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Items: 1 to 50 of 65

1.

An innovative study design to assess the community effect of interventions to mitigate HIV epidemics using transmission-chain phylodynamics.

Magiorkinis G, Karamitros T, Vasylyeva TI, Williams LD, Mbisa JL, Hatzakis A, Paraskevis D, Friedman SR.

Am J Epidemiol. 2018 Aug 7. doi: 10.1093/aje/kwy160. [Epub ahead of print]

PMID:
30101288
2.

Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations.

Karamitros T, van Wilgenburg B, Wills M, Klenerman P, Magiorkinis G.

BMC Genomics. 2018 Aug 2;19(1):577. doi: 10.1186/s12864-018-4949-6.

3.

Impact of Interferon-α Receptor-1 Promoter Polymorphisms on the Transcriptome of the Hepatitis B Virus-Associated Hepatocellular Carcinoma.

Karamitros T, Papatheodoridis G, Paraskevis D, Hatzakis A, Mbisa JL, Georgopoulou U, Klenerman P, Magiorkinis G.

Front Immunol. 2018 Apr 16;9:777. doi: 10.3389/fimmu.2018.00777. eCollection 2018.

4.

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.

5.

Molecular Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Infected Individuals in a Network-Based Intervention (Transmission Reduction Intervention Project): Phylogenetics Identify HIV-1-Infected Individuals With Social Links.

Kostaki EG, Nikolopoulos GK, Pavlitina E, Williams L, Magiorkinis G, Schneider J, Skaathun B, Morgan E, Psichogiou M, Daikos GL, Sypsa V, Smyrnov P, Korobchuk A, Malliori M, Hatzakis A, Friedman SR, Paraskevis D.

J Infect Dis. 2018 Jul 24;218(5):707-715. doi: 10.1093/infdis/jiy239.

PMID:
29697829
6.

Spatiotemporal Characteristics of the HIV-1 CRF02_AG/CRF63_02A1 Epidemic in Russia and Central Asia.

Kostaki EG, Karamitros T, Bobkova M, Oikonomopoulou M, Magiorkinis G, Garcia F, Hatzakis A, Paraskevis D.

AIDS Res Hum Retroviruses. 2018 May;34(5):415-420. doi: 10.1089/AID.2017.0233. Epub 2018 Apr 5.

PMID:
29455562
7.

Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine.

Vasylyeva TI, Liulchuk M, Friedman SR, Sazonova I, Faria NR, Katzourakis A, Babii N, Scherbinska A, Thézé J, Pybus OG, Smyrnov P, Mbisa JL, Paraskevis D, Hatzakis A, Magiorkinis G.

Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):1051-1056. doi: 10.1073/pnas.1701447115. Epub 2018 Jan 16.

8.

Multiplexed Targeted Sequencing for Oxford Nanopore MinION: A Detailed Library Preparation Procedure.

Karamitros T, Magiorkinis G.

Methods Mol Biol. 2018;1712:43-51. doi: 10.1007/978-1-4939-7514-3_4.

PMID:
29224067
9.

Detailed Molecular Surveillance of the HIV-1 Outbreak Among People who Inject Drugs (PWID) in Athens During a Period of Four Years.

Kostaki E, Magiorkinis G, Psichogiou M, Flampouris A, Iliopoulos P, Papachristou E, Daikos GL, Bonovas S, Otelea D, Friedman SR, Hatzakis A, Paraskevis D.

Curr HIV Res. 2017;15(6):396-404. doi: 10.2174/1570162X15666171120104048.

PMID:
29165088
10.

Roles of Endogenous Retroviruses in Early Life Events.

Magiorkinis G, Katzourakis A, Lagiou P.

Trends Microbiol. 2017 Nov;25(11):876-877. doi: 10.1016/j.tim.2017.09.002. Epub 2017 Sep 29.

PMID:
28969881
11.

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data.

Santander CG, Gambron P, Marchi E, Karamitros T, Katzourakis A, Magiorkinis G.

Virus Evol. 2017 Aug 21;3(2):vex023. doi: 10.1093/ve/vex023. eCollection 2017 Jul.

12.

Prevalence of drug resistance among HIV-1 treatment-naive patients in Greece during 2003-2015: Transmitted drug resistance is due to onward transmissions.

Paraskevis D, Kostaki E, Magiorkinis G, Gargalianos P, Xylomenos G, Magiorkinis E, Lazanas M, Chini M, Nikolopoulos G, Skoutelis A, Papastamopoulos V, Antoniadou A, Papadopoulos A, Psichogiou M, Daikos GL, Oikonomopoulou M, Zavitsanou A, Chrysos G, Paparizos V, Kourkounti S, Sambatakou H, Sipsas NV, Lada M, Panagopoulos P, Maltezos E, Drimis S, Hatzakis A.

