Pavel Skums

Summary

Affiliation: Centers for Disease Control and Prevention
Country: USA

Publications

  1. pmc Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity
    Pavel Skums
    Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333 and
    Proc Natl Acad Sci U S A 112:6653-8. 2015
  2. pmc Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows
    Pavel Skums
    Laboratory of Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, 1600 Clifton Road NE, 30333 Atlanta, GA, USA
    BMC Bioinformatics 14:S2. 2013
  3. doi request reprint Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response
    Pavel Skums
    Division of Viral Hepatitis, Centers of Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA
    In Silico Biol 11:263-9. 2011
  4. pmc Efficient error correction for next-generation sequencing of viral amplicons
    Pavel Skums
    Laboratory of Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
    BMC Bioinformatics 13:S6. 2012
  5. doi request reprint Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling
    Pavel Skums
    Division of Viral Hepatitis, Centers of Disease Control and Prevention, Atlanta, GA, USA, Department of Computer Science, Georgia State University, Atlanta, GA, USA and Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    Bioinformatics 31:682-90. 2015
  6. doi request reprint Reconstructing viral quasispecies from NGS amplicon reads
    Nicholas Mancuso
    Department of Computer Science, Georgia State University, Atlanta, GA, USA
    In Silico Biol 11:237-49. 2011
  7. pmc Intra-host diversity and evolution of hepatitis C virus endemic to Côte d'Ivoire
    Joseph C Forbi
    Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
    J Med Virol 86:765-71. 2014
  8. doi request reprint Nosocomial hepatitis C virus transmission from tampering with injectable anesthetic opioids
    Rikita I Hatia
    Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA
    Hepatology 62:101-10. 2015

Collaborators

Detail Information

Publications8

  1. pmc Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity
    Pavel Skums
    Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA 30333 and
    Proc Natl Acad Sci U S A 112:6653-8. 2015
    ..The proposed mechanism is supported by empirical observations of intrahost HCV evolution. Interference with AC is a potential strategy for interruption and prevention of chronic HCV infection. ..
  2. pmc Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows
    Pavel Skums
    Laboratory of Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, 1600 Clifton Road NE, 30333 Atlanta, GA, USA
    BMC Bioinformatics 14:S2. 2013
    ..Although a few approaches were developed for this task, accurate reconstruction of quasispecies populations remains greatly unresolved...
  3. doi request reprint Numerical detection, measuring and analysis of differential interferon resistance for individual HCV intra-host variants and its influence on the therapy response
    Pavel Skums
    Division of Viral Hepatitis, Centers of Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA
    In Silico Biol 11:263-9. 2011
    ....
  4. pmc Efficient error correction for next-generation sequencing of viral amplicons
    Pavel Skums
    Laboratory of Molecular Epidemiology and Bioinformatics, Division of Viral Hepatitis, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
    BMC Bioinformatics 13:S6. 2012
    ..All these parameters are strongly sequence specific and should be incorporated into the calibration of error-correction algorithms designed for amplicon sequencing...
  5. doi request reprint Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling
    Pavel Skums
    Division of Viral Hepatitis, Centers of Disease Control and Prevention, Atlanta, GA, USA, Department of Computer Science, Georgia State University, Atlanta, GA, USA and Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
    Bioinformatics 31:682-90. 2015
    ..Although a number of pooling strategies for consensus sequencing of DNA samples and detection of SNPs have been proposed, these strategies cannot be applied to sequencing of highly heterogeneous viral populations...
  6. doi request reprint Reconstructing viral quasispecies from NGS amplicon reads
    Nicholas Mancuso
    Department of Computer Science, Georgia State University, Atlanta, GA, USA
    In Silico Biol 11:237-49. 2011
    ..All algorithms have been implemented and made available at https://bitbucket.org/nmancuso/bioa/...
  7. pmc Intra-host diversity and evolution of hepatitis C virus endemic to Côte d'Ivoire
    Joseph C Forbi
    Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
    J Med Virol 86:765-71. 2014
    ..Collectively, the results indicate a complex HCV evolution in Côte d'Ivoire, similar to the rest of West Africa, and suggest a unique HCV epidemic history in the country...
  8. doi request reprint Nosocomial hepatitis C virus transmission from tampering with injectable anesthetic opioids
    Rikita I Hatia
    Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA
    Hepatology 62:101-10. 2015
    ..0046%; SE = 0.0033%). To pose a 50% patient transmission risk, an infected surgeon may take 30 years, compared to <1 year for a PWID tamperer, and weeks or days for a PWID tamperer who intensifies access to opioids...