Linda Van Dyk, PhD

Publications

• Diebel, K.W., Smith, A.L., and van Dyk, L.F. (2010). Mature and functional miRNAs transcribed from novel RNA polymerase III promoters of gammaherpesvirus 68. RNA 16:170-185. PMID: 19948768.
• Vannella KM, Luckhardt TR, Wilke CA, van Dyk LF, Toews GB, Moore BB. 2010. Latent herpesvirus infection augments experimental pulmonary fibrosis. Am J Respir Crit Care Med.:181:465-77. PMID: 20185751.
• Orioli, A., Pascali, C., Quartararo, J., Diebel K.D., Praz, V., Romascano, D., Percudani, R., van Dyk, L.F., Hernandez, N., Teichmann, M. and Dieci, G. (2011). Widespread occurrence of non-canonical transcription termination by human RNA polymerase III. Nucleic Acids Research, doi:10.1093/nar/gkr074, Mar 17 [Epub ahead of print].
• Suárez AL, Kong R, George T, He L, Yue Z, and van Dyk LF. (2011). Gammaherpesvirus 68 infection of endothelial cells requires both host autophagy genes and viral oncogenes for optimal survival and persistence. J Virol. 185:6293-308.
• Wu Q, van Dyk LF, Jiang D, Dakhama A, Li L, White SR, Gross A, Chu HW. Interleukin-1 receptor-associated kinase M (IRAK-M) promotes human rhinovirus infection in lung epithelial cells via the autophagic pathway. Virology. 2013 Nov;446(1-2):199-206. PubMed PMID: 24074582
• Rubtsova K, Rubtsov AV, van Dyk LF, Kappler JW, Marrack P. T-box transcription factor T-bet, a key player in a unique type of B-cell activation essential for effective viral clearance. Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3216-24. PubMed PMID: 23922396
• Ashley SL, Jegal Y, Moore TA, van Dyk LF, Laouar Y and BB Moore. gammaHerpes virus-68, but not Psuedomonas aeruginosa or Influenza A (H1N1) Exacerbate Established Murine Lung Fibrosis. Accepted, Am J Physiol Lung Cell Mol Physiol.
• Diebel KW, Claypool DJ, and LF van Dyk. (2014). A conserved RNA polymerase III promoter required for gammaherpesvirus TMER transcription and microRNA processing. Accepted, Gene.
• Feldman ER, Kara M, Coleman CB, Grau KR, Oko L, Krueger BJ, Renne R, van Dyk LF and Tibbetts SA. (2014). Virus-encoded miRNAs facilitate gamma-herpesvirus latency and pathogenesis in vivo. In revision for mBio.
• Diebel KW, Oko L, Medina EM, Claypool DJ, Warren C, Tibbetts SA, Clambey ET and van Dyk LF. (2014). Gammaherpesvirus small non-coding RNAs contribute to virulence in vivo. In revision for mBio.
• Lee KS, Suarez AL, Claypool DJ, Armstrong TK, Buckingham EM and van Dyk LF. 2012. Viral Cyclins Mediate Separate Phases of Infection by Integrating Functions of Distinct Mammalian Cyclins. PLoS Pathogens Feb;8(2):e1002496.
• Diebel KW, Oko LM, Medina EM, Niemeyer BF, Warren CJ, Claypool DJ, Tibbetts SA, Cool CD, Clambey ET, van Dyk LF. Gammaherpesvirus small noncoding RNAs are bifunctional elements that regulate infection and contribute to virulence in vivo. MBio. 2015 Feb 17;6(1):e01670-14. PubMed PMID: 25691585
• Larson J.D., J.M. Thurman, A.V. Rubtsov, D. Claypool, P. Marrack, L.F. van Dyk, R.M. Torres, and R. Pelanda. (2012). Murine gammaherpesvirus 68 infection protects lupus-prone mice from the development of autoimmunity. PNAS, doi: 10.1073/pnas.1203019109.
• Lee K.S., Suarez A.L., Claypool D.J., Armstrong T.K., Buckingham E.M. and van Dyk L.F. (2012). Viral Cyclins Mediate Separate Phases of Infection by Integrating Functions of Distinct Mammalian Cyclins. PLoS Pathogens Feb;8(2):e1002496.
• Larson J.D., J.M. Thurman, A.V. Rubtsov, D. Claypool, P. Marrack, L.F. van Dyk, R.M. Torres, and R. Pelanda. (2012). Murine gammaherpesvirus 68 infection protects lupus-prone mice from the development of autoimmunity. PNAS, doi: 10.1073/pnas.1203019109.
