-4686, 2001.
  • Vohradsky J: Neural network model of gene expression. FASEB Journal. 15: 846-854, 2001.
  • Mikulik K, Suchan P, Bobek J. Changes in ribosome function induced by protein kinase associated with ribosomes of Streptomyces collinus producing kirromycin.Biochem Biophys Res Commun. 2001 Nov 30;289(2):434-443.

2000

  • Bobek J, Hercik K, Dobrova Z, Branny P, Nadvornik R, Janecek J. Evidence for phosphoprotein phosphatase in Streptomyces granaticolor. Folia Microbiol (Praha). 2000;45(4):310-312.
  • Vohradsky J, Li XM, Dale G, Folcher M, Nguyen L, Viollier PH and Thompson CJ: Developmental control of stress stimulons in Streptomyces coelicolor revealed by statistical analyses of global gene expression patterns. Journal of Bacteriology. 182: 4979 4986, 2000.

1999

  • Panek J and Vohradsky J: Point pattern matching in the analysis of two-dimensional gel electropherograms. Electrophoresis. 20: 3483-3491, 1999.
  • Chiu ML, Folcher M, Katoh T, Puglia AM, Vohradsky J, Yun BS, Seto H and Thompson CJ: Broad spectrum thiopeptide recognition specificity of the Streptomyces lividans TipAL protein and its role in regulating gene expression. Journal of Biological Chemistry. 274: 20578-20586, 1999.

1998

  • Ramsden JJ and Vohradsky J: Zipf-like behavior in procaryotic protein expression. Physical Review E. 58: 7777-7780, 1998.
  • Hlavacek O, Adamec J, Vomastek T, Babkova L, Sedlak M, Vohradsky J, Vachova L and Chaloupka J: Expression of dnaK and groESL operons during sporulation of Bacillus megateriumFEMS Microbiology Letters. 165: 181-186, 1998.

1997

  • Vohradsky J: Adaptive classification of two-dimensional gel electrophoretic spot patterns by neural networks and cluster analysis. Electrophoresis. 18: 2749-2754, 1997.
  • Vohradsky J, Li XM and Thompson CJ: Identification of procaryotic developmental stages by statistical analyses of two-dimensional gel patterns. Electrophoresis. 18: 1418 1428, 1997.
  • Panek J and Vohradsky J: Object-oriented developmental environment for image-analysis applications: Implementation for 2D gel electrophoretogram analysis. Computer Applications in the Biosciences. 13: 257-262, 1997.
  • Nesvera J, Patek M, Hochmannova J, Abrhamova Z, Becvarova V, Jelinkova M and Vohradsky J: Plasmid pGA1 from Corynebacterium glutamicum codes for a gene product that positively influences plasmid copy number. Journal of Bacteriology. 179: 1525-1532, 1997.
  • Nesvera J, Abrhamova Z, Patek M, Hochmanova J and Vohradsky J: A positively acting element is involved in regulation of copy number of the plasmid pGA1 from Corynebacterium glutamicumPlasmid. 37: 225, 1997.

1995

  • Puglia AM, Vohradsky J and Thompson CJ: Developmental control of the heat-shock stress regulon in Streptomyces coelicolor. Molecular Microbiology. 17: 737-746, 1995.
  • Nguyen LT, Nguyen KT, Kopecký J, Nová P, Novotná J and B?hal V: Purification and characterization of a novel valine dehydrogenase from Streptomyces aureofaciens. Biochemica et Biophysica Acta 1251, 186-190 (1995).
  • Novotna J, Li XM, Novotna J, Vohradsky J and Weiser J: Protein profiles of Streptomyces aureofaciens producing tetracyclines - Reappraisal of the effect of benzyl thiocyanate. Current Microbiology. 31: 84-91, 1995.

1994

  • Li XM, Vohradsky J and Weiser J: The use of protein-synthesis elongation-factor EF-Tu as internal calibration standard in 2-dimensional electrophoretic studies of differentiation in Streptomyces. Electrophoresis. 15: 1198-1204, 1994.

1993

  • Sedlak M, Vinter V, Adamec J, Vohradsky J, Voburka Z and Chaloupka J: Heat-shock applied early in sporulation affects heat-resistance of Bacillus megaterium spores. Journal of Bacteriology. 175: 8049-8052, 1993.
  • Vohradsky J and Panek J: Quantitative-analysis of gel electrophoretograms by image-analysis and least-squares modeling. Electrophoresis. 14: 601-612, 1993.

