The University of Southampton
Woelk lab

Publications

Click here for a searchable list on Pubmed. 

 

Published articles

39. Bonczkowski P., De Spiegelaere W., Bosque A., White C.H., Van Nuffel A., Malatinkova E, Kiselinova M., Trypsteen W., Witkowski W., Vermeire J., Verhasselt B., Martins L., Woelk C.H., Planelles V. and Vandekerckhove L. (2014) Replication competent virus as an important source of bias in HIV latency models utilizing single round viral constructs. Retrovirology. 11:70.

38. Al-Daghri N., Attas O., Johnston H., Singhania A., Alokail M., Alkharfy K., Abd-Alrahman S., Sabico S., Roumeliotis T., Manousopoulou-Garbis A., Townsend P., Woelk C.H., Chrousos G., and Garbis S. (In Press) Whole serum 3D LC-nESI-FTMS quantitative proteomics reveals sexual dimorphism in the Milieu Intérieur of overweight and obese adults. Journal of Proteome Research, ##-####.

37. Beliakova-Bethell N., Jain S., Woelk C.H., Witt M.D., Sun X., Lada S.M., Spina C.A., Goicoechea M., Rought S.E., Haubrich R., and Dubé M.P. (2014) Maraviroc intensification in patients with suppressed HIV viremia has limited effects on CD4+ T cell recovery and gene expression. Antiviral Research. 107:42-49.

36. Beliakova-Bethell N.*, Massanella M.*, White C.H., Lada S., Du P., Vaida F., Blanco J., Spina C.A., and Woelk C.H. (2013) The effect of cell subset isolation method on gene expression in leukocytes. Cytometry Part A, 85(1): 94-104. [Highlighted Article]

35. Spina C.A, Anderson J., Archin N.M., Bosque A., Chan J., Greene W.C., Famiglietti M., Kashuba A., Lewin S.R., Mau M., Margolis D.M., Ruelas D., Saleh S., Shirakawa K., Siliciano R., Singhania A., Soto P.C., Terry V.H., Verdin E., Woelk C.H., Wooden S., Xing S., and Planelles V. (2013) An in-depth comparison of latent HIV-1 reactivation in multiple cell model systems and resting CD4+ T cells from aviremic patients. PLoS Pathogens, 9(12): e1003834.

34. Massanella M.*, Singhania A.*, Beliakova-Bethell N., Pier R., Lada S., White C.H., Pérez-Santiago J., Blanco J., Richman D.D., Little S.J. and Woelk C.H. (2013) Differential Gene Expression in HIV-Infected Individuals Following ART. Antiviral Research, 100(2): 420-428 [Highlighted Article]

33. Viriyakosol S.*, Singhania A.*, Fierer J., Goldberg J., Kirkland T.N.† and Woelk C.H.† (2013) Gene expression in human fungal pathogen Coccidioides immitis changes as mycelia differentiate into spherules and mature. BMC Microbiology, 13: 121.

32. Glatt S.J., Tylee D., Chandler S.D., Pazol J., Nievergelt C., Woelk C.H., Litz B.T., Baker D., Lohr J.B., Kremen W.S. and Ming T. Tsuang (2013) Blood-Based Gene-Expression Predictors of PTSD Risk and Resilience among Deployed Marines: A Pilot Study. American Journal of Medical Genetics Part B. Neuropsychiatric Genetics, 162(4): 313-326.

31. Strain M.C., Lada S., Luong T., Rought S.E., Gianella S., Terry V., Spina C.A., Woelk C.H. and Richman D.D. (2013) Highly Precise Measurement of HIV DNA by Droplet Digital PCR. PLoS ONE, 8(4): e55943.

30. Beliakova-Bethell N., Zhang J.X., Singhania A., Lee V., Terry V.H., Richman D.D., Spina C.A. and Woelk C.H. (2013) Suberoylanilide hydroxamic acid (SAHA) induces limited changes in the transcriptome of primary CD4+ T cells. AIDS, 27(1): 29-37.

