Christopher H Woelk

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T-cell recovery
    Christopher H Woelk
    Department of Medicine, University of California, San Diego, La Jolla, USA
    AIDS 24:217-22. 2010
  2. pmc Factors regulated by interferon gamma and hypoxia-inducible factor 1A contribute to responses that protect mice from Coccidioides immitis infection
    Christopher H Woelk
    Veterans Affairs San Diego Healthcare System, Mail Code 9111 F, San Diego, California 92161, USA
    BMC Microbiol 12:218. 2012
  3. pmc Evolution of the interferon alpha gene family in eutherian mammals
    Christopher H Woelk
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Gene 397:38-50. 2007
  4. ncbi request reprint Interferon gene expression following HIV type 1 infection of monocyte-derived macrophages
    Christopher H Woelk
    Department of Pathology, University of California San Diego, La Jolla, California 92093 0679, USA
    AIDS Res Hum Retroviruses 20:1210-22. 2004
  5. ncbi request reprint GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006
  6. pmc Differential gene expression in HIV-infected individuals following ART
    Marta Massanella
    Fundació irsiCaixa HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol IGTP, Hospital Germans Trias, Universitat Autonoma de Barcelona, 08916 Badalona, Spain Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Antiviral Res 100:420-8. 2013
  7. pmc Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature
    Suganya Viriyakosol
    Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
    BMC Microbiol 13:121. 2013
  8. pmc A public health model for the molecular surveillance of HIV transmission in San Diego, California
    Davey M Smith
    University of California San Diego, La Jolla, CA 92093 0679, USA
    AIDS 23:225-32. 2009
  9. pmc Highly precise measurement of HIV DNA by droplet digital PCR
    Matthew C Strain
    University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 8:e55943. 2013
  10. doi request reprint A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia
    Josué Pérez-Santiago
    Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
    J Psychiatr Res 46:1464-74. 2012

