Julio Vera

Summary

Affiliation: University of Rostock
Country: Germany

Publications

  1. doi request reprint MicroRNA-regulated networks: the perfect storm for classical molecular biology, the ideal scenario for systems biology
    Julio Vera
    Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
    Adv Exp Med Biol 774:55-76. 2013
  2. doi request reprint Systems biology of JAK-STAT signalling in human malignancies
    Julio Vera
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
    Prog Biophys Mol Biol 106:426-34. 2011
  3. doi request reprint Dynamical effects of epigenetic silencing of 14-3-3sigma expression
    Julio Vera
    Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, 18051 Rostock, Germany
    Mol Biosyst 6:264-73. 2010
  4. ncbi request reprint Exploration of homodimer receptor: homodimer protein interactions
    Julio Vera
    Group of Systems Biology and Bioinformatics, Department of Computer Science, University of Rostock, 18051 Rostock, Germany
    Int J Bioinform Res Appl 5:447-57. 2009
  5. doi request reprint Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network
    Julio Vera
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock
    Cancer Res 73:3511-24. 2013
  6. pmc Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs
    Xin Lai
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
    Nucleic Acids Res 40:8818-34. 2012
  7. doi request reprint Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic
    Faiz M Khan
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany
    Biochim Biophys Acta 1844:289-98. 2014
  8. pmc 14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence
    Julia Schultz
    Department of Cardiac Surgery, University of Rostock, Rostock, Germany
    Mol Cancer 8:53. 2009
  9. pmc A Systems' Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks
    Xin Lai
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany Laboratory of Systems Tumor Immunology, Department of Dermatology, Faculty of Medicine, University of Erlangen Nuremberg, Ulmenweg 18, 91054 Erlangen, Germany
    Biomed Res Int 2013:703849. 2013
  10. doi request reprint Modeling miRNA regulation in cancer signaling systems: miR-34a regulation of the p53/Sirt1 signaling module
    Xin Lai
    Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany
    Methods Mol Biol 880:87-108. 2012

