Publications

The following journal articles were published using Core technology. Others relate to the lab and the processes utilized by the core.

Sequencing/Bioinformatics

Dittmer, D. P., Yang, D., Sanders, M., Xiong, J., Texier, J., & Bigi, R. (2015). VIRONOMICS: The study of viral genomics in human cancer and disease. In Next Generation Sequencing in Cancer Research, Volume 2: From Basepairs to Bedsides. (pp. 345-366). Springer International Publishing. 10.1007/978-3-319-15811-2_20

  1. Complete Genome Sequences of Mandrillus leucophaeus and Papio ursinus Cytomegaloviruses.
    Earl Linwood Blewett, Carly J. Sherrod, Jordan R. Texier, Tom M. Conrad, Dirk P. Dittmer.
    Genome Announc. 2015 Aug 6;3(4). pii: e00781-15. doi: 10.1128/genomeA.00781-15.

  2. Hepatitis C Virus (HCV) NS3 sequence diversity and antiviral resistance-associated variant frequency in HCV/HIV coinfection.
    Jabara CB, Hu F, Mollan KR, Williford SE, Menezes P, Yang Y, Eron JJ, Fried MW, Hudgens MG, Jones CD, Swanstrom R, Lemon SM.
    Antimicrob Agents Chemother. 2014 Oct;58(10):6079-92. doi: 10.1128/AAC.03466-14. Epub 2014 Aug 4.

  3. Complete genome sequence of cell culture-attenuated Guinea pig cytomegalovirus cloned as an infectious bacterial artificial chromosome.
    Yang D, Alam Z, Cui X, Chen M, Sherrod CJ, McVoy MA, Schleiss MR, Dittmer DP.
    Genome Announc. 2014 Oct 16;2(5). pii: e00928-14. doi: 10.1128/genomeA.00928-14. 
  4. Recent cancer incidence trends in an observational clinical cohort of HIV-infected patients in the US, 2000 to 2011.
    Yanik EL, Tamburro K, Eron JJ, Damania B, Napravnik S, Dittmer DP.
    Infect Agent Cancer. 2013 May 24;8(1):18. 
  5.  Poisson factor models with applications to non-normalized microRNA profiling.
    Lee S, Chugh PE, Shen H, Eberle R, Dittmer DP.
    Bioinformatics. 2013 May 1;29(9):1105-11. 
  6. Complete genome sequence of pathogenic Guinea pig cytomegalovirus from salivary gland homogenates of infected animals.
    Yang D, Tamburro K, Dittmer D, Cui X, McVoy MA, Hernandez-Alvarado N, Schleiss MR.
    Genome Announc. 2013 Mar 14;1(2):e0005413.
  7. Vironome of Kaposi sarcoma associated herpesvirus-inflammatory cytokine syndrome in an AIDS patient reveals co-infection of human herpesvirus 8 and human herpesvirus 6A.
    Tamburro KM, Yang D, Poisson J, Fedoriw Y, Roy D, Lucas A, Sin SH, Malouf N, Moylan V, Damania B, Moll S, van der Horst C, Dittmer DP. 
    Virology. 2012 Nov 10;433(1):220-5.

Viral qPCR assays (recent) 

  1.  Kaposi's Sarcoma-Associated Herpesvirus Latency Locus Compensates for Interleukin-6 in Initial B Cell Activation.
    Sin SH, Kang SA, Kim Y, Eason A, Tan K, An H, Dittmer DP. 
    J Virol. 2015 Dec 9;90(4):2150-4. doi: 10.1128/JVI.02456-15.

  2. Modulation of the cGAS-STING DNA sensing pathway by gammaherpesviruses.
    Ma Z, Jacobs SR, West JA, Stopford C, Zhang Z, Davis Z, Barber GN, Glaunsinger BA, Dittmer DP, Damania B.
    Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4306-15. doi: 10.1073/pnas.1503831112. Epub 2015 Jul 21.

  3. Characteristics and survival for HIV-associated multicentric Castleman disease in Malawi. 
    Gopal S, Liomba NG, Montgomery ND, Moses A, Kaimila B, Nyasosela R, Chikasema M, Dhungel BM, Kampani C, Sanders MK, Krysiak R, Dittmer DP, Fedoriw Y. 
    J Int AIDS Soc. 2015 Aug 3;18:20122. doi: 10.7448/IAS.18.1.20122. eCollection 2015.

