J Vohradsky

Summary

Affiliation: Academy of Sciences of the Czech Republic
Country: Czech Republic

Publications

  1. pmc Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes
    Jiri Vohradsky
    Laboratory of Bioinformatics, Institute of Microbiology ASCR, v v i, Videnska 1083, 14220 Prague, Czech Republic
    Nucleic Acids Res 40:7096-103. 2012
  2. pmc A parallel genetic algorithm for single class pattern classification and its application for gene expression profiling in Streptomyces coelicolor
    Cuong C To
    Laboratory of Bioinformatics, Institute of Microbiology, ASCR, Videnska 1083, 142 20 Prague, Czech Republic
    BMC Genomics 8:49. 2007
  3. pmc Biocomputational prediction of small non-coding RNAs in Streptomyces
    Josef Panek
    Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    BMC Genomics 9:217. 2008
  4. pmc Supervised inference of gene-regulatory networks
    Cuong C To
    Laboratory of Bioinformatics, Institute of Microbiology ASCR, Prague, Czech Republic
    BMC Bioinformatics 9:2. 2008
  5. ncbi request reprint Comparative analysis of gene expression on mRNA and protein level during development of Streptomyces cultures by using singular value decomposition
    Jiri Vohradsky
    Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska, Prague, Czech Republic
    Proteomics 7:3853-66. 2007
  6. pmc Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation
    Jiri Vohradsky
    Institute of Microbiology ASCR vvi, Prague, Czech Republic
    Nucleic Acids Res 38:4579-85. 2010
  7. ncbi request reprint Identification of procaryotic developmental stages by statistical analyses of two-dimensional gel patterns
    J Vohradsky
    Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
    Electrophoresis 18:1418-28. 1997
  8. ncbi request reprint Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions
    Jiri Vohradsky
    Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
    Proteomics 6:785-93. 2006
  9. ncbi request reprint Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server
    Jiri Vohradsky
    Institute of Microbiology, CAS, Prague, Czech Republic
    Proteomics 3:1874-82. 2003
  10. ncbi request reprint Neural model of the genetic network
    J Vohradsky
    Institute of Microbiology CAS, Videnska 1083, 142 20 Prague, Czech Republic
    J Biol Chem 276:36168-73. 2001

Detail Information

Publications14

  1. pmc Stochastic simulation for the inference of transcriptional control network of yeast cyclins genes
    Jiri Vohradsky
    Laboratory of Bioinformatics, Institute of Microbiology ASCR, v v i, Videnska 1083, 14220 Prague, Czech Republic
    Nucleic Acids Res 40:7096-103. 2012
    ..Level of influence of individual regulators in control of the regulated genes is defined. Simulation results indicate particular mechanism of regulatory activity of protein complexes involved in the control of cyclins...
  2. pmc A parallel genetic algorithm for single class pattern classification and its application for gene expression profiling in Streptomyces coelicolor
    Cuong C To
    Laboratory of Bioinformatics, Institute of Microbiology, ASCR, Videnska 1083, 142 20 Prague, Czech Republic
    BMC Genomics 8:49. 2007
    ..Identification of coordinately regulated genes according to the level of their expression during the time course of a process allows for discovering functional relationships among genes involved in the process...
  3. pmc Biocomputational prediction of small non-coding RNAs in Streptomyces
    Josef Panek
    Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
    BMC Genomics 9:217. 2008
    ..This study was based on sequence conservation in intergenic regions of Streptomyces, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs...
  4. pmc Supervised inference of gene-regulatory networks
    Cuong C To
    Laboratory of Bioinformatics, Institute of Microbiology ASCR, Prague, Czech Republic
    BMC Bioinformatics 9:2. 2008
    ..Inference of protein interaction networks from various sources of data has become an important topic of both systems and computational biology. Here we present a supervised approach to identification of gene expression regulatory networks...
  5. ncbi request reprint Comparative analysis of gene expression on mRNA and protein level during development of Streptomyces cultures by using singular value decomposition
    Jiri Vohradsky
    Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska, Prague, Czech Republic
    Proteomics 7:3853-66. 2007
    ....
  6. pmc Numerical modelling of microRNA-mediated mRNA decay identifies novel mechanism of microRNA controlled mRNA downregulation
    Jiri Vohradsky
    Institute of Microbiology ASCR vvi, Prague, Czech Republic
    Nucleic Acids Res 38:4579-85. 2010
    ..Genes associated with this process were identified and parameters of the model for all miRNA-124a affected mRNAs were computed...
  7. ncbi request reprint Identification of procaryotic developmental stages by statistical analyses of two-dimensional gel patterns
    J Vohradsky
    Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
    Electrophoresis 18:1418-28. 1997
    ....
  8. ncbi request reprint Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions
    Jiri Vohradsky
    Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
    Proteomics 6:785-93. 2006
    ..The observation that enzymes representing principal metabolic pathways displayed their own distinctive average kinetic profiles suggested that expression of a "high-flux backbone" may dominate regulation of metabolic flux...
  9. ncbi request reprint Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server
    Jiri Vohradsky
    Institute of Microbiology, CAS, Prague, Czech Republic
    Proteomics 3:1874-82. 2003
    ..In its current state, the SWICZ proteome database provides a platform for the incorporation of new data emerging from extended functional studies on the C. crescentus proteome...
  10. ncbi request reprint Neural model of the genetic network
    J Vohradsky
    Institute of Microbiology CAS, Videnska 1083, 142 20 Prague, Czech Republic
    J Biol Chem 276:36168-73. 2001
    ..Reverse engineering of the biochemical pathways from proteomics and DNA micro array data using the suggested neural network model is discussed...
  11. ncbi request reprint Neural network model of gene expression
    J Vohradsky
    Institute of Microbiology, CAS, 142 20 Prague, Czech Republic
    FASEB J 15:846-54. 2001
    ..Vohradsk√Ĺ, J. Neural network model of gene expression...
  12. doi request reprint Effect of protein degradation on spot M(r) distribution in 2-D gels--a case study of proteolysis during development of Streptomyces coelicolor cultures
    Jiri Vohradsky
    Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
    Proteomics 8:2371-5. 2008
    ..The observations were supported by a numerical model of degradation and its influence on the M(r) distribution. Simple statistics could be used to distinguish between normal and degradative 2-D gel electrophoretic patterns...
  13. ncbi request reprint Adaptive classification of two-dimensional gel electrophoretic spot patterns by neural networks and cluster analysis
    J Vohradsky
    Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
    Electrophoresis 18:2749-54. 1997
    ..Artificially created training sets with added random noise can be used for network training. The analysis was applied on the Streptomyces coelicolor developmental two-dimensional (2-D) gel database...
  14. pmc Plasmid pGA1 from Corynebacterium glutamicum codes for a gene product that positively influences plasmid copy number
    J Nesvera
    Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague
    J Bacteriol 179:1525-32. 1997
    ..The related plasmids pGA1, pSR1, and pNG2 lacking significant homology with any other plasmid seem to be representatives of a new group of plasmids replicating in the rolling-circle mode...