Deng, W., D. N. Nickle, G. H. Learn, B. Maust, and J. I. Mullins. 2007.
ViroBLAST: A stand-alone BLAST web server for flexible queries of multiple
databases and user's datasets.
Bioinformatics
23: 2334-2336
[abstract].
|
Rolland, M., D. C. Nickle, W. Deng, N. Frahm, C. Brander, G. H. Learn,
D. Heckerman, N. Jojic, V. Jojic, B. D. Walker, and J. I. Mullins. 2007.
Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity
to human proteins.
PLoS ONE
2: e823
[abstract].
|
Rolland, M., M. A. Jensen, D. C. Nickle, J. Yan, G. H. Learn, L.
Heath, D. Weiner, and J. I. Mullins. 2007.
Reconstruction and function of ancestral Center-of-Tree (COT) human immunodeficiency
virus type 1 proteins.
Journal of
Virology 81: 8507-8514
[abstract].
|
Rousseau, C. M., G. H. Learn, T. Bhattacharya, D. C. Nickle, D.
Heckerman, S. Chetty, C. Brander, P. J. Goulder, B. D. Walker, P.
Kiepiela, B. T. Korber, and J. I. Mullins. 2007.
Extensive intrasubtype recombination in South African human
immunodeficiency virus type 1 subtype C infections.
Journal of Virology
81: 4492-4500
[abstract].
|
Bhattacharya, T., M. Daniels, D. Heckerman, B. Foley, N. Frahm,
C. Kadie, J. Carlson, K. Yusim, B. McMahon, B. Gaschen, S. Mallal, J. I.
Mullins, D. C. Nickle, J. Herbeck, C. Rousseau, G. H. Learn, T. Miura,
C. Brander, B. Walker, and B. Korber. 2007. Founder effects in the
assessment of HIV polymorphisms and HLA allele associations.
Science 135: 1583-1586
[abstract].
|
Kiepiela, P., K. Ngumbela, C. Thobakgale, D. Ramduth, I. Honeyborne, E.
Moodley, S. Reddy, C. de Pierres, Z. Mncube, N. Mkhwanazi, K. Bishop, M. van der Stok,
K. Nair, N. Khan, H. Crawford, R. Payne, A. Leslie, J. Prado, A. Prendergast, J.
Frater, N. McCarthy, C. Brander, G. H. Learn, D. Nickle, C. Rousseau, H. Coovadia,
J. I. Mullins, D. Heckerman, B. D. Walker, and P. Goulder. 2007.
CD8+ T-cell responses to different HIV proteins have discordant associations
with viral load.
Nature Medicine
13: 46-53
[abstract].
|
Rousseau, C. M., B. A. Birditt, A. R. McKay, J. N. Stoddard, T. C. Lee, S. McLaughlin,
S. W. Moore, N. Shindo, G. H. Learn, B. T. Korber, C. Brander, P. J. R. Goulder, P.
Kiepiela, B. D. Walker, and J. I. Mullins. 2006.
Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes.
Journal of Virological Methods
136: 118-125
[abstract].
|
Herbeck, J. T., D. C. Nickle, G. H. Learn, G. S. Gottlieb, M. E. Curlin,
L. Heath, and J. I. Mullins. 2006. Human immunodeficiency virus type 1 env
evolves toward ancestral states upon transmission to a new host.
Journal of Virology
80: 1637-1644
[abstract].
Iversen, A. K., G. Stewart-Jones, G. H. Learn, N. Christie, C. Sylvester-Hviid, A. E. Armitage,
R. Kaul, T. Beattie, J. K. Lee, Y. Li, P. Chotiyarnwong, T. Dong T, X. Xu, M. A. Luscher, K. MacDonald,
H. Ullum, B. Klarlund-Pedersen, P. Skinøj, L. Fugger, S. Buus, J. I. Mullins, E. Y. Jones, P. A. van
der Merwe, and A. J. McMichael. 2006. Conflicting selective forces affect T cell receptor contacts in
an immunodominant human immunodeficiency virus epitope.
Nature Immunology 7: 179-189
[abstract].
|
Doria-Rose, N. A., G. H. Learn, A. G. Rodrigo, D. C. Nickle, F. Li, M. Mahalanabis,
M. T. Hensel, S. McLaughlin, P. F. Edmonson, D. Montefiori, S. W. Barnett, N. L. Haigwood,
and J. I. Mullins. 2005. 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.