Collaborators

Detail Information

Publications22

  1. pmc Gene expression before HAART initiation predicts HIV-infected individuals at risk of poor CD4+ T-cell recovery
    Christopher H Woelk
    Department of Medicine, University of California, San Diego, La Jolla, USA
    AIDS 24:217-22. 2010
    ..To identify a pre-HAART gene expression signature in peripheral blood mononuclear cells (PBMCs) predictive of CD4 T-cell recovery during HAART in HIV-infected individuals...
  2. pmc Factors regulated by interferon gamma and hypoxia-inducible factor 1A contribute to responses that protect mice from Coccidioides immitis infection
    Christopher H Woelk
    Veterans Affairs San Diego Healthcare System, Mail Code 9111 F, San Diego, California 92161, USA
    BMC Microbiol 12:218. 2012
    ..Mouse models of the disease have identified strains that are resistant (e.g. DBA/2) or susceptible (e.g. C57BL/6) to these pathogens. However, the genetic and immunological basis for this difference has not been fully characterized...
  3. pmc Evolution of the interferon alpha gene family in eutherian mammals
    Christopher H Woelk
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Gene 397:38-50. 2007
    ..Gene conversion, similar to duplication, provides a mechanism by which the protein product of a specific IFNA gene can be increased...
  4. ncbi request reprint Interferon gene expression following HIV type 1 infection of monocyte-derived macrophages
    Christopher H Woelk
    Department of Pathology, University of California San Diego, La Jolla, California 92093 0679, USA
    AIDS Res Hum Retroviruses 20:1210-22. 2004
    ..The nuclear factor in activated T cells (NFAT) and members of the interferon family of transcription factors appeared to be responsible for the upregulation of this set of interferon-stimulated genes following HIV-1 exposure...
  5. ncbi request reprint GARD: a genetic algorithm for recombination detection
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 22:3096-8. 2006
    ..The evolution of recombinant sequences can not be properly explained by a single phylogenetic tree, but several phylogenies may be used to correctly model the evolution of non-recombinant fragments...
  6. pmc Differential gene expression in HIV-infected individuals following ART
    Marta Massanella
    Fundació irsiCaixa HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol IGTP, Hospital Germans Trias, Universitat Autonoma de Barcelona, 08916 Badalona, Spain Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
    Antiviral Res 100:420-8. 2013
    ..In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized. ..
  7. pmc Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature
    Suganya Viriyakosol
    Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
    BMC Microbiol 13:121. 2013
    ..immitis mycelia with early (day 2) and late stage (day 8) spherules grown in vitro. All hybridizations were done in quadruplicate and stringent criteria were used to identify significantly differentially expressed genes...
  8. pmc A public health model for the molecular surveillance of HIV transmission in San Diego, California
    Davey M Smith
    University of California San Diego, La Jolla, CA 92093 0679, USA
    AIDS 23:225-32. 2009
    ..Here, we investigate how molecular epidemiology can be used to identify highly related HIV networks within a population and how voluntary contact tracing of sexual partners can be used to selectively target these networks...
  9. pmc Highly precise measurement of HIV DNA by droplet digital PCR
    Matthew C Strain
    University of California San Diego, La Jolla, California, United States of America
    PLoS ONE 8:e55943. 2013
    ..The improved sensitivity and precision of measurement of these rare events should facilitate measurements to characterize the latent HIV reservoir and interventions to eradicate it...
  10. doi request reprint A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia
    Josué Pérez-Santiago
    Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
    J Psychiatr Res 46:1464-74. 2012
    ..In conclusion, this combined analysis has resulted in a statistically robust identification of genes whose dysregulation may contribute to the mechanism of schizophrenia...
  11. pmc The effect of cell subset isolation method on gene expression in leukocytes
    Nadejda Beliakova-Bethell
    Department of Medicine, University of California San Diego, La Jolla, California, 92093
    Cytometry A 85:94-104. 2014
    ..2013 International Society for Advancement of Cytometry. ..
  12. pmc Comparison of algorithms that interpret genotypic HIV-1 drug resistance to determine the prevalence of transmitted drug resistance
    Lin Liu
    University of California San Diego, La Jolla, California 92093 0679, USA
    AIDS 22:835-9. 2008
    ..We compared eight genotypic interpretation methods to determine whether the method used would affect the rates of reported transmitted drug resistance...
  13. ncbi request reprint Automated phylogenetic detection of recombination using a genetic algorithm
    Sergei L Kosakovsky Pond
    Department of Pathology, University of California San Diego, USA
    Mol Biol Evol 23:1891-901. 2006
    ..Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection...
  14. ncbi request reprint Maraviroc intensification in patients with suppressed HIV viremia has limited effects on CD4+ T cell recovery and gene expression
    Nadejda Beliakova-Bethell
    University of California San Diego, La Jolla, CA 92093, USA Electronic address
    Antiviral Res 107:42-9. 2014
    ..However, the modest changes in T cell composition, including reduction of the percentages of Tregs, proliferating CD4+ T cells and senescent CD8+ T cells, suggest immunologically favorable effects of MVC. ..
  15. doi request reprint The utility of gene expression in blood cells for diagnosing neuropsychiatric disorders
    Christopher H Woelk
    Department of Medicine, University of California San Diego, La Jolla, California, USA
    Int Rev Neurobiol 101:41-63. 2011
    ....
  16. pmc Suberoylanilide hydroxamic acid induces limited changes in the transcriptome of primary CD4(+) T cells
    Nadejda Beliakova-Bethell
    Department of Medicine, University of California San Diego, La Jolla CA 92093 0679, USA
    AIDS 27:29-37. 2013
    ..To assess the off-target effects of the histone deacetylase inhibitor (HDACi) suberoylanilide hydroxamic acid (SAHA) in human primary CD4 T cells...
  17. ncbi request reprint Codon volatility does not reflect selective pressure on the HIV-1 genome
    Satish K Pillai
    University of California, San Diego, Stein Clinical Research Building, Room 325, 9500 Gilman Drive 0679, La Jolla 92093, USA
    Virology 336:137-43. 2005
    ..Volatility failed to correlate with the results of any of the comparative methods demonstrating that it is not a reliable indicator of selection pressure...
  18. doi request reprint Improving reverse vaccinology with a machine learning approach
    Brett N Bowman
    Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA 92182, USA
    Vaccine 29:8156-64. 2011
    ..05). This paper describes a superior workflow for performing reverse vaccinology studies and provides a benchmark training data set that can be used to evaluate future methodological improvements...
  19. doi request reprint Antiretroviral drug resistance and risk behavior among recently HIV-infected men who have sex with men
    Pamina M Gorbach
    Department of Epidemiology, School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095 7353, USA
    J Acquir Immune Defic Syndr 47:639-43. 2008
    ..Examine associations among behaviors including substance use during sexual encounters, and transmitted HIV drug resistance in recently HIV-infected men who have sex with men (MSM)...
  20. pmc Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes
    Marc Choisy
    CEPM, UMR CNRS IRD 9926, Montpellier, France
    J Virol 78:1962-70. 2004
    ..We found a significant tendency for positively selected sites to fall outside T-helper epitopes and for positively selected sites to be strongly associated with N glycosylation sites...
  21. ncbi request reprint Genetic constraints and the adaptive evolution of rabies virus in nature
    Edward C Holmes
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Virology 292:247-57. 2002
    ..Assuming that the average rate of synonymous change does not vary among species, we estimated that the current genetic diversity in lyssavirus genotype 1 may have arisen only during the last 500 years...
  22. ncbi request reprint Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections
    Christopher H Woelk
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
    J Gen Virol 83:1419-30. 2002
    ..Finally, using H gene data, we estimated the rate of molecular evolution for SSPE strains as 3.4 x 10(-4) substitutions/site/year, which is similar to previous estimates obtained for acute strains...

Research Grants2

  1. Gene expression biomarkers of immune recovery in HIV infected patients
    Christopher H Woelk; Fiscal Year: 2010
    ..This proposal will also identify which drugs an HIV-infected patient should be treated with in order to maximize the extent of their immune recovery. ..
  2. Gene expression biomarkers of immune recovery in HIV infected patients
    Christopher H Woelk; Fiscal Year: 2011
    ..This proposal will also identify which drugs an HIV-infected patient should be treated with in order to maximize the extent of their immune recovery. ..