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Genomic programming of IRF4-expressing human Langerhans cells.

Sirvent S, Vallejo AF, Davies J, Clayton K, Wu Z, Woo J, Riddell J, Chaudhri VK, Stumpf P, Nazlamova LA, Wheway G, Rose-Zerilli M, West J, Pujato M, Chen X, Woelk CH, MacArthur B, Ardern-Jones M, Friedmann PS, Weirauch MT, Singh H, Polak ME.

Nat Commun. 2020 Jan 16;11(1):313. doi: 10.1038/s41467-019-14125-x.


An evaluation of different classification algorithms for protein sequence-based reverse vaccinology prediction.

Heinson AI, Ewing RM, Holloway JW, Woelk CH, Niranjan M.

PLoS One. 2019 Dec 13;14(12):e0226256. doi: 10.1371/journal.pone.0226256. eCollection 2019.


Long non-coding RNAs and latent HIV - A search for novel targets for latency reversal.

Trypsteen W, White CH, Mukim A, Spina CA, De Spiegelaere W, Lefever S, Planelles V, Bosque A, Woelk CH, Vandekerckhove L, Beliakova-Bethell N.

PLoS One. 2019 Nov 11;14(11):e0224879. doi: 10.1371/journal.pone.0224879. eCollection 2019.


A deep learning genome-mining strategy for biosynthetic gene cluster prediction.

Hannigan GD, Prihoda D, Palicka A, Soukup J, Klempir O, Rampula L, Durcak J, Wurst M, Kotowski J, Chang D, Wang R, Piizzi G, Temesi G, Hazuda DJ, Woelk CH, Bitton DA.

Nucleic Acids Res. 2019 Oct 10;47(18):e110. doi: 10.1093/nar/gkz654.


Immunological biomarkers as indicators for outcome after discontinuation of nucleos(t)ide analogue therapy in patients with HBeAg-negative chronic hepatitis B.

Kranidioti H, Manolakopoulos S, Kontos G, Breen MS, Kourikou A, Deutsch M, Quesada-Del-Bosque ME, Martinez-Nunez RT, Naiyer MM, Woelk CH, Sanchez-Elsner T, Hadziyannis E, Papatheodoridis G, Khakoo SI.

J Viral Hepat. 2019 Jun;26(6):697-709. doi: 10.1111/jvh.13068. Epub 2019 Feb 27.


HPV, tumour metabolism and novel target identification in head and neck squamous cell carcinoma.

Fleming JC, Woo J, Moutasim K, Mellone M, Frampton SJ, Mead A, Ahmed W, Wood O, Robinson H, Ward M, Woelk CH, Ottensmeier CH, King E, Kim D, Blaydes JP, Thomas GJ.

Br J Cancer. 2019 Feb;120(3):356-367. doi: 10.1038/s41416-018-0364-7. Epub 2019 Jan 17.


Patients with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus species.

Osman KL, Jefferies JMC, Woelk CH, Devos N, Pascal TG, Mortier MC, Devaster JM, Wilkinson TMA, Cleary DW, Clarke SC; AERIS Study Group.

Sci Rep. 2018 Oct 3;8(1):14734. doi: 10.1038/s41598-018-32973-3.


Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment.

White CH, Beliakova-Bethell N, Lada SM, Breen MS, Hurst TP, Spina CA, Richman DD, Frater J, Magiorkinis G, Woelk CH.

Front Immunol. 2018 Apr 12;9:603. doi: 10.3389/fimmu.2018.00603. eCollection 2018.


The adhesins of non-typeable Haemophilus influenzae.

Osman KL, Jefferies JM, Woelk CH, Cleary DW, Clarke SC.

Expert Rev Anti Infect Ther. 2018 Mar;16(3):187-196. doi: 10.1080/14787210.2018.1438263. Epub 2018 Feb 21. Review.


Head and Neck Squamous Cell Carcinomas Are Characterized by a Stable Immune Signature Within the Primary Tumor Over Time and Space.

Wood O, Clarke J, Woo J, Mirza AH, Woelk CH, Thomas GJ, Vijayanand P, King E, Ottensmeier CH.

