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Items: 1 to 50 of 63

1.

Upregulation of Mobility in Pancreatic Cancer Cells by Secreted S100A11 Through Activation of Surrounding Fibroblasts.

Mitsui Y, Tomonobu N, Watanabe M, Kinoshita R, Sumardika IW, Youyi C, Murata H, Yamamoto KI, Sadahira T, Rodrigo AGH, Takamatsu H, Araki K, Yamauchi A, Yamamura M, Fujiwara H, Inoue Y, Futami J, Saito K, Iioka H, Kondo E, Nishibori M, Toyooka S, Yamamoto Y, Nasu Y, Sakaguchi M.

Oncol Res. 2019 Aug 8;27(8):945-956. doi: 10.3727/096504019X15555408784978. Epub 2019 Apr 17.

PMID:
31046874
2.

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations.

Wong TKF, Ranjard L, Lin Y, Rodrigo AG.

BMC Bioinformatics. 2018 Oct 22;19(1):389. doi: 10.1186/s12859-018-2424-7.

3.
4.

Identifying predictors of time-inhomogeneous viral evolutionary processes.

Bielejec F, Baele G, Rodrigo AG, Suchard MA, Lemey P.

Virus Evol. 2016 Sep 6;2(2):vew023. eCollection 2016 Jul.

5.

Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution.

Nascimento FF, Rodrigo AG.

PLoS One. 2016 Sep 20;11(9):e0162454. doi: 10.1371/journal.pone.0162454. eCollection 2016.

6.

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals.

Wu SH, Rodrigo AG.

BMC Bioinformatics. 2015 Nov 4;16:357. doi: 10.1186/s12859-015-0810-y.

7.

Frequency-dependent selection drives HBeAg seroconversion in chronic hepatitis B virus infection.

Warner BG, Abbott WG, Rodrigo AG.

Evol Med Public Health. 2014 Jan;2014(1):1-9. doi: 10.1093/emph/eot023. Epub 2013 Dec 13.

8.

HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study.

Ping LH, Jabara CB, Rodrigo AG, Hudelson SE, Piwowar-Manning E, Wang L, Eshleman SH, Cohen MS, Swanstrom R.

PLoS One. 2013 Sep 24;8(9):e71557. doi: 10.1371/journal.pone.0071557. eCollection 2013.

9.

Transient compartmentalization of simian immunodeficiency virus variants in the breast milk of african green monkeys.

Ho C, Wu S, Amos JD, Colvin L, Smith SD, Wilks AB, Demarco CT, Brinkley C, Denny TN, Schmitz JE, Rodrigo AG, Permar SR.

J Virol. 2013 Oct;87(20):11292-9. doi: 10.1128/JVI.01643-13. Epub 2013 Aug 7.

10.

A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels.

Wu SH, Black MA, North RA, Rodrigo AG.

BMC Bioinformatics. 2012 Jun 19;13:137. doi: 10.1186/1471-2105-13-137.

11.

Time-dependent rates of molecular evolution.

Ho SY, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A.

Mol Ecol. 2011 Aug;20(15):3087-101. doi: 10.1111/j.1365-294X.2011.05178.x. Epub 2011 Jul 8. Review.

PMID:
21740474
12.

Evidence for reduced selection pressure on the hepatitis B virus core gene in hepatitis B e antigen-negative chronic hepatitis B.

Warner BG, Tsai P, Rodrigo AG, 'ofanoa M, Gane EJ, Munn SR, Abbott WG.

J Gen Virol. 2011 Aug;92(Pt 8):1800-8. doi: 10.1099/vir.0.030478-0. Epub 2011 Apr 20.

PMID:
21508187
13.

The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats.

Hayward JJ, Rodrigo AG.

Arch Virol. 2010 Mar;155(3):411-6. doi: 10.1007/s00705-010-0598-z. Epub 2010 Jan 29. No abstract available.

PMID:
20112119
14.

Covariation of branch lengths in phylogenies of functionally related genes.

Li WL, Rodrigo AG.

PLoS One. 2009 Dec 29;4(12):e8487. doi: 10.1371/journal.pone.0008487.

15.

Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus).

Hayward JJ, Rodrigo AG.

Vet Immunol Immunopathol. 2010 Mar 15;134(1-2):68-74. doi: 10.1016/j.vetimm.2009.10.011. Epub 2009 Oct 14. Review.

16.

Associations between HLA class I alleles and escape mutations in the hepatitis B virus core gene in New Zealand-resident Tongans.

Abbott WG, Tsai P, Leung E, Trevarton A, Ofanoa M, Hornell J, Gane EJ, Munn SR, Rodrigo AG.

J Virol. 2010 Jan;84(1):621-9. doi: 10.1128/JVI.01471-09.

18.

A statistical model to identify differentially expressed proteins in 2D PAGE gels.

Wu SH, Black MA, North RA, Atkinson KR, Rodrigo AG.

PLoS Comput Biol. 2009 Sep;5(9):e1000509. doi: 10.1371/journal.pcbi.1000509. Epub 2009 Sep 18.

19.

Selecting taxa to save or sequence: desirable criteria and a greedy solution.

Bordewich M, Rodrigo AG, Semple C.

Syst Biol. 2008 Dec;57(6):825-34. doi: 10.1080/10635150802552831.

PMID:
19085326
20.

Recombination in feline immunodeficiency virus from feral and companion domestic cats.

Hayward JJ, Rodrigo AG.

Virol J. 2008 Jun 17;5:76. doi: 10.1186/1743-422X-5-76.

21.

Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.

Goode M, Rodrigo AG.

Curr Protoc Bioinformatics. 2004 May;Chapter 6:Unit 6.8. doi: 10.1002/0471250953.bi0608s05.

