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Austin Hughes

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

Research Profile (preview)

Phenomena

Molecular Evolution

Concepts & Ideas

Genes & Molecular Sequences

Chemicals & Drugs

Physiology

Living Beings

Procedures

Sequence Alignment

Anatomy

Cytotoxic T-Lymphocytes

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Co-Publications
Name
42
Friedman, Robert
35
Watkins, David
17
O'Connor, David
14
Piontkivska, Helen
12
Letvin, Norman
9
Sette, Alessandro
8
Sidney, John
8
Chen, Zheng
8
Yeager, M
7
Allen, Todd
6
Dodds, Elizabeth
6
Friedrich, Thomas
6
Golos, Thaddeus
6
Jongwutiwes, Somchai
6
Boyson, Jonathan

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Publications

TOP 3
Hughes Austin L
Small effective population sizes and rare nonsynonymous variants in potyviruses.
Hughes Austin L
Relaxation of purifying selection on the SAD lineage of live attenuated oral vaccines for rabies virus.
Bimber Benjamin N; Burwitz Benjamin J; O'Connor Shelby; Detmer Ann; Gostick Emma; Lank Simon M; Price David A; Hughes Austin; O'Connor David
Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques.

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All Publications

2009: Hughes Austin L
Small effective population sizes and rare nonsynonymous variants in potyviruses.
Virology 2009;393(1):127-34.
2009: Hughes Austin L
Relaxation of purifying selection on the SAD lineage of live attenuated oral vaccines for rabies virus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2009;9(5):827-31.
2009: Bimber Benjamin N; Burwitz Benjamin J; O'Connor Shelby; Detmer Ann; Gostick Emma; Lank Simon M; Price David A; Hughes Austin; O'Connor David
Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques.
Journal of virology 2009;83(16):8247-53.
2009: Hughes Austin L; Friedman Robert
A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes.
Evolution & development 2009;11(4):382-90.
2009: Putaporntip Chaturong; Jongwutiwes Somchai; Hughes Austin L
Natural selection maintains a stable polymorphism at the circumsporozoite protein locus of Plasmodium falciparum in a low endemic area.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2009;9(4):567-73.
2009: Hughes Austin L; Friedman Robert
More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size.
Gene 2009;440(1-2):50-6.
2009: Bondarenko Gennadiy I; Dambaeva Svetlana V; Grendell Richard L; Hughes Austin L; Durning Maureen; Garthwaite Mark A; Golos Thaddeus G
Characterization of cynomolgus and vervet monkey placental MHC class I expression: diversity of the nonhuman primate AG locus.
Immunogenetics 2009;61(6):431-42.
2009: Conley A J; Corbin C J; Hughes A L
Adaptive evolution of mammalian aromatases: lessons from Suiformes.
Journal of experimental zoology. Part A, Ecological genetics and physiology 2009;311(5):346-57.
2009: Hughes Austin L
Relaxation of purifying selection on live attenuated vaccine strains of the family Paramyxoviridae.
Vaccine 2009;27(11):1685-90.
2009: Campbell Kevin J; Detmer Ann M; Karl Julie A; Wiseman Roger W; Blasky Alex J; Hughes Austin L; Bimber Benjamin N; O'Connor Shelby L; O'Connor David H
Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques.
Immunogenetics 2009;61(3):177-87.
2009: Hughes Austin L
Evolution in the post-genome era.
Perspectives in biology and medicine 2009;52(2):332-7.
2008: Putaporntip Chaturong; Jongwutiwes Somchai; Hughes Austin L
Differential selective pressures on the merozoite surface protein 2 locus of Plasmodium falciparum in a low endemic area.
Gene 2008;427(1-2):51-7.
2008: Hughes Austin L; Friedman Robert
Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes.
Molecular biology and evolution 2008;25(12):2681-8.
2008: Bimber Benjamin N; Moreland Anna J; Wiseman Roger W; Hughes Austin L; O'Connor David H
Complete characterization of killer Ig-like receptor (KIR) haplotypes in Mauritian cynomolgus macaques: novel insights into nonhuman primate KIR gene content and organization.
Journal of immunology (Baltimore, Md. : 1950) 2008;181(9):6301-8.
2008: Hughes Austin L; Friedman Robert; Rivailler Pierre; French Jeffrey O
Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes.
Molecular biology and evolution 2008;25(10):2199-209.
2008: Hughes Austin L; Friedman Robert
Alternative splicing, gene duplication and connectivity in the genetic interaction network of the nematode worm Caenorhabditis elegans.
Genetica 2008;134(2):181-6.
2008: Hughes Austin L
The origin of adaptive phenotypes.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(36):13193-4.
2008: Hughes Austin L; Friedman Robert
Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes.
Immunogenetics 2008;60(9):495-506.
2008: Irausquin Stephanie Jiménez; Hughes Austin L
Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.
The Journal of general virology 2008;89(Pt 8):1921-9.
2008: Pendley Chad J; Becker Ericka A; Karl Julie A; Blasky Alex J; Wiseman Roger W; Hughes Austin L; O'Connor Shelby L; O'Connor David H
MHC class I characterization of Indonesian cynomolgus macaques.
Immunogenetics 2008;60(7):339-51.
2008: Hughes Austin L; Welch Robert; Puri Vinita; Matthews Casey; Haque Kashif; Chanock Stephen J; Yeager Meredith
Genome-wide SNP typing reveals signatures of population history.
Genomics 2008;92(1):1-8.
2008: Maness Nicholas J; Yant Levi J; Chung Chungwon; Loffredo John T; Friedrich Thomas C; Piaskowski Shari M; Furlott Jessica; May Gemma E; Soma Taeko; León Enrique J; Wilson Nancy A; Piontkivska Helen; Hughes Austin L; Sidney John; Sette Alessandro; Watkins David I
Comprehensive immunological evaluation reveals surprisingly few differences between elite controller and progressor Mamu-B*17-positive Simian immunodeficiency virus-infected rhesus macaques.
Journal of virology 2008;82(11):5245-54.
2008: Hughes Austin L; Piontkivska Helen
Functional diversification of the toll-like receptor gene family.
Immunogenetics 2008;60(5):249-56.
2008: Hughes Austin L; Piontkivska Helen
Nucleotide sequence polymorphism in circoviruses.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2008;8(2):130-8.