Journal of Virology
79: 11214-11224
[abstract].
|
Tobin, N. H., G. H. Learn, S. E. Holte, Y. Wang, A. J. Melvin, J. L. McKernan,
D. M. Pawluk, K. M. Mohan, P. F. Lewis, J. I. Mullins, and L. M. Frenkel. 2005.
Evidence that low-Level viremias during effective highly active antiretroviral
therapy result from two processes: Expression of archival virus and replication of virus.
Journal of Virology
79: 9625-9634
[abstract].
|
Iversen, A. K. N., G. H. Learn, P. Skinhøj, J. I. Mullins, A. J. McMichael,
A. Rambaut. 2005. Preferential detection of HIV subtype C' over subtype A in
cervical cells from a dually-infected woman.
AIDS 19: 990-993.
|
Learn, G. H., and J. I. Mullins.
2004. The microbial forensic use of HIV sequences.
pp. 22-37.
In HIV Sequence Compendium 2003 T. Leitner, B. Foley, B. Hahn, P. Marx,
F. McCutchan J. Mellors, S. Wolinksy, and B. Korber, (eds.), Los Alamos
National Laboratory, Los Alamos, NM.
|
Liu, Y., D. C. Nickle, D. Shriner, M. A. Jensen, G. H. Learn, Jr.,
J. E. Mittler and J. I. Mullins 2004. Molecular clock-like evolution of human
immunodeficiency virus type 1. Virology 329: 101-108
[abstract].
|
Mullins, J. I., D. C. Nickle, L. Heath, A. G. Rodrigo, G. H.
Learn. 2004. Immunogen sequence: the fourth tier of AIDS vaccine design.
Expert Review of Vaccines 3: S151-159
[abstract].
|
Zhu, T., S.-L. Hu, F. Feng, P. Polacino, H. Liu, Y. Hwangbo,
G. H. Learn, J. I. Mullins, and L. Corey. 2004.
Persistence of low levels of simian immunodeficiency virus in macaques that were
transiently viremic by conventional testing.
Virology 323: 208-219
[abstract].
|
Gottlieb, G. S., D. C. Nickle, M. A. Jensen,
K. G. Wong, J. Grobler, F. Li, S.-L. Liu, C. Rademeyer, G. H. Learn, S.
S. A. Karim, C. Williamson, L. Corey, J. B. Margolick, J. I.
Mullins. 2004. Dual HIV-1 infection associated with rapid disease
progression.
The Lancet 363: 619-622
[abstract].
|
Anderson, J. P., G. H. Learn, A. G. Rodrigo, X. He,
Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins.
2003. Predicting demographic group structures based on DNA sequence data.
Molecular Biology and Evolution 20: 1168-1180
[abstract].
|
Zhu, T., L. Corey, Y. Hwangbo, J. M. Lee, G. H. Learn,
J. I. Mullins, and M. J. McElrath. 2003. Persistence of extraordinarily
low levels of genetically homogeneous human immunodeficiency virus type
1 in exposed seronegative individuals.
Journal of Virology, 77: 6108-6116
[abstract].
|
Frenkel L. M., Y. Wang, G. H. Learn, J. L. McKernan,
G. M. Ellis, K. M. Mohan, S. E. Holte, S. M. De Vange, D. M. Pawluk, A. J. Melvin,
P. F. Lewis, L. M. Heath, I. A. Beck, M. Mahalanabis, W. E. Naugler, N. H. Tobin,
and J. I. Mullins. 2003 Multiple viral genetic analyses detect low-level human
immunodeficiency virus type 1 replication during effective highly active
antiretroviral therapy.
Journal of Virology, 77: 5721-5730
[abstract].
|
Nickle, D.C., M. A. Jensen, G. S. Gottlieb, D. Shriner, G. H. Learn,
A. G. Rodrigo, and J. I. Mullins. 2003.
Consensus and ancestral state HIV vaccines.
Science, 299: 1515-1517.
|
Learn, G. H., D. Muthui, S. J. Brodie, T. Zhu, K. Diem,
J. I. Mullins, and L. Corey.
2002. Virus population homogenization following acute human immunodeficiency virus
type 1 infection.
Journal of Virology, 76: 11953-11959
[abstract].
|
| Anderson, J. P., M. Rain, D. Shriner, A. G. Rodrigo, Y. Wang, D. Nickle, G. H. Learn,
W. E. Naugler and J. I. Mullins. 2002. The genetics of HIV-1. pp. 44-99. In
The Human
Immunodeficiency Virus. E. A. Emini (ed.), Princeton University Press, Princeton, N.J.
