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Items: 1 to 50 of 150

1.

Entropy of mitochondrial DNA circulating in blood is associated with hepatocellular carcinoma.

Campo DS, Nayak V, Srinivasamoorthy G, Khudyakov Y.

BMC Med Genomics. 2019 Jun 6;12(Suppl 4):74. doi: 10.1186/s12920-019-0506-7.

2.

HCV transmission in high-risk communities in Bulgaria.

Ganova-Raeva L, Dimitrova Z, Alexiev I, Punkova L, Sue A, Xia GL, Gancheva A, Dimitrova R, Kostadinova A, Golkocheva-Markova E, Khudyakov Y.

PLoS One. 2019 Mar 5;14(3):e0212350. doi: 10.1371/journal.pone.0212350. eCollection 2019.

3.

Recent and occult hepatitis B virus infections among blood donors in the United States.

Ramachandran S, Groves JA, Xia GL, Saá P, Notari EP, Drobeniuc J, Poe A, Khudyakov N, Schillie SF, Murphy TV, Kamili S, Teo CG, Dodd RY, Khudyakov YE, Stramer SL.

Transfusion. 2019 Feb;59(2):601-611. doi: 10.1111/trf.15057. Epub 2018 Nov 30.

PMID:
30499591
4.

A large HCV transmission network enabled a fast-growing HIV outbreak in rural Indiana, 2015.

Ramachandran S, Thai H, Forbi JC, Galang RR, Dimitrova Z, Xia GL, Lin Y, Punkova LT, Pontones PR, Gentry J, Blosser SJ, Lovchik J, Switzer WM, Teshale E, Peters P, Ward J, Khudyakov Y; Hepatitis C Investigation Team.

EBioMedicine. 2018 Nov;37:374-381. doi: 10.1016/j.ebiom.2018.10.007. Epub 2018 Nov 15.

5.

Automated quality control for a molecular surveillance system.

Sims S, Longmire AG, Campo DS, Ramachandran S, Medrzycki M, Ganova-Raeva L, Lin Y, Sue A, Thai H, Zelikovsky A, Khudyakov Y.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):358. doi: 10.1186/s12859-018-2329-5.

6.

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants.

Tsyvina V, Campo DS, Sims S, Zelikovsky A, Khudyakov Y, Skums P.

BMC Bioinformatics. 2018 Oct 22;19(Suppl 11):360. doi: 10.1186/s12859-018-2333-9.

7.

HCV adaptation to HIV coinfection.

Lara J, Teka MA, Sims S, Xia GL, Ramachandran S, Khudyakov Y.

Infect Genet Evol. 2018 Nov;65:216-225. doi: 10.1016/j.meegid.2018.07.039. Epub 2018 Jul 31.

PMID:
30075255
8.

Intelligent Network DisRuption Analysis (INDRA): A targeted strategy for efficient interruption of hepatitis C transmissions.

Campo DS, Khudyakov Y.

Infect Genet Evol. 2018 Sep;63:204-215. doi: 10.1016/j.meegid.2018.05.028. Epub 2018 May 31.

9.

Reactivation of a Vaccine Escape Hepatitis B Virus Mutant in a Cambodian Patient During Anti-Hepatitis C Virus Therapy.

Fusco DN, Ganova-Raeva L, Khudyakov Y, Punkova L, Mohamed A, Cheon SSY, Koirala P, Andersson KL, Jourdain G, Sureau C, Chung RT, Lauer G.

Front Med (Lausanne). 2018 Apr 30;5:97. doi: 10.3389/fmed.2018.00097. eCollection 2018.

10.

QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data.

Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y.

Bioinformatics. 2018 Jan 1;34(1):163-170. doi: 10.1093/bioinformatics/btx402.

11.

Inference of genetic relatedness between viral quasispecies from sequencing data.

Glebova O, Knyazev S, Melnyk A, Artyomenko A, Khudyakov Y, Zelikovsky A, Skums P.

BMC Genomics. 2017 Dec 6;18(Suppl 10):918. doi: 10.1186/s12864-017-4274-5.

12.

GHOST: global hepatitis outbreak and surveillance technology.