2008: Karl Julie A; Wiseman Roger W; Campbell Kevin J; Blasky Alex J; Hughes Austin L; Ferguson Betsy; Read Daniel S; O'Connor David H
Identification of MHC class I sequences in Chinese-origin rhesus macaques.
Immunogenetics 2008;60(1):37-46.
2008: Hughes Austin L
Near neutrality: leading edge of the neutral theory of molecular evolution.
Annals of the New York Academy of Sciences 2008;1133():162-79.
2008: Grynberg Priscila; Fontes Cor Jesus F; Hughes Austin L; Braga Erika M
Polymorphism at the apical membrane antigen 1 locus reflects the world population history of Plasmodium vivax.
BMC evolutionary biology 2008;8():123.
2007: Hughes Austin L; Hughes Mary Ann K
More effective purifying selection on RNA viruses than in DNA viruses.
Gene 2007;404(1-2):117-25.
2007: Hughes Austin L; Rivailler Pierre
Phylogeny and recombination history of gallid herpesvirus 2 (Marek's disease virus) genomes.
Virus research 2007;130(1-2):28-33.
2007: Maness Nicholas J; Valentine Laura E; May Gemma E; Reed Jason; Piaskowski Shari M; Soma Taeko; Furlott Jessica; Rakasz Eva G; Friedrich Thomas C; Price David A; Gostick Emma; Hughes Austin L; Sidney John; Sette Alessandro; Wilson Nancy A; Watkins David I
AIDS virus specific CD8+ T lymphocytes against an immunodominant cryptic epitope select for viral escape.
The Journal of experimental medicine 2007;204(11):2505-12.
2007: Corbin C J; Hughes A L; Heffelfinger J R; Berger T; Waltzek T B; Roser J F; Santos T C; Miglino M A; Oliveira M F; Braga F C; Meirelles F V; Conley A J
Evolution of suiform aromatases: ancestral duplication with conservation of tissue-specific expression in the collared peccary (Pecari tayassu).
Journal of molecular evolution 2007;65(4):403-12.
2007: Hughes A L
Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level.
Heredity 2007;99(4):364-73.
2007: Hughes Austin L; Friedman Robert
The effect of branch lengths on phylogeny: an empirical study using highly conserved orthologs from mammalian genomes.
Molecular phylogenetics and evolution 2007;45(1):81-8.
2007: Hughes Austin L; Piontkivska Helen; Foppa Ivo
Rapid fixation of a distinctive sequence motif in the 3' noncoding region of the clade of West Nile virus invading North America.
Gene 2007;399(2):152-61.
2007: Hughes Austin L
Evolution of the lung surfactant proteins in birds and mammals.
Immunogenetics 2007;59(7):565-72.
2007: Conley A J; Corbin C J; Browne P; Mapes S M; Place N J; Hughes A L; Glickman S E
Placental expression and molecular characterization of aromatase cytochrome P450 in the spotted hyena (Crocuta crocuta).
Placenta 2007;28(7):668-75.
2007: Averdam Anne; Kuhl Heiner; Sontag Mario; Becker Tamara; Hughes Austin L; Reinhardt Richard; Walter Lutz
Genomics and diversity of the common marmoset monkey NK complex.
Journal of immunology (Baltimore, Md. : 1950) 2007;178(11):7151-61.
2007: O'Connor Shelby L; Blasky Alex J; Pendley Chad J; Becker Ericka A; Wiseman Roger W; Karl Julie A; Hughes Austin L; O'Connor David H
Comprehensive characterization of MHC class II haplotypes in Mauritian cynomolgus macaques.
Immunogenetics 2007;59(6):449-62.
2007: Hughes Austin L
Micro-scale signature of purifying selection in Marburg virus genomes.
Gene 2007;392(1-2):266-72.
2007: Hughes Austin L; Hughes Mary Ann K
Coding sequence polymorphism in avian mitochondrial genomes reflects population histories.
Molecular ecology 2007;16(7):1369-76.
2007: Schwarz Ryan S; Hodes-Villamar Linda; Fitzpatrick Kelly A; Fain Matthew G; Hughes Austin L; Cadavid Luis F
A gene family of putative immune recognition molecules in the hydroid Hydractinia.
Immunogenetics 2007;59(3):233-46.
2007: Westover Kristi M; Hughes Austin L
Evolution of cytotoxic T-lymphocyte epitopes in hepatitis B virus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2007;7(2):254-62.
2007: Hughes Austin L; Langley Katherine J
Nucleotide usage, synonymous substitution pattern, and past recombination in genomes of Streptococcus pyogenes.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2007;7(2):188-96.
2007: Hughes Austin L; Friedman Robert
Sharing of transcription factors after gene duplication in the yeast Saccharomyces cerevisiae.
Genetica 2007;129(3):301-8.
2007: Hughes Austin L; Hughes Mary Ann K; Friedman Robert
Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus.
Virus research 2007;123(2):147-53.
2007: Friedman Robert; Hughes Austin L
Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods.
Molecular phylogenetics and evolution 2007;42(2):388-93.
2007: Hughes Austin L; French Jeffrey O
Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium.
Gene 2007;387(1-2):31-7.
2007: Hughes Austin L; Hughes Mary Ann K
Nucleotide substitution at the highly polymorphic K1 locus of human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus).
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2007;7(1):110-5.
2007: Loffredo John T; Friedrich Thomas C; León Enrique J; Stephany Jason J; Rodrigues Denise S; Spencer Sean P; Bean Alex T; Beal Dominic R; Burwitz Benjamin J; Rudersdorf Richard A; Wallace Lyle T; Piaskowski Shari M; May Gemma E; Sidney John; Gostick Emma; Wilson Nancy A; Price David A; Kallas Esper G; Piontkivska Helen; Hughes Austin L; Sette Alessandro; Watkins David I
CD8+ T cells from SIV elite controller macaques recognize Mamu-B*08-bound epitopes and select for widespread viral variation.
PloS one 2007;2(11):e1152.
2006: Hughes Austin L
Evolutionary relationships of vertebrate NACHT domain-containing proteins.
Immunogenetics 2006;58(10):785-91.
2006: Hughes Austin L; Friedman Robert
Across-tissue expression and evolution of genes controlled by the Aire transcription factor.
Genomics 2006;88(4):462-7.
2006: Chakrabarty Anindita; MacLean James A; Hughes Austin L; Roberts R Michael; Green Jonathan A
Rapid evolution of the trophoblast kunitz domain proteins (TKDPs)-a multigene family in ruminant ungulates.
Journal of molecular evolution 2006;63(2):274-82.
2006: Friedman Robert; Hughes Austin L
Pattern of gene duplication in the Cotesia congregata Bracovirus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2006;6(4):315-22.
2006: Slukvin I I; Grendell R L; Rao D S; Hughes A L; Golos T G
Cloning of rhesus monkey LILRs.
Tissue antigens 2006;67(4):331-7.