Clin Cancer Res. 2017 Dec 15;23(24):7641-7649. doi: 10.1158/1078-0432.CCR-17-0373. Epub 2017 Sep 26.


Multitissue Transcriptomics Delineates the Diversity of Airway T Cell Functions in Asthma.

Singhania A, Wallington JC, Smith CG, Horowitz D, Staples KJ, Howarth PH, Gadola SD, Djukanović R, Woelk CH, Hinks TSC.

Am J Respir Cell Mol Biol. 2018 Feb;58(2):261-270. doi: 10.1165/rcmb.2017-0162OC.


PTSD Blood Transcriptome Mega-Analysis: Shared Inflammatory Pathways across Biological Sex and Modes of Trauma.

Breen MS, Tylee DS, Maihofer AX, Neylan TC, Mehta D, Binder EB, Chandler SD, Hess JL, Kremen WS, Risbrough VB, Woelk CH, Baker DG, Nievergelt CM, Tsuang MT, Buxbaum JD, Glatt SJ.

Neuropsychopharmacology. 2018 Feb;43(3):469-481. doi: 10.1038/npp.2017.220. Epub 2017 Sep 19.


Gene Expression Signatures in Tuberculosis Have Greater Overlap with Autoimmune Diseases Than with Infectious Diseases.

Clayton K, Polak ME, Woelk CH, Elkington P.

Am J Respir Crit Care Med. 2017 Sep 1;196(5):655-656. doi: 10.1164/rccm.201706-1248LE. No abstract available.


IFN-γ Influences Epithelial Antiviral Responses via Histone Methylation of the RIG-I Promoter.

Spalluto CM, Singhania A, Cellura D, Woelk CH, Sanchez-Elsner T, Staples KJ, Wilkinson TMA.

Am J Respir Cell Mol Biol. 2017 Oct;57(4):428-438. doi: 10.1165/rcmb.2016-0392OC.


Enhancing the Biological Relevance of Machine Learning Classifiers for Reverse Vaccinology.

Heinson AI, Gunawardana Y, Moesker B, Hume CC, Vataga E, Hall Y, Stylianou E, McShane H, Williams A, Niranjan M, Woelk CH.

Int J Mol Sci. 2017 Feb 1;18(2). pii: E312. doi: 10.3390/ijms18020312.


Altered Epithelial Gene Expression in Peripheral Airways of Severe Asthma.

Singhania A, Rupani H, Jayasekera N, Lumb S, Hales P, Gozzard N, Davies DE, Woelk CH, Howarth PH.

PLoS One. 2017 Jan 3;12(1):e0168680. doi: 10.1371/journal.pone.0168680. eCollection 2017.


Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model.

White CH, Moesker B, Beliakova-Bethell N, Martins LJ, Spina CA, Margolis DM, Richman DD, Planelles V, Bosque A, Woelk CH.

PLoS Pathog. 2016 Nov 29;12(11):e1006026. doi: 10.1371/journal.ppat.1006026. eCollection 2016 Nov.


Sex-specific vitamin D effects on blood coagulation among overweight adults.

Al-Daghri NM, Alokail MS, Manousopoulou A, Heinson A, Al-Attas O, Al-Saleh Y, Sabico S, Yakout S, Woelk CH, Chrousos GP, Garbis SD.

Eur J Clin Invest. 2016 Dec;46(12):1031-1040. doi: 10.1111/eci.12688. Epub 2016 Nov 1.


Systems proteomic analysis reveals that clusterin and tissue inhibitor of metalloproteinases 3 increase in leptomeningeal arteries affected by cerebral amyloid angiopathy.

Manousopoulou A, Gatherer M, Smith C, Nicoll JAR, Woelk CH, Johnson M, Kalaria R, Attems J, Garbis SD, Carare RO.

Neuropathol Appl Neurobiol. 2017 Oct;43(6):492-504. doi: 10.1111/nan.12342. Epub 2016 Oct 5.


