| Year |
Citation |
Score |
| 2016 |
Bailey AL, Lauck M, Ghai RR, Nelson CW, Heimbruch K, Hughes AL, Goldberg TL, Kuhn JH, Jasinska AJ, Freimer NB, Apetrei C, O'Connor DH. Arteriviruses, pegiviruses, and lentiviruses are common among wild African monkeys. Journal of Virology. PMID 27170760 DOI: 10.1128/Jvi.00573-16 |
0.332 |
|
| 2016 |
Moncla LH, Zhong G, Nelson CW, Dinis JM, Mutschler J, Hughes AL, Watanabe T, Kawaoka Y, Friedrich TC. Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus. Cell Host & Microbe. 19: 169-80. PMID 26867176 DOI: 10.1016/J.Chom.2016.01.011 |
0.32 |
|
| 2015 |
Putaporntip C, Kuamsab N, Kosuwin R, Tantiwattanasub W, Vejakama P, Sueblinvong T, Seethamchai S, Jongwutiwes S, Hughes AL. Natural selection on K13 mutants of Plasmodium falciparum in response to artemisinin combination therapies in Thailand. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. PMID 26548510 DOI: 10.1016/J.Cmi.2015.10.027 |
0.313 |
|
| 2015 |
Gellerup D, Balgeman A, Nelson CW, Ericsen A, Scarlotta M, Hughes AL, O'Connor S. Conditional immune escape during chronic SIV infection. Journal of Virology. PMID 26491171 DOI: 10.1128/Jvi.02587-15 |
0.319 |
|
| 2015 |
Nelson CW, Moncla LH, Hughes AL. SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data. Bioinformatics (Oxford, England). PMID 26227143 DOI: 10.1093/Bioinformatics/Btv449 |
0.438 |
|
| 2015 |
Hughes AL. Life-history evolution at the molecular level: adaptive amino acid composition of avian vitellogenins. Proceedings. Biological Sciences / the Royal Society. 282: 20151105. PMID 26224713 DOI: 10.1098/Rspb.2015.1105 |
0.35 |
|
| 2015 |
Luo H, Thompson LR, Stingl U, Hughes AL. Selection maintains low genomic GC content in marine SAR11 lineages. Molecular Biology and Evolution. PMID 26116859 DOI: 10.1093/Molbev/Msv149 |
0.571 |
|
| 2015 |
Nelson CW, Hughes AL. Within-host nucleotide diversity of virus populations: insights from next-generation sequencing. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 30: 1-7. PMID 25481279 DOI: 10.1016/J.Meegid.2014.11.026 |
0.385 |
|
| 2014 |
Hughes AL. Evolutionary diversification of insect innexins. Journal of Insect Science (Online). 14. PMID 25502029 DOI: 10.1093/Jisesa/Ieu083 |
0.414 |
|
| 2014 |
Hughes AL, Friedman R. Evolutionary diversification of the vertebrate transferrin multi-gene family. Immunogenetics. 66: 651-61. PMID 25142446 DOI: 10.1007/S00251-014-0798-X |
0.578 |
|
| 2014 |
Hughes AL. Evolutionary diversification of aminopeptidase N in Lepidoptera by conserved clade-specific amino acid residues. Molecular Phylogenetics and Evolution. 76: 127-33. PMID 24675701 DOI: 10.1016/J.Ympev.2014.03.014 |
0.407 |
|
| 2014 |
Bailey AL, Lauck M, Weiler A, Sibley SD, Dinis JM, Bergman Z, Nelson CW, Correll M, Gleicher M, Hyeroba D, Tumukunde A, Weny G, Chapman C, Kuhn JH, Hughes AL, et al. High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population. Plos One. 9: e90714. PMID 24651479 DOI: 10.1371/Journal.Pone.0090714 |
0.363 |
|
| 2014 |
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA. Comparing effective population sizes of dominant marine alphaproteobacteria lineages. Environmental Microbiology Reports. 6: 167-72. PMID 24596290 DOI: 10.1111/1758-2229.12129 |
0.517 |
|
| 2014 |
Luo H, Swan BK, Stepanauskas R, Hughes AL, Moran MA. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. The Isme Journal. 8: 1428-39. PMID 24451207 DOI: 10.1038/Ismej.2013.248 |
0.574 |
|
| 2013 |
Wilker PR, Dinis JM, Starrett G, Imai M, Hatta M, Nelson CW, O'Connor DH, Hughes AL, Neumann G, Kawaoka Y, Friedrich TC. Selection on haemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses. Nature Communications. 4: 2636. PMID 24149915 DOI: 10.1038/Ncomms3636 |
0.308 |
|
| 2013 |
Luo H, Csuros M, Hughes AL, Moran MA. Evolution of divergent life history strategies in marine alphaproteobacteria. Mbio. 4. PMID 23839216 DOI: 10.1128/Mbio.00373-13 |
0.563 |
|
| 2013 |
Hughes AL. Evolution of the salivary apyrases of blood-feeding arthropods. Gene. 527: 123-30. PMID 23791653 DOI: 10.1016/J.Gene.2013.05.087 |
0.378 |
|
| 2013 |
Lauck M, Sibley SD, Lara J, Purdy MA, Khudyakov Y, Hyeroba D, Tumukunde A, Weny G, Switzer WM, Chapman CA, Hughes AL, Friedrich TC, O'Connor DH, Goldberg TL. A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate. Journal of Virology. 87: 8971-81. PMID 23740998 DOI: 10.1128/Jvi.00888-13 |
0.393 |
|
| 2013 |
Walsh AD, Bimber BN, Das A, Piaskowski SM, Rakasz EG, Bean AT, Mudd PA, Ericsen AJ, Wilson NA, Hughes AL, O'Connor DH, Maness NJ. Acute phase CD8+ T lymphocytes against alternate reading frame epitopes select for rapid viral escape during SIV infection. Plos One. 8: e61383. PMID 23671565 DOI: 10.1371/Journal.Pone.0061383 |