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Nickle, D. C., G. H. Learn, M. W. Rain, J.
I. Mullins and J. E. Mittler. 2002. Curiously modern DNA for a “250 million
year old” bacterium.
Journal of Molecular Evolution, 54: 134-137
[abstract].
|
Shankarappa, R., R. Chatterjee, G. H. Learn,
D. Neogi, M. Ding, P. Roy, A. Ghosh, L. Kingsley, L. Harrison, J. I. Mullins
and P. Gupta. 2001. Human immunodeficiency virus type 1 (HIV-1) env
sequences from Calcutta in Eastern India: Identification of features that
distinguish subtype C sequences in India from other subtype C sequences.
Journal of Virology, 75: 10479-10487
[abstract].
|
Holterman, L., R. Dubbes, J. Mullins, G. Learn,
H. Niphuis, W. Koornstra, G. Koopman, E.-M. Kuhn, A. Wade-Evans, B. Rosenwirth,
J. Haaijman and J. Heeney. 2001. Distinct characteristics of a pathogenic
molecular clone of an end-stage variant of simian immunodeficiency virus
(SIVF359) .
Journal of Virology, 75: 9328-9338
[abstract].
|
Anderson, J. P., A. G. Rodrigo, G. H. Learn, Y. Wang,
H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins.
2001. Substitution model of sequence evolution for the human immunodeficiency
virus type 1 subtype B gp120 gene over the C2-V5 region.
Journal of Molecular Evolution, 53: 55-62
[abstract].
|
Rodrigo, A. G., and G. H. Learn, Jr. (editors) 2001. Computational
and Evolutionary Analyses of HIV Sequences. Kluwer Academic Publishers, Boston.
|
Rodrigo, A. G., E. W. Hanley, P. C. Goracke, and G. H. Learn,
Jr. 2001. Sampling and processing HIV molecular sequences: a computational
evolutionary biologist's perspective. pp. 1-17. In Computational and
Evolutionary Analyses of HIV Sequences. A. G. Rodrigo and G. H.
Learn, Jr. (eds.), Kluwer Academic Publishers,
Boston.
|
Anderson, J. P., A. G. Rodrigo, G. H. Learn, A. Madan, C.
Delahunty, M. Coon, M. Girard, S. Osmanov, L. Hood, and J. I. Mullins.
2000. Testing the hypothesis of a recombinant origin of human immunodeficiency
virus type 1 subtype E.
Journal of Virology, 74: 10752-10765
[abstract].
|
Kliks, S., C. H. Contag, H. Corliss, G. Learn, A. Rodrigo,
D. Wara, J. I. Mullins, and J. A. Levy. 2000. Genetic analysis of viral
variants selected in transmission of human immunodeficiency viruses to newborns.
AIDS Research and Human Retroviruses, 16: 1223-1233
[abstract].
|
Robertson, D. L., J. P. Anderson, J. A. Bradac, J. K. Carr, B.
Foley, R .K. Funkhouser, F. Gao, B. H. Hahn, M. L. Kalish, C. Kuiken,
G. H. Learn, T. Leitner, F. McCutchan, S. Osmanov, M. Peeters,
D. Pieniazek, M. Salminen, P. M. Sharp, S. Wolinsky, and B. Korber. 2000.
HIV-1 nomenclature proposal: A reference guide to HIV-1 classification.
pp. 492-505. In Human Retroviruses and AIDS 1999: A Compilation and
Analysis of Nucleic Acid and Amino Acid Sequences.
C. L. Kuiken, B. Foley, B. Hahn, B. Korber, F. McCutchan, P. A. Marx,
J. W. Mellors, J. I. Mullins, J. Sodroski, and S. Wolinksy (eds.), Los
Alamos National Laboratory, Los Alamos, NM.
|
Robertson, D. L., J. P. Anderson, J. A. Bradac, J. K. Carr, B.
Foley, R. K. Funkhouser, F. Gao, B. H. Hahn, M. L. Kalish, C. Kuiken,
G. H. Learn, T. Leitner, F. McCutchan, S. Osmanov, M. Peeters,
D. Pieniazek, M. Salminen, P. M. Sharp, S. Wolinsky and B. Korber. 2000.
HIV-1 nomenclature proposal.
Science, 288: 55.
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Iversen A. K., G. H. Learn, L. Fugger, J. Gerstoft, J. I.
