Alexei Vazquez

Summary

Affiliation: Institute for Advanced Study
Country: USA

Publications

  1. pmc Genome-wide associations of signaling pathways in glioblastoma multiforme
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Med Genomics 6:11. 2013
  2. ncbi Epidemic outbreaks on structured populations
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute for Advanced Study, Einstein Dr, Princeton, NJ 08540, USA
    J Theor Biol 245:125-9. 2007
  3. pmc Impact of the solvent capacity constraint on E. coli metabolism
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
    BMC Syst Biol 2:7. 2008
  4. pmc Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
    PLoS Comput Biol 4:e1000195. 2008
  5. doi Quality control methodology for high-throughput protein-protein interaction screening
    Alexei Vazquez
    Department of Radiation Oncology, The Cancer Institute of New Jersey and UMDNJ Robert Wood Johnson Medical School, New Brunswick, NJ, USA
    Methods Mol Biol 781:279-94. 2011
  6. pmc Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology
    Alexei Vazquez
    Department of Radiation Oncology, Robert Wood Johnson Medical School and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey, United States of America
    PLoS ONE 6:e19538. 2011
  7. doi A genetic variant in a PP2A regulatory subunit encoded by the PPP2R2B gene associates with altered breast cancer risk and recurrence
    Alexei Vazquez
    Department of Radiation Oncology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ, USA
    Int J Cancer 128:2335-43. 2011
  8. pmc Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation
    Alexei Vazquez
    Division of Bioinformatics and Surveillance, Department of Radiation Oncology, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
    PLoS ONE 6:e25881. 2011
  9. pmc Optimization of personalized therapies for anticancer treatment
    Alexei Vazquez
    Department of Radiation Oncology and Center for Systems Biology, The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 195 Little Albany St, New Brunswick, NJ 08903, USA
    BMC Syst Biol 7:31. 2013
  10. doi Overexpression of the mitochondrial folate and glycine-serine pathway: a new determinant of methotrexate selectivity in tumors
    Alexei Vazquez
    Center for Systems Biology and Department of Radiation Oncology, Graduate School of Biomedical Sciences, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey, USA
    Cancer Res 73:478-82. 2013