Infect Genet Evol. 2017 Oct;54:183-191. doi: 10.1016/j.meegid.2017.07.003. Epub 2017 Jul 5.

PMID:
28688977
13.

Epigenetic Control of Human Endogenous Retrovirus Expression: Focus on Regulation of Long-Terminal Repeats (LTRs).

Hurst TP, Magiorkinis G.

Viruses. 2017 May 31;9(6). pii: E130. doi: 10.3390/v9060130. Review.

14.

A network intervention that locates and intervenes with recently HIV-infected persons: The Transmission Reduction Intervention Project (TRIP).

Nikolopoulos GK, Pavlitina E, Muth SQ, Schneider J, Psichogiou M, Williams LD, Paraskevis D, Sypsa V, Magiorkinis G, Smyrnov P, Korobchuk A, Vasylyeva TI, Skaathun B, Malliori M, Kafetzopoulos E, Hatzakis A, Friedman SR.

Sci Rep. 2016 Dec 5;6:38100. doi: 10.1038/srep38100.

15.

Reducing HIV infection in people who inject drugs is impossible without targeting recently-infected subjects.

Vasylyeva TI, Friedman SR, Lourenco J, Gupta S, Hatzakis A, Pybus OG, Katzourakis A, Smyrnov P, Karamitros T, Paraskevis D, Magiorkinis G.

AIDS. 2016 Nov 28;30(18):2885-2890.

16.

A contaminant-free assessment of Endogenous Retroviral RNA in human plasma.

Karamitros T, Paraskevis D, Hatzakis A, Psichogiou M, Elefsiniotis I, Hurst T, Geretti AM, Beloukas A, Frater J, Klenerman P, Katzourakis A, Magiorkinis G.

Sci Rep. 2016 Sep 19;6:33598. doi: 10.1038/srep33598.

17.

The application of HIV molecular epidemiology to public health.

Paraskevis D, Nikolopoulos GK, Magiorkinis G, Hodges-Mameletzis I, Hatzakis A.

Infect Genet Evol. 2016 Dec;46:159-168. doi: 10.1016/j.meegid.2016.06.021. Epub 2016 Jun 14. Review.

PMID:
27312102
18.

De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

Karamitros T, Harrison I, Piorkowska R, Katzourakis A, Magiorkinis G, Mbisa JL.

PLoS One. 2016 Jun 16;11(6):e0157600. doi: 10.1371/journal.pone.0157600. eCollection 2016.

19.

The global spread of HIV-1 subtype B epidemic.

Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB; SPREAD program, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D.

Infect Genet Evol. 2016 Dec;46:169-179. doi: 10.1016/j.meegid.2016.05.041. Epub 2016 Jun 2.

20.

Integrating molecular epidemiology and social network analysis to study infectious diseases: Towards a socio-molecular era for public health.

Vasylyeva TI, Friedman SR, Paraskevis D, Magiorkinis G.

Infect Genet Evol. 2016 Dec;46:248-255. doi: 10.1016/j.meegid.2016.05.042. Epub 2016 Jun 2. Review.

21.

Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada.

Jacka B, Applegate T, Poon AF, Raghwani J, Harrigan PR, DeBeck K, Milloy MJ, Krajden M, Olmstead A, Joy JB, Marshall BD, Hayashi K, Pybus OG, Lima VD, Magiorkinis G, Montaner J, Lamoury F, Dore GJ, Wood E, Grebely J.

J Hepatol. 2016 Jun;64(6):1247-55. doi: 10.1016/j.jhep.2016.02.031. Epub 2016 Feb 26.

22.

Human endogenous retrovirus (HERV) expression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency.

Hurst T, Pace M, Katzourakis A, Phillips R, Klenerman P, Frater J, Magiorkinis G.

Retrovirology. 2016 Feb 6;13:10. doi: 10.1186/s12977-016-0242-4.

23.

Enhanced HIV-1 surveillance using molecular epidemiology to study and monitor HIV-1 outbreaks among intravenous drug users (IDUs) in Athens and Bucharest.

Paraskevis D, Paraschiv S, Sypsa V, Nikolopoulos G, Tsiara C, Magiorkinis G, Psichogiou M, Flampouris A, Mardarescu M, Niculescu I, Batan I, Malliori M, Otelea D, Hatzakis A.

Infect Genet Evol. 2015 Oct;35:109-21. doi: 10.1016/j.meegid.2015.08.004. Epub 2015 Aug 4.

PMID:
26247720
24.

A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits.

Karamitros T, Magiorkinis G.

