INSTITUTE OF MICROBIOLOGY OF THE CZECH ACADEMY OF SCIENCES

• The SMN complex drives structural changes in human snRNAs to enable snRNP assembly
  • Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat Commun. 2023 Oct 18;14(1):6580. doi: 10.1038/s41467-023-42324-0. PMID: 37852981; PMCID: PMC10584915.
• Retinitis pigmentosa–associated mutations in mouse Prpf8 cause misexpression of circRNAs and degeneration of cerebellar granule cells
  • Krausová, M., Kreplová, M., Banik P., Cvačková, Z., Kubovčiak, J. Modrák, M., Zudová, D., Lindovský, J., Kubik-Zahorodna, A., Pálková, M., Kolář, M., Procházka, J., Sedláček, R., Staněk, D. (2023), Life Science Alliance 6 (6) e202201855; DOI: 10.26508/lsa.202201855  
    

• Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation
  • Vohradský, J. (2022) Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation. Biology 11(12), 1729.
• Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control
  • Wagner, S., Bohlen, J., Herrmannova, A.,  Jelínek, J., Preiss, T., Valášek, L.S. & Teleman, A. A.(2022) Selective footprinting of 40S and 80S ribosome subpopulations (Sel-TCP-seq) to study translation and its control. Nature Protocols 17, 2139–2187.
• Simulation-Based Calibration Checking for Bayesian Computation: The Choice of Test Quantities Shapes Sensitivity
  • Modrák, M., Moon, A. H., and Kim, S., Bürkner, P., Huurre, N., Faltejsková, K., Gelman, A., Vehtari, A. (2022) Simulation-Based Calibration Checking for Bayesian Computation: The Choice of Test Quantities Shapes Sensitivity. Arxiv preprint 2211.02383.
• Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
  • Vaňková Hausnerová, V.,  Marvalová, O., Šiková, M. Shoman, M., Havelková, J., Kambová, M., Janoušková, M., Kumar, D., Halada, P., Schwarz, M., Krásný, L., Hnilicová, J., Pánek, J. (2022) Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search. Frontiers in Microbiology 13:848536.
• Clinical prediction models for mortality in patients with covid-19: external validation and individual participant data meta-analysis
  • de Jong, V.M.T, Rousset, R. Z., Antonio-Villa, N.E., ... , Modrak, M., ... , Debray, T.P.A. (2022) Clinical prediction models for mortality in patients with covid-19: external validation and individual participant data meta-analysis. BMJ 378:e069881.
• Nicotinic Acetylcholine Receptors Expressed by Striatal Interneurons Inhibit Striatal Activity and Control Striatal-Dependent Behaviors
  • Abbondanza, A., Ribeiro Bas, I., Modrak, M., Capek, M., Minich, J., Tyshkevich, A., Naser, S., Rangotis, R., Houdek, P., Sumova, A., Dumas, S., Bernard, V., and Janickova, H. (2022) Nicotinic Acetylcholine Receptors Expressed by Striatal Interneurons Inhibit Striatal Activity and Control Striatal-Dependent Behaviors Journal of Neuroscience 42 (13), pp. 2786-2803
    

• Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
  • Waterhouse, R.M., Adam-Blondon, A.F., Agosti D., et al., Vohradsky, J., Nunes-Jorge, A., Willassen, N. P. , Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR . F1000Research 2021, 10(ELIXIR):1238
• Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy
  • Schierova, D.; Roubalova, R.; Kolar, M.; Stehlikova, Z.; Rob, F.; Jackova, Z.; Coufal, S.; Thon, T.; Mihula, M.; Modrak, M.; Kverka, M.; Bajer, L.; Kostovcikova, K.; Drastich, P.; Hercogova, J.; Novakova, M.; Vasatko, M.; Lukas, M.; Tlaskalova-Hogenova, H.; Jiraskova Zakostelska, Z. (2021) Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy. Cells 2021, 10, 3188
• Disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic in March–October 2020: An exploratory analysis
  • Modrák, M, Bürkner, P-C, Sieger, T, Slisz, T, Vašáková, M, Mesežnikov, G, et al. (2021) Disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic in March–October 2020: An exploratory analysis. PLoS ONE 16(10): e0245103
• Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression
  • Mangiola, S., McCoy, P., Modrak, M. et al. (2021) Transcriptome sequencing and multi-plex imaging of prostate cancer microenvironment reveals a dominant role for monocytic cells in progression. BMC Cancer 21, 846.
• Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth
  • Vohradský, J., Schwarz, M., Ramaniuk, O., Ruiz-Larrabeiti, O., Vaňková Hausnerová V., Šanderová, H., Krásný, L. (2021) Kinetic Modeling and Meta-Analysis of the Bacillus subtilis SigB Regulon during Spore Germination and Outgrowth. Microorganisms, 9 (1), 112.
• LinX: A Software Tool for Uncommon Cross-Linking Chemistry
  • Kukačka, Z., Rosůlek, M., Jelínek J., Slavata, L., Kavan, D., Novák, P. (2021) LinX: A Software Tool for Uncommon Cross-Linking Chemistry, Journal of Proteome Research, 20 (4), pp. 2021-2027.
• Probabilistic outlier identification for RNA sequencing generalized linear models
  • Mangiola, S., Thomas, E. A., Modrák, M.,, Vehtari, A., Papenfuss, A. T. (2021) Probabilistic outlier identification for RNA sequencing generalized linear models, NAR Genomics and Bioinformatics, lqab005
• rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output
  • Schwarz, M, Vohradský, J., Pánek, J. (2021) rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output, Bioinformatics, btab073