Collaborators

Detail Information

Publications24

  1. pmc Genome-wide associations of signaling pathways in glioblastoma multiforme
    Stefan Wuchty
    National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    BMC Med Genomics 6:11. 2013
    ..However, genes mediate their biological roles in groups rather than in isolation, prompting us to extend the concept of eQTLs to whole gene pathways...
  2. ncbi Epidemic outbreaks on structured populations
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute for Advanced Study, Einstein Dr, Princeton, NJ 08540, USA
    J Theor Biol 245:125-9. 2007
    ..Finally, I present empirical data for the AIDS epidemics supporting the model predictions...
  3. pmc Impact of the solvent capacity constraint on E. coli metabolism
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
    BMC Syst Biol 2:7. 2008
    ..Molecular crowding in a cell's cytoplasm is one such potential constraint, as it limits the solvent capacity available to metabolic enzymes...
  4. pmc Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
    PLoS Comput Biol 4:e1000195. 2008
    ..cerevisiae at physiological growth conditions, and that a full kinetic model together with the limited solvent capacity constraint can be used to predict both metabolite concentrations and enzyme activities in vivo...
  5. doi Quality control methodology for high-throughput protein-protein interaction screening
    Alexei Vazquez
    Department of Radiation Oncology, The Cancer Institute of New Jersey and UMDNJ Robert Wood Johnson Medical School, New Brunswick, NJ, USA
    Methods Mol Biol 781:279-94. 2011
    ..In this chapter, we discuss experimental and statistical methodologies to quantify error rates in high-throughput protein-protein interactions screens...
  6. pmc Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology
    Alexei Vazquez
    Department of Radiation Oncology, Robert Wood Johnson Medical School and The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey, United States of America
    PLoS ONE 6:e19538. 2011
    ..Addition of this constraint to metabolic flux balance models can explain several observations of mammalian cell metabolism under steady state conditions...
  7. doi A genetic variant in a PP2A regulatory subunit encoded by the PPP2R2B gene associates with altered breast cancer risk and recurrence
    Alexei Vazquez
    Department of Radiation Oncology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ, USA
    Int J Cancer 128:2335-43. 2011
    ..Taken together these results indicate that the A variant of the rs319217 SNP is a marker of better prognosis in breast cancer...
  8. pmc Serine biosynthesis with one carbon catabolism and the glycine cleavage system represents a novel pathway for ATP generation
    Alexei Vazquez
    Division of Bioinformatics and Surveillance, Department of Radiation Oncology, The Cancer Institute of New Jersey and University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, United States of America
    PLoS ONE 6:e25881. 2011
    ....
  9. pmc Optimization of personalized therapies for anticancer treatment
    Alexei Vazquez
    Department of Radiation Oncology and Center for Systems Biology, The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 195 Little Albany St, New Brunswick, NJ 08903, USA
    BMC Syst Biol 7:31. 2013
    ..Given the documented side effects of anticancer drugs, it is clear that such a strategy is unfeasible...
  10. doi Overexpression of the mitochondrial folate and glycine-serine pathway: a new determinant of methotrexate selectivity in tumors
    Alexei Vazquez
    Center for Systems Biology and Department of Radiation Oncology, Graduate School of Biomedical Sciences, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey, USA
    Cancer Res 73:478-82. 2013
    ..We propose that patients whose tumors show this phenotype will be sensitive to folate antagonists targeting thymidylate or purine biosynthesis...
  11. pmc Metabolic states following accumulation of intracellular aggregates: implications for neurodegenerative diseases
    Alexei Vazquez
    Department of Radiation Oncology and Center for Systems Biology, The Cancer Institute of New Jersey, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, New Brunswick, New Jersey, United States of America
    PLoS ONE 8:e63822. 2013
    ..Ultimately this maximum capacity becomes zero when the protein aggregates reach a concentration of about 9.3 mM, predicting the cessation of neuronal activity...
  12. pmc Allele-specific p53 mutant reactivation
    Xin Yu
    The Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
    Cancer Cell 21:614-25. 2012
    ..This activity depends upon the zinc ion chelating properties of the compound as well as redox changes. These data identify NSC319726 as a p53(R175) mutant reactivator and as a lead compound for p53-targeted drug development...
  13. pmc Inference of synergy/antagonism between anticancer drugs from the pooled analysis of clinical trials
    Wenfeng Kang
    Department of Radiation Oncology and Center for Systems Biology, The Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
    BMC Med Res Methodol 13:77. 2013
    ..In some instances these interactions can be anticipated based on pre-clinical models. However, the anticipation of drug interactions in the clinical context is in general a challenging task...
  14. pmc Molecular classification of prostate cancer using curated expression signatures
    Elke K Markert
    Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA
    Proc Natl Acad Sci U S A 108:21276-81. 2011
    ..This classification is independent of Gleason score and therefore provides useful unique molecular profiles for prostate cancer prognosis, helping to predict poor outcome in patients with low or average Gleason scores...
  15. pmc Polymorphic variants in TSC1 and TSC2 and their association with breast cancer phenotypes
    Madhura S Mehta
    Department of Medicine, Division of Medical Oncology, The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
    Breast Cancer Res Treat 125:861-8. 2011
    ....
  16. pmc Catabolic efficiency of aerobic glycolysis: the Warburg effect revisited
    Alexei Vazquez
    Department of Radiation Oncology, The Cancer Institute of New Jersey and UMDNJ Robert Wood Johnson Medical School, New Brunswick, NJ 08963, USA
    BMC Syst Biol 4:58. 2010
    ..The maintenance of this mixed metabolic phenotype is seemingly counterintuitive given that aerobic glycolysis is far less efficient in terms of ATP yield per moles of glucose than mitochondrial respiration...
  17. doi Higher order Boolean networks as models of cell state dynamics
    Elke K Markert
    Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Dr, Princeton, NJ 08540, USA
    J Theor Biol 264:945-51. 2010
    ..Finally, we illustrate how the model can be expanded considering higher levels and higher order dynamics...
  18. doi A polymorphic variant in human MDM4 associates with accelerated age of onset of estrogen receptor negative breast cancer
    Diptee A Kulkarni
    Department of Medicine Division of Medical Oncology, The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA
    Carcinogenesis 30:1910-5. 2009
    ..2 years (P = 7 x 10(-5)) earlier than CC carriers in cohorts 1 and 2, respectively. No association was seen in ER-positive ductal cancers suggesting that the SNP in MDM4 only has a functional association in ER-negative breast cancer...
  19. doi Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects
    Alexei Vazquez
    Department of Radiation Oncology, The Cancer Institute of New Jersey and UMDNJ Robert Wood Johnson Medical School, 195 Little Albany St, New Brunswick, NJ 08903, USA
    J Theor Biol 264:356-9. 2010
    ..More important, the predicted optimal density is in the range of the experimentally determined density of Escherichia coli...
  20. ncbi Impact of non-Poissonian activity patterns on spreading processes
    Alexei Vazquez
    The Simons Center for Systems Biology, Institute of Advanced Study, Einstein Drive, Princeton, New Jersey 08540, USA
    Phys Rev Lett 98:158702. 2007
    ....
  21. doi Chemosensitivity profiles identify polymorphisms in the p53 network genes 14-3-3tau and CD44 that affect sarcoma incidence and survival
    Alexei Vazquez
    The Institute for Advanced Study, Princeton, New Jersey, USA
    Cancer Res 70:172-80. 2010
    ..89 relative risk, P=0.011) and an earlier age of diagnosis (up to 10.7 years earlier, P=0.002). Our findings define genetic markers in 14-3-3tau and CD44 that might improve the treatment and prognosis of soft-tissue sarcomas...
  22. pmc Fine-scale detection of population-specific linkage disequilibrium using haplotype entropy in the human genome
    Hideaki Mizuno
    The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA
    BMC Genet 11:27. 2010
    ..Several methods have been proposed to detect linkage disequilibrium (LD), which is indicative of natural selection, from genome-wide profiles of common genetic variations but are designed for large regions...
  23. pmc High-quality binary protein interaction map of the yeast interactome network
    Haiyuan Yu
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 322:104-10. 2008
    ..Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy...
  24. ncbi Global protein function prediction from protein-protein interaction networks
    Alexei Vazquez
    Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
    Nat Biotechnol 21:697-700. 2003
    ..The robustness of the approach is tested in a system containing a high percentage of unclassified proteins and also in cases of deletion and insertion of specific protein interactions...