0.337 |
|
| 2013 |
Putaporntip C, Hughes AL, Jongwutiwes S. Low level of sequence diversity at merozoite surface protein-1 locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai isolates. Plos One. 8: e58962. PMID 23536840 DOI: 10.1371/Journal.Pone.0058962 |
0.35 |
|
| 2013 |
Hughes AL. Accumulation of slightly deleterious mutations in the mitochondrial genome: a hallmark of animal domestication. Gene. 515: 28-33. PMID 23237775 DOI: 10.1016/J.Gene.2012.11.064 |
0.417 |
|
| 2012 |
Luo H, Hughes AL. d(N)/d(S) does not show positive selection drives separation of polar-tropical SAR11 populations. Molecular Systems Biology. 8: 625. PMID 23169001 DOI: 10.1038/Msb.2012.58 |
0.531 |
|
| 2012 |
Hughes AL, Becker EA, Lauck M, Karl JA, Braasch AT, O'Connor DH, O'Connor SL. SIV genome-wide pyrosequencing provides a comprehensive and unbiased view of variation within and outside CD8 T lymphocyte epitopes. Plos One. 7: e47818. PMID 23112852 DOI: 10.1371/Journal.Pone.0047818 |
0.398 |
|
| 2012 |
Luo H, Arndt W, Zhang Y, Shi G, Alekseyev MA, Tang J, Hughes AL, Friedman R. Phylogenetic analysis of genome rearrangements among five mammalian orders. Molecular Phylogenetics and Evolution. 65: 871-82. PMID 22929217 DOI: 10.1016/J.Ympev.2012.08.008 |
0.694 |
|
| 2012 |
Becker EA, Burns CM, León EJ, Rajabojan S, Friedman R, Friedrich TC, O'Connor SL, Hughes AL. Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes. Genome Biology and Evolution. 4: 457-65. PMID 22436995 DOI: 10.1093/Gbe/Evs029 |
0.603 |
|
| 2012 |
Boggs JM, South AH, Hughes AL. Phylogenetic analysis supports horizontal gene transfer of L-amino acid oxidase gene in Streptococcus oligofermentans. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 12: 1005-9. PMID 22414918 DOI: 10.1016/J.Meegid.2012.02.014 |
0.384 |
|
| 2012 |
Hughes AL. Evolution of the βGRP/GNBP/β-1,3-glucanase family of insects. Immunogenetics. 64: 549-58. PMID 22410636 DOI: 10.1007/S00251-012-0610-8 |
0.404 |
|
| 2012 |
Hughes AL. Evolution of adaptive phenotypic traits without positive Darwinian selection. Heredity. 108: 347-53. PMID 22045380 DOI: 10.1038/Hdy.2011.97 |
0.311 |
|
| 2012 |
Hughes AL. Evolution of the heme peroxidases of Culicidae (Diptera) Psyche (New York). DOI: 10.1155/2012/146387 |
0.48 |
|
| 2011 |
Hughes AL, Friedman R. Distinctive amino acid composition profiles in salivary proteins of the tick Ixodes scapularis. Ticks and Tick-Borne Diseases. 2: 219-24. PMID 22108016 DOI: 10.1016/J.Ttbdis.2011.09.004 |
0.53 |
|
| 2011 |
Hughes AL, Piontkivska H. Evolutionary diversification of the avian fatty acid-binding proteins. Gene. 490: 1-5. PMID 21986036 DOI: 10.1016/J.Gene.2011.09.016 |
0.373 |
|
| 2011 |
Callendret B, Bukh J, Eccleston HB, Heksch R, Hasselschwert DL, Purcell RH, Hughes AL, Walker CM. Transmission of clonal hepatitis C virus genomes reveals the dominant but transitory role of CD8⺠T cells in early viral evolution. Journal of Virology. 85: 11833-45. PMID 21900166 DOI: 10.1128/Jvi.02654-10 |
0.366 |
|
| 2011 |
Hughes AL. Recombinational histories of avian infectious bronchitis virus and turkey coronavirus. Archives of Virology. 156: 1823-9. PMID 21744259 DOI: 10.1007/S00705-011-1061-5 |
0.443 |
|
| 2011 |
Knapp EW, Irausquin SJ, Friedman R, Hughes AL. PolyAna: analyzing synonymous and nonsynonymous polymorphic sites. Conservation Genetics Resources. 3: 429-431. PMID 21731595 DOI: 10.1007/S12686-010-9372-5 |
0.794 |
|
| 2011 |
Creager HM, Becker EA, Sandman KK, Karl JA, Lank SM, Bimber BN, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH. Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques. Immunogenetics. 63: 611-8. PMID 21614582 DOI: 10.1007/S00251-011-0537-5 |
0.337 |
|
| 2011 |
Li H, Hughes AL, Bano N, McArdle S, Livingston S, Deubner H, McMahon BJ, Townshend-Bulson L, McMahan R, Rosen HR, Gretch DR. Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time. Plos One. 6: e19562. PMID 21573177 DOI: 10.1371/Journal.Pone.0019562 |
0.319 |
|
| 2011 |
Luo H, Friedman R, Tang J, Hughes AL. Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Molecular Biology and Evolution. 28: 2751-60. PMID 21531921 DOI: 10.1093/Molbev/Msr081 |
0.71 |
|
| 2011 |
Hughes AL, Friedman R. A survey of schistosome protein domain types: insights into unique biological properties. Molecular and Biochemical Parasitology. 177: 100-5. PMID 21315771 DOI: 10.1016/J.Molbiopara.2011.02.001 |
0.57 |
|
| 2011 |
Irausquin SJ, Hughes AL. Conflicting selection pressures on T-cell epitopes in HIV-1 subtype B. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 483-8. PMID 21232634 DOI: 10.1016/J.Meegid.2010.12.011 |