Quantitative Non-canonical Amino Acid Tagging (QuaNCAT) Proteomics Identifies Distinct Patterns of Protein Synthesis Rapidly Induced by Hypertrophic Agents in Cardiomyocytes, Revealing New Aspects of Metabolic Remodeling.

Liu R, Kenney JW, Manousopoulou A, Johnston HE, Kamei M, Woelk CH, Xie J, Schwarzer M, Garbis SD, Proud CG.

Mol Cell Proteomics. 2016 Oct;15(10):3170-3189. Epub 2016 Aug 9.


Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors.

Wood O, Woo J, Seumois G, Savelyeva N, McCann KJ, Singh D, Jones T, Peel L, Breen MS, Ward M, Garrido Martin E, Sanchez-Elsner T, Thomas G, Vijayanand P, Woelk CH, King E, Ottensmeier C; SPARC Consortium.

Oncotarget. 2016 Aug 30;7(35):56781-56797. doi: 10.18632/oncotarget.10788.


Lithium-responsive genes and gene networks in bipolar disorder patient-derived lymphoblastoid cell lines.

Breen MS, White CH, Shekhtman T, Lin K, Looney D, Woelk CH, Kelsoe JR.

Pharmacogenomics J. 2016 Oct;16(5):446-53. doi: 10.1038/tpj.2016.50. Epub 2016 Jul 12.


Upregulated Glucose Metabolism Correlates Inversely with CD8+ T-cell Infiltration and Survival in Squamous Cell Carcinoma.

Ottensmeier CH, Perry KL, Harden EL, Stasakova J, Jenei V, Fleming J, Wood O, Woo J, Woelk CH, Thomas GJ, Thirdborough SM.

Cancer Res. 2016 Jul 15;76(14):4136-48. doi: 10.1158/0008-5472.CAN-15-3121. Epub 2016 May 20.


Hypothalamus proteomics from mouse models with obesity and anorexia reveals therapeutic targets of appetite regulation.

Manousopoulou A, Koutmani Y, Karaliota S, Woelk CH, Manolakos ES, Karalis K, Garbis SD.

Nutr Diabetes. 2016 Apr 25;6:e204. doi: 10.1038/nutd.2016.10.


Vitamin D Metabolites Inhibit Hepatitis C Virus and Modulate Cellular Gene Expression.

Gutierrez JA, Jones KA, Flores R, Singhania A, Woelk CH, Schooley RT, Wyles DL.

J Virol Antivir Res. 2014 Oct 6;3(3). doi: 10.4172/2324-8955.1000129.


Structural and Functional Changes of the Invariant NKT Clonal Repertoire in Early Rheumatoid Arthritis.

Mansour S, Tocheva AS, Sanderson JP, Goulston LM, Platten H, Serhal L, Parsons C, Edwards MH, Woelk CH, Elkington PT, Elliott T, Cooper C, Edwards CJ, Gadola SD.

J Immunol. 2015 Dec 15;195(12):5582-91. doi: 10.4049/jimmunol.1501092. Epub 2015 Nov 9.


Acute psychological stress induces short-term variable immune response.

Breen MS, Beliakova-Bethell N, Mujica-Parodi LR, Carlson JM, Ensign WY, Woelk CH, Rana BK.

Brain Behav Immun. 2016 Mar;53:172-182. doi: 10.1016/j.bbi.2015.10.008. Epub 2015 Oct 22.


The interaction of genetic determinants in the outcome of HCV infection: evidence for discrete immunological pathways.

Hydes TJ, Moesker B, Traherne JA, Ashraf S, Alexander GJ, Dimitrov BD, Woelk CH, Trowsdale J, Khakoo SI.

Tissue Antigens. 2015 Oct;86(4):267-75. doi: 10.1111/tan.12650.


Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency.

White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N.

Antiviral Res. 2015 Nov;123:78-85. doi: 10.1016/j.antiviral.2015.09.002. Epub 2015 Sep 4.


Dose-responsive gene expression in suberoylanilide hydroxamic acid-treated resting CD4+ T cells.

Reardon B, Beliakova-Bethell N, Spina CA, Singhania A, Margolis DM, Richman DR, Woelk CH.