Longmire AG, Sims S, Rytsareva I, Campo DS, Skums P, Dimitrova Z, Ramachandran S, Medrzycki M, Thai H, Ganova-Raeva L, Lin Y, Punkova LT, Sue A, Mirabito M, Wang S, Tracy R, Bolet V, Sukalac T, Lynberg C, Khudyakov Y.

BMC Genomics. 2017 Dec 6;18(Suppl 10):916. doi: 10.1186/s12864-017-4268-3.

13.

Transmissibility of intra-host hepatitis C virus variants.

Campo DS, Zhang J, Ramachandran S, Khudyakov Y.

BMC Genomics. 2017 Dec 6;18(Suppl 10):881. doi: 10.1186/s12864-017-4267-4.

14.
15.

Efficient detection of viral transmissions with Next-Generation Sequencing data.

Rytsareva I, Campo DS, Zheng Y, Sims S, Thankachan SV, Tetik C, Chirag J, Chockalingam SP, Sue A, Aluru S, Khudyakov Y.

BMC Genomics. 2017 May 24;18(Suppl 4):372. doi: 10.1186/s12864-017-3732-4.

16.

Molecular epidemiology of hepatitis B virus infection in Tanzania.

Forbi JC, Dillon M, Purdy MA, Drammeh BS, Tejada-Strop A, McGovern D, Xia GL, Lin Y, Ganova-Raeva LM, Campo DS, Thai H, Vaughan G, Haule D, Kutaga RP, Basavaraju SV, Kamili S, Khudyakov YE.

J Gen Virol. 2017 May 25. doi: 10.1099/jgv.0.000776. [Epub ahead of print]

PMID:
28537543
17.

Transmission of Hepatitis A Virus through Combined Liver-Small Intestine-Pancreas Transplantation.

Foster MA, Weil LM, Jin S, Johnson T, Hayden-Mixson TR, Khudyakov Y, Annambhotla PD, Basavaraju SV, Kamili S, Ritter JM, Nelson N, Mazariegos G, Green M, Himes RW, Kuhar DT, Kuehnert MJ, Miller JA, Wiseman R, Moorman AC.

Emerg Infect Dis. 2017 Apr;23(4):590-596. doi: 10.3201/eid2304.161532.

18.

Increased Mitochondrial Genetic Diversity in Persons Infected With Hepatitis C Virus.

Campo DS, Roh HJ, Pearlman BL, Fierer DS, Ramachandran S, Vaughan G, Hinds A, Dimitrova Z, Skums P, Khudyakov Y.

Cell Mol Gastroenterol Hepatol. 2016 May 26;2(5):676-684. doi: 10.1016/j.jcmgh.2016.05.012. eCollection 2016 Sep.

19.

Hepatitis C virus transmission in a skilled nursing facility, North Dakota, 2013.

Calles DL, Collier MG, Khudyakov Y, Mixson-Hayden T, VanderBusch L, Weninger S, Miller TK; North Dakota Hepatitis C Virus Investigation Team.

Am J Infect Control. 2017 Feb 1;45(2):126-132. doi: 10.1016/j.ajic.2016.08.013. Epub 2016 Nov 2.

PMID:
27816216
20.

Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction.

Xu X, Thai H, Kitrinos KM, Xia G, Gaggar A, Paulson M, Ganova-Raeva L, Khudyakov Y, Lara J.

BMC Bioinformatics. 2016 Aug 31;17 Suppl 8:280. doi: 10.1186/s12859-016-1116-4.

21.

HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014-2015.

Peters PJ, Pontones P, Hoover KW, Patel MR, Galang RR, Shields J, Blosser SJ, Spiller MW, Combs B, Switzer WM, Conrad C, Gentry J, Khudyakov Y, Waterhouse D, Owen SM, Chapman E, Roseberry JC, McCants V, Weidle PJ, Broz D, Samandari T, Mermin J, Walthall J, Brooks JT, Duwve JM; Indiana HIV Outbreak Investigation Team.

N Engl J Med. 2016 Jul 21;375(3):229-39. doi: 10.1056/NEJMoa1515195.

22.

Notes from the Field: Health Care-Associated Hepatitis A Outbreak - Texas, 2015.