• Freeman ML, Burkum CE, Cookenham T, Roberts AD, Lanzer KG, Huston GE, Jensen MK, Sidney J, Peters B, Kohlmeier JE, Woodland DL, van Dyk LF, Sette A, Blackman MA. CD4 T cells specific for a latency-associated ?-herpesvirus epitope are polyfunctional and cytotoxic. J Immunol. 2014 Dec 15;193(12):5827-34. PubMed PMID: 25378595
• Ashley SL, Jegal Y, Moore TA, van Dyk LF, Laouar Y, Moore BB. ?-Herpes virus-68, but not Pseudomonas aeruginosa or influenza A (H1N1), exacerbates established murine lung fibrosis. Am J Physiol Lung Cell Mol Physiol. 2014 Aug 1;307(3):L219-30. PubMed PMID: 24879051
• Feldman ER, Kara M, Coleman CB, Grau KR, Oko LM, Krueger BJ, Renne R, van Dyk LF, Tibbetts SA. Virus-encoded microRNAs facilitate gammaherpesvirus latency and pathogenesis in vivo. MBio. 2014 May 27;5(3):e00981-14. PubMed PMID: 24865551
• Diebel KW, Claypool DJ, van Dyk LF. A conserved RNA polymerase III promoter required for gammaherpesvirus TMER transcription and microRNA processing. Gene. 2014 Jul 1;544(1):8-18. PubMed PMID: 24747015
• Getahun A., Smith M.J., Kogut I., van Dyk L.F. and J.C. Cambier. (2012). Retention of Anergy and Inhibition of Antibody Responses During Acute Gammaherpesvirus 68 Infection. J Immunol189:2965-74. PMID: 22904300.
• Klionsky, D.J.….van Dyk L.F.….Zuckerbraun, B. (2012). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy ;8:445-544. PMID: 22966490.
• Zhou X, Loomis-King H, Gurczynski SJ, Wilke CA, Konopka KE, Ptaschinski C, Coomes SM, Iwakura Y, van Dyk LF, Lukacs NW, Moore BB. Bone marrow transplantation alters lung antigen-presenting cells to promote T(H)17 response and the development of pneumonitis and fibrosis following gammaherpesvirus infection. Mucosal Immunol. 2015 Sep 16. [Epub ahead of print] PubMed PMID: 26376362
• Williams LM, Niemeyer BF, Franklin DS, Clambey ET, van Dyk LF. A Conserved Gammaherpesvirus Cyclin Specifically Bypasses Host p18(INK4c) To Promote Reactivation from Latency. J Virol. 2015 Nov;89(21):10821-31. PubMed PMID: 26292318
• Wu Q, Jiang D, Huang C, van Dyk LF, Li L, Chu HW. Trehalose-mediated autophagy impairs the anti-viral function of human primary airway epithelial cells. PLoS One. 2015;10(4):e0124524. PubMed PMID: 25879848
• Diebel KW, Oko LM, Medina EM, Niemeyer BF, Warren CJ, Claypool DJ, Tibbetts SA, Cool CD, Clambey ET, van Dyk LF. Gammaherpesvirus small noncoding RNAs are bifunctional elements that regulate infection and contribute to virulence in vivo. MBio. 2015 Feb 17;6(1):e01670-14. PubMed PMID: 25691585
• Feldman ER, Kara M, Oko LM, Grau KR, Krueger BJ, Zhang J, Feng P, van Dyk LF, Renne R, Tibbetts SA. A Gammaherpesvirus Noncoding RNA Is Essential for Hematogenous Dissemination and Establishment of Peripheral Latency. mSphere. 2016 Apr;1(2). PubMed PMID: 27110595
• Niemeyer BF, Oko LM, Medina EM, Oldenburg DG, White DW, Cool CD, Clambey ET, van Dyk LF. Host Tumor Suppressor p18(INK4c) functions as a potent cell-intrinsic inhibitor of ?HV68 reactivation and pathogenesis. J Virol. 2018 Jan 3. [Epub ahead of print] PubMed PMID: 29298882
• Kimball AK, Oko LM, Bullock BL, Nemenoff RA, van Dyk LF, Clambey ET. A Beginner's Guide to Analyzing and Visualizing Mass Cytometry Data. J Immunol. 2018 Jan 1;200(1):3-22. PubMed PMID: 29255085
• Zhou X, Loomis-King H, Gurczynski SJ, Wilke CA, Konopka KE, Ptaschinski C, Coomes SM, Iwakura Y, van Dyk LF, Lukacs NW, Moore BB. Bone marrow transplantation alters lung antigen-presenting cells to promote TH17 response and the development of pneumonitis and fibrosis following gammaherpesvirus infection. Mucosal Immunol. 2016 May;9(3):610-20. PubMed PMID: 26376362
• Getahun A, Wemlinger SM, Rudra P, Santiago ML, van Dyk LF, Cambier JC. Impaired B cell function during viral infections due to PTEN-mediated inhibition of the PI3K pathway. J Exp Med. 2017 Apr 3;214(4):931-941. PubMed PMID: 28341640
• Clambey, E.T. & van Dyk, L.F. Curr Clin Micro Rpt (2016) 3: 162. doi:10.1007/s40588-016-0042-6