2006: Putaporntip Chaturong; Jongwutiwes Somchai; Iwasaki Takuya; Kanbara Hiroji; Hughes Austin L
Ancient common ancestry of the merozoite surface protein 1 of Plasmodium vivax as inferred from its homologue in Plasmodium knowlesi.
Molecular and biochemical parasitology 2006;146(1):105-8.
2006: Piontkivska Helen; Hughes Austin L
Patterns of sequence evolution at epitopes for host antibodies and cytotoxic T-lymphocytes in human immunodeficiency virus type 1.
Virus research 2006;116(1-2):98-105.
2006: Hughes Austin L; Glenn Nancy L
Contrasting patterns of transcript abundance in tumour tissue and cancer cell lines.
Applied bioinformatics 2006;5(4):201-10.
2005: Hughes Austin L; Friedman Robert
Gene duplication and the properties of biological networks.
Journal of molecular evolution 2005;61(6):758-64.
2005: Hughes Austin L; Packer Bernice; Welch Robert; Chanock Stephen J; Yeager Meredith
High level of functional polymorphism indicates a unique role of natural selection at human immune system loci.
Immunogenetics 2005;57(11):821-7.
2005: Hughes Austin L; Piontkivska Helen; Krebs Kendall C; O'Connor David H; Watkins David I
Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus.
Bioinformatics (Oxford, England) 2005;21 Suppl 3():iii39-44.
2005: Hughes Austin L
Consistent across-tissue signatures of differential gene expression in Crohn's disease.
Immunogenetics 2005;57(10):709-16.
2005: Piontkivska Helen; Hughes Austin L
Environmental kinetoplastid-like 18S rRNA sequences and phylogenetic relationships among Trypanosomatidae: paraphyly of the genus Trypanosoma.
Molecular and biochemical parasitology 2005;144(1):94-9.
2005: Hughes Austin L; Hughes Mary Ann K
Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes.
Virus research 2005;113(2):81-8.
2005: Krebs Kendall C; Jin ZheYuan; Rudersdorf Richard; Hughes Austin L; O'Connor David H
Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques.
Journal of immunology (Baltimore, Md. : 1950) 2005;175(8):5230-9.
2005: Hughes Austin L; Friedman Robert
Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum.
Molecular and biochemical parasitology 2005;142(2):170-6.
2005: Jongwutiwes Somchai; Putaporntip Chaturong; Iwasaki Takuya; Ferreira Marcelo U; Kanbara Hiroji; Hughes Austin L
Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax.
Molecular biology and evolution 2005;22(8):1733-9.
2005: Hughes Austin L; Packer Bernice; Welch Robert; Bergen Andrew W; Chanock Stephen J; Yeager Meredith
Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding Loci.
Genetics 2005;170(3):1181-7.
2005: Hughes Austin L
Gene duplication and the origin of novel proteins.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(25):8791-2.
2005: Hughes Austin L; Friedman Robert
Loss of ancestral genes in the genomic evolution of Ciona intestinalis.
Evolution & development 2005;7(3):196-200.
2005: Hughes Austin L; Friedman Robert
Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes.
Molecular biology and evolution 2005;22(5):1320-4.
2005: Friedman Robert; Hughes Austin L
The pattern of nucleotide difference at individual codons among mouse, rat, and human.
Molecular biology and evolution 2005;22(5):1285-9.
2005: Hughes Austin L; Ekollu Vikram; Friedman Robert; Rose John R
Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology.
Systematic biology 2005;54(2):268-76.
2005: Hughes Austin L; Friedman Robert
Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus.
Journal of bacteriology 2005;187(8):2698-704.
2005: Biron David G; Moura Hercules; Marché Laurent; Hughes Austin L; Thomas Frédéric
Towards a new conceptual approach to "parasitoproteomics".
Trends in parasitology 2005;21(4):162-8.
2005: Hughes Austin L; Friedman Robert
Poxvirus genome evolution by gene gain and loss.
Molecular phylogenetics and evolution 2005;35(1):186-95.
2005: Friedman Robert; Hughes Austin L
Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons.
Molecular biology and evolution 2005;22(3):542-6.
2005: Hughes Austin L; Friedman Robert
Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana.
Journal of molecular evolution 2005;60(2):247-56.
2005: Hughes Austin L
Evidence for abundant slightly deleterious polymorphisms in bacterial populations.
Genetics 2005;169(2):533-8.
2005: Hughes Austin L; Piontkivska Helen
DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size.
BMC evolutionary biology 2005;5(1):12.
2004: Hughes Austin L; Friedman Robert
Patterns of sequence divergence in 5' intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories.
Genetics 2004;168(4):1795-803.
2004: Hughes Austin L; Friedman Robert
Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals.
Journal of molecular evolution 2004;59(6):827-33.
2004: O'Connor David H; McDermott Adrian B; Krebs Kendall C; Dodds Elizabeth J; Miller Jacqueline E; Gonzalez Edna J; Jacoby Timothy J; Yant Levi; Piontkivska Helen; Pantophlet Ralph; Burton Dennis R; Rehrauer William M; Wilson Nancy; Hughes Austin L; Watkins David I
A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation.
Journal of virology 2004;78(24):14012-22.
2004: Patil Amar; Hughes Austin L; Zhang Guolong
Rapid evolution and diversification of mammalian alpha-defensins as revealed by comparative analysis of rodent and primate genes.
Physiological genomics 2004;20(1):1-11.
2004: Hughes Austin L
Evolutionary origin of the Jiv90 gene of Pestivirus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2004;4(4):329-33.
2004: Piontkivska Helen; Hughes Austin L
Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisons.
Journal of virology 2004;78(21):11758-65.
2004: Friedman Robert; Ekollu Vikram; Rose John R; Hughes Austin L
Dblox: a genome-wide test for ancient segmental duplication.
Bioinformatics (Oxford, England) 2004;20(16):2834-5.
2004: Hughes Austin L
The evolution of amino acid repeat arrays in Plasmodium and other organisms.
Journal of molecular evolution 2004;59(4):528-35.
2004: Eck Peter; Erichsen Hans Christian; Taylor James G; Yeager Meredith; Hughes Austin L; Levine Mark; Chanock Stephen
Comparison of the genomic structure and variation in the two human sodium-dependent vitamin C transporters, SLC23A1 and SLC23A2.
