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Items: 30

1.

Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection.

Wagh K, Bhattacharya T, Williamson C, Robles A, Bayne M, Garrity J, Rist M, Rademeyer C, Yoon H, Lapedes A, Gao H, Greene K, Louder MK, Kong R, Karim SA, Burton DR, Barouch DH, Nussenzweig MC, Mascola JR, Morris L, Montefiori DC, Korber B, Seaman MS.

PLoS Pathog. 2016 Mar 30;12(3):e1005520. doi: 10.1371/journal.ppat.1005520. eCollection 2016 Mar.

2.

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants.

Hraber P, Korber B, Wagh K, Giorgi EE, Bhattacharya T, Gnanakaran S, Lapedes AS, Learn GH, Kreider EF, Li Y, Shaw GM, Hahn BH, Montefiori DC, Alam SM, Bonsignori M, Moody MA, Liao HX, Gao F, Haynes BF.

Viruses. 2015 Oct 21;7(10):5443-75. doi: 10.3390/v7102881.

3.

Impact of clade, geography, and age of the epidemic on HIV-1 neutralization by antibodies.

Hraber P, Korber BT, Lapedes AS, Bailer RT, Seaman MS, Gao H, Greene KM, McCutchan F, Williamson C, Kim JH, Tovanabutra S, Hahn BH, Swanstrom R, Thomson MM, Gao F, Harris L, Giorgi E, Hengartner N, Bhattacharya T, Mascola JR, Montefiori DC.

J Virol. 2014 Nov;88(21):12623-43. doi: 10.1128/JVI.01705-14. Epub 2014 Aug 20.

4.

Antigenicity and immunogenicity of transmitted/founder, consensus, and chronic envelope glycoproteins of human immunodeficiency virus type 1.

Liao HX, Tsao CY, Alam SM, Muldoon M, Vandergrift N, Ma BJ, Lu X, Sutherland LL, Scearce RM, Bowman C, Parks R, Chen H, Blinn JH, Lapedes A, Watson S, Xia SM, Foulger A, Hahn BH, Shaw GM, Swanstrom R, Montefiori DC, Gao F, Haynes BF, Korber B.

J Virol. 2013 Apr;87(8):4185-201. doi: 10.1128/JVI.02297-12. Epub 2013 Jan 30.

5.

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections.

Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, Decamp AC, Magaret CA, Schief WR, Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B.

PLoS Pathog. 2011 Sep;7(9):e1002209. doi: 10.1371/journal.ppat.1002209. Epub 2011 Sep 29.

6.

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.

Gnanakaran S, Daniels MG, Bhattacharya T, Lapedes AS, Sethi A, Li M, Tang H, Greene K, Gao H, Haynes BF, Cohen MS, Shaw GM, Seaman MS, Kumar A, Gao F, Montefiori DC, Korber B.

PLoS Comput Biol. 2010 Oct 7;6(10):e1000955. doi: 10.1371/journal.pcbi.1000955.

7.

Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies.

Seaman MS, Janes H, Hawkins N, Grandpre LE, Devoy C, Giri A, Coffey RT, Harris L, Wood B, Daniels MG, Bhattacharya T, Lapedes A, Polonis VR, McCutchan FE, Gilbert PB, Self SG, Korber BT, Montefiori DC, Mascola JR.

J Virol. 2010 Feb;84(3):1439-52. doi: 10.1128/JVI.02108-09. Epub 2009 Nov 25.

8.

Breadth of human immunodeficiency virus-specific neutralizing activity in sera: clustering analysis and association with clinical variables.

Doria-Rose NA, Klein RM, Daniels MG, O'Dell S, Nason M, Lapedes A, Bhattacharya T, Migueles SA, Wyatt RT, Korber BT, Mascola JR, Connors M.

J Virol. 2010 Feb;84(3):1631-6. doi: 10.1128/JVI.01482-09. Epub 2009 Nov 18.

9.

Influenza vaccine strain selection and recent studies on the global migration of seasonal influenza viruses.

Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, Gust ID, Hampson AW, Hay AJ, Hurt AC, de Jong JC, Kelso A, Klimov AI, Kageyama T, Komadina N, Lapedes AS, Lin YP, Mosterin A, Obuchi M, Odagiri T, Osterhaus AD, Rimmelzwaan GF, Shaw MW, Skepner E, Stohr K, Tashiro M, Fouchier RA, Smith DJ.

Vaccine. 2008 Sep 12;26 Suppl 4:D31-4. Review.

PMID:
19230156
10.

Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India.

Kulkarni SS, Lapedes A, Tang H, Gnanakaran S, Daniels MG, Zhang M, Bhattacharya T, Li M, Polonis VR, McCutchan FE, Morris L, Ellenberger D, Butera ST, Bollinger RC, Korber BT, Paranjape RS, Montefiori DC.

Virology. 2009 Mar 15;385(2):505-20. doi: 10.1016/j.virol.2008.12.032. Epub 2009 Jan 23.

11.

