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Items: 18

1.

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.

Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN.

Stat Appl Genet Mol Biol. 2015 Aug;14(4):375-89. doi: 10.1515/sagmb-2014-0078.

2.

Cryptic species of Paracoccidioides brasiliensis: impact on paracoccidioidomycosis immunodiagnosis.

Machado GC, Moris DV, Arantes TD, Silva LR, Theodoro RC, Mendes RP, Vicentini AP, Bagagli E.

Mem Inst Oswaldo Cruz. 2013 Aug;108(5):637-43.

3.

GenColors-based comparative genome databases for small eukaryotic genomes.

Felder M, Romualdi A, Petzold A, Platzer M, Sühnel J, Glöckner G.

Nucleic Acids Res. 2013 Jan;41(Database issue):D692-9. doi: 10.1093/nar/gks1176.

4.

Short communication: new HIV infections at Southern New England academic institutions: implications for prevention.

Chan PA, Kazi S, Rana A, Blazar I, Dejong CC, Mayer KH, Huard TK, Carleton K, Gillani F, Alexander N, Parillo Z, Flanigan TP, Kantor R.

AIDS Res Hum Retroviruses. 2013 Jan;29(1):25-9. doi: 10.1089/AID.2012.0130.

5.

Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

Delong AK, Wu M, Bennett D, Parkin N, Wu Z, Hogan JW, Kantor R.

AIDS Res Hum Retroviruses. 2012 Aug;28(8):894-901. doi: 10.1089/AID.2011.0120.

6.

Analysis of selection pressure and mutational pattern of HIV type 1 reverse transcriptase region among treated and nontreated patients.

Shanmugasundaram U, Solomon S, Madhavan V, Kailapuri MG, Nagalingeswaran K, Solomon SS, Mayer KH, Pachamuthu B.

AIDS Res Hum Retroviruses. 2010 Oct;26(10):1093-6. doi: 10.1089/aid.2009.0300.

7.

Short communication: Nucleotide variation and positively selected sites in HIV type 1 reverse transcriptase among heterosexual transmission pairs.

Shanmugasundaram U, Solomon S, Murugavel KG, Nagalingeswaran K, Solomon SS, Mayer KH, Pachamuthu B.

AIDS Res Hum Retroviruses. 2010 Aug;26(8):895-9. doi: 10.1089/aid.2010.0003.

8.

Diversity and evolution of the small multidrug resistance protein family.

Bay DC, Turner RJ.

BMC Evol Biol. 2009 Jun 23;9:140. doi: 10.1186/1471-2148-9-140.

9.

Genetic characterization of hepatitis B virus in peripheral blood leukocytes: evidence for selection and compartmentalization of viral variants with the immune escape G145R mutation.

Datta S, Panigrahi R, Biswas A, Chandra PK, Banerjee A, Mahapatra PK, Panda CK, Chakrabarti S, Bhattacharya SK, Biswas K, Chakravarty R.

J Virol. 2009 Oct;83(19):9983-92. doi: 10.1128/JVI.01905-08.

10.

Learning to count: robust estimates for labeled distances between molecular sequences.

O'Brien JD, Minin VN, Suchard MA.

Mol Biol Evol. 2009 Apr;26(4):801-14. doi: 10.1093/molbev/msp003.

11.

Genetic diversity of the Leptospiral immunoglobulin-like (Lig) genes in pathogenic Leptospira spp.

McBride AJ, Cerqueira GM, Suchard MA, Moreira AN, Zuerner RL, Reis MG, Haake DA, Ko AI, Dellagostin OA.

Infect Genet Evol. 2009 Mar;9(2):196-205. doi: 10.1016/j.meegid.2008.10.012.

12.

HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL.

Mitsuya Y, Winters MA, Fessel WJ, Rhee SY, Slome S, Flamm J, Horberg M, Hurley L, Klein D, Shafer RW.

J Acquir Immune Defic Syndr. 2006 Sep;43(1):56-9.

13.

The distribution and evolutionary history of the PRP8 intein.

Butler MI, Gray J, Goodwin TJ, Poulter RT.

BMC Evol Biol. 2006 May 31;6:42.

14.

Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain.

Lemey P, Derdelinckx I, Rambaut A, Van Laethem K, Dumont S, Vermeulen S, Van Wijngaerden E, Vandamme AM.

J Virol. 2005 Sep;79(18):11981-9.

15.

Laboratory-based surveillance and molecular epidemiology of influenza virus in Taiwan.

Shih SR, Chen GW, Yang CC, Yang WZ, Liu DP, Lin JH, Chiu SC, Chen HY, Tsao KC, Huang CG, Huang YL, Mok CK, Chen CJ, Lin TY, Wang JR, Kao CL, Lin KH, Chen LK, Eng HL, Liu YC, Chen PY, Lin JS, Wang JH, Lin CW, Chan YJ, Lu JJ, Hsiung CA, Chen PJ, Su IJ.

J Clin Microbiol. 2005 Apr;43(4):1651-61.

16.

HIV sequence databases.

Kuiken C, Korber B, Shafer RW.

AIDS Rev. 2003 Jan-Mar;5(1):52-61. Review.

17.

Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation.

Gonzales MJ, Delwart E, Rhee SY, Tsui R, Zolopa AR, Taylor J, Shafer RW.

J Infect Dis. 2003 Aug 1;188(3):397-405.

18.

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