Human genetics 2004;115(4):285-94.
2004: Xiao Yanjing; Hughes Austin L; Ando Junko; Matsuda Yoichi; Cheng Jan-Fang; Skinner-Noble Donald; Zhang Guolong
A genome-wide screen identifies a single beta-defensin gene cluster in the chicken: implications for the origin and evolution of mammalian defensins.
BMC genomics 2004;5(1):56.
2004: Pollack Henry; Hou Zhiying; Hughes Austin L; Borkowsky William
Perinatal transmission and viral evolution of hepatitis C virus quasispecies in infants coinfected with HIV.
Journal of acquired immune deficiency syndromes (1999) 2004;36(4):890-9.
2004: Hughes Austin L; Friedman Robert
Recent mammalian gene duplications: robust search for functionally divergent gene pairs.
Journal of molecular evolution 2004;59(1):114-20.
2004: Friedman Robert; Drake John W; Hughes Austin L
Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles.
Genetics 2004;167(3):1507-12.
2004: Hughes Austin L; Friedman Robert
Pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish.
Molecular phylogenetics and evolution 2004;32(1):337-43.
2004: Hughes A L
Comparative genomics: mining the crucial 1%.
Heredity 2004;93(1):5.
2004: Hughes Austin L; Friedman Robert
Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale.
Genetica 2004;121(2):181-5.
2004: Hughes Austin L
Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2004;4(2):143-52.
2004: Friedman Robert; Hughes Austin L
Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse.
Molecular biology and evolution 2004;21(6):1008-13.
2004: Friedrich Thomas C; Dodds Elizabeth J; Yant Levi J; Vojnov Lara; Rudersdorf Richard; Cullen Candice; Evans David T; Desrosiers Ronald C; Mothé Bianca R; Sidney John; Sette Alessandro; Kunstman Kevin; Wolinsky Steven; Piatak Michael; Lifson Jeffrey; Hughes Austin L; Wilson Nancy; O'Connor David H; Watkins David I
Reversion of CTL escape-variant immunodeficiency viruses in vivo.
Nature medicine 2004;10(3):275-81.
2004: Friedrich Thomas C; Frye Christopher A; Yant Levi J; O'Connor David H; Kriewaldt Nancy A; Benson Meghan; Vojnov Lara; Dodds Elizabeth J; Cullen Candice; Rudersdorf Richard; Hughes Austin L; Wilson Nancy; Watkins David I
Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an immunodominant cytotoxic-T-lymphocyte response.
Journal of virology 2004;78(5):2581-5.
2004: Hughes Austin L; Friedman Robert
Differential loss of ancestral gene families as a source of genomic divergence in animals.
Proceedings. Biological sciences / The Royal Society 2004;271 Suppl 3():S107-9.
2004: Hughes Austin L
Birth-and-death evolution of protein-coding regions and concerted evolution of non-coding regions in the multi-component genomes of nanoviruses.
Molecular phylogenetics and evolution 2004;30(2):287-94.
2003: Hughes Austin L; Packer Bernice; Welch Robert; Bergen Andrew W; Chanock Stephen J; Yeager Meredith
Widespread purifying selection at polymorphic sites in human protein-coding loci.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(26):15754-7.
2003: Hughes Austin L; Friedman Robert; Ekollu Vikram; Rose John R
Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana.
Molecular phylogenetics and evolution 2003;29(3):410-6.
2003: Hughes Austin L; Green Jonathan A; Piontkivska Helen; Roberts R Michael
Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins.
Molecular biology and evolution 2003;20(11):1940-5.
2003: O'Connor David H; Mothe Bianca R; Weinfurter Jason T; Fuenger Sarah; Rehrauer William M; Jing Peicheng; Rudersdorf Richard R; Liebl Max E; Krebs Kendall; Vasquez Joshua; Dodds Elizabeth; Loffredo John; Martin Sarah; McDermott Adrian B; Allen Todd M; Wang Chenxi; Doxiadis G G; Montefiori David C; Hughes Austin; Burton Dennis R; Allison David B; Wolinsky Steven M; Bontrop Ronald; Picker Louis J; Watkins David I
Major histocompatibility complex class I alleles associated with slow simian immunodeficiency virus disease progression bind epitopes recognized by dominant acute-phase cytotoxic-T-lymphocyte responses.
Journal of virology 2003;77(16):9029-40.
2003: Hughes Austin L; Friedman Robert
Parallel evolution by gene duplication in the genomes of two unicellular fungi.
Genome research 2003;13(6A):1259-64.
2003: Hughes Austin L; Friedman Robert
Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses.
Molecular biology and evolution 2003;20(6):979-87.
2003: Hughes Austin L; Friedman Robert
Parallel evolution by gene duplication in the genomes of two unicellular fungi.
Genome research 2003;13(5):794-9.
2003: Hughes Austin L; Piontkivska Helen
Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera.
Molecular biology and evolution 2003;20(4):644-52.
2003: Sette Alessandro; Sidney John; Livingston Brian D; Dzuris John L; Crimi Claire; Walker Christopher M; Southwood Scott; Collins Edward J; Hughes Austin L
Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution.
Immunogenetics 2003;54(12):830-41.
2003: Piontkivska Helen; Hughes Austin L
Evolution of vertebrate voltage-gated ion channel alpha chains by sequential gene duplication.
Journal of molecular evolution 2003;56(3):277-85.
2003: Hughes Austin L
Genomes of mice and men.
Heredity 2003;90(2):115-7.
2003: Friedman Robert; Hughes Austin L
The temporal distribution of gene duplication events in a set of highly conserved human gene families.
Molecular biology and evolution 2003;20(1):154-61.
2003: Bashirova Arman A; Wu Li; Cheng Jie; Martin Thomas D; Martin Maureen P; Benveniste Raoul E; Lifson Jeffrey D; KewalRamani Vineet N; Hughes Austin; Carrington Mary
Novel member of the CD209 (DC-SIGN) gene family in primates.
Journal of virology 2003;77(1):217-27.
2003: Hughes Austin L; Friedman Robert
2R or not 2R: testing hypotheses of genome duplication in early vertebrates.
Journal of structural and functional genomics 2003;3(1-4):85-93.
2002: Hughes Austin L
Natural selection and the diversification of vertebrate immune effectors.
Immunological reviews 2002;190():161-8.
2002: Flügge Perris; Zimmermann Elke; Hughes Austin L; Günther Eberhard; Walter Lutz
Characterization and phylogenetic relationship of prosimian MHC class I genes.
Journal of molecular evolution 2002;55(6):768-75.
2002: Hughes Austin L; Friedman Robert; Murray Megan
Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.
Emerging infectious diseases 2002;8(11):1342-6.
2002: Hughes Austin L
Evolution of the human killer cell inhibitory receptor family.
Molecular phylogenetics and evolution 2002;25(2):330-40.
2002: Vogel Thorsten U; Friedrich Thomas C; O'Connor David H; Rehrauer William; Dodds Elizabeth J; Hickman Heather; Hildebrand William; Sidney John; Sette Alessandro; Hughes Austin; Horton Helen; Vielhuber Kathy; Rudersdorf Richard; De Souza Ivna P; Reynolds Matthew R; Allen Todd M; Wilson Nancy; Watkins David I
Escape in one of two cytotoxic T-lymphocyte epitopes bound by a high-frequency major histocompatibility complex class I molecule, Mamu-A*02: a paradigm for virus evolution and persistence?
Journal of virology 2002;76(22):11623-36.
2002: Hughes Austin L
Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2002;2(1):3-10.
2002: Jongwutiwes Somchai; Putaporntip Chaturong; Friedman Robert; Hughes Austin L
The extent of nucleotide polymorphism is highly variable across a 3-kb region on Plasmodium falciparum chromosome 2.
Molecular biology and evolution 2002;19(9):1585-90.
2002: Hughes Austin L
Adaptive evolution after gene duplication.
Trends in genetics : TIG 2002;18(9):433-4.
2002: Hughes Austin L; Verra Federica
Extensive polymorphism and ancient origin of Plasmodium falciparum.
Trends in parasitology 2002;18(8):348-51.
2002: Hughes Austin L
Strength in numbers.
Nature 2002;417(6891):795.
2002: O'Connor David H; Allen Todd M; Vogel Thorsten U; Jing Peicheng; DeSouza Ivan P; Dodds Elizabeth; Dunphy Edward J; Melsaether Cheri; Mothé Bianca; Yamamoto Hiroshi; Horton Helen; Wilson Nancy; Hughes Austin L; Watkins David I
Acute phase cytotoxic T lymphocyte escape is a hallmark of simian immunodeficiency virus infection.
Nature medicine 2002;8(5):493-9.
2002: Lipovich Leonard; Hughes Austin L; King Mary Claire; Abkowitz Janis L; Quigley John G
Genomic structure and evolutionary context of the human feline leukemia virus subgroup C receptor (hFLVCR) gene: evidence for block duplications and de novo gene formation within duplicons of the hFLVCR locus.
Gene 2002;286(2):203-13.
2002: Friedman Robert; Hughes Austin L
Molecular evolution of the NF-kappaB signaling system.
Immunogenetics 2002;53(10-11):964-74.
2002: Hughes Austin L
Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues.
Journal of molecular evolution 2002;54(1):90-101.
2001: Hughes A L
Evolutionary change of predicted cytotoxic T cell epitopes of dengue virus.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2001;1(2):123-30.
2001: Erickson A L; Kimura Y; Igarashi S; Eichelberger J; Houghton M; Sidney J; McKinney D; Sette A; Hughes A L; Walker C M
The outcome of hepatitis C virus infection is predicted by escape mutations in epitopes targeted by cytotoxic T lymphocytes.
Immunity 2001;15(6):883-95.
2001: Grendell R L; Hughes A L; Golos T G
Cloning of rhesus monkey killer-cell Ig-like receptors (KIRs) from early pregnancy decidua.
Tissue antigens 2001;58(5):329-34.
2001: Friedman R; Hughes A L
Pattern and timing of gene duplication in animal genomes.
Genome research 2001;11(11):1842-7.
2001: O'Connor D; Friedrich T; Hughes A; Allen T M; Watkins D
Understanding cytotoxic T-lymphocyte escape during simian immunodeficiency virus infection.
Immunological reviews 2001;183():115-26.
2001: Westover K M; Hughes A L
Molecular evolution of viral fusion and matrix protein genes and phylogenetic relationships among the Paramyxoviridae.
Molecular phylogenetics and evolution 2001;21(1):128-34.
2001: Hughes A L; Verra F
Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum.
Proceedings. Biological sciences / The Royal Society 2001;268(1478):1855-60.
2001: Hughes A L; Westover K; da Silva J; O'Connor D H; Watkins D I
Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus.
Journal of virology 2001;75(17):7966-72.
2001: Hughes A L; da Silva J; Friedman R
Ancient genome duplications did not structure the human Hox-bearing chromosomes.
Genome research 2001;11(5):771-80.
2001: Friedman R; Hughes A L
Gene duplication and the structure of eukaryotic genomes.
Genome research 2001;11(3):373-81.
2001: Wang X; Hughes A L; Tsukamoto T; Ando T; Kao T
Evidence that intragenic recombination contributes to allelic diversity of the S-RNase gene at the self-incompatibility (S) locus in Petunia inflata.
Plant physiology 2001;125(2):1012-22.
2001: Hughes A L
Evolution of the integrin alpha and beta protein families.
Journal of molecular evolution 2001;52(1):63-72.
2000: Hughes A L; Friedman R
Evolutionary diversification of protein-coding genes of hantaviruses.
Molecular biology and evolution 2000;17(10):1558-68.
2000: Allen T M; O'Connor D H; Jing P; Dzuris J L; Mothé B R; Vogel T U; Dunphy E; Liebl M E; Emerson C; Wilson N; Kunstman K J; Wang X; Allison D B; Hughes A L; Desrosiers R C; Altman J D; Wolinsky S M; Sette A; Watkins D I
Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia.
Nature 2000;407(6802):386-90.
2000: Hughes A L; Pontarotti P
Gene duplication and MHC origins.
Immunogenetics 2000;51(11):982-3.
2000: Hughes A L; Roberts R M
Independent origin of IFN-alpha and IFN-beta in birds and mammals.
Journal of interferon & cytokine research : the official journal of the International Society for Interferon and Cytokine Research 2000;20(8):737-9.
2000: Hughes A L
Evolution of introns and exons of class II major histocompatibility complex genes of vertebrates.
Immunogenetics 2000;51(6):473-86.
2000: Hughes A L; Green J A; Garbayo J M; Roberts R M
Adaptive diversification within a large family of recently duplicated, placentally expressed genes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(7):3319-23.
2000: Hughes A L
Modes of evolution in the protease and kringle domains of the plasminogen-prothrombin family.
Molecular phylogenetics and evolution 2000;14(3):469-78.
2000: Urvater J A; Otting N; Loehrke J H; Rudersdorf R; Slukvin I I; Piekarczyk M S; Golos T G; Hughes A L; Bontrop R E; Watkins D I
Mamu-I: a novel primate MHC class I B-related locus with unusually low variability.
Journal of immunology (Baltimore, Md. : 1950) 2000;164(3):1386-98.