• Bayesian Workflow
  • Gelman, A., Vehtari, A., Simpson, D., Margossian, C. C., Carpenter, B., Yao, Y., Kennedy, L., Gabry, J., Bürkner, P.-C., Modrák, M. (2020). Bayesian Workflow, Arxiv preprint 2011.01808
• Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature
  • Carneiro, C.F.D., Queiroz, V.G.S., Moulin, T.C., ... Modrák, M., et al. (2020) Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature. Res Integr Peer Rev 5.
• Bacterial nanotubes as a manifestation of cell death
  • Pospíšil, J., Vítovská, D., Kofroňová, O., Muchová, K., Šanderová, H., Hubálek, M., Šiková, M., Modrák, M., Benada, O., Barák, I., Krásný, L. (2020). Bacterial nanotubes as a manifestation of cell death. Nat Commun 11, 4963.
• MicroRNA dilution during oocyte growth disables the microRNA pathway in mammalian oocytes
  • Kataruka, S, Modrak, M., Kinterova, V., Malik, R., Zeitler, D. M., Horvat, F., Kanka, J., Meister, G., Svoboda, P. (2020). MicroRNA dilution during oocyte growth disables the microRNA pathway in mammalian oocytes. Nucleic Acids Research, gkaa543
• A Comparison of Protein and mRNA Expression during Development of the Soil Dwelling Prokaryote (S. coelicolor )
  • Pospíšil, J., Strunin, D., Ziková, A., Hubálek, M., Vohradský, J. (2020). A Comparison of Protein and mRNA Expression during Development of the Soil Dwelling Prokaryote (S. coelicolor). Proteomics, Early view.
• rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output
  • Schwarz, M., Vohradský, J., Modrák, M. and Pánek, J., (2020). rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output. Frontiers in Genetics, 11, p.675.

• Meta-analysis of genotype-phenotype associations in Bardet-Biedl Syndrome uncovers differences among causative genes
  • Niederlová, V., Modrák, M., Tsyklauri, O., Huranová, M. & Štěpánek, O. (2019). Meta-analysis of genotype-phenotype associations in Bardet-Biedl Syndrome uncovers differences among causative genes. Human Mutation, 40 (11), pp. 2068-2087.
  • Supplementary Figures, Supplementary Tables, Supplementary Statistical Analysis
  • Publisher Version (Paywalled)
• rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots
  • Jelínek, J., Hoksza, D., Hajič, J., Pešek, J., Drozen, J., Hladík, T., Klimpera, M., Vohradský, J. & Pánek, J. (2019) rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. Database, baz047

• DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
  • Šmídová, K., Ziková, A., Pospíšil, J., Schwarz, M., Bobek, J., & Vohradský, J. (2018). DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor. Nucleic acids research, 47(2), 621-633.

• σ^I from Bacillus subtilis: Impact on Gene Expression and Characterization of σ^I-Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements
  • Ramaniuk, O., Převorovský, M., Pospíšil, J., Vítovská, D., Kofroňová, O., Benada, O., Schwarz, M., Šanderová, H., Hnilicová, J., Krásný, L. (2018). σ^I from Bacillus subtilis: Impact on Gene Expression and Characterization of σ^I-Dependent Transcription That Requires New Types of Promoters with Extended −35 and −10 Elements. Journal of Bacteriology, 200(17), e00251-18.
    