0.79 |
|
| 2011 |
Silva JC, Egan A, Friedman R, Munro JB, Carlton JM, Hughes AL. Genome sequences reveal divergence times of malaria parasite lineages. Parasitology. 138: 1737-49. PMID 21118608 DOI: 10.1017/S0031182010001575 |
0.547 |
|
| 2011 |
Luo H, Tang J, Friedman R, Hughes AL. Ongoing purifying selection on intergenic spacers in group A streptococcus. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 11: 343-8. PMID 21115137 DOI: 10.1016/J.Meegid.2010.11.005 |
0.721 |
|
| 2011 |
Hughes AL. Runaway evolution of the male-specific exon of the doublesex gene in Diptera. Gene. 472: 1-6. PMID 21059384 DOI: 10.1016/J.Gene.2010.10.015 |
0.315 |
|
| 2010 |
Hughes AL. Reduced microsatellite heterozygosity in island endemics supports the role of long-term effective population size in avian microsatellite diversity. Genetica. 138: 1271-6. PMID 21104002 DOI: 10.1007/S10709-010-9527-Z |
0.31 |
|
| 2010 |
Bhoumik P, Hughes AL. Reassortment of ancient neuraminidase and recent hemagglutinin in pandemic (H1N1) 2009 virus. Emerging Infectious Diseases. 16: 1748-50. PMID 21029534 DOI: 10.3201/Eid1611.100361 |
0.765 |
|
| 2010 |
Hughes AL. Origin and diversification of the L-amino oxidase family in innate immune defenses of animals. Immunogenetics. 62: 753-9. PMID 20878154 DOI: 10.1007/S00251-010-0482-8 |
0.378 |
|
| 2010 |
Bimber BN, Dudley DM, Lauck M, Becker EA, Chin EN, Lank SM, Grunenwald HL, Caruccio NC, Maffitt M, Wilson NA, Reed JS, Sosman JM, Tarosso LF, Sanabani S, Kallas EG, ... Hughes AL, et al. Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing. Journal of Virology. 84: 12087-92. PMID 20844037 DOI: 10.1128/Jvi.01378-10 |
0.359 |
|
| 2010 |
Putaporntip C, Jongwutiwes S, Thongaree S, Seethamchai S, Grynberg P, Hughes AL. Ecology of malaria parasites infecting Southeast Asian macaques: evidence from cytochrome b sequences. Molecular Ecology. 19: 3466-76. PMID 20646216 DOI: 10.1111/J.1365-294X.2010.04756.X |
0.314 |
|
| 2010 |
Hughes AL, Verra F. Malaria parasite sequences from chimpanzee support the co-speciation hypothesis for the origin of virulent human malaria (Plasmodium falciparum). Molecular Phylogenetics and Evolution. 57: 135-43. PMID 20541613 DOI: 10.1016/J.Ympev.2010.06.004 |
0.325 |
|
| 2010 |
Hughes AL, O'Connor S, Dudley DM, Burwitz BJ, Bimber BN, O'Connor D. Dynamics of haplotype frequency change in a CD8+TL epitope of simian immunodeficiency virus. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 10: 555-60. PMID 20149896 DOI: 10.1016/J.Meegid.2010.02.001 |
0.344 |
|
| 2010 |
Irausquin SJ, Hughes AL. Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b. Virus Research. 147: 202-7. PMID 19896990 DOI: 10.1016/J.Virusres.2009.11.001 |
0.751 |
|
| 2010 |
Hughes AL, Irausquin S, Friedman R. The evolutionary biology of poxviruses. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 10: 50-9. PMID 19833230 DOI: 10.1016/J.Meegid.2009.10.001 |
0.801 |
|
| 2009 |
Hughes AL. Small effective population sizes and rare nonsynonymous variants in potyviruses. Virology. 393: 127-34. PMID 19695658 DOI: 10.1016/J.Virol.2009.07.016 |
0.457 |
|
| 2009 |
Putaporntip C, Jongwutiwes S, Grynberg P, Cui L, Hughes AL. Nucleotide sequence polymorphism at the apical membrane antigen-1 locus reveals population history of Plasmodium vivax in Thailand. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 9: 1295-300. PMID 19643205 DOI: 10.1016/J.Meegid.2009.07.005 |
0.388 |
|
| 2009 |
Hughes AL, Friedman R. A phylogenetic approach to gene expression data: evidence for the evolutionary origin of mammalian leukocyte phenotypes. Evolution & Development. 11: 382-90. PMID 19601972 DOI: 10.1111/J.1525-142X.2009.00345.X |
0.594 |
|
| 2009 |
Hughes AL. Evolution in the post-genome era. Perspectives in Biology and Medicine. 52: 332-7. PMID 19496291 DOI: 10.1353/Pbm.0.0090 |
0.355 |
|
| 2009 |
Putaporntip C, Jongwutiwes S, Hughes AL. 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. 9: 567-73. PMID 19460323 DOI: 10.1016/J.Meegid.2009.02.006 |
0.423 |
|
| 2009 |
Hughes AL. 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. 9: 827-31. PMID 19409512 DOI: 10.1016/J.Meegid.2009.04.016 |
0.368 |
|
| 2009 |
Hughes AL, Friedman R. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene. 440: 50-6. PMID 19332110 DOI: 10.1016/J.Gene.2009.03.012 |
0.613 |
|
| 2009 |
Hughes AL. Relaxation of purifying selection on live attenuated vaccine strains of the family Paramyxoviridae. Vaccine. 27: 1685-90. PMID 19195493 DOI: 10.1016/J.Vaccine.2009.01.036 |
0.345 |
|
| 2009 |