Nucleic Acids Res. 2015 Dec 15;43(22):e152. doi: 10.1093/nar/gkv773. Epub 2015 Aug 3.

25.

Dating the origin of hepatitis B virus reveals higher substitution rate and adaptation on the branch leading to F/H genotypes.

Paraskevis D, Angelis K, Magiorkinis G, Kostaki E, Ho SY, Hatzakis A.

Mol Phylogenet Evol. 2015 Dec;93:44-54. doi: 10.1016/j.ympev.2015.07.010. Epub 2015 Jul 26.

PMID:
26220838
26.

Activation of the innate immune response by endogenous retroviruses.

Hurst TP, Magiorkinis G.

J Gen Virol. 2015 Jun;96(Pt 6):1207-18. doi: 10.1099/jgv.0.000017. Review. Erratum in: J Gen Virol. 2015 Aug;96(8):2470.

PMID:
26068187
27.

The interferon receptor-1 promoter polymorphisms affect the outcome of Caucasians with HBeAg-negative chronic HBV infection.

Karamitros T, Papatheodoridis G, Dimopoulou E, Papageorgiou MV, Paraskevis D, Magiorkinis G, Sypsa V, Hatzakis A.

Liver Int. 2015 Dec;35(12):2506-13. doi: 10.1111/liv.12859. Epub 2015 May 17.

PMID:
25939635
28.

Prevention of early HIV transmissions might be more important in emerging or generalizing epidemics.

Vasylyeva TI, Friedman SR, Magiorkinis G.

Proc Natl Acad Sci U S A. 2015 Mar 31;112(13):E1515. doi: 10.1073/pnas.1424168112. Epub 2015 Mar 3. No abstract available.

29.

The decline of human endogenous retroviruses: extinction and survival.

Magiorkinis G, Blanco-Melo D, Belshaw R.

Retrovirology. 2015 Feb 2;12:8. doi: 10.1186/s12977-015-0136-x.

30.

Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia.

Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, Struck D, Vercauteren J, Wensing AM, Alexiev I, Åsjö B, Balotta C, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej S, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Boucher CA, Kaplan L, Vandamme AM, Paraskevis D.

J Infect Dis. 2015 Jun 1;211(11):1735-44. doi: 10.1093/infdis/jiu666. Epub 2014 Dec 15.

PMID:
25512631
31.

Phylogenetic clustering of hepatitis C virus among people who inject drugs in Vancouver, Canada.

Jacka B, Applegate T, Krajden M, Olmstead A, Harrigan PR, Marshall B, DeBeck K, Milloy MJ, Lamoury F, Pybus OG, Lima VD, Magiorkinis G, Montoya V, Montaner J, Joy J, Woods C, Dobrer S, Dore GJ, Poon AF, Grebely J.

Hepatology. 2014 Nov;60(5):1571-1580. doi: 10.1002/hep.27310. Epub 2014 Sep 29.

32.

Larger mammalian body size leads to lower retroviral activity.

Katzourakis A, Magiorkinis G, Lim AG, Gupta S, Belshaw R, Gifford R.

PLoS Pathog. 2014 Jul 17;10(7):e1004214. doi: 10.1371/journal.ppat.1004214. eCollection 2014 Jul.

33.

Unfixed endogenous retroviral insertions in the human population.

Marchi E, Kanapin A, Magiorkinis G, Belshaw R.

J Virol. 2014 Sep 1;88(17):9529-37. doi: 10.1128/JVI.00919-14. Epub 2014 Jun 11.

34.

Prevalence and clinical manifestations of ankylosing spondylitis in young Greek males.

Kassimos DG, Vassilakos J, Magiorkinis G, Garyfallos A.

Clin Rheumatol. 2014 Sep;33(9):1303-6. doi: 10.1007/s10067-014-2574-6. Epub 2014 Mar 20.

PMID:
24647983
35.

Neanderthal and Denisovan retroviruses in modern humans.

Marchi E, Kanapin A, Byott M, Magiorkinis G, Belshaw R.

Curr Biol. 2013 Nov 18;23(22):R994-R995. doi: 10.1016/j.cub.2013.10.028. No abstract available.

36.

Socially-integrated transdisciplinary HIV prevention.

Friedman SR, Downing MJ Jr, Smyrnov P, Nikolopoulos G, Schneider JA, Livak B, Magiorkinis G, Slobodianyk L, Vasylyeva TI, Paraskevis D, Psichogiou M, Sypsa V, Malliori MM, Hatzakis A.

AIDS Behav. 2014 Oct;18(10):1821-34. doi: 10.1007/s10461-013-0643-5.

37.

Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses.

Pavesi A, Magiorkinis G, Karlin DG.