29. Wie S.H., Du P., Luong T.Q., Rought S.E., Beliakova-Bethell N., Lozach J., Corbeil J., Kornbluth R.S., Richman D.D. and Woelk C.H. (2013) HIV Downregulates Interferon Stimulated Genes in Primary Macrophages. Journal of Interferon and Cytokine Research, 33(2): 90-95.

28. Pérez-Santiago J.*, Diez-Alarcia R.*, Callado L.F., Zhang J.X., Chana G., White C., Glatt S., Tsuang M., Everall I.P., Meana J.J. and Woelk C.H. (2012) Identification of genes implicated in schizophrenia by a meta-analysis of microarray gene expression studies of the human prefrontal cortex. Journal of Psychiatric Research, 46(11): 1464-1474.

27. Woelk C.H.*, Zhang J.X.*, Walls L., Viriyakosol S., Singhania A., Kirkland T. and Fierer J. (2012) Factors regulated by interferon gamma and hypoxia-inducible factor 1A contribute to responses that protect mice from Coccidioides immitis infection. BMC Microbiology, 12: 218.

26. Sirois M., Robitaille L., Allary R., Shah M., Woelk C.H., Estaquier J. and Corbeil J.C. (2011) TRAF6 and IRF7 control HIV replication in macrophages. PLoS ONE, 6(11): e28125.

25. Bowman B.N., McAdam P.M., Vivona S., Zhang J., Luong T., Belew R.K., Sahota H., Guiney D., Valafar F., Fierer J. and Woelk C.H. (2011) Improving reverse vaccinology with a machine learning approach. Vaccine, 29: 8156–8164.

24. Woelk C.H., Beliakova-Bethell N., Goicoechea M., Zhao Y., Du P., Rought S.E., Lozach J., Pérez-Santiago J., Richman D.D. and Little S.J. (2010) Gene Expression Predicts HIV-infected Individuals at Risk of Poor CD4+ T Cell Recovery Before Initiation of Highly Active Antiretroviral Treatment (HAART). AIDS, 24 (2): 217-222.

23. Kozak I., Cheng L., Rought S., Woelk C.H., Barron E.C., Schrier R.D., Corbeil J. and Freeman W.R. (2010) Characterization of cytokine gene expression associated with noninfectious human immunodeficiency virus retinopathy in human autopsy eyes. Retina, 30 (6): 952-957.

22. Chana G., Lucero G., Salaria S., Lozach J., Du P., Woelk C.H. and Everall I. (2009) Upregulation of NRG-1 and VAMP-1 in Human Brain Aggregates Exposed to Clozapine. Schizophrenia Research, 113(2-3): 273-276.

21. Smith D.M., May S., Tweeten S., Drumright L., Pacold M.E., Kosakovsky Pond S.L., Pesano R.L., Lie Y.S., Richman D.D., Frost S.D.W., Woelk C.H., and Little S.J. (2009) A Public Health Model for the Molecular Surveillance of HIV Transmission in San Diego, California. AIDS, 23(2): 225-232.

20. Gorbach P.M., Drumright L.N., Javanbakht M., Kosakovsky Pond S.L., Woelk C.H., Daar E.S. & Little S.J. (2008) Antiretroviral drug resistance and risk behavior among recently HIV-infected men who have sex with men (MSM). Journal of Acquired Immunodeficiency Syndromes, 47(5):639-43.

19. Liu L., Richman, D.D., Hecht F.M., Markowitz M., Daar E.S., Routy J-P., Margolick J.B., Collier A.C., Woelk C.H., Little S.J. & Smith D.M. (2008) Comparison of algorithms that interpret genotypic HIV-1 drug resistance to determine the prevalence of transmitted drug resistance. AIDS, 22: 1-5.

18. Woelk, C.H., Frost, S.D.W., Richman, D.D., Higley, P.E., & Kosakovsky Pond, S.L. (2007) Evolution of the interferon alpha gene family in eutherian mammals. Gene, 397(1-2): 38-50.