2000: Yeager M; Carrington M; Hughes A L
Class I and class II MHC bind self peptide sets that are strikingly different in their evolutionary characteristics.
Immunogenetics 2000;51(1):8-15.
2000: Verra F; Hughes A L
Evidence for ancient balanced polymorphism at the Apical Membrane Antigen-1 (AMA-1) locus of Plasmodium falciparum.
Molecular and biochemical parasitology 2000;105(1):149-53.
1999: Hughes A L
Concerted evolution of exons and introns in the MHC-linked tenascin-X gene of mammals.
Molecular biology and evolution 1999;16(11):1558-67.
1999: Evans D T; O'Connor D H; Jing P; Dzuris J L; Sidney J; da Silva J; Allen T M; Horton H; Venham J E; Rudersdorf R A; Vogel T; Pauza C D; Bontrop R E; DeMars R; Sette A; Hughes A L; Watkins D I
Virus-specific cytotoxic T-lymphocyte responses select for amino-acid variation in simian immunodeficiency virus Env and Nef.
Nature medicine 1999;5(11):1270-6.
1999: Hughes A L
Evolutionary diversification of the mammalian defensins.
Cellular and molecular life sciences : CMLS 1999;56(1-2):94-103.
1999: da Silva J; Hughes A L
Molecular phylogenetic evidence of cytotoxic T lymphocyte (CTL) selection on human immunodeficiency virus type 1 (HIV-1)
Molecular biology and evolution 1999;16(10):1420-2.
1999: Verra F; Hughes A L
Natural selection on apical membrane antigen-1 of Plasmodium falciparum.
Parassitologia 1999;41(1-3):93-5.
1999: Verra F; Hughes A L
Biased amino acid composition in repeat regions of Plasmodium antigens.
Molecular biology and evolution 1999;16(5):627-33.
1999: Hughes A L
Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history.
Journal of molecular evolution 1999;48(5):565-76.
1999: Vogel T U; Evans D T; Urvater J A; O'Connor D H; Hughes A L; Watkins D I
Major histocompatibility complex class I genes in primates: co-evolution with pathogens.
Immunological reviews 1999;167():327-37.
1999: Yeager M; Hughes A L
Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution.
Immunological reviews 1999;167():45-58.
1999: Tasaki Y; Fukuda S; Iio M; Miura R; Imai T; Sugano S; Yoshie O; Hughes A L; Nomiyama H
Chemokine PARC gene (SCYA18) generated by fusion of two MIP-1alpha/LD78alpha-like genes.
Genomics 1999;55(3):353-7.
1999: Hughes A L; Yeager M
Coevolution of the mammalian chemokines and their receptors.
Immunogenetics 1999;49(2):115-24.
1999: Hughes A L
Evolution of the arthropod prophenoloxidase/hexamerin protein family.
Immunogenetics 1999;49(2):106-14.
1999: Boyson J E; Iwanaga K K; Urvater J A; Hughes A L; Golos T G; Watkins D I
Evolution of a new nonclassical MHC class I locus in two Old World primate species.
Immunogenetics 1999;49(2):86-98.
1999: Hughes A L; Yeager M; Ten Elshof A E; Chorney M J
A new taxonomy of mammalian MHC class I molecules.
Immunology today 1999;20(1):22-6.
1999: Hughes A L
Genomic catastrophism and the origin of vertebrate immunity.
Archivum immunologiae et therapiae experimentalis 1999;47(6):347-53.
1998: da Silva J; Hughes A L
Conservation of cytotoxic T lymphocyte (CTL) epitopes as a host strategy to constrain parasite adaptation: evidence from the nef gene of human immunodeficiency virus 1 (HIV-1).
Molecular biology and evolution 1998;15(10):1259-68.
1998: Hughes A L; Verra F
Ancient polymorphism and the hypothesis of a recent bottleneck in the malaria parasite Plasmodium falciparum.
Genetics 1998;150(1):511-3.
1998: Hughes A L
Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1.
Molecular biology and evolution 1998;15(7):854-70.
1998: Hughes A L; Yeager M
Natural selection and the evolutionary history of major histocompatibility complex loci.
Frontiers in bioscience : a journal and virtual library 1998;3():d509-16.
1998: Hughes A L
Protein phylogenies provide evidence of a radical discontinuity between arthropod and vertebrate immune systems.
Immunogenetics 1998;47(4):283-96.
1998: Hughes A L; Yeager M
Natural selection at major histocompatibility complex loci of vertebrates.
Annual review of genetics 1998;32():415-35.
1997: Cadavid L F; Shufflebotham C; Ruiz F J; Yeager M; Hughes A L; Watkins D I
Evolutionary instability of the major histocompatibility complex class I loci in New World primates.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(26):14536-41.
1997: Yeager M; Kumar S; Hughes A L
Sequence convergence in the peptide-binding region of primate and rodent MHC class Ib molecules.
Molecular biology and evolution 1997;14(10):1035-41.
1997: Hughes A L; Yeager M
Molecular evolution of the vertebrate immune system.
BioEssays : news and reviews in molecular, cellular and developmental biology 1997;19(9):777-86.
1997: Hughes A L; Yeager M
Comparative evolutionary rates of introns and exons in murine rodents.
Journal of molecular evolution 1997;45(2):125-30.
1997: Evans D T; Piekarczyk M S; Allen T M; Boyson J E; Yeager M; Hughes A L; Gotch F M; Hinshaw V S; Watkins D I
Immunodominance of a single CTL epitope in a primate species with limited MHC class I polymorphism.
Journal of immunology (Baltimore, Md. : 1950) 1997;159(3):1374-82.
1997: Schwiebert L M; Hughes A; Monos D S; Ono S J
HLA-DRA promoter polymorphism and diversity generation within the immune system.
Human genetics 1997;99(6):801-5.
1997: Hughes A L; Yeager M
Coordinated amino acid changes in the evolution of mammalian defensins.
Journal of molecular evolution 1997;44(6):675-82.
1997: Cereb N; Kim C; Hughes A L; Yang S Y
Molecular analysis of HLA-B35 alleles and their relationship to HLA-B15 alleles.
Tissue antigens 1997;49(4):389-96.
1997: Cereb N; Hughes A L; Yang S Y
Cw*1701, a new HLA-C allelic lineage with an unusual transmembrane domain.
Tissue antigens 1997;49(3 Pt 1):252-5.
1997: Hughes A L
Rapid evolution of immunoglobulin superfamily C2 domains expressed in immune system cells.
Molecular biology and evolution 1997;14(1):1-5.
1997: Cereb N; Hughes A L; Yang S Y
Locus-specific conservation of the HLA class I introns by intra-locus homogenization.
Immunogenetics 1997;47(1):30-6.
1997: Hughes A L
Evolution of the proteasome components.
Immunogenetics 1997;46(2):82-92.
1997: Tay G K; Leelayuwat C; Chorney M J; Cattley S K; Hollingsworth P N; Witt C S; Daly L N; Hughes A; Dawkins R L