PLoS Comput Biol. 2013;9(8):e1003162. doi: 10.1371/journal.pcbi.1003162. Epub 2013 Aug 15.

38.

Evolutionary analysis of hepatitis C virus gene sequences from 1953.

Gray RR, Tanaka Y, Takebe Y, Magiorkinis G, Buskell Z, Seeff L, Alter HJ, Pybus OG.

Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12;368(1626):20130168. doi: 10.1098/rstb.2013.0168. Print 2013 Sep 19.

39.

'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era.

Magiorkinis G, Belshaw R, Katzourakis A.

Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12;368(1626):20120504. doi: 10.1098/rstb.2012.0504. Print 2013 Sep 19. Review.

40.

Mediterranean diet intervention for patients with hyperuricemia: a pilot study.

Chatzipavlou M, Magiorkinis G, Koutsogeorgopoulou L, Kassimos D.

Rheumatol Int. 2014 Jun;34(6):759-62. doi: 10.1007/s00296-013-2690-7. Epub 2013 Feb 13.

PMID:
23404078
41.

Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics.

Magiorkinis G, Sypsa V, Magiorkinis E, Paraskevis D, Katsoulidou A, Belshaw R, Fraser C, Pybus OG, Hatzakis A.

PLoS Comput Biol. 2013;9(1):e1002876. doi: 10.1371/journal.pcbi.1002876. Epub 2013 Jan 31.

42.

Dating the origin and dispersal of hepatitis B virus infection in humans and primates.

Paraskevis D, Magiorkinis G, Magiorkinis E, Ho SY, Belshaw R, Allain JP, Hatzakis A.

Hepatology. 2013 Mar;57(3):908-16. doi: 10.1002/hep.26079. Epub 2013 Feb 7.

PMID:
22987324
43.

Env-less endogenous retroviruses are genomic superspreaders.

Magiorkinis G, Gifford RJ, Katzourakis A, De Ranter J, Belshaw R.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):7385-90. doi: 10.1073/pnas.1200913109. Epub 2012 Apr 23.

44.

Molecular typing of the recently expanding subtype B HIV-1 epidemic in Romania: evidence for local spread among MSMs in Bucharest area.

Paraschiv S, Otelea D, Batan I, Baicus C, Magiorkinis G, Paraskevis D.

Infect Genet Evol. 2012 Jul;12(5):1052-7. doi: 10.1016/j.meegid.2012.03.003. Epub 2012 Mar 10.

45.

Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships.

Beloukas A, Magiorkinis E, Magiorkinis G, Zavitsanou A, Karamitros T, Hatzakis A, Paraskevis D.

Virus Res. 2012 Jun;166(1-2):54-60. doi: 10.1016/j.virusres.2012.03.002. Epub 2012 Mar 12.

PMID:
22429620
46.

A novel bunyavirus in China.

Magiorkinis G.

N Engl J Med. 2011 Sep 1;365(9):864; author reply 864-5. doi: 10.1056/NEJMc1106000. No abstract available.

PMID:
21879911
47.

Mouse viruses and human disease.

Magiorkinis G.

Lancet Infect Dis. 2011 Apr;11(4):264. doi: 10.1016/S1473-3099(11)70081-0. No abstract available.

PMID:
21453870
48.

Appearance of a single amino acid insertion at position 33 in HIV type 1 protease under a lopinavir-containing regimen, associated with reduced protease inhibitor susceptibility.

Magiorkinis E, Paraskevis D, Detsika MG, Lu L, Magiorkinis G, Lazanas M, Imbrechts S, Van Laethem K, Vandamme AM, Pilot-Matias T, Molla A, Camacho RJ, Hatzakis A.

AIDS Res Hum Retroviruses. 2011 Nov;27(11):1223-9. doi: 10.1089/AID.2010.0275. Epub 2011 May 13.

PMID:
21417947
49.

The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis.

Magiorkinis G, Magiorkinis E, Paraskevis D, Ho SY, Shapiro B, Pybus OG, Allain JP, Hatzakis A.

PLoS Med. 2009 Dec;6(12):e1000198. doi: 10.1371/journal.pmed.1000198. Epub 2009 Dec 15.

50.

Quantitative detection of the M204V hepatitis B virus minor variants by amplification refractory mutation system real-time PCR combined with molecular beacon technology.

Ntziora F, Paraskevis D, Haida C, Magiorkinis E, Manesis E, Papatheodoridis G, Manolakopoulos S, Beloukas A, Chryssoy S, Magiorkinis G, Sypsa V, Hatzakis A.

J Clin Microbiol. 2009 Aug;47(8):2544-50. doi: 10.1128/JCM.00045-09. Epub 2009 Jun 24.

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