Campbell KJ, Detmer AM, Karl JA, Wiseman RW, Blasky AJ, Hughes AL, Bimber BN, O'Connor SL, O'Connor DH. Characterization of 47 MHC class I sequences in Filipino cynomolgus macaques. Immunogenetics. 61: 177-87. PMID 19107381 DOI: 10.1007/S00251-008-0351-X |
0.401 |
|
| 2009 |
Conley AJ, Corbin CJ, Hughes AL. Adaptive evolution of mammalian aromatases: lessons from Suiformes. Journal of Experimental Zoology. Part a, Ecological Genetics and Physiology. 311: 346-57. PMID 18381772 DOI: 10.1002/Jez.451 |
0.391 |
|
| 2009 |
Burwitz BJ, Bimber BN, O'Connor S, Detmer A, Gostick E, Lank SM, Price DA, Hughes A, O'Connor D. P20-16. Ultra-deep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in SIV-infected macaques Retrovirology. 6: P386. DOI: 10.1186/1742-4690-6-S3-P386 |
0.345 |
|
| 2008 |
Bimber BN, Moreland AJ, Wiseman RW, Hughes AL, O'Connor DH. 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). 181: 6301-8. PMID 18941221 DOI: 10.4049/Jimmunol.181.9.6301 |
0.375 |
|
| 2008 |
Putaporntip C, Jongwutiwes S, Hughes AL. Differential selective pressures on the merozoite surface protein 2 locus of Plasmodium falciparum in a low endemic area. Gene. 427: 51-7. PMID 18840512 DOI: 10.1016/J.Gene.2008.09.009 |
0.39 |
|
| 2008 |
Hughes AL, Friedman R. Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes. Molecular Biology and Evolution. 25: 2681-8. PMID 18820253 DOI: 10.1093/Molbev/Msn207 |
0.642 |
|
| 2008 |
Hughes AL. The origin of adaptive phenotypes. Proceedings of the National Academy of Sciences of the United States of America. 105: 13193-4. PMID 18768803 DOI: 10.1073/Pnas.0807440105 |
0.334 |
|
| 2008 |
Hughes AL, Friedman R, Rivailler P, French JO. Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Molecular Biology and Evolution. 25: 2199-209. PMID 18667439 DOI: 10.1093/Molbev/Msn166 |
0.792 |
|
| 2008 |
Irausquin SJ, Hughes AL. Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures. The Journal of General Virology. 89: 1921-9. PMID 18632963 DOI: 10.1099/Vir.0.2008/000992-0 |
0.784 |
|
| 2008 |
Hughes AL, Friedman R. Codon-based tests of positive selection, branch lengths, and the evolution of mammalian immune system genes. Immunogenetics. 60: 495-506. PMID 18581108 DOI: 10.1007/S00251-008-0304-4 |
0.561 |
|
| 2008 |
Hughes AL. Near neutrality: leading edge of the neutral theory of molecular evolution. Annals of the New York Academy of Sciences. 1133: 162-79. PMID 18559820 DOI: 10.1196/Annals.1438.001 |
0.374 |
|
| 2008 |
Pendley CJ, Becker EA, Karl JA, Blasky AJ, Wiseman RW, Hughes AL, O'Connor SL, O'Connor DH. MHC class I characterization of Indonesian cynomolgus macaques. Immunogenetics. 60: 339-51. PMID 18504574 DOI: 10.1007/S00251-008-0292-4 |
0.354 |
|
| 2008 |
Hughes AL, Welch R, Puri V, Matthews C, Haque K, Chanock SJ, Yeager M. Genome-wide SNP typing reveals signatures of population history. Genomics. 92: 1-8. PMID 18485661 DOI: 10.1016/J.Ygeno.2008.03.005 |
0.393 |
|
| 2008 |
Grynberg P, Fontes CJ, Hughes AL, Braga EM. Polymorphism at the apical membrane antigen 1 locus reflects the world population history of Plasmodium vivax. Bmc Evolutionary Biology. 8: 123. PMID 18445274 DOI: 10.1186/1471-2148-8-123 |
0.34 |
|
| 2008 |
Hughes AL, Piontkivska H. Functional diversification of the toll-like receptor gene family. Immunogenetics. 60: 249-56. PMID 18415094 DOI: 10.1007/S00251-008-0283-5 |
0.382 |
|
| 2008 |
Maness NJ, Yant LJ, Chung C, Loffredo JT, Friedrich TC, Piaskowski SM, Furlott J, May GE, Soma T, León EJ, Wilson NA, Piontkivska H, Hughes AL, Sidney J, Sette A, et al. 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. 82: 5245-54. PMID 18385251 DOI: 10.1128/Jvi.00292-08 |
0.321 |
|
| 2008 |
Karl JA, Wiseman RW, Campbell KJ, Blasky AJ, Hughes AL, Ferguson B, Read DS, O'Connor DH. Identification of MHC class I sequences in Chinese-origin rhesus macaques. Immunogenetics. 60: 37-46. PMID 18097659 DOI: 10.1007/S00251-007-0267-X |
0.36 |
|
| 2008 |
Hughes AL, Piontkivska H. Nucleotide sequence polymorphism in circoviruses. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 8: 130-8. PMID 18093882 DOI: 10.1016/J.Meegid.2007.11.001 |
0.457 |
|
| 2008 |
Hughes AL, Friedman R. Alternative splicing, gene duplication and connectivity in the genetic interaction network of the nematode worm Caenorhabditis elegans. Genetica. 134: 181-6. PMID 18026854 DOI: 10.1007/S10709-007-9223-9 |
0.6 |
|
| 2007 |
Hughes AL, Hughes MA. More effective purifying selection on RNA viruses than in DNA viruses. Gene. 404: 117-25. PMID 17928171 DOI: 10.1016/J.Gene.2007.09.013 |
0.316 |
|
| 2007 |
Corbin CJ, Hughes AL, Heffelfinger JR, Berger T, Waltzek TB, Roser JF, Santos TC, Miglino MA, Oliveira MF, Braga FC, Meirelles FV, Conley AJ. Evolution of suiform aromatases: ancestral duplication with conservation of tissue-specific expression in the collared peccary (Pecari tayassu). Journal of Molecular Evolution. 65: 403-12. PMID 17912474 DOI: 10.1007/S00239-007-9021-0 |