Mullins and P. Skinhøj. 1999. Presence of multiple HIV subtypes and a
high frequency of subtype chimeric viruses in heterosexually infected
women.
Journal of Acquired Immune Deficiency Syndromes, 22:
325-332
[abstract].
|
Shankarappa, R., J. B. Margolick, S. J. Gange, A. G. Rodrigo, D.
Upchurch, H. Farzadegan, P. Gupta, C. R. Rinaldo, G. H. Learn, X.
He, X.-L. Huang, and J. I. Mullins. 1999. Consistent viral evolutionary
changes asscociated with the progression of human immunodeficiency virus
type 1 infection.
Journal of Virology, 73: 10489-10502
[abstract].
|
Wolinsky, S., and G. H. Learn. 1999. Levels of diversity
within and among host individuals. pp. 275-314. In The Evolution of HIV.
K. A. Crandall (ed.), Johns Hopkins University Press, Baltimore,
MD.
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Poss, M., A. G. Rodrigo, J. J. Gosink, G. H. Learn, D. de
Vange Panteleeff, H. L. Martin, Jr., J. Bwayo, Joan K. Kreiss, and J. Overbaugh.
1998. Evolution of envelope sequences from the genital tract and peripheral
blood of women infected with clade A human immunodeficiency virus type
1. Journal
of Virology, 72: 8240-8251
[abstract].
|
Ostrowski, M. A., D. C. Krakauer, Y. Li, S. J. Justement, G.
Learn, L. A. Ehler, S. K. Stanley, M. Nowak, and A. S. Fauci. 1998.
Effect of immune activation on the dynamics of human immunodeficiency virus
replication and on the distribution of viral quasispecies.
Journal of Virology, 72: 7772-7784
[abstract].
|
Frenkel, L., J. I. Mullins, G. H. Learn, L. Manns-Arcuino,
B. L. Herring, M. L. Kalish, R. W. Steketee, D. M. Thea, J. E. Nichols,
S.-L. Liu, A. Harmache, X. He, D. Muthui, A. Madan, L. Hood, A. T. Haase,
M. Zupancic, K. Staskus, S. M. Wolinsky, P. Krogstad, J. Zhao, I. Chen,
R. Koup, D. D. Ho, B. T. Korber, R. J. Apple, R. W. Coombs, S. Pahwa,
and N. J. Roberts, Jr. 1998. Genetic evaluation of suspected cases of
transient HIV-1 infection of infants.
Science, 280:1073-1077
[abstract].
|
Shankarappa, R., P. Gupta, G. H. Learn, Jr., A. G. Rodrigo,
C. R. Rinaldo, Jr., M. C. Gorry, J. I. Mullins, P. L. Nara, and G. D. Ehrlich.
1998. Evolution of human immunodefiency virus type 1 envelope sequences
in infected individuals with differing disease progression profiles.
Virology, 241:251-259
[abstract].
|
Paladin, F. J. E., O. T. Monzon, H. Tsuchie, M. R. A. Aplasca,
G. H. Learn, Jr., and T. Kurimura. 1998. Genetics subtypes of
HIV-1 in the Philippines. AIDS, 12: 291-300
[abstract].
|
Delwart, E. L., J. I. Mullins, P. Gupta, G. H. Learn, Jr.,
M. Holodniy, D. Katzenstein, B. D. Walker, and M. K. Singh. 1998. Human immunodeficiency virus type I populations in blood and semen.
Journal of Virology, 72: 617-623
[abstract].
|
Edmonson, P., M. Murphey-Corb, L. N. Martin, C. Delahunty, J. Heeney,
H. Kornfeld, P. R. Donohue, G. H. Learn, L. Hood, and J. I. Mullins.
1998. Evolution of a simian immunodeficiency virus pathogen.
Journal of
Virology, 72: 405-414
[abstract].
|
Bachmann, M. B., C. Mathiason-Dubard, G. H. Learn,
A. G. Rodrigo, D. L. Sodora, P. Mazzetti, E. A. Hoover, and J. I. Mullins.
1997. Genetic diversity of feline immunodeficiency virus: dual infection,
recombination, and distinct evolutionary rates among envelope sequence
clades.
Journal of Virology, 71:4241-4253
[abstract].
|
Contag, C. H., A. Ehrnst, J. Duda, A.-B. Bohlin, S. Lindgren,
G. H. Learn, and J. I. Mullins. 1997. Mother-to-infant transmission
of human immunodeficiency virus type 1 involving five envelope sequence subtypes.