AIDS. 2015 Nov;29(17):2235-44. doi: 10.1097/QAD.0000000000000839.


Are you also what your mother eats? Distinct proteomic portrait as a result of maternal high-fat diet in the cerebral cortex of the adult mouse.

Manousopoulou A, Woo J, Woelk CH, Johnston HE, Singhania A, Hawkes C, Garbis SD, Carare RO.

Int J Obes (Lond). 2015 Aug;39(8):1325-8. doi: 10.1038/ijo.2015.35. Epub 2015 Mar 23.


Gene networks specific for innate immunity define post-traumatic stress disorder.

Breen MS, Maihofer AX, Glatt SJ, Tylee DS, Chandler SD, Tsuang MT, Risbrough VB, Baker DG, O'Connor DT, Nievergelt CM, Woelk CH.

Mol Psychiatry. 2015 Dec;20(12):1538-45. doi: 10.1038/mp.2015.9. Epub 2015 Mar 10.


The promise of reverse vaccinology.

Heinson AI, Woelk CH, Newell ML.

Int Health. 2015 Mar;7(2):85-9. doi: 10.1093/inthealth/ihv002. Review.


Gender-dependent differences in plasma matrix metalloproteinase-8 elevated in pulmonary tuberculosis.

Sathyamoorthy T, Sandhu G, Tezera LB, Thomas R, Singhania A, Woelk CH, Dimitrov BD, Agranoff D, Evans CA, Friedland JS, Elkington PT.

PLoS One. 2015 Jan 30;10(1):e0117605. doi: 10.1371/journal.pone.0117605. eCollection 2015.


Blood-based gene-expression biomarkers of post-traumatic stress disorder among deployed marines: A pilot study.

Tylee DS, Chandler SD, Nievergelt CM, Liu X, Pazol J, Woelk CH, Lohr JB, Kremen WS, Baker DG, Glatt SJ, Tsuang MT; Marine Resiliency Study Investigators.

Psychoneuroendocrinology. 2015 Jan;51:472-94. doi: 10.1016/j.psyneuen.2014.09.024. Epub 2014 Sep 30.


Replication competent virus as an important source of bias in HIV latency models utilizing single round viral constructs.

Bonczkowski P, De Spiegelaere W, Bosque A, White CH, Van Nuffel A, Malatinkova E, Kiselinova M, Trypsteen W, Witkowski W, Vermeire J, Verhasselt B, Martins L, Woelk CH, Planelles V, Vandekerckhove L.

Retrovirology. 2014 Aug 21;11:70. doi: 10.1186/s12977-014-0070-3.


Whole serum 3D LC-nESI-FTMS quantitative proteomics reveals sexual dimorphism in the milieu intérieur of overweight and obese adults.

Al-Daghri NM, Al-Attas OS, Johnston HE, Singhania A, Alokail MS, Alkharfy KM, Abd-Alrahman SH, Sabico SL, Roumeliotis TI, Manousopoulou-Garbis A, Townsend PA, Woelk CH, Chrousos GP, Garbis SD.

J Proteome Res. 2014 Nov 7;13(11):5094-105. doi: 10.1021/pr5003406. Epub 2014 Jul 29.


Maraviroc intensification in patients with suppressed HIV viremia has limited effects on CD4+ T cell recovery and gene expression.

Beliakova-Bethell N, Jain S, Woelk CH, Witt MD, Sun X, Lada SM, Spina CA, Goicoechea M, Rought SE, Haubrich R, Dubé MP.

Antiviral Res. 2014 Jul;107:42-9. doi: 10.1016/j.antiviral.2014.04.005. Epub 2014 Apr 24.


The effect of cell subset isolation method on gene expression in leukocytes.

Beliakova-Bethell N, Massanella M, White C, Lada S, Du P, Vaida F, Blanco J, Spina CA, Woelk CH.

Cytometry A. 2014 Jan;85(1):94-104. doi: 10.1002/cyto.a.22352. Epub 2013 Sep 20.


Differential gene expression in HIV-infected individuals following ART.