The MHC contains multiple genes potentially relevant to hemochromatosis.
Immunogenetics 1997;45(5):336-40.
1996: Hughes A L; Yeager M; Carrington M
Peptide binding function and the paradox of HLA disease associations.
Immunology and cell biology 1996;74(5):444-8.
1996: Cadavid L F; Hughes A L; Watkins D I
MHC class I-processed pseudogenes in New World primates provide evidence for rapid turnover of MHC class I genes.
Journal of immunology (Baltimore, Md. : 1950) 1996;157(6):2403-9.
1996: Hughes A L
Gene duplication and recombination in the evolution of mammalian Fc receptors.
Journal of molecular evolution 1996;43(1):4-10.
1996: Boyson J E; Shufflebotham C; Cadavid L F; Urvater J A; Knapp L A; Hughes A L; Watkins D I
The MHC class I genes of the rhesus monkey. Different evolutionary histories of MHC class I and II genes in primates.
Journal of immunology (Baltimore, Md. : 1950) 1996;156(12):4656-65.
1996: Greenberg A S; Hughes A L; Guo J; Avila D; McKinney E C; Flajnik M F
A novel "chimeric" antibody class in cartilaginous fish: IgM may not be the primordial immunoglobulin.
European journal of immunology 1996;26(5):1123-9.
1996: Hughes A L
Evolution of the src-related protein tyrosine kinases.
Journal of molecular evolution 1996;42(2):247-56.
1996: Milewicz D M; Byers P H; Reveille J; Hughes A L; Duvic M
A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific.
Journal of molecular evolution 1996;42(2):117-23.
1996: Allen T M; Lanchbury J S; Hughes A L; Watkins D I
The T-cell receptor beta chain-encoding gene repertoire of a New World primate species, the cotton-top tamarin.
Immunogenetics 1996;45(2):151-60.
1996: Yeager M; Hughes A L
Interallelic recombination has not played a major role in the history of the HLA-C locus.
Immunogenetics 1996;44(2):128-33.
1995: Hughes A L
The evolution of the type I interferon gene family in mammals.
Journal of molecular evolution 1995;41(5):539-48.
1995: Hughes A L; Hughes M K
Small genomes for better flyers.
Nature 1995;377(6548):391.
1995: Seibert S A; Howell C Y; Hughes M K; Hughes A L
Natural selection on the gag, pol, and env genes of human immunodeficiency virus 1 (HIV-1).
Molecular biology and evolution 1995;12(5):803-13.
1995: McAdam S N; Boyson J E; Liu X; Garber T L; Hughes A L; Bontrop R E; Watkins D I
Chimpanzee MHC class I A locus alleles are related to only one of the six families of human A locus alleles.
Journal of immunology (Baltimore, Md. : 1950) 1995;154(12):6421-9.
1995: Hughes M K; Hughes A L
Natural selection on Plasmodium surface proteins.
Molecular and biochemical parasitology 1995;71(1):99-113.
1995: Greenberg A S; Avila D; Hughes M; Hughes A; McKinney E C; Flajnik M F
A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks.
Nature 1995;374(6518):168-73.
1995: Weiner A; Erickson A L; Kansopon J; Crawford K; Muchmore E; Hughes A L; Houghton M; Walker C M
Persistent hepatitis C virus infection in a chimpanzee is associated with emergence of a cytotoxic T lymphocyte escape variant.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(7):2755-9.
1995: Hughes A L
Origin and evolution of HLA class I pseudogenes.
Molecular biology and evolution 1995;12(2):247-58.
1995: Boyson J E; McAdam S N; Gallimore A; Golos T G; Liu X; Gotch F M; Hughes A L; Watkins D I
The MHC E locus in macaques is polymorphic and is conserved between macaques and humans.
Immunogenetics 1995;41(2-3):59-68.
1995: Hughes A L; Hughes M K
Natural selection on the peptide-binding regions of major histocompatibility complex molecules.
Immunogenetics 1995;42(4):233-43.
1995: Hughes A L; Hughes M K
Self peptides bound by HLA class I molecules are derived from highly conserved regions of a set of evolutionarily conserved proteins.
Immunogenetics 1995;41(5):257-62.
1994: Hughes A L
Evolution of cysteine proteinases in eukaryotes.
Molecular phylogenetics and evolution 1994;3(4):310-21.
1994: Jongwutiwes S; Tanabe K; Hughes M K; Kanbara H; Hughes A L
Allelic variation in the circumsporozoite protein of Plasmodium falciparum from Thai field isolates.
The American journal of tropical medicine and hygiene 1994;51(5):659-68.
1994: Hughes A L; Hughes M K; Howell C Y; Nei M
Natural selection at the class II major histocompatibility complex loci of mammals.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1994;346(1317):359-66; discussion 366-7.
1994: Hughes A L
Evolution of the ATP-binding-cassette transmembrane transporters of vertebrates.
Molecular biology and evolution 1994;11(6):899-910.
1994: Hughes A L
Evolution of the interleukin-1 gene family in mammals.
Journal of molecular evolution 1994;39(1):6-12.
1994: McAdam S N; Boyson J E; Liu X; Garber T L; Hughes A L; Bontrop R E; Watkins D I
A uniquely high level of recombination at the HLA-B locus.
Proceedings of the National Academy of Sciences of the United States of America 1994;91(13):5893-7.
1994: Hughes A L
The evolution of functionally novel proteins after gene duplication.
Proceedings. Biological sciences / The Royal Society 1994;256(1346):119-24.
1994: Hughes A L
Phylogeny of the C3/C4/C5 complement-component gene family indicates that C5 diverged first.
Molecular biology and evolution 1994;11(3):417-25.
1994: Hughes A L
Conserved proteins as immunogens: glutathione S-transferase of Schistosoma.
Parasitology today (Personal ed.) 1994;10(4):149-51.
1994: Garber T L; Hughes A L; Watkins D I; Templeton J W
Evidence for at least three transcribed BoLA class I loci.
Immunogenetics 1994;39(4):257-65.
1993: Hughes M K; Hughes A L
Evolution of duplicate genes in a tetraploid animal, Xenopus laevis.
Molecular biology and evolution 1993;10(6):1360-9.
1993: Wagner A G; Hughes A L; Iandoli M L; Stewart D; Herbert S; Watkins D I; Hurley C K; Rosen-Bronson S
HLA-A*8001 is a member of a newly discovered ancient family of HLA-A alleles.
Tissue antigens 1993;42(5):522-9.
1993: Hughes A L
Contrasting evolutionary rates in the duplicate chaperonin genes of Mycobacterium tuberculosis and M. leprae.
Molecular biology and evolution 1993;10(6):1343-59.
1993: Hughes A L; Hughes M K
Adaptive evolution in the rat olfactory receptor gene family.
Journal of molecular evolution 1993;36(3):249-54.
1993: Hughes A L
