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A. Hughes · SciRah

Researcher profile · Semantic Scholar

A. Hughes

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A. Hughes — researcher profile on SciRah

h-index: 71
Works: 373
Citations: 21K

Most-cited papers

SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data
Chase W. Nelson, Louise H. Moncla, A. Hughes
2015Bioinform.165 citations Open access
Semantic Scholar
The Evolutionary Biology of Poxviruses
A. Hughes, S. Irausquin, R. Friedman
2009Infection, Genetics and Evolution158 citations Open access
Semantic Scholar
A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate
M. Lauck, S. D. Sibley, J. Lara, M. Purdy +10 more
2013Journal of Virology100 citations Open access
Semantic Scholar
Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria
Haiwei Luo, Miklós Csűros, A. Hughes, M. Moran
2013mBio100 citations Open access
Semantic Scholar
Within-Host Nucleotide Diversity of Virus Populations: Insights from Next-Generation Sequencing
Chase W. Nelson, A. Hughes
2014Infection, Genetics and Evolution99 citations Open access
Semantic Scholar
Selection on hemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses
Peter R. Wilker, J. Dinis, G. Starrett, M. Imai +7 more
2013Nature Communications91 citations Open access
Semantic Scholar
MHC heterozygote advantage in simian immunodeficiency virus-infected Mauritian cynomolgus macaques
S. O'Connor, Jennifer J. Lhost, Ericka A. Becker, A. Detmer +16 more
2010Science Translational Medicine89 citations Open access
Semantic Scholar
Ultradeep Pyrosequencing Detects Complex Patterns of CD8+ T-Lymphocyte Escape in Simian Immunodeficiency Virus-Infected Macaques
B. Bimber, B. Burwitz, S. O'Connor, A. Detmer +5 more
2009Journal of Virology82 citations Open access
Semantic Scholar
Selective bottlenecks shape evolutionary pathways taken during mammalian adaptation of a 1918-like avian influenza virus
Louise H. Moncla, G. Zhong, Chase W. Nelson, J. Dinis +5 more
2016Cell Host and Microbe69 citations Open access
Semantic Scholar
Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing
B. Bimber, D. Dudley, M. Lauck, Ericka A. Becker +13 more
2010Journal of Virology69 citations Open access
Semantic Scholar
Selection-Driven Immune Escape Is Not a Significant Factor in the Failure of CD4 T Cell Responses in Persistent Hepatitis C Virus Infection
M. Fuller, N. Shoukry, Toshifumi Gushima, D. Bowen +5 more
2010Hepatology68 citations Open access
Semantic Scholar
Evolution of adaptive phenotypic traits without positive Darwinian selection
A. Hughes
2011Heredity66 citations Open access
Semantic Scholar
Evolution of the βGRP/GNBP/β-1,3-glucanase family of insects
A. Hughes
2012Immunogenetics60 citations
Semantic Scholar
Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters
Haiwei Luo, B. Swan, R. Stepanauskas, A. Hughes +1 more
2014The ISME Journal56 citations Open access
Semantic Scholar
Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing
M. Lauck, M. V. Alvarado-Mora, Ericka A. Becker, Dipankar Bhattacharya +5 more
2012Journal of Virology56 citations Open access
Semantic Scholar
Genome sequences reveal divergence times of malaria parasite lineages
Joana C. Silva, Amy Egan, R. Friedman, James B. Munro +2 more
2010Parasitology50 citations Open access
Semantic Scholar
Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages.
Haiwei Luo, L. Thompson, U. Stingl, A. Hughes
2015Molecular biology and evolution49 citations
Semantic Scholar
Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus.
Haiwei Luo, R. Friedman, Jijun Tang, A. Hughes
2011Molecular biology and evolution49 citations Open access
Semantic Scholar
High Genetic Diversity and Adaptive Potential of Two Simian Hemorrhagic Fever Viruses in a Wild Primate Population
A. Bailey, M. Lauck, A. Weiler, S. D. Sibley +14 more
2014PLoS ONE42 citations Open access
Semantic Scholar
Escape from CD8+ T Cell Responses in Mamu-B*00801+ Macaques Differentiates Progressors from Elite Controllers
P. Mudd, A. Ericsen, B. Burwitz, N. Wilson +3 more
2012Journal of Immunology39 citations Open access
Semantic Scholar
Cross-clade simultaneous HIV drug resistance genotyping for reverse transcriptase, protease, and integrase inhibitor mutations by Illumina MiSeq
D. Dudley, A. Bailey, S. Mehta, A. Hughes +3 more
2014Retrovirology38 citations Open access
Semantic Scholar
Bottleneck Effects on Vaccine-Candidate Antigen Diversity of Malaria Parasites in Thailand
S. Jongwutiwes, C. Putaporntip, A. Hughes
2010Vaccine35 citations Open access
Semantic Scholar
Conditional CD8 T Cell Escape during Acute Simian Immunodeficiency Virus Infection
S. O'Connor, Ericka A. Becker, J. Weinfurter, E. Chin +8 more
201134 citations
Semantic Scholar
Origin and diversification of the L-amino oxidase family in innate immune defenses of animals
A. Hughes
2010Immunogenetics34 citations Open access
Semantic Scholar
Genetic Diversity of Near Genome-Wide Hepatitis C Virus Sequences during Chronic Infection: Evidence for Protein Structural Conservation Over Time
Hui Li, A. Hughes, Nazneen Bano, S. Mcardle +7 more