Massanella M, Singhania A, Beliakova-Bethell N, Pier R, Lada SM, White CH, Pérez-Santiago J, Blanco J, Richman DD, Little SJ, Woelk CH.

Antiviral Res. 2013 Nov;100(2):420-8. doi: 10.1016/j.antiviral.2013.07.017. Epub 2013 Aug 6.


Gene expression in human fungal pathogen Coccidioides immitis changes as arthroconidia differentiate into spherules and mature.

Viriyakosol S, Singhania A, Fierer J, Goldberg J, Kirkland TN, Woelk CH.

BMC Microbiol. 2013 May 28;13:121. doi: 10.1186/1471-2180-13-121.


Blood-based gene-expression predictors of PTSD risk and resilience among deployed marines: a pilot study.

Glatt SJ, Tylee DS, Chandler SD, Pazol J, Nievergelt CM, Woelk CH, Baker DG, Lohr JB, Kremen WS, Litz BT, Tsuang MT; Marine Resiliency Study Investigators.

Am J Med Genet B Neuropsychiatr Genet. 2013 Jun;162B(4):313-26. doi: 10.1002/ajmg.b.32167. Epub 2013 May 3.


Highly precise measurement of HIV DNA by droplet digital PCR.

Strain MC, Lada SM, Luong T, Rought SE, Gianella S, Terry VH, Spina CA, Woelk CH, Richman DD.

PLoS One. 2013;8(4):e55943. doi: 10.1371/journal.pone.0055943. Epub 2013 Apr 3.


HIV downregulates interferon-stimulated genes in primary macrophages.

Wie SH, Du P, Luong TQ, Rought SE, Beliakova-Bethell N, Lozach J, Corbeil J, Kornbluth RS, Richman DD, Woelk CH.

J Interferon Cytokine Res. 2013 Feb;33(2):90-5. doi: 10.1089/jir.2012.0052. Epub 2012 Dec 31.


Suberoylanilide hydroxamic acid induces limited changes in the transcriptome of primary CD4(+) T cells.

Beliakova-Bethell N, Zhang JX, Singhania A, Lee V, Terry VH, Richman DD, Spina CA, Woelk CH.

AIDS. 2013 Jan 2;27(1):29-37. doi: 10.1097/QAD.0b013e32835b3e26.


Factors regulated by interferon gamma and hypoxia-inducible factor 1A contribute to responses that protect mice from Coccidioides immitis infection.

Woelk CH, Zhang JX, Walls L, Viriyakosol S, Singhania A, Kirkland TN, Fierer J.

BMC Microbiol. 2012 Sep 24;12:218. doi: 10.1186/1471-2180-12-218.


A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia.

Pérez-Santiago J, Diez-Alarcia R, Callado LF, Zhang JX, Chana G, White CH, Glatt SJ, Tsuang MT, Everall IP, Meana JJ, Woelk CH.

J Psychiatr Res. 2012 Nov;46(11):1464-74. doi: 10.1016/j.jpsychires.2012.08.005. Epub 2012 Sep 3.


TRAF6 and IRF7 control HIV replication in macrophages.

Sirois M, Robitaille L, Allary R, Shah M, Woelk CH, Estaquier J, Corbeil J.

PLoS One. 2011;6(11):e28125. doi: 10.1371/journal.pone.0028125. Epub 2011 Nov 28.


The utility of gene expression in blood cells for diagnosing neuropsychiatric disorders.

Woelk CH, Singhania A, Pérez-Santiago J, Glatt SJ, Tsuang MT.

Int Rev Neurobiol. 2011;101:41-63. doi: 10.1016/B978-0-12-387718-5.00003-1. Review.


Improving reverse vaccinology with a machine learning approach.

Bowman BN, McAdam PR, Vivona S, Zhang JX, Luong T, Belew RK, Sahota H, Guiney D, Valafar F, Fierer J, Woelk CH.

Vaccine. 2011 Oct 19;29(45):8156-64. doi: 10.1016/j.vaccine.2011.07.142. Epub 2011 Aug 22.


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