Rates of amino acid evolution in the 26- and 28-kDa glutathione S-transferases of Schistosoma.
Molecular and biochemical parasitology 1993;58(1):43-52.
1993: Hughes A L; Hughes M K; Watkins D I
Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci.
Genetics 1993;133(3):669-80.
1993: Hughes A L
Nonlinear relationships among evolutionary rates identify regions of functional divergence in heat-shock protein 70 genes.
Molecular biology and evolution 1993;10(1):243-55.
1993: Chen Z W; Hughes A L; Ghim S H; Letvin N L; Watkins D I
Two more chimpanzee Patr-A locus alleles related to the HLA-A1/A3/A11 family.
Immunogenetics 1993;38(3):238-40.
1993: Hughes A L
Evidence of positive selection at the Lyb-2 locus of the mouse.
Immunogenetics 1993;38(1):54-6.
1993: Garber T L; Hughes A L; Letvin N L; Templeton J W; Watkins D I
Sequence and evolution of cattle MHC class I cDNAs: concerted evolution has not taken place in cattle.
Immunogenetics 1993;38(1):11-20.
1993: Hughes A L; Nei M
Evolutionary relationships of the classes of major histocompatibility complex genes.
Immunogenetics 1993;37(5):337-46.
1992: Chen Z W; Shen L; Miller M D; Ghim S H; Hughes A L; Letvin N L
Cytotoxic T lymphocytes do not appear to select for mutations in an immunodominant epitope of simian immunodeficiency virus gag.
Journal of immunology (Baltimore, Md. : 1950) 1992;149(12):4060-6.
1992: Hughes A L; Nei M
Models of host-parasite interaction and MHC polymorphism.
Genetics 1992;132(3):863-4.
1992: Gaur L K; Hughes A L; Heise E R; Gutknecht J
Maintenance of DQB1 polymorphisms in primates.
Molecular biology and evolution 1992;9(4):599-609.
1992: Hughes A L
Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum.
Molecular biology and evolution 1992;9(3):381-93.
1992: Chen Z W; McAdam S N; Hughes A L; Dogon A L; Letvin N L; Watkins D I
Molecular cloning of orangutan and gibbon MHC class I cDNA. The HLA-A and -B loci diverged over 30 million years ago.
Journal of immunology (Baltimore, Md. : 1950) 1992;148(8):2547-54.
1992: Hughes A L
Coevolution of the vertebrate integrin alpha- and beta-chain genes.
Molecular biology and evolution 1992;9(2):216-34.
1992: Hughes A L; Nei M
Maintenance of MHC polymorphism.
Nature 1992;355(6359):402-3.
1992: Levinson G; Hughes A L; Letvin N L
Sequence and diversity of rhesus monkey T-cell receptor beta chain genes.
Immunogenetics 1992;35(2):75-88.
1991: Zhou L J; Ord D C; Hughes A L; Tedder T F
Structure and domain organization of the CD19 antigen of human, mouse, and guinea pig B lymphocytes. Conservation of the extensive cytoplasmic domain.
Journal of immunology (Baltimore, Md. : 1950) 1991;147(4):1424-32.
1991: Miller M D; Yamamoto H; Hughes A L; Watkins D I; Letvin N L
Definition of an epitope and MHC class I molecule recognized by gag-specific cytotoxic T lymphocytes in SIVmac-infected rhesus monkeys.
Journal of immunology (Baltimore, Md. : 1950) 1991;147(1):320-9.
1991: Hughes A L
Evolutionary origin and diversification of the mammalian CD1 antigen genes.
Molecular biology and evolution 1991;8(2):185-201.
1991: Hughes A L
Circumsporozoite protein genes of malaria parasites (Plasmodium spp.): evidence for positive selection on immunogenic regions.
Genetics 1991;127(2):345-53.
1991: Hughes A L
Independent gene duplications, not concerted evolution, explain relationships among class I MHC genes of murine rodents.
Immunogenetics 1991;33(5-6):367-73.
1991: Hughes A L
Testing for interlocus genetic exchange in the MHC: a reply to Andersson and co-workers.
Immunogenetics 1991;33(4):243-6.
1991: Watkins D I; Chen Z W; Garber T L; Hughes A L; Letvin N L
Segmental exchange between MHC class I genes in a higher primate: recombination in the gorilla between the ancestor of a human non-functional gene and an A locus gene.
Immunogenetics 1991;34(3):185-91.
1991: Watkins D I; Garber T L; Chen Z W; Toukatly G; Hughes A L; Letvin N L
Unusually limited nucleotide sequence variation of the expressed major histocompatibility complex class I genes of a New World primate species (Saguinus oedipus).
Immunogenetics 1991;33(2):79-89.
1990: Hughes A L; Ota T; Nei M
Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules.
Molecular biology and evolution 1990;7(6):515-24.
1990: Watkins D I; Chen Z W; Hughes A L; Lagos A; Lewis A M; Shadduck J A; Letvin N L
Syrian hamsters express diverse MHC class I gene products.
Journal of immunology (Baltimore, Md. : 1950) 1990;145(10):3483-90.
1990: Hughes A L; Nei M
Evolutionary relationships of class II major-histocompatibility-complex genes in mammals.
Molecular biology and evolution 1990;7(6):491-514.
1990: Watkins D I; Chen Z W; Hughes A L; Evans M G; Tedder T F; Letvin N L
Evolution of the MHC class I genes of a New World primate from ancestral homologues of human non-classical genes.
Nature 1990;346(6279):60-3.
1990: Watkins D I; Chen Z W; Hughes A L; Hodi F S; Letvin N L
Genetically distinct cell populations in naturally occurring bone marrow-chimeric primates express similar MHC class I gene products.
Journal of immunology (Baltimore, Md. : 1950) 1990;144(10):3726-35.
1990: Watkins D I; Letvin N L; Hughes A L; Tedder T F
Molecular cloning of cDNA that encode MHC class I molecules from a New World primate (Saguinus oedipus). Natural selection acts at positions that may affect peptide presentation to T cells.
Journal of immunology (Baltimore, Md. : 1950) 1990;144(3):1136-43.
1989: Hughes A L; Nei M
Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals.
Molecular biology and evolution 1989;6(6):559-79.
1989: Hughes A L
Interaction between strains in the social relations of inbred mice.
Behavior genetics 1989;19(5):685-700.
1989: Hughes A L; Nei M
Ancient interlocus exon exchange in the history of the HLA-A locus.
Genetics 1989;122(3):681-6.
1989: Hughes A L; Nei M
Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(3):958-62.
1988: Hughes A L; Nei M
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection.
Nature 1988;335(6186):167-70.
1982: Fagg S L; Hughes A; Fielding J W; Dawson-Edwards P; Hughes M A; Howie A
Retinoic acid receptor in human bladder tumours.
Clinical oncology 1982;8(4):329-34.

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