• cpPredictor: a web server for template-based prediction of RNA secondary structure
  • Jelínek, J., & Pánek, J. (2018). cpPredictor: a web server for template-based prediction of RNA secondary structure. Bioinformatics, bty753.
• The Sm-core mediates the retention of partially-assembled spliceosomal snRNPs in Cajal bodies until their full maturation
  • Roithová, A., Klimešová, K., Pánek, J., Will, C. L., Lührmann, R., Staněk, D., & Girard, C. (2018). The Sm-core mediates the retention of partially-assembled spliceosomal snRNPs in Cajal bodies until their full maturation. Nucleic acids research, 46(7), 3774-3790.
• Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data
  • Modrák, M., & Vohradský, J. (2018). Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data. BMC bioinformatics, 19(1), 137.
• Reparametrizing the Sigmoid Model of Gene Regulation for Bayesian Inference
  • Modrák, M. (2018). Reparametrizing the Sigmoid Model of Gene Regulation for Bayesian Inference. In International Conference on Computational Methods in Systems Biology (pp. 309-312). Springer, Cham.
• ODE model of gene regulation
  • Modrák, M. (2018). ODE model of gene regulation. StanCon Helsinki

• Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth Supplementary material Publisher version
  • Ramaniuk, O., Cerny, M., Krasny, L., Vohradsky, J. (2017) Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth. BBA Gene Regulatory Mechanisms 1860 (8), 894-904
• Does eIF3 promote reinitiation after translation of short upstream ORFs also in mammalian cells?
  • Hronova, V., Mohammad, M. P., Wagner, S., Panek, J., Gunisova, S., Zeman, J.,  Poncova, K., Shivaya Valasek, L. (2017) Does eIF3 promote reinitiation after translation of short upstream ORFs also in mammalian cells? RNA Biology In press.
• An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences
  • Panek, J., Modrak, M., Schwarz, M. (2017) An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences. Frontiers in Genetics (8), 147.
• Lambda phage genetic switch as a system with critical behaviour
  • Vohradsky, J. (2017) Lambda phage genetic switch as a system with critical behaviour. Journal of Theoretical Biology 431, 32 - 38.

• Template-based prediction of RNA tertiary structure
  • R. Galvanek, D. Hoksza and J. Pánek (2016) Template-based prediction of RNA tertiary structure, IEEE International Conference on Bioinformatics and Biomedicine 2016, pp. 1897-1900.
• A systematic computational analysis of the rRNA–3′ UTR sequence complementarity suggests a regulatory mechanism influencing post-termination events in metazoan translation
  • Panek, J., Kolar, M., Herrmannova, A., Shivaya Valasek, L. (2016). A systematic computational analysis of the rRNA–3′ UTR sequence complementarity suggests a regulatory mechanism influencing post-termination events in metazoan translation. RNA 22, 957-967

• Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria
  • Hnilicova J, Jirat Matejckova J, Sikova M, Pospisil J, Halada P, Panek J, Krasny L: Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria. Nucleic Acids Res 2014, 42(18), 11763-11776.
• Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote.
  • Strakova, E., Zikova, A. and Vohradsky, J. (2014) Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote. Nucleic Acids Res 42(2), 748-763.
• Template-Based Prediction of Ribosomal RNA Secondary Structure
  • Josef Pánek, Jan Hajič jr., David Hoksza. Template-Based Prediction of Ribosomal RNA Secondary Structure, 2014 IEEE International Conference on Bioinformatics and Biomedicine, pp. 18-20, IEEE, 2014.
• Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor
  • Bobek, J., Strakova, E., Zikova, A. and Vohradsky,J. (2014) Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor. BMC Genomics 15:1173-
    

• Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination.
  • Strakova, E., Bobek, J., Zikova, A. and Vohradsky, J. (2013) Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination. PLoS One, 8, e72842.
• Systems insight into the spore germination of Streptomyces coelicolor.
  • Strakova, E., Bobek, J., Zikova, A., Rehulka, P., Benada, O., Rehulkova, H., Kofronova, O. and Vohradsky, J. (2013) Systems insight into the spore germination of Streptomyces coelicolor. J Proteome Res, 12, 525-536.
• An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5' UTRs and its implications for eukaryotic gene translation regulation
  • Panek, J., Kolar, M., Vohradsky, J. and Shivaya Valasek, L. (2013) An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5' UTRs and its implications for eukaryotic gene translation regulation. Nucleic Acids Res,41, 7625-7634. 

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 E, Vohradsky 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 J, Panek 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. Proteomics, 8, 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 Genomics, 9, 217.
• To, C.C. and Vohradsky, J. (2008) Supervised inference of gene-regulatory networks. BMC Bioinformatics, 9, 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 Biochem, 311, 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 Genomics, 8, 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 Res, 35, 279-287.
• Panek, J.,Eidhammer, I., Aasland, R.(2007)Using hydropathy features for function prediction of membrane proteins, Mol Membr Biol, 24, 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, Proteomics, 6, 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 J, Vohradsky 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 J, Vohradsky 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 megaterium. FEMS 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 glutamicum. Plasmid. 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 aureofaciens. FEMS 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).