• Niemeyer BF, Oko LM, Medina EM, Oldenburg DG, White DW, Cool CD, Clambey ET, van Dyk LF. Host Tumor Suppressor p18(INK4c) Functions as a Potent Cell-Intrinsic Inhibitor of Murine Gammaherpesvirus 68 Reactivation and Pathogenesis. J Virol. 2018 Mar 15;92(6). PubMed PMID: 29298882
• Kimball AK, Oko LM, Bullock BL, Nemenoff RA, van Dyk LF, Clambey ET. A Beginner's Guide to Analyzing and Visualizing Mass Cytometry Data. J Immunol. 2018 Jan 1;200(1):3-22. PubMed PMID: 29255085
• Kimball AK, Oko LM, Kaspar RE, van Dyk LF, Clambey ET. High-Dimensional Characterization of IL-10 Production and IL-10-Dependent Regulation during Primary Gammaherpesvirus Infection. Immunohorizons. 2019 Mar 21;3(3):94-109. PubMed PMID: 31356152
• O'Grady T, Feswick A, Hoffman BA, Wang Y, Medina EM, Kara M, van Dyk LF, Flemington EK, Tibbetts SA. Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68. Cell Rep. 2019 Jun 25;27(13):3988-4002.e5. PubMed PMID: 31242428
• Oko LM, Kimball AK, Kaspar RE, Knox AN, Coleman CB, Rochford R, Chang T, Alderete B, van Dyk LF, Clambey ET. Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression. PLoS Pathog. 2019 Jun;15(6):e1007849. PubMed PMID: 31166996
• Ashley N. Knox, Alice Mueller, Eva M. Medina, Eric T. Clambey, Linda F. van Dyk. Lytic infection with murine gammaherpesvirus 68 activates host and viral RNA polymerase III-dependent promoters to enhance non-coding RNA expression. bioRxiv 795278; doi: https://doi.org/10.1101/795278
• Niemeyer BF, Gibson J, Berger J, Oko L, Medina E, Clambey ET and van Dyk LF. The gammaherpesvirus 68 viral cyclin facilitates reactivation by promoting latent gene expression. In revision for PLoS Pathogens (PPathogens-D-19-01728; preprint available at BioRxiv doi: https://doi.org/10.1101/761700)
• Knox A, Mueller A, Medina E, Clambey ET, van Dyk LF. Lytic infection with murine gammaherpesvirus 68 activates host and viral RNA polymerase III-dependent promoters to enhance non-coding RNA expression. In revision for J Virol (JVI01721-19; preprint available BioRxiv doi: https://doi.org/10.1101/795278).
• Berger J, Sanford B, Kimball A, Oko L, Kaspar R, Niemeyer BF, Jones KL, Clambey ET and van Dyk LF. Redefining De Novo Gammaherpesvirus Infection Through High-Dimensional, Single-Cell Analysis of Virus and Host. in revision for eLIFE (27-08-2020-RA-eLife-62541; preprint available at BioRxiv doi: https://doi.org/10.1101/2020.08.11.203117).
• Brian F Niemeyer, Joy E Gibson, Jennifer N Berger, Lauren M Oko, Eva Medina, Eric T Clambey, Linda F van Dyk. The gammaherpesvirus 68 viral cyclin facilitates reactivation by promoting latent gene expression. bioRxiv 761700; doi: https://doi.org/10.1101/761700
• Niemeyer BF, Sanford B, Gibson JE, Berger JN, Oko LM, Medina E, Clambey ET, van Dyk LF. The gammaherpesvirus 68 viral cyclin facilitates expression of LANA. PLoS Pathog. 2021 Nov;17(11):e1010019. PubMed PMID: 34780571
• Knox AN, Mueller A, Medina EM, Clambey ET, van Dyk LF. Lytic Infection with Murine Gammaherpesvirus 68 Activates Host and Viral RNA Polymerase III Promoters and Enhances Noncoding RNA Expression. J Virol. 2021 Jun 24;95(14):e0007921. PubMed PMID: 33910955
• Riggs JB, Medina EM, Perrenoud LJ, Bonilla DL, Clambey ET, van Dyk LF, Berg LJ. Optimized Detection of Acute MHV68 Infection With a Reporter System Identifies Large Peritoneal Macrophages as a Dominant Target of Primary Infection. Front Microbiol. 2021;12:656979. PubMed PMID: 33767688
• Gammaherpesvirus ncRNAs share conserved features of binding and virulence despite lack of sequence conservation Ashley N. Knox, Eva M. Medina, Darby G. Oldenburg, Eric T. Clambey, Linda F. van Dyk bioRxiv 2022.05.09.491269; doi: https://doi.org/10.1101/2022.05.09.491269
• Vragel G, Gomez BD, Kostelecky RE, Noell KS, Tseng A, Cohen S, Dalwadi M, Medina EM, Nail EA, Goodspeed A, Clambey ET, van Dyk LF. Murine Gammaherpesvirus 68 Efficiently Infects Myeloid Cells Resulting In An Atypical, Restricted Form Of Infection. bioRxiv. 2023 Jun 29. PubMed PMID: 37425871