  4. Viral profiling identifies multiple subtypes of Kaposi's sarcoma.
    Hosseinipour MC, Sweet KM, Xiong J, Namarika D, Mwafongo A, Nyirenda M, Chiwoko L, Kamwendo D, Hoffman I, Lee J, Phiri S, Vahrson W, Damania B, Dittmer DP.
    MBio. 2014 Sep 23;5(5):e01633-14. doi: 10.1128/mBio.01633-14.

  5. Multicentric Castleman's disease in Malawi.
    Gopal S, Fedoriw Y, Montgomery ND, Kampani C, Krysiak R, Sanders MK, Dittmer DP, Liomba NG.
    Lancet. 2014 Sep 20;384(9948):1158. doi: 10.1016/S0140-6736(14)61366-0.

  6. An important role for mitochondrial antiviral signaling protein in the Kaposi's sarcoma-associated herpesvirus life cycle.
    West JA, Wicks M, Gregory SM, Chugh P, Jacobs SR, Zhang Z, Host KM, Dittmer DP, Damania B.
    J Virol. 2014 May;88(10):5778-87. doi: 10.1128/JVI.03226-13. Epub 2014 Mar 12.

  7. Maribavir inhibits Epstein-Barr virus transcription through the EBV protein kinase.
    Whitehurst CB, Sanders MK, Law M, Wang FZ, Xiong J, Dittmer DP, Pagano JS.
    J Virol. 2013 May;87(9):5311-5. 
  8. Tousled-like kinases modulate reactivation of gammaherpesviruses from latency.
    Dillon PJ, Gregory SM, Tamburro K, Sanders MK, Johnson GL, Raab-Traub N, Dittmer DP, Damania B.
    Cell Host Microbe. 2013 Feb 13;13(2):204-14. 
  9. mTOR inhibitors block Kaposi sarcoma growth by inhibiting essential autocrine growth factors and tumor angiogenesis.
    Roy D, Sin SH, Lucas A, Venkataramanan R, Wang L, Eason A, Chavakula V, Hilton IB, Tamburro KM, Damania B, Dittmer DP.
    Cancer Res. 2013 Apr 1;73(7):2235-46. 
  10. Latent Kaposi's sarcoma-associated herpesvirus infection of monocytes downregulates expression of adaptive immune response costimulatory receptors and proinflammatory cytokines.
    Gregory SM, Wang L, West JA, Dittmer DP, Damania B.
    J Virol. 2012 Apr;86(7):3916-23. 
  11. Rapamycin with antiretroviral therapy in AIDS-associated Kaposi sarcoma: an AIDS Malignancy Consortium study.
    Krown SE, Roy D, Lee JY, Dezube BJ, Reid EG, Venkataramanan R, Han K, Cesarman E, Dittmer DP.
    J Acquir Immune Defic Syndr. 2012 Apr 15;59(5):447-54. 

miRNA assays

  1. Toll-like receptor-3 is dispensable for the innate microRNA response to West Nile virus (WNV).
    Chugh PE, Damania BA, Dittmer DP.
    PLoS One. 2014 Aug 15;9(8):e104770. doi: 10.1371/journal.pone.0104770. eCollection 2014.