Wiseman R, Weil LM, Lozano C, Johnson TJ Jr, Jin S, Moorman AC, Foster MA, Mixson-Hayden T, Khudyakov Y, Kuhar DT, Graves J.

MMWR Morb Mortal Wkly Rep. 2016 Apr 29;65(16):425-6. doi: 10.15585/mmwr.mm6516a5.

23.

The spread of hepatitis C virus genotype 1a in North America: a retrospective phylogenetic study.

Joy JB, McCloskey RM, Nguyen T, Liang RH, Khudyakov Y, Olmstead A, Krajden M, Ward JW, Harrigan PR, Montaner JSG, Poon AFY.

Lancet Infect Dis. 2016 Jun;16(6):698-702. doi: 10.1016/S1473-3099(16)00124-9. Epub 2016 Mar 30.

24.

Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana.

Forbi JC, Layden JE, Phillips RO, Mora N, Xia GL, Campo DS, Purdy MA, Dimitrova ZE, Owusu DO, Punkova LT, Skums P, Owusu-Ofori S, Sarfo FS, Vaughan G, Roh H, Opare-Sem OK, Cooper RS, Khudyakov YE.

PLoS One. 2015 Dec 18;10(12):e0145530. doi: 10.1371/journal.pone.0145530. eCollection 2015.

25.

Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings.

Campo DS, Xia GL, Dimitrova Z, Lin Y, Forbi JC, Ganova-Raeva L, Punkova L, Ramachandran S, Thai H, Skums P, Sims S, Rytsareva I, Vaughan G, Roh HJ, Purdy MA, Sue A, Khudyakov Y.

J Infect Dis. 2016 Mar 15;213(6):957-65. doi: 10.1093/infdis/jiv542. Epub 2015 Nov 17.

26.

Cryptic Hepatitis B and E in Patients With Acute Hepatitis of Unknown Etiology.

Ganova-Raeva L, Punkova L, Campo DS, Dimitrova Z, Skums P, Vu NH, Dat do T, Dalton HR, Khudyakov Y.

J Infect Dis. 2015 Dec 15;212(12):1962-9. doi: 10.1093/infdis/jiv315. Epub 2015 Jun 8.

PMID:
26155829
27.

Antigenic cooperation among intrahost HCV variants organized into a complex network of cross-immunoreactivity.

Skums P, Bunimovich L, Khudyakov Y.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6653-8. doi: 10.1073/pnas.1422942112. Epub 2015 May 4.

28.

A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events.

Olmstead AD, Joy JB, Montoya V, Luo I, Poon AF, Jacka B, Lamoury F, Applegate T, Montaner J, Khudyakov Y, Grebely J, Cook D, Harrigan PR, Krajden M.

Infect Genet Evol. 2015 Jul;33:101-9. doi: 10.1016/j.meegid.2015.04.017. Epub 2015 Apr 24.

29.

Epidemiology of Acute Hepatitis B in the United States From Population-Based Surveillance, 2006-2011.

Iqbal K, Klevens RM, Kainer MA, Baumgartner J, Gerard K, Poissant T, Sweet K, Vonderwahl C, Knickerbocker T, Khudyakov Y, Xia GL, Roberts H, Teshale E.

Clin Infect Dis. 2015 Aug 15;61(4):584-92. doi: 10.1093/cid/civ332. Epub 2015 Apr 22.

PMID:
25904365
30.

A re-evaluation of the origin of hepatitis C virus genotype 2 in West Africa.

Purdy MA, Forbi JC, Sue A, Layden JE, Switzer WM, Opare-Sem OK, Phillips RO, Khudyakov YE.

J Gen Virol. 2015 Aug;96(8):2157-64. doi: 10.1099/vir.0.000153. Epub 2015 Apr 17.

31.

Hepatitis A outbreak among adults with developmental disabilities in group homes--Michigan, 2013.

Bohm SR, Berger KW, Hackert PB, Renas R, Brunette S, Parker N, Padro C, Hocking A, Hedemark M, Edwards R, Bush RL, Khudyakov Y, Nelson NP, Teshale EH; Centers for Disease Control and Prevention (CDC).