0.447 |
|
| 2007 |
Hughes AL. Looking for Darwin in all the wrong places: The misguided quest for positive selection at the nucleotide sequence level Heredity. 99: 364-373. PMID 17622265 DOI: 10.1038/Sj.Hdy.6801031 |
0.401 |
|
| 2007 |
Hughes AL, Piontkivska H, Foppa I. Rapid fixation of a distinctive sequence motif in the 3' noncoding region of the clade of West Nile virus invading North America. Gene. 399: 152-61. PMID 17587514 DOI: 10.1016/J.Gene.2007.05.007 |
0.392 |
|
| 2007 |
Hughes AL, Friedman R. The effect of branch lengths on phylogeny: an empirical study using highly conserved orthologs from mammalian genomes. Molecular Phylogenetics and Evolution. 45: 81-8. PMID 17574446 DOI: 10.1016/J.Ympev.2007.04.022 |
0.589 |
|
| 2007 |
Hughes AL, Rivailler P. Phylogeny and recombination history of gallid herpesvirus 2 (Marek's disease virus) genomes. Virus Research. 130: 28-33. PMID 17566585 DOI: 10.1016/J.Virusres.2007.05.008 |
0.375 |
|
| 2007 |
Averdam A, Kuhl H, Sontag M, Becker T, Hughes AL, Reinhardt R, Walter L. Genomics and diversity of the common marmoset monkey NK complex. Journal of Immunology (Baltimore, Md. : 1950). 178: 7151-61. PMID 17513764 DOI: 10.4049/Jimmunol.178.11.7151 |
0.444 |
|
| 2007 |
Hughes AL. Evolution of the lung surfactant proteins in birds and mammals. Immunogenetics. 59: 565-72. PMID 17457583 DOI: 10.1007/S00251-007-0218-6 |
0.381 |
|
| 2007 |
Hughes AL, Hughes MA. Coding sequence polymorphism in avian mitochondrial genomes reflects population histories. Molecular Ecology. 16: 1369-76. PMID 17391262 DOI: 10.1111/J.1365-294X.2007.03242.X |
0.379 |
|
| 2007 |
Hughes AL. Micro-scale signature of purifying selection in Marburg virus genomes. Gene. 392: 266-72. PMID 17306473 DOI: 10.1016/J.Gene.2006.12.038 |
0.462 |
|
| 2007 |
Schwarz RS, Hodes-Villamar L, Fitzpatrick KA, Fain MG, Hughes AL, Cadavid LF. A gene family of putative immune recognition molecules in the hydroid Hydractinia. Immunogenetics. 59: 233-46. PMID 17216438 DOI: 10.1007/S00251-006-0179-1 |
0.442 |
|
| 2007 |
Westover KM, Hughes AL. Evolution of cytotoxic T-lymphocyte epitopes in hepatitis B virus. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 7: 254-62. PMID 17140859 DOI: 10.1016/J.Meegid.2006.10.004 |
0.413 |
|
| 2007 |
Hughes AL, French JO. Homologous recombination and the pattern of nucleotide substitution in Ehrlichia ruminantium. Gene. 387: 31-7. PMID 17005333 DOI: 10.1016/J.Gene.2006.08.003 |
0.799 |
|
| 2007 |
Hughes AL, Hughes MA, Friedman R. Variable intensity of purifying selection on cytotoxic T-lymphocyte epitopes in hepatitis C virus. Virus Research. 123: 147-53. PMID 17005284 DOI: 10.1016/J.Virusres.2006.08.012 |
0.619 |
|
| 2007 |
Hughes AL, Langley KJ. 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. 7: 188-96. PMID 17000138 DOI: 10.1016/J.Meegid.2006.08.003 |
0.454 |
|
| 2007 |
Friedman R, Hughes AL. 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. 42: 388-93. PMID 16959502 DOI: 10.1016/J.Ympev.2006.07.015 |
0.603 |
|
| 2007 |
Hughes AL, Friedman R. Sharing of transcription factors after gene duplication in the yeast Saccharomyces cerevisiae. Genetica. 129: 301-8. PMID 16897462 DOI: 10.1007/S10709-006-0011-8 |
0.627 |
|
| 2007 |
Hughes AL, Hughes MA. 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. 7: 110-5. PMID 16861055 DOI: 10.1016/J.Meegid.2006.06.002 |
0.386 |
|
| 2006 |
Hughes AL. Evolutionary relationships of vertebrate NACHT domain-containing proteins. Immunogenetics. 58: 785-91. PMID 17006665 DOI: 10.1007/S00251-006-0148-8 |
0.36 |
|
| 2006 |
Chakrabarty A, MacLean JA, Hughes AL, Roberts RM, Green JA. Rapid evolution of the trophoblast kunitz domain proteins (TKDPs)-a multigene family in ruminant ungulates. Journal of Molecular Evolution. 63: 274-82. PMID 16830095 DOI: 10.1007/S00239-005-0264-3 |
0.333 |
|
| 2006 |
Hughes AL, Friedman R. Across-tissue expression and evolution of genes controlled by the Aire transcription factor Genomics. 88: 462-467. PMID 16806803 DOI: 10.1016/J.Ygeno.2006.05.006 |
0.576 |
|
| 2006 |
Slukvin II, Grendell RL, Rao DS, Hughes AL, Golos TG. Cloning of rhesus monkey LILRs. Tissue Antigens. 67: 331-7. PMID 16634871 DOI: 10.1111/J.1399-0039.2006.00579.X |
0.301 |
|
| 2006 |
Friedman R, Hughes AL. Pattern of gene duplication in the Cotesia congregata Bracovirus Infection, Genetics and Evolution. 6: 315-322. PMID 16386964 DOI: 10.1016/J.Meegid.2005.10.001 |
0.619 |
|
| 2006 |