17. Kosakovsky Pond S.L., Posada D., Gravenor M.B., Woelk C.H. & Frost S.D. (2006) GARD: a genetic algorithm for recombination detection. Bioinformatics, 22 (24): 3096-3098.

16. Kosakovsky Pond S.L., Posada D., Gravenor M.B., Woelk C.H. & Frost S.D. (2006) Automated phylogenetic detection of recombination using a genetic algorithm. Molecular Biology and Evolution, 23 (10): 1891-1901.

15. Pillai S.K., Kosakovsky Pond S.L., Woelk C.H., Richman, D.D., Smith D.M. (2005) "Codon Volatility" does not reflect selective pressure on the HIV-1 genome. Virology, 336 (2): 137-143.

14. Woelk C.H., Ottones F., Plotkin C.R., Pinyi Du, Royer C.D., Rought S.E., Lozach J., Sasik R., Kornbluth R.S., Richman D. & Corbeil J. (2004) Interferon gene expression following HIV-1 infection of monocyte-derived macrophages. AIDS Research and Human Retroviruses 20 (11): 1210-1222.

13. Choisy M., Woelk C.H., Guégan J.F. & Robertson D. L. (2004) A comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. Journal of Virology, 78 (4): 1962-1970.

12. Sasik R., Woelk C.H., Corbeil J. (2004) Microarrays: Truths and Consequences. Journal of Molecular Endocrinology, 33 (1): 1-9.

11. Twiddy S.S., Woelk C.H., & Holmes E.C. (2002) Phylogenetic evidence for adaptive evolution of dengue viruses in nature. Journal of General Virology 83: 1679-1689.

10. Woelk C.H. & Holmes E.C. (2002) Reduced positive selection in vector-borne RNA viruses. Molecular Biology and Evolution 19 (12): 2333-2336.

9. Woelk C.H., Jin L., Brown D.W.G., & Holmes E.C. (2002) Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections. Journal of General Virology 83: 1419-1430.

8. Holmes E.C., Woelk C.H., Kassis R., & Bourhy H. (2002) Genetic constraints and the adaptive evolution of rabies virus in nature. Virology 292: 247-257.

7. Brault A.C., Powers A.M., Holmes E.C., Woelk C.H., & Weaver S.C. (2002) Positively charged amino acid substitutions in the E2 envelope glycoprotein are associated with the emergence of Venezuelan equine encephalitis virus. Journal of Virology 76 (4): 1718-1730.

6. Woelk C.H., Jin L., Holmes E.C., & Brown D.W.G. (2001) Immune and artificial selection in the hemagglutinin (H) glycoprotein of measles virus. Journal of General Virology 82: 2463-2474.

5. Jenkins G.M., Worobey M., Woelk C.H., & Holmes E.C. (2001) Evidence for the non-quasispecies evolution of RNA viruses. Molecular Biology and Evolution 18 (6): 987-994.

4. Woelk C.H. & Holmes E.C. (2001) Variable immune-driven natural selection in the attachment (G) glycoprotein of respiratory syncytial virus. Journal of Molecular Evolution 52: 182-192.

3. Ballingall K.T., Waibochi L., Holmes E.C., Woelk C.H., MacHugh N.D., Lutje V., & McKeever D.J. (2001) The CD45 locus in cattle: allelic polymorphism and evidence for exceptional positive natural selection. Immunogenetics 52 (3-4): 276-283.

2. Jenkins G.A., Woelk C.H., Rambaut A., & Holmes E.C. (2000) Testing the extent of sequence similarity among viroids, satellite RNAs and hepatitis delta virus. Journal of Molecular Evolution 50: 98-102.

1. Dellamary L.A., Tarara T.E., Smith D.J., Woelk C.H., Adractas A., Costello M.L., Gill H., & Weers J.G. (2000) Hollow porous particles in metered dose inhalers. Pharmaceutical Research, 17 (2): 168-174.

 

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