MMWR Morb Mortal Wkly Rep. 2015 Feb 20;64(6):148-52.

32.

High frequency of active HCV infection among seropositive cases in west Africa and evidence for multiple transmission pathways.

Layden JE, Phillips RO, Owusu-Ofori S, Sarfo FS, Kliethermes S, Mora N, Owusu D, Nelson K, Opare-Sem O, Dugas L, Luke A, Shoham D, Forbi JC, Khudyakov YE, Cooper RS.

Clin Infect Dis. 2015 Apr 1;60(7):1033-41. doi: 10.1093/cid/ciu965. Epub 2014 Dec 4.

PMID:
25477425
33.

Outbreak of hepatitis C virus infection associated with narcotics diversion by an hepatitis C virus-infected surgical technician.

Warner AE, Schaefer MK, Patel PR, Drobeniuc J, Xia G, Lin Y, Khudyakov Y, Vonderwahl CW, Miller L, Thompson ND.

Am J Infect Control. 2015 Jan;43(1):53-8. doi: 10.1016/j.ajic.2014.09.012. Epub 2014 Nov 20.

34.

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling.

Skums P, Artyomenko A, Glebova O, Ramachandran S, Mandoiu I, Campo DS, Dimitrova Z, Zelikovsky A, Khudyakov Y.

Bioinformatics. 2015 Mar 1;31(5):682-90. doi: 10.1093/bioinformatics/btu726. Epub 2014 Oct 29.

PMID:
25359889
35.

Outbreak of hepatitis A in the USA associated with frozen pomegranate arils imported from Turkey: an epidemiological case study.

Collier MG, Khudyakov YE, Selvage D, Adams-Cameron M, Epson E, Cronquist A, Jervis RH, Lamba K, Kimura AC, Sowadsky R, Hassan R, Park SY, Garza E, Elliott AJ, Rotstein DS, Beal J, Kuntz T, Lance SE, Dreisch R, Wise ME, Nelson NP, Suryaprasad A, Drobeniuc J, Holmberg SD, Xu F; Hepatitis A Outbreak Investigation Team.

Lancet Infect Dis. 2014 Oct;14(10):976-81. doi: 10.1016/S1473-3099(14)70883-7. Epub 2014 Sep 3.

PMID:
25195178
36.

Recent population expansions of hepatitis B virus in the United States.

Ramachandran S, Purdy MA, Xia GL, Campo DS, Dimitrova ZE, Teshale EH, Teo CG, Khudyakov YE.

J Virol. 2014 Dec;88(24):13971-80. doi: 10.1128/JVI.01594-14. Epub 2014 Sep 3.

37.

Genetic history of hepatitis C virus in Pakistan.

ur Rehman I, Vaughan G, Purdy MA, Xia GL, Forbi JC, Rossi LM, Butt S, Idrees M, Khudyakov YE.

Infect Genet Evol. 2014 Oct;27:318-24. doi: 10.1016/j.meegid.2014.08.005. Epub 2014 Aug 13.

PMID:
25131452
38.

Next-generation sequencing reveals large connected networks of intra-host HCV variants.

Campo DS, Dimitrova Z, Yamasaki L, Skums P, Lau DT, Vaughan G, Forbi JC, Teo CG, Khudyakov Y.

BMC Genomics. 2014;15 Suppl 5:S4. doi: 10.1186/1471-2164-15-S5-S4. Epub 2014 Jul 14.

39.

Computational models of liver fibrosis progression for hepatitis C virus chronic infection.

Lara J, López-Labrador F, González-Candelas F, Berenguer M, Khudyakov YE.

BMC Bioinformatics. 2014;15 Suppl 8:S5. doi: 10.1186/1471-2105-15-S8-S5. Epub 2014 Jul 14.

40.

Hepatitis C virus hypervariable region 1 variants presented on hepatitis B virus capsid-like particles induce cross-neutralizing antibodies.

Lange M, Fiedler M, Bankwitz D, Osburn W, Viazov S, Brovko O, Zekri AR, Khudyakov Y, Nassal M, Pumpens P, Pietschmann T, Timm J, Roggendorf M, Walker A.