  2. Expression profile of microRNAs in Epstein-Barr virus-infected AGS gastric carcinoma cells.
    Marquitz AR, Mathur A, Chugh PE, Dittmer DP, Raab-Traub N.
    J Virol. 2014 Jan;88(2):1389-93. doi: 10.1128/JVI.02662-13. Epub 2013 Nov 13.
  3. Viral latency locus complements miR-155 deficiency in vivo.
    Sin SH, Kim YB, Dittmer DP.
    J Virol. 2013 Aug 21. 
  4. Systemically Circulating Viral and Tumor-Derived MicroRNAs in KSHV-Associated Malignancies.
    Chugh PE, Sin SH, Ozgur S, Henry DH, Menezes P, Griffith J, Eron JJ, Damania B, Dittmer DP.
    PLoS Pathog. 2013 Jul;9(7):e1003484. 
  5. Potential pitfalls in microRNA profiling.
    Chugh P, Dittmer DP.
    Wiley Interdiscip Rev RNA. 2012 Sep-Oct;3(5):601-16. 
  6. Interferon-γ production by neutrophils during bacterial pneumonia in mice.
    Yamada M, Gomez JC, Chugh PE, Lowell CA, Dinauer MC, Dittmer DP, Doerschuk CM.
    Am J Respir Crit Care Med. 2011 May 15;183(10):1391-401. 
  7. Profiling of pre-micro RNAs and microRNAs using quantitative real-time PCR (qPCR) arrays.
    Chugh P, Tamburro K, Dittmer DP.
    J Vis Exp. 2010 Dec 3;(46). http://www.jove.com/index/details.stp?id=2210, doi: 10.3791/2210
  1. Pre-micro RNA signatures delineate stages of endothelial cell transformation in Kaposi sarcoma.
    O'Hara AJ, Chugh P, Wang L, Netto EM, Luz E, Harrington WJ, Dezube BJ, Damania B, Dittmer DP.
    PLoS Pathog. 2009 Apr;5(4):e1000389. 
  2. Tumor suppressor microRNAs are underrepresented in primary effusion lymphoma and Kaposi sarcoma.
    O'Hara AJ, Wang L, Dezube BJ, Harrington WJ Jr, Damania B, Dittmer DP.
    Blood. 2009 Jun 4;113(23):5938-41. 
  3. EBV microRNAs in primary lymphomas and targeting of CXCL-11 by ebv-mir-BHRF1-3.
    Xia T, O'Hara A, Araujo I, Barreto J, Carvalho E, Sapucaia JB, Ramos JC, Luz E, Pedroso C, Manrique M, Toomey NL, Brites C, Dittmer DP, Harrington WJ Jr.
    Cancer Res. 2008 Mar 1;68(5):1436-42. d
  4. Gene alteration and precursor and mature microRNA transcription changes contribute to the miRNA signature of primary effusion lymphoma.
    O'Hara AJ, Vahrson W, Dittmer DP.
    Blood. 2008 Feb 15;111(4):2347-53. 

(2010 and older):