Piontkivska H, Hughes AL. Patterns of sequence evolution at epitopes for host antibodies and cytotoxic T-lymphocytes in human immunodeficiency virus type 1 Virus Research. 116: 98-105. PMID 16214253 DOI: 10.1016/J.Virusres.2005.09.001 |
0.399 |
|
| 2005 |
Hughes AL, Friedman R. Gene duplication and the properties of biological networks Journal of Molecular Evolution. 61: 758-764. PMID 16315107 DOI: 10.1007/S00239-005-0037-Z |
0.555 |
|
| 2005 |
Hughes AL, Piontkivska H, Krebs KC, O'Connor DH, Watkins DI. Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus. Bioinformatics (Oxford, England). 21: iii39-44. PMID 16306391 DOI: 10.1093/Bioinformatics/Bti1203 |
0.377 |
|
| 2005 |
Hughes AL, Packer B, Welch R, Chanock SJ, Yeager M. High level of functional polymorphism indicates a unique role of natural selection at human immune system loci Immunogenetics. 57: 821-827. PMID 16261383 DOI: 10.1007/S00251-005-0052-7 |
0.432 |
|
| 2005 |
Piontkivska H, Hughes AL. Environmental kinetoplastid-like 18S rRNA sequences and phylogenetic relationships among trypanosomatidae : Paraphyly of the genus Trypanosoma Molecular and Biochemical Parasitology. 144: 94-99. PMID 16169099 DOI: 10.1016/J.Molbiopara.2005.08.007 |
0.349 |
|
| 2005 |
Hughes AL, Ekollu V, Friedman R, Rose JR. Gene Family Content-Based Phylogeny of Prokaryotes: The Effect of Criteria for Inferring Homology Systematic Biology. 54: 268-276. PMID 16012097 DOI: 10.1080/10635150590923335 |
0.633 |
|
| 2005 |
Hughes AL, Friedman R. Amino acid sequence constraint and gene expression pattern across the life history in the malaria parasite Plasmodium falciparum Molecular and Biochemical Parasitology. 142: 170-176. PMID 15978954 DOI: 10.1016/J.Molbiopara.2005.02.014 |
0.581 |
|
| 2005 |
Hughes AL. Gene duplication and the origin of novel proteins Proceedings of the National Academy of Sciences of the United States of America. 102: 8791-8792. PMID 15956198 DOI: 10.1073/Pnas.0503922102 |
0.448 |
|
| 2005 |
Hughes AL, Hughes MA. Patterns of nucleotide difference in overlapping and non-overlapping reading frames of papillomavirus genomes. Virus Research. 113: 81-8. PMID 15913825 DOI: 10.1016/J.Virusres.2005.03.030 |
0.365 |
|
| 2005 |
Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M. Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding loci Genetics. 170: 1181-1187. PMID 15911586 DOI: 10.1534/Genetics.104.037077 |
0.411 |
|
| 2005 |
Jongwutiwes S, Putaporntip C, Iwasaki T, Ferreira MU, Kanbara H, Hughes AL. Mitochondrial genome sequences support ancient population expansion in Plasmodium vivax. Molecular Biology and Evolution. 22: 1733-9. PMID 15901839 DOI: 10.1093/Molbev/Msi168 |
0.356 |
|
| 2005 |
Hughes AL, Friedman R. Loss of ancestral genes in the genomic evolution of Ciona intestinalis. Evolution & Development. 7: 196-200. PMID 15876192 DOI: 10.1111/J.1525-142X.2005.05022.X |
0.651 |
|
| 2005 |
Hughes AL, Friedman R. Nucleotide substitution and recombination at orthologous loci in Staphylococcus aureus Journal of Bacteriology. 187: 2698-2704. PMID 15805516 DOI: 10.1128/Jb.187.8.2698-2704.2005 |
0.648 |
|
| 2005 |
Hughes AL, Friedman R. Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana. Journal of Molecular Evolution. 60: 247-56. PMID 15785853 DOI: 10.1007/s00239-004-0171-z |
0.574 |
|
| 2005 |
Hughes AL, Friedman R. Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes. Molecular Biology and Evolution. 22: 1320-4. PMID 15746015 DOI: 10.1093/Molbev/Msi120 |
0.526 |
|
| 2005 |
Hughes AL, Friedman R. Poxvirus genome evolution by gene gain and loss. Molecular Phylogenetics and Evolution. 35: 186-195. PMID 15737590 DOI: 10.1016/J.Ympev.2004.12.008 |
0.657 |
|
| 2005 |
Friedman R, Hughes AL. The pattern of nucleotide difference at individual codons among mouse, rat, and human Molecular Biology and Evolution. 22: 1285-1289. PMID 15716467 DOI: 10.1093/Molbev/Msi113 |
0.565 |
|
| 2005 |
Hughes AL, Piontkivska H. DNA repeat arrays in chicken and human genomes and the adaptive evolution of avian genome size. Bmc Evolutionary Biology. 5: 12-12. PMID 15694002 DOI: 10.1186/1471-2148-5-12 |
0.345 |
|
| 2005 |
Hughes AL. Evidence for abundant slightly deleterious polymorphisms in bacterial populations Genetics. 169: 533-538. PMID 15545641 DOI: 10.1534/Genetics.104.036939 |
0.354 |
|
| 2005 |
Friedman R, Hughes AL. Codon Volatility As an Indicator of Positive Selection: Data from Eukaryotic Genome Comparisons Molecular Biology and Evolution. 22: 542-546. PMID 15525698 DOI: 10.1093/Molbev/Msi038 |
0.629 |
|
| 2005 |
Eck P, Erichsen HC, Taylor JG, Yeager M, Hughes AL, Levine M, Chanock S. Comparison of the genomic structure and variation in the two human sodium-dependent vitamin C transporters, SLC23A1 and SLC23A2. Human Genetics. 115: 285-94. PMID 15316768 DOI: 10.1007/S00439-004-1167-X |