PLoS One. 2014 Jul 11;9(7):e102235. doi: 10.1371/journal.pone.0102235. eCollection 2014.

41.

Genetic host specificity of hepatitis E virus.

Lara J, Purdy MA, Khudyakov YE.

Infect Genet Evol. 2014 Jun;24:127-39. doi: 10.1016/j.meegid.2014.03.011. Epub 2014 Mar 22.

42.

Intra-host diversity and evolution of hepatitis C virus endemic to Côte d'Ivoire.

Forbi JC, Campo DS, Purdy MA, Dimitrova ZE, Skums P, Xia GL, Punkova LT, Ganova-Raeva LM, Vaughan G, Ben-Ayed Y, Switzer WM, Khudyakov YE.

J Med Virol. 2014 May;86(5):765-71. doi: 10.1002/jmv.23897. Epub 2014 Feb 12.

43.

Drug resistance of a viral population and its individual intrahost variants during the first 48 hours of therapy.

Campo DS, Skums P, Dimitrova Z, Vaughan G, Forbi JC, Teo CG, Khudyakov Y, Lau DT.

Clin Pharmacol Ther. 2014 Jun;95(6):627-35. doi: 10.1038/clpt.2014.20. Epub 2014 Jan 31.

44.

Full-length genome characterization and genetic relatedness analysis of hepatitis A virus outbreak strains associated with acute liver failure among children.

Vaughan G, Forbi JC, Xia GL, Fonseca-Ford M, Vazquez R, Khudyakov YE, Montiel S, Waterman S, Alpuche C, Gonçalves Rossi LM, Luna N.

J Med Virol. 2014 Feb;86(2):202-8. doi: 10.1002/jmv.23843. Epub 2013 Nov 5.

PMID:
24243548
45.

Genetic relatedness among hepatitis A virus strains associated with food-borne outbreaks.

Vaughan G, Xia G, Forbi JC, Purdy MA, Rossi LM, Spradling PR, Khudyakov YE.

PLoS One. 2013 Nov 6;8(11):e74546. doi: 10.1371/journal.pone.0074546. eCollection 2013.

46.

Hepatitis A virus: host interactions, molecular epidemiology and evolution.

Vaughan G, Goncalves Rossi LM, Forbi JC, de Paula VS, Purdy MA, Xia G, Khudyakov YE.

Infect Genet Evol. 2014 Jan;21:227-43. doi: 10.1016/j.meegid.2013.10.023. Epub 2013 Nov 5. Review.

PMID:
24200587
47.

Hepatitis B outbreak associated with a home health care agency serving multiple assisted living facilities in Texas, 2008-2010.

Zheteyeva YA, Tosh P, Patel PR, Martinez D, Kilborn C, Awosika-Olumo D, Khuwaja S, Ibrahim S, Ryder A, Tohme RA, Khudyakov Y, Thai H, Drobeniuc J, Heseltine G, Guh AY.

Am J Infect Control. 2014 Jan;42(1):77-81. doi: 10.1016/j.ajic.2013.06.016. Epub 2013 Oct 29.

48.

Hepatitis B virus transmissions associated with a portable dental clinic, West Virginia, 2009.

Radcliffe RA, Bixler D, Moorman A, Hogan VA, Greenfield VS, Gaviria DM, Patel PR, Schaefer MK, Collins AS, Khudyakov YE, Drobeniuc J, Gooch BF, Cleveland JL.

J Am Dent Assoc. 2013;144(10):1110-8. Erratum in: J Am Dent Assoc. 2013 Nov;144(11):1228.

49.

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.

Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A.

BMC Bioinformatics. 2013;14 Suppl 9:S2. doi: 10.1186/1471-2105-14-S9-S2. Epub 2013 Jun 28.

50.

Disparate distribution of hepatitis B virus genotypes in four sub-Saharan African countries.

Forbi JC, Ben-Ayed Y, Xia GL, Vaughan G, Drobeniuc J, Switzer WM, Khudyakov YE.

J Clin Virol. 2013 Sep;58(1):59-66. doi: 10.1016/j.jcv.2013.06.028. Epub 2013 Jul 17.

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