Detail Information

Publications23

  1. doi request reprint MicroRNA-regulated networks: the perfect storm for classical molecular biology, the ideal scenario for systems biology
    Julio Vera
    Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
    Adv Exp Med Biol 774:55-76. 2013
    ....
  2. doi request reprint Systems biology of JAK-STAT signalling in human malignancies
    Julio Vera
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
    Prog Biophys Mol Biol 106:426-34. 2011
    ..We describe the modelling workflow that realises a systems biology approach and give an example for interferon-γ signalling in pancreatic stellate cells...
  3. doi request reprint Dynamical effects of epigenetic silencing of 14-3-3sigma expression
    Julio Vera
    Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, 18051 Rostock, Germany
    Mol Biosyst 6:264-73. 2010
    ....
  4. ncbi request reprint Exploration of homodimer receptor: homodimer protein interactions
    Julio Vera
    Group of Systems Biology and Bioinformatics, Department of Computer Science, University of Rostock, 18051 Rostock, Germany
    Int J Bioinform Res Appl 5:447-57. 2009
    ..Finally, we found a prevalence of homodimer-homodimer interactions in signalling systems in human cells...
  5. doi request reprint Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network
    Julio Vera
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock
    Cancer Res 73:3511-24. 2013
    ....
  6. pmc Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs
    Xin Lai
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
    Nucleic Acids Res 40:8818-34. 2012
    ..In addition, we find that high abundance of miRNAs, in combination with cooperativity, can enhance noise buffering for the transcription of target hubs...
  7. doi request reprint Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic
    Faiz M Khan
    Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock, Germany
    Biochim Biophys Acta 1844:289-98. 2014
    ..This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications. Guest Editor: Yudong Cai. ..
  8. pmc 14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence
    Julia Schultz
    Department of Cardiac Surgery, University of Rostock, Rostock, Germany
    Mol Cancer 8:53. 2009
    ..The 14-3-3sigma isoform acts as a tumor suppressor and is often inactivated during tumor development...
  9. pmc A Systems' Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks
    Xin Lai
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany Laboratory of Systems Tumor Immunology, Department of Dermatology, Faculty of Medicine, University of Erlangen Nuremberg, Ulmenweg 18, 91054 Erlangen, Germany
    Biomed Res Int 2013:703849. 2013
    ..Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts. ..
  10. doi request reprint Modeling miRNA regulation in cancer signaling systems: miR-34a regulation of the p53/Sirt1 signaling module
    Xin Lai
    Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany
    Methods Mol Biol 880:87-108. 2012
    ....
  11. pmc Dynamics of receptor and protein transducer homodimerisation
    Julio Vera
    University of Rostock, Rostock, Germany
    BMC Syst Biol 2:92. 2008
    ..Several authors have suggested in recent times that dimerisation relates to a series of physical and biological outcomes used by the cell in the regulation of signal transduction...
  12. doi request reprint A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis
    Xin Lai
    Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, 18051 Rostock, Germany
    Comput Biol Chem 33:312-24. 2009
    ....
  13. doi request reprint A system biology approach to understand functional activity of cell communication systems
    Julio Vera
    Department of Computer Science, University of Rostock, 18051 Rostock, Germany
    Methods Cell Biol 90:399-415. 2008
    ..We, furthermore, show the use of such a methodology in a case study, analyzing receptor and transcription factor modulation affecting the responsiveness of the JAK2/STAT5 pathway...
  14. doi request reprint Computational analysis and modeling the effectiveness of 'Zanamivir' targeting neuraminidase protein in pandemic H1N1 strains
    Shailendra K Gupta
    Department of Bioinformatics, Indian Institute of Toxicology Research, CSIR, Lucknow, India
    Infect Genet Evol 11:1072-82. 2011
    ..To further evaluate the effectiveness of the antiviral drugs, we derived, calibrated and analyzed an ordinary differential equations based mathematical model for H1N1 infection dynamics and drug mediated virus deactivation...
  15. pmc Non-coding RNA detection methods combined to improve usability, reproducibility and precision
    Peter Raasch
    Systems Biology and Bioinformatics Group, University of Rostock, Rostock, Germany
    BMC Bioinformatics 11:491. 2010
    ..Also, for genomic scans they often need to be incorporated in detection workflows using custom scripts, which decreases transparency and reproducibility...
  16. doi request reprint Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models
    Julio Vera
    Systems Biology and Bioinformatics Group, University of Rostock, 18051 Rostock, Germany
    Mol Biosyst 6:2174-91. 2010
    ..This later result suggests that dynamic modulation of signal inhibitors during stimulation may be a regulatory mechanism in ERK signalling and other pathways...
  17. pmc Systems biologists seek fuller integration of systems biology approaches in new cancer research programs
    Olaf Wolkenhauer
    University of Rostock, Rostock, Germany
    Cancer Res 70:12-3. 2010
    ....
  18. pmc A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway
    Julio Vera
    Systems Biology and Bioinformatics Group, Department of Computer Science, University of Rostock, Rostock, Germany
    BMC Syst Biol 2:38. 2008
    ..Despite of the apparent importance of signal amplification, there have been few attempts to formalise this concept...
  19. doi request reprint Tumors as chaotic attractors
    Svetoslav Nikolov
    Department of Systems Biology and Bioinformatics, Institute for Informatics, University of Rostock, 18051 Rostock, Germany
    Mol Biosyst 10:172-9. 2013
    ....
  20. doi request reprint Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach
    Daniel V Guebel
    Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany
    Mol Biosyst 8:1230-42. 2012
    ..Other model predictions include expected levels of the nuclear complex β-catenin_TCF4 and the anti-apoptotic protein Survivin for both normal and tumorigenic colonic stem cells...
  21. ncbi request reprint Detection of potential enzyme targets by metabolic modelling and optimization: application to a simple enzymopathy
    Julio Vera
    Systems Biology and Bioinformatics Group, University of Rostock, Albert Einstein Street 21, 18051, Germany
    Bioinformatics 23:2281-9. 2007
    ..Each solution consists of a set of predicted values for metabolites, initial substrates and enzyme activities, which describe a biologically acceptable steady state of the system that shifts the pathologic state towards a healthy state...
  22. ncbi request reprint PLMaddon: a power-law module for the Matlab SBToolbox
    Julio Vera
    Systems Biology and Bioinformatics Group, Department of Computer Science University of Rostock, 18051 Rostock, Germany
    Bioinformatics 23:2638-40. 2007
    ..g. Michaelis-Menten type models), as well as algorithms to estimate steady-states. The robustness and sensitivity of the models can also be analysed and visualized by computing the power-law's logarithmic gains and sensitivities...
  23. ncbi request reprint Power-law models of signal transduction pathways
    Julio Vera
    Systems Biology and Bioinformatics Group, Department of Computer Sciences, University of Rostock, 18051 Rostock, Germany
    Cell Signal 19:1531-41. 2007
    ..In particular, the investigation on the effects of signal inhibition and feedback loops and the validation of structural hypotheses are discussed...