0.379 |
|
| 2005 |
Piontkivska H, Hughes AL. Between-Host Evolution of Cytotoxic T-Lymphocyte Epitopes in Human Immunodeficiency Virus Type 1: an Approach Based on Phylogenetically Independent Comparisons Journal of Virology. 79: 1981-1982. DOI: 10.1128/Jvi.78.21.11758-11765.2004 |
0.42 |
|
| 2005 |
Hughes AL, Friedman R. Expression patterns of duplicate genes in the developing root in Arabidopsis thaliana Journal of Molecular Evolution. 60: 247-256. DOI: 10.1007/S00239-004-0171-Z |
0.616 |
|
| 2004 |
Hughes AL. The evolution of amino acid repeat arrays in Plasmodium and other organisms Journal of Molecular Evolution. 59: 528-535. PMID 15638464 DOI: 10.1007/S00239-004-2645-4 |
0.331 |
|
| 2004 |
Hughes AL, Friedman R. Patterns of sequence divergence in 5′ intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories Genetics. 168: 1795-1803. PMID 15611157 DOI: 10.1534/Genetics.104.032979 |
0.652 |
|
| 2004 |
Hughes AL, Friedman R. Shedding genomic ballast: Extensive parallel loss of ancestral gene families in animals Journal of Molecular Evolution. 59: 827-833. PMID 15599514 DOI: 10.1007/S00239-004-0115-7 |
0.587 |
|
| 2004 |
O'Connor DH, McDermott AB, Krebs KC, Dodds EJ, Miller JE, Gonzalez EJ, Jacoby TJ, Yant L, Piontkivska H, Pantophlet R, Burton DR, Rehrauer WM, Wilson N, Hughes AL, Watkins DI. A dominant role for CD8+-T-lymphocyte selection in simian immunodeficiency virus sequence variation. Journal of Virology. 78: 14012-22. PMID 15564508 DOI: 10.1128/Jvi.78.24.14012-14022.2004 |
0.323 |
|
| 2004 |
Patil A, Hughes AL, Zhang G. Rapid evolution and diversification of mammalian alpha-defensins as revealed by comparative analysis of rodent and primate genes. Physiological Genomics. 20: 1-11. PMID 15494476 DOI: 10.1152/Physiolgenomics.00150.2004 |
0.37 |
|
| 2004 |
Piontkivska H, Hughes AL. Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisons. Journal of Virology. 78: 11758-65. PMID 15479817 DOI: 10.1128/JVI.78.21.11758-11765.2004 |
0.306 |
|
| 2004 |
Hughes AL, Friedman R. Recent mammalian gene duplications: Robust search for functionally divergent gene pairs Journal of Molecular Evolution. 59: 114-120. PMID 15383914 DOI: 10.1007/S00239-004-2616-9 |
0.618 |
|
| 2004 |
Hughes AL. Evolutionary origin of the Jiv90 gene of Pestivirus Infection, Genetics and Evolution. 4: 329-333. PMID 15374530 DOI: 10.1016/J.Meegid.2004.04.001 |
0.442 |
|
| 2004 |
Hughes AL, Friedman R. Transposable element distribution in the yeast genome reflects a role in repeated genomic rearrangement events on an evolutionary time scale Genetica. 121: 181-185. PMID 15330117 DOI: 10.1023/B:Gene.0000040383.51611.E3 |
0.602 |
|
| 2004 |
Xiao Y, Hughes AL, Ando J, Matsuda Y, Cheng JF, Skinner-Noble D, Zhang G. 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. 5: 56. PMID 15310403 DOI: 10.1186/1471-2164-5-56 |
0.377 |
|
| 2004 |
Friedman R, Drake JW, Hughes AL. Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles. Genetics. 167: 1507-12. PMID 15280258 DOI: 10.1534/Genetics.104.026344 |
0.604 |
|
| 2004 |
Hughes AL, Friedman R. Pattern of divergence of amino acid sequences encoded by paralogous genes in human and pufferfish Molecular Phylogenetics and Evolution. 32: 337-343. PMID 15186818 DOI: 10.1016/J.Ympev.2003.12.007 |
0.645 |
|
| 2004 |
Hughes AL. Phylogeny of the Picornaviridae and differential evolutionary divergence of picornavirus proteins Infection, Genetics and Evolution. 4: 143-152. PMID 15157632 DOI: 10.1016/J.Meegid.2004.03.001 |
0.397 |
|
| 2004 |
Friedman R, Ekollu V, Rose JR, Hughes AL. Dblox: a genome-wide test for ancient segmental duplication. Bioinformatics (Oxford, England). 20: 2834-5. PMID 15145815 DOI: 10.1093/Bioinformatics/Bth275 |
0.548 |
|
| 2004 |
Hughes AL, Friedman R. Differential loss of ancestral gene families as a source of genomic divergence in animals Proceedings of the Royal Society B: Biological Sciences. 271. PMID 15101434 DOI: 10.1098/Rsbl.2003.0124 |
0.62 |
|
| 2004 |
Friedrich TC, Dodds EJ, Yant LJ, Vojnov L, Rudersdorf R, Cullen C, Evans DT, Desrosiers RC, Mothé BR, Sidney J, Sette A, Kunstman K, Wolinsky S, Piatak M, Lifson J, ... Hughes AL, et al. Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nature Medicine. 10: 275-81. PMID 14966520 DOI: 10.1038/Nm998 |
0.333 |
|
| 2004 |
Friedrich TC, Frye CA, Yant LJ, O'Connor DH, Kriewaldt NA, Benson M, Vojnov L, Dodds EJ, Cullen C, Rudersdorf R, Hughes AL, Wilson N, Watkins DI. Extraepitopic compensatory substitutions partially restore fitness to simian immunodeficiency virus variants that escape from an immunodominant cytotoxic-T-lymphocyte response. Journal of Virology. 78: 2581-5. PMID 14963161 DOI: 10.1128/Jvi.78.5.2581-2585.2004 |