1992

  • Štastná J, Goodfellow M, Krištufek V,Novotná J, Jizba J, Cáslavská J, Kofronová O, Blumauerová M: Taxonomic and chemical studies on a variant of Streptomyces globisporus forming endospores in submerged cultures. Folia Microbiologica 37, 111-116 (1992).
  • Vohradsky J, Janda I and Weiser J: Procedure for quantitative analysis of gel electrophoresis densitograms. Methods in Molecular and Cellular Biology. 3: 6-14, 1992.

1990

  • Vohradsky J and Sovova H: Measurement of local velocities of drops in a liquid-liquid-extraction vibrating plate column. Chemical Engineering Science. 45: 3563-3570, 1990.
  • Hoštálek Z, Novotná J, Starý V, Kalachová L, Voríšek J: Subcellular organization of Streptomyces aureofaciens and overproduction of chlortetracycline. Biotechnology Advances 8, 131-139 (1990).
  • Vohradsky J, Maresova H, Vecerek B and Kyslik P: Determination of plasmid copy number in continuous culture by fluorescence densitometry and image analysis. Methods in Molecular and Cellular Biology. 1: 223-233, 1990.

1989

  • Novotná J, Neužil J, Hoš?álek Z: Spectrophotometric identification of 8-hydroxy-5-deazaflavin: NADPH oxidoreductase activity in streptomycetes producing tetracyclines. FEMS Microbiological Letters 59, 241-246 (1989)
  • Weiser J, Morava P and Vohradsky J: Content, distribution and stability of protein-synthesis elongation-factor Tu in subcellular-fractions of vegetative cells and spores of Streptomyces aureofaciensFEMS Microbiology Letters. 65: 11-15, 1989.
  • Neužil J, Novotná J, Behal V, Hoštálek Z: A direct-injection reversed-phase liquid chromatographic micromethod for studying the kinetics of terminal reactions of tetracycline biosynthesis. Analytical Biochemistry 181, 125-129 (1989).

1988

  • Neužil J, Novotná J, Vancurová, Behal V, Hoštálek Z: High-performance liquid chromatography of derivatives involved in the terminal steps of tetracycline biosynthesis in Streptomyces aureofaciens. Journal of Liquid Chromatography 11, 2789-2800 (1988).
  • Neužil J, Novotná J, Erban V, B?hal V, Hoš?álek Z: Glucose-6-phosphate dehydrogenase from a tetracycline producing strain Streptomyces aureofaciens: some properties and regulatory aspects of the enzyme. Biochemistry International 17, 187-196 (1988).
  • Vancurová I, Volc J, Flieger M, Neužil J, Novotná J, Vlach J, Behal V: Isolation of pure anhydrotetracycline oxygenase from Streptomyces aureofaciens. Biochemical Journal 253, 263-267 (1988).

1987

  • Vancurová I, Flieger M, Volc J, Beneš MJ, Novotná J, Neužil J, B?hal V: Partial purification and characterization of anhydrotetracycline oxygenase of Streptomyces aureofaciens. Journal of Basic Microbiology 9, 529-533 (1987).
  • Erban V, Trilisenko LV, Novotná J, Behal V, Kulaev IS, Hoš?álek Z: Subcellular localization of enzymes in Streptomyces aureofaciens and its alteration by benzylthiocyanate. II. Anhydrotetracycline oxygenase and glucose-6-phosphate dehydrogenase. Folia Microbiologica 32, 411-416 (1987).
  • Trilisenko LV, Novotná J, Erban V, Behal V, Hoš?álek Z, Kulaev IS: Subcellular localization of enzymes in Streptomyces aureofaciens and its alteration by benzyl thiocyanate. I. Phosphatases and ATP-glucokinase. Folia Microbiologica 32, 402-410 (1987).

1986

  • Neužil J, Novotná J, Behal V, Hoštálek Z: Inhibition studies of glucose-6-phosphate dehydrogenase from tetracycline-producing Streptomyces aureofaciens. Biotechnology and Applied Biochemistry 8, 375-378 (1986).

1985

  • Novotná J, Hoštálek Z: Phosphorylation of hexoses in Streptomyces aureofaciens: evidence that the phosphoenolpyruvate:sugar phosphotransferase system is not operative. FEMS Microbiological Letters 28, 347-350 (1985).

1983

  • Erban V, Novotná J, Behal V, Hoštálek Z: Growth rate, sugar consumption, chlortetracycline production and anhydrotetracycline oxygenase activity in Streptomyces aureofaciens. Folia Microbiologica 28, 262-267 (1983).

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