2011PLoS ONE33 citations Open access
Semantic Scholar
Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand
C. Putaporntip, S. Jongwutiwes, P. Grynberg, Li-Wang Cui +1 more
2009Infection, Genetics and Evolution33 citations Open access
Semantic Scholar
Transmission of Clonal Hepatitis C Virus Genomes Reveals the Dominant but Transitory Role of CD8+ T Cells in Early Viral Evolution
Benoît Callendret, J. Bukh, Heather B. Eccleston, Ryan A. Heksch +4 more
2011Journal of Virology31 citations Open access
Semantic Scholar
Reduced variance of gene expression at numerous loci in a population of chickens selected for high feather pecking.
A. Hughes, A. Buitenhuis
2010Poultry Science30 citations Open access
Semantic Scholar
Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys
A. Bailey, M. Lauck, R. Ghai, Chase W. Nelson +8 more
2016Journal of Virology29 citations Open access
Semantic Scholar
Small Effective Population Sizes and Rare Nonsynonymous Variants in Potyviruses
A. Hughes
2009Virology28 citations Open access
Semantic Scholar
Comparing effective population sizes of dominant marine alphaproteobacteria lineages.
Haiwei Luo, B. Swan, R. Stepanauskas, A. Hughes +1 more
2014Environmental Microbiology Reports27 citations
Semantic Scholar
Phylogenetic Analysis of Genome Rearrangements among Five Mammalian Orders
Haiwei Luo, W. Arndt, Yiwei Zhang, G. Shi +4 more
2012Molecular Phylogenetics and Evolution26 citations Open access
Semantic Scholar
Malaria Parasite Sequences from Chimpanzee Support the Co-Speciation Hypothesis for the Origin of Virulent Human Malaria (Plasmodium falciparum)
A. Hughes, F. Verra
2010Molecular Phylogenetics and Evolution25 citations Open access
Semantic Scholar
Low Level of Sequence Diversity at Merozoite Surface Protein-1 Locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai Isolates
C. Putaporntip, A. Hughes, S. Jongwutiwes
2013PLoS ONE23 citations Open access
Semantic Scholar
Recombinational histories of avian infectious bronchitis virus and turkey coronavirus
A. Hughes
2011Archives of Virology22 citations Open access
Semantic Scholar
Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques
Hannah M. Creager, Ericka A. Becker, Kelly K. Sandman, J. Karl +6 more
2011Immunogenetics22 citations Open access
Semantic Scholar
More Radical Amino Acid Replacements in Primates than in Rodents: Support for the Evolutionary Role of Effective Population Size
A. Hughes, R. Friedman
2009Gene22 citations Open access
Semantic Scholar
Evolutionary Diversifaction of Aminopeptidase N in Lepidoptera by Conserved Clade-specific Amino Acid Residues
A. Hughes
2014Molecular Phylogenetics and Evolution19 citations Open access
Semantic Scholar
Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes
Ericka A. Becker, Charles M. Burns, Enrique J. Léon, Saravanan Rajabojan +4 more
2012Genome Biology and Evolution19 citations Open access
Semantic Scholar
Evolutionary diversification of the avian fatty acid-binding proteins
A. Hughes, H. Piontkivska
2011Gene19 citations Open access
Semantic Scholar
Evolution of the salivary apyrases of blood-feeding arthropods.
A. Hughes
2013Gene17 citations
Semantic Scholar
Characterization of cynomolgus and vervet monkey placental MHC class I expression: diversity of the nonhuman primate AG locus
G. Bondarenko, S. Dambaeva, R. L. Grendell, A. Hughes +3 more
2009Immunogenetics17 citations Open access
Semantic Scholar
Sickle cell trait is not associated with an increased risk of heart failure or abnormalities of cardiac structure and function.
Natalie A. Bello, H. Hyacinth, Nicholas S. Roetker, S. Seals +21 more
2017Blood16 citations Open access
Semantic Scholar
Evolutionary Diversification of the Vertebrate Transferrin Multi-gene Family
A. Hughes, R. Friedman
2014Immunogenetics16 citations Open access
Semantic Scholar
Accumulation of Slightly Deleterious Mutations in the Mitochondrial Genome: a Hallmark of Animal Domestication
A. Hughes
2012Gene16 citations Open access
Semantic Scholar
Origin of Ecdysosteroid UDP-glycosyltransferases of Baculoviruses through Horizontal Gene Transfer from Lepidoptera
A. Hughes
2013Coevolution15 citations Open access
Semantic Scholar
Behavioral correlates of post-breeding weight change in a captive flock of American flamingos (Phoenicopterus ruber ruber).
A. Hughes, A. Raynes, C. Driscoll, Jenna Babler
2013Zoo Biology13 citations
Semantic Scholar
Phylogenetic analysis supports horizontal gene transfer of L-amino acid oxidase gene in Streptococcus oligofermentans
J. Boggs, A. H. South, A. Hughes
2012Infection, Genetics and Evolution13 citations Open access
Semantic Scholar
SIV Genome-Wide Pyrosequencing Provides a Comprehensive and Unbiased View of Variation within and outside CD8 T Lymphocyte Epitopes
A. Hughes, Ericka A. Becker, M. Lauck, J. Karl +3 more
2012PLoS ONE13 citations Open access
Semantic Scholar
Reduced microsatellite heterozygosity in island endemics supports the role of long-term effective population size in avian microsatellite diversity
A. Hughes
2010Genetica13 citations Open access
Semantic Scholar

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