PMID:
18428729
22.

Viral quasi-species evolution during hepatitis Be antigen seroconversion.

Lim SG, Cheng Y, Guindon S, Seet BL, Lee LY, Hu P, Wasser S, Peter FJ, Tan T, Goode M, Rodrigo AG.

Gastroenterology. 2007 Sep;133(3):951-8. Epub 2007 Jun 20.

PMID:
17854598
23.

SQUINT: a multiple alignment program and editor.

Goode MG, Rodrigo AG.

Bioinformatics. 2007 Jun 15;23(12):1553-5. Epub 2007 May 7.

PMID:
17485434
24.

Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand.

Hayward JJ, Taylor J, Rodrigo AG.

J Virol. 2007 Mar;81(6):2999-3004. Epub 2006 Dec 27.

25.

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes.

Ross HA, Nickle DC, Liu Y, Heath L, Jensen MA, Rodrigo AG, Mullins JI.

Evol Bioinform Online. 2007 Jan 13;2:53-76.

26.

Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope.

Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, Barnett SW, Haigwood NL, Mullins JI.

J Virol. 2005 Sep;79(17):11214-24.

27.

Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1.

Meintjes PL, Rodrigo AG.

J Bioinform Comput Biol. 2005 Feb;3(1):157-68.

PMID:
15751118
28.

Pervasive genomic recombination of HIV-1 in vivo.

Shriner D, Rodrigo AG, Nickle DC, Mullins JI.

Genetics. 2004 Aug;167(4):1573-83.

29.

Modeling the site-specific variation of selection patterns along lineages.

Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP.

Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12957-62. Epub 2004 Aug 23.

30.

Immunogen sequence: the fourth tier of AIDS vaccine design.

Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH.

Expert Rev Vaccines. 2004 Aug;3(4 Suppl):S151-9. Review.

PMID:
15285713
31.

Inferring evolutionary rates using serially sampled sequences from several populations.

Rodrigo AG, Goode M, Forsberg R, Ross HA, Drummond A.

Mol Biol Evol. 2003 Dec;20(12):2010-8. Epub 2003 Aug 29.

PMID:
12949147
32.

Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars.

Biek R, Rodrigo AG, Holley D, Drummond A, Anderson CR Jr, Ross HA, Poss M.

J Virol. 2003 Sep;77(17):9578-89.

33.

Predicting demographic group structures based on DNA sequence data.

Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI.

Mol Biol Evol. 2003 Jul;20(7):1168-80. Epub 2003 May 30.

PMID:
12777527
34.

DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises.

Ross HA, Lento GM, Dalebout ML, Goode M, Ewing G, McLaren P, Rodrigo AG, Lavery S, Baker CS.

J Hered. 2003 Mar-Apr;94(2):111-4. Review.

PMID:
12721222
35.

Consensus and ancestral state HIV vaccines.

Nickle DC, Jensen MA, Gottlieb GS, Shriner D, Learn GH, Rodrigo AG, Mullins JI.

Science. 2003 Mar 7;299(5612):1515-8; author reply 1515-8. No abstract available.

PMID:
12624248
36.

[Human immunodeficiency virus infection. Dermatologic perspective].

Rodrigo FG, Rodrigo AG.

Acta Med Port. 2002 Jul-Aug;15(4):293-309. Review. Portuguese.

38.

Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS.

Liu SL, Mittler JE, Nickle DC, Mulvania TM, Shriner D, Rodrigo AG, Kosloff B, He X, Corey L, Mullins JI.

J Virol. 2002 Nov;76(21):10674-84.

39.
40.

Likelihood-based tests of topologies in phylogenetics.

Goldman N, Anderson JP, Rodrigo AG.

Syst Biol. 2000 Dec;49(4):652-70.

PMID:
12116432
41.

Combinability of phylogenies and bootstrap confidence envelopes.

Rodrigo AG.

Syst Biol. 1998 Dec;47(4):727-33. No abstract available.

PMID:
12066315
42.

A heteroduplex method for detection of targeted sub-populations of bacterial communities.

Turner SJ, Saul DJ, Rodrigo AG, Lewis GD.

FEMS Microbiol Lett. 2002 Feb 19;208(1):9-13.

43.

Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region.

Anderson JP, Rodrigo AG, Learn GH, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI.

J Mol Evol. 2001 Jul;53(1):55-62.

PMID:
11683323
44.

The inference of stepwise changes in substitution rates using serial sequence samples.

Drummond A, Forsberg R, Rodrigo AG.

Mol Biol Evol. 2001 Jul;18(7):1365-71.

PMID:
11420374
45.
46.

Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E.

Anderson JP, Rodrigo AG, Learn GH, Madan A, Delahunty C, Coon M, Girard M, Osmanov S, Hood L, Mullins JI.

J Virol. 2000 Nov;74(22):10752-65.

47.

Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection.

Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI.

J Virol. 1999 Dec;73(12):10489-502.

48.

HIV evolutionary genetics.

Rodrigo AG.

Proc Natl Acad Sci U S A. 1999 Sep 14;96(19):10559-61. Review. No abstract available.

49.

HIV-1 dynamics in children.

Melvin AJ, Rodrigo AG, Mohan KM, Lewis PA, Manns-Arcuino L, Coombs RW, Mullins JI, Frenkel LM.

J Acquir Immune Defic Syndr Hum Retrovirol. 1999 Apr 15;20(5):468-73.

PMID:
10225229
50.

Coalescent estimates of HIV-1 generation time in vivo.

Rodrigo AG, Shpaer EG, Delwart EL, Iversen AK, Gallo MV, Brojatsch J, Hirsch MS, Walker BD, Mullins JI.

Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):2187-91.

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