Journal
of Virology, 71:1292-1300
[abstract].
|
Sabino, E. C., R. S. Diaz, L. F. Brigido, G. H. Learn, J.
I. Mullins, A. L. Reingold, A. J. S. Duarte, A. Mayer, and M. P. Busch. 1996.
Distribution of HIV-1 subtypes seen an AIDS clinic in Sao Paulo City, Brazil.
AIDS 10:1579-1584 [abstract].
|
Yoshimura, F. K., K. Diem, G. H. Learn, Jr., S. Riddell,
and L. Corey. 1996. Intrapatient sequence variation of gag gene of human
immunodeficiency virus type 1 plasma virions.
Journal of Virology, 70:8879-8887
[abstract].
|
Liu, S.-L., A. G. Rodrigo, R. Shankarappa, G. H. Learn, L.
P. Zhao, H. Li, O. Davidov, and J. I. Mullins. 1996. HIV quasispecies and
resampling.
Science, 273:415-416.
|
Learn, G. H., Jr., B. T. M. Korber, B. Foley, B. H. Hahn,
S. M. Wolinsky, and J. I. Mullins. 1996. Maintaining the integrity of human
immunodeficiency virus sequence databases.
Journal of Virology, 70:5720-5730
[abstract].
|
Korber, B. T. M., G. Learn, J. I. Mullins, B. H. Hahn, and
S. Wolinsky. 1995. Protecting HIV databases. Nature 378:242-243.
|
Förster, H., G. Learn, and M. D. Coffey. 1995. Towards
a better understanding of the evolutionary history of species of the genus
Phytophthora using isozymes, DNA RFLPs and ribosomal DNA spacer
sequences. pp. 42-54. In Phytophthora infestans 150. L. J. Dowley,
E. Bannon, L. R. Cooke, T. Keane, and E. O'Sullivan (eds.), Boole Press
Ltd., Dublin, Ireland.
|
Durbin, M. L., G. H. Learn, Jr., G. A. Huttley, and M. T.
Clegg. 1995. Evolution of the chalcone synthase gene family in the genus
Ipomoea.
Proceedings of the National Academy of Sciences, U.S.A., 92:
3338-3342
[abstract].
|
Eguiarte, L. E., M. R. Duvall, G. H. Learn, Jr., and M. T.
Clegg. 1994. The systematic status of the Agavaceae and Nolinaceae and
related Asparagales in the Monocotyledons: An analysis based on the
rbcL gene sequence. Boletín de la Sociedad Botánica
de México, 54:35-56.
|
Clegg, M. T., B. S. Gaut, G. H. Learn, Jr., and B. R. Morton.
1994. Rates and patterns of chloroplast DNA evolution.
Proceedings of the National Academy of Sciences, U.S.A., 91:
6795-6801
[abstract].
|
Lee, K., F. Y. Bih, G. H. Learn, Jr., J. T. L. Ting, C. Sellers,
J. T. C. Tzen, and A. H. C. Huang. 1994. Oleosins in the gametophytes of
Pinus and Brassica and their relation to those in the sporophytes of various
species. Planta, 193:461-469 [abstract].
|
Duvall, M. R., G. H. Learn, Jr., L. E. Eguiarte, and M. T.
Clegg. 1993. Phylogenetic analysis of rbcL sequences identifies
Acorus calamus as the primal extant monocotyledon.
Proceedings of the National Academy of Sciences, U.S.A., 90:
4641-4644
[abstract].
|
Learn, G. H., Jr., J. S. Shore, G. R. Furnier, G. Zurawski,
and M. T. Clegg. 1992. Constraints on the evolution of chloroplast introns:
the intron in the gene encoding tRNA-Val(UAC).
Molecular Biology and Evolution, 9:856-871
[abstract].
|
Giannasi, D. E., G. Zurawski, G. Learn, and M. T. Clegg. 1992. Evolutionary
relationships of the Caryophillidae based on comparative rbcL sequences.
Systematic Botany, 17:1-15.
|
Clegg, M. T., G. H. Learn, and E. M. Golenberg. 1991. Molecular
evolution of chloroplast DNA. pp. 135-149. In Evolution at the Molecular
Level. R.K. Selander, A. G. Clark and T. S. Whittam (eds.), Sinauer
Associates, Sunderland, MA.
|
Learn, G. H., Jr., and B. A. Schaal. 1987. Population subdivision
for ribosomal DNA repeat variants in Clematis fremontii.
Evolution,
41:433-438.
|