0.307 |
|
| 2004 |
Friedman R, Hughes AL. Two Patterns of Genome Organization in Mammals: the Chromosomal Distribution of Duplicate Genes in Human and Mouse Molecular Biology and Evolution. 21: 1008-1013. PMID 14963098 DOI: 10.1093/Molbev/Msh076 |
0.593 |
|
| 2004 |
Hughes AL. 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. 30: 287-294. PMID 14715221 DOI: 10.1016/S1055-7903(03)00189-1 |
0.406 |
|
| 2004 |
Hughes AL, Friedman R, Ekollu V, Rose JR. Non-random association of transposable elements with duplicated genomic blocks in Arabidopsis thaliana. Molecular Phylogenetics and Evolution. 29: 410-6. PMID 14615183 DOI: 10.1016/S1055-7903(03)00262-8 |
0.602 |
|
| 2004 |
Hughes AL. Malaria Parasites: Genomes and Molecular Biology Infection, Genetics and Evolution. 4: 371. DOI: 10.1016/J.Meegid.2004.05.005 |
0.303 |
|
| 2003 |
Hughes AL, Packer B, Welch R, Bergen AW, Chanock SJ, Yeager M. Widespread purifying selection at polymorphic sites in human protein-coding loci Proceedings of the National Academy of Sciences of the United States of America. 100: 15754-15757. PMID 14660790 DOI: 10.1073/Pnas.2536718100 |
0.431 |
|
| 2003 |
Hughes AL, Piontkivska H. Molecular phylogenetics of Trypanosomatidae: contrasting results from 18S rRNA and protein phylogenies Kinetoplastid Biology and Disease. 2: 15-15. PMID 14613495 DOI: 10.1186/1475-9292-2-15 |
0.441 |
|
| 2003 |
Hughes AL, Green JA, Piontkivska H, Roberts RM. Aspartic proteinase phylogeny and the origin of pregnancy-associated glycoproteins. Molecular Biology and Evolution. 20: 1940-5. PMID 12949149 DOI: 10.1093/Molbev/Msg217 |
0.375 |
|
| 2003 |
Hughes AL, Friedman R. Parallel evolution by gene duplication in the genomes of two unicellular fungi Genome Research. 13: 1259-1264. PMID 12901373 DOI: 10.1101/Gr.714603 |
0.64 |
|
| 2003 |
Hughes AL, Friedman R. 2R or not 2R: Testing hypotheses of genome duplication in early vertebrates Journal of Structural and Functional Genomics. 3: 85-93. PMID 12836688 DOI: 10.1023/A:1022681600462 |
0.624 |
|
| 2003 |
Hughes AL, Friedman R. Parallel evolution by gene duplication in the genomes of two unicellular fungi. Genome Research. 13: 794-9. PMID 12727899 DOI: 10.1101/gr.714603 |
0.599 |
|
| 2003 |
Hughes AL, Friedman R. Genome-wide survey for genes horizontally transferred from cellular organisms to baculoviruses Molecular Biology and Evolution. 20: 979-987. PMID 12716988 DOI: 10.1093/Molbev/Msg107 |
0.627 |
|
| 2003 |
Hughes AL, Piontkivska H. Phylogeny of Trypanosomatidae and Bodonidae (Kinetoplastida) based on 18S rRNA: evidence for paraphyly of Trypanosoma and six other genera. Molecular Biology and Evolution. 20: 644-52. PMID 12679543 DOI: 10.1093/Molbev/Msg062 |
0.347 |
|
| 2003 |
Sette A, Sidney J, Livingston BD, Dzuris JL, Crimi C, Walker CM, Southwood S, Collins EJ, Hughes AL. Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution. Immunogenetics. 54: 830-41. PMID 12671733 DOI: 10.1007/S00251-002-0530-0 |
0.307 |
|
| 2003 |
Hughes AL. Genomes of mice and men Heredity. 90: 115-116. PMID 12634812 DOI: 10.1038/Sj.Hdy.6800222 |
0.467 |
|
| 2003 |
Piontkivska H, Hughes AL. Evolution of Vertebrate Voltage-Gated Ion Channel α Chains by Sequential Gene Duplication Journal of Molecular Evolution. 56: 277-285. PMID 12612831 DOI: 10.1007/S00239-002-2399-9 |
0.331 |
|
| 2003 |
Friedman R, Hughes AL. The temporal distribution of gene duplication events in a set of highly conserved human gene families Molecular Biology and Evolution. 20: 154-161. PMID 12519918 DOI: 10.1093/Molbev/Msg017 |
0.648 |
|
| 2003 |
Bashirova AA, Wu L, Cheng J, Martin TD, Martin MP, Benveniste RE, Lifson JD, KewalRamani VN, Hughes A, Carrington M. Novel member of the CD209 (DC-SIGN) gene family in primates. Journal of Virology. 77: 217-27. PMID 12477827 DOI: 10.1128/Jvi.77.1.217-227.2003 |
0.354 |
|
| 2002 |
Hughes AL. Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts Infection, Genetics and Evolution. 2: 3-10. PMID 12797996 DOI: 10.1016/S1567-1348(02)00040-0 |
0.443 |
|
| 2002 |
Hughes AL. Natural selection and the diversification of vertebrate immune effectors Immunological Reviews. 190: 161-168. PMID 12493013 DOI: 10.1034/J.1600-065X.2002.19012.X |
0.383 |
|
| 2002 |
Flügge P, Zimmermann E, Hughes AL, Günther E, Walter L. Characterization and phylogenetic relationship of prosimian MHC class I genes. Journal of Molecular Evolution. 55: 768-75. PMID 12486535 DOI: 10.1007/S00239-002-2372-7 |
0.44 |
|
| 2002 |
Hughes AL, Friedman R, Murray MB. Genomewide Pattern of Synonymous Nucleotide