1. Efficiency clustering for low-density microarrays and its application to QPCR.
Lock EF, Ziemiecke R, Marron J, Dittmer DP.
BMC Bioinformatics. 2010 Jul 20;11:386.
PMID: 20646303 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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2. Genome-wide real-time PCR for West Nile virus reduces the false-negative rate and facilitates new strain discovery.
Papin JF, Vahrson W, Larson L, Dittmer DP.
J Virol Methods. 2010 Oct;169(1):103-11. Epub 2010 Jul 14.
PMID: 20637239 [PubMed - in process]
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3. Molecular and clinical assessment in the treatment of AIDS Kaposi sarcoma with valproic Acid.
Lechowicz M, Dittmer DP, Lee JY, Krown SE, Wachsman W, Aboulafia D, Dezube BJ, Ratner L, Said J, Ambinder RF.
Clin Infect Dis. 2009 Dec 15;49(12):1946-9.
PMID: 19911999 [PubMed - indexed for MEDLINE]
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4. Maribavir inhibits epstein-barr virus transcription in addition to viral DNA replication.
Wang FZ, Roy D, Gershburg E, Whitehurst CB, Dittmer DP, Pagano JS.
J Virol. 2009 Dec;83(23):12108-17. Epub 2009 Sep 16.
PMID: 19759127 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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5. General and target-specific RNA binding properties of Epstein-Barr virus SM posttranscriptional regulatory protein.
Han Z, Verma D, Hilscher C, Dittmer DP, Swaminathan S.
J Virol. 2009 Nov;83(22):11635-44. Epub 2009 Sep 2.
PMID: 19726500 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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6. Disruption of LANA in rhesus rhadinovirus generates a highly lytic recombinant virus.
Wen KW, Dittmer DP, Damania B.
J Virol. 2009 Oct;83(19):9786-802. Epub 2009 Jul 8.
PMID: 19587030 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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7. Multiple pathways for Epstein-Barr virus episome loss from nasopharyngeal carcinoma.
Dittmer DP, Hilscher CJ, Gulley ML, Yang EV, Chen M, Glaser R.
Int J Cancer. 2008 Nov 1;123(9):2105-12.
PMID: 18688856 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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8. EBV microRNAs in primary lymphomas and targeting of CXCL-11 by ebv-mir-BHRF1-3.
Xia T, O'Hara A, Araujo I, Barreto J, Carvalho E, Sapucaia JB, Ramos JC, Luz E, Pedroso C, Manrique M, Toomey NL, Brites C, Dittmer DP, Harrington WJ Jr.
Cancer Res. 2008 Mar 1;68(5):1436-42.
PMID: 18316607 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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9. Development of a fluorescence-based assay to screen antiviral drugs against Kaposi's sarcoma associated herpesvirus.
Nun TK, Kroll DJ, Oberlies NH, Soejarto DD, Case RJ, Piskaut P, Matainaho T, Hilscher C, Wang L, Dittmer DP, Gao SJ, Damania B.
Mol Cancer Ther. 2007 Aug;6(8):2360-70.
PMID: 17699731 [PubMed - indexed for MEDLINE] Free Article
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10. In vivo-restricted and reversible malignancy induced by human herpesvirus-8 KSHV: a cell and animal model of virally induced Kaposi's sarcoma.
Mutlu AD, Cavallin LE, Vincent L, Chiozzini C, Eroles P, Duran EM, Asgari Z, Hooper AT, La Perle KM, Hilsher C, Gao SJ, Dittmer DP, Rafii S, Mesri EA.
Cancer Cell. 2007 Mar;11(3):245-58. Erratum in: Cancer Cell. 2007 May;11(5):471.
PMID: 17349582 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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11. Functional p53 signaling in Kaposi's sarcoma-associated herpesvirus lymphomas: implications for therapy.
Petre CE, Sin SH, Dittmer DP.
J Virol. 2007 Feb;81(4):1912-22. Epub 2006 Nov 22.
PMID: 17121789 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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12. Reactivation of Kaposi's sarcoma-associated herpesvirus by natural products from Kaposi's sarcoma endemic regions.
Whitby D, Marshall VA, Bagni RK, Miley WJ, McCloud TG, Hines-Boykin R, Goedert JJ, Conde BA, Nagashima K, Mikovits J, Dittmer DP, Newman DJ.
Int J Cancer. 2007 Jan 15;120(2):321-8.
PMID: 17066452 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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13. Faster quantitative real-time PCR protocols may lose sensitivity and show increased variability.
Hilscher C, Vahrson W, Dittmer DP.
Nucleic Acids Res. 2005 Nov 27;33(21):e182.
PMID: 16314296 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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14. Role of Notch signal transduction in Kaposi's sarcoma-associated herpesvirus gene expression.
Chang H, Dittmer DP, Shin YC, Hong Y, Jung JU.
J Virol. 2005 Nov;79(22):14371-82. Erratum in: J Virol. 2006 Apr;80(8):4203. Chul, Shin-Young [corrected to Shin, Young C].
PMID: 16254371 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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15. Whole-genome transcription profiling of rhesus monkey rhadinovirus.
Dittmer DP, Gonzalez CM, Vahrson W, DeWire SM, Hines-Boykin R, Damania B.
J Virol. 2005 Jul;79(13):8637-50.
PMID: 15956606 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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16. Real-time quantitative PCR analysis of viral transcription.
Papin J, Vahrson W, Hines-Boykin R, Dittmer DP.
Methods Mol Biol. 2005;292:449-80.
PMID: 15507725 [PubMed - indexed for MEDLINE]
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17. SYBR green-based real-time quantitative PCR assay for detection of West Nile Virus circumvents false-negative results due to strain variability.
Papin JF, Vahrson W, Dittmer DP.
J Clin Microbiol. 2004 Apr;42(4):1511-8.
PMID: 15070997 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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18. Transcription profile of Kaposi's sarcoma-associated herpesvirus in primary Kaposi's sarcoma lesions as determined by real-time PCR arrays.
Dittmer DP.
Cancer Res. 2003 May 1;63(9):2010-5.
PMID: 12727810 [PubMed - indexed for MEDLINE] Free Article
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19. Charting latency transcripts in Kaposi's sarcoma-associated herpesvirus by whole-genome real-time quantitative PCR.
Fakhari FD, Dittmer DP.
J Virol. 2002 Jun;76(12):6213-23.
PMID: 12021355 [PubMed - indexed for MEDLINE] Free PMC Article Free text
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