The global circulation of seasonal influenza A (H3N2) viruses.

Russell CA, Jones TC, Barr IG, Cox NJ, Garten RJ, Gregory V, Gust ID, Hampson AW, Hay AJ, Hurt AC, de Jong JC, Kelso A, Klimov AI, Kageyama T, Komadina N, Lapedes AS, Lin YP, Mosterin A, Obuchi M, Odagiri T, Osterhaus AD, Rimmelzwaan GF, Shaw MW, Skepner E, Stohr K, Tashiro M, Fouchier RA, Smith DJ.

Science. 2008 Apr 18;320(5874):340-6. doi: 10.1126/science.1154137.

12.

Antigenic and genetic evolution of swine influenza A (H3N2) viruses in Europe.

de Jong JC, Smith DJ, Lapedes AS, Donatelli I, Campitelli L, Barigazzi G, Van Reeth K, Jones TC, Rimmelzwaan GF, Osterhaus AD, Fouchier RA.

J Virol. 2007 Apr;81(8):4315-22. Epub 2007 Feb 7.

13.

Mutations, drift, and the influenza archipelago.

Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Jones TC, Rimmelzwaan GF, Osterhaus AD, Fouchier RA.

Discov Med. 2004 Dec;4(24):371-7.

14.

Mapping the antigenic and genetic evolution of influenza virus.

Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, Fouchier RA.

Science. 2004 Jul 16;305(5682):371-6. Epub 2004 Jun 24.

15.

Recognition of homo- and heterosubtypic variants of influenza A viruses by human CD8+ T lymphocytes.

Boon AC, de Mutsert G, van Baarle D, Smith DJ, Lapedes AS, Fouchier RA, Sintnicolaas K, Osterhaus AD, Rimmelzwaan GF.

J Immunol. 2004 Feb 15;172(4):2453-60.

16.

Probabilistic code for DNA recognition by proteins of the EGR family.

Benos PV, Lapedes AS, Stormo GD.

J Mol Biol. 2002 Nov 1;323(4):701-27.

PMID:
12419259
17.

Is there a code for protein-DNA recognition? Probab(ilistical)ly. . .

Benos PV, Lapedes AS, Stormo GD.

Bioessays. 2002 May;24(5):466-75. Review.

PMID:
12001270
18.

Genetic correlations in mutation processes.

Ben-Naim E, Lapedes AS.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Jun;59(6):7000-7.

PMID:
11969688
19.

Superadditive correlation.

Giraud BG, Heumann JM, Lapedes AS.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 May;59(5 Pt A):4983-91.

PMID:
11969452
20.

Complex systems analysis: a tool for shock research.

Buchman TG, Cobb JP, Lapedes AS, Kepler TB.

Shock. 2001 Oct;16(4):248-51. Review.

PMID:
11580104
21.

The geometry of shape space: application to influenza.

Lapedes A, Farber R.

J Theor Biol. 2001 Sep 7;212(1):57-69.

PMID:
11527445
22.

Exploring protein sequence space using knowledge-based potentials.

Babajide A, Farber R, Hofacker IL, Inman J, Lapedes AS, Stadler PF.

J Theor Biol. 2001 Sep 7;212(1):35-46.

PMID:
11527443
23.

SAMIE: statistical algorithm for modeling interaction energies.

Benos PV, Lapedes AS, Fields DS, Stormo GD.

Pac Symp Biocomput. 2001:115-26.

24.

Timing the ancestor of the HIV-1 pandemic strains.

Korber B, Muldoon M, Theiler J, Gao F, Gupta R, Lapedes A, Hahn BH, Wolinsky S, Bhattacharya T.

Science. 2000 Jun 9;288(5472):1789-96.

25.

Neural net representations of empirical protein potentials.

Grossman T, Farber R, Lapedes A.

Proc Int Conf Intell Syst Mol Biol. 1995;3:154-61.

PMID:
7584432
26.

Neural networks for determining protein specificity and multiple alignment of binding sites.

Heumann JM, Lapedes AS, Stormo GD.

Proc Int Conf Intell Syst Mol Biol. 1994;2:188-94.

PMID:
7584389
27.

Domain growth, wetting, and scaling in porous media.

Grunau DW, Lookman T, Chen SY, Lapedes AS.

Phys Rev Lett. 1993 Dec 20;71(25):4198-4201. No abstract available.

PMID:
10055181
28.

Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis.

Korber BT, Farber RM, Wolpert DH, Lapedes AS.

Proc Natl Acad Sci U S A. 1993 Aug 1;90(15):7176-80.

29.

Determination of eukaryotic protein coding regions using neural networks and information theory.

Farber R, Lapedes A, Sirotkin K.

J Mol Biol. 1992 Jul 20;226(2):471-9.

PMID:
1640461
30.

Predicting protein secondary structure using neural net and statistical methods.

Stolorz P, Lapedes A, Xia Y.

J Mol Biol. 1992 May 20;225(2):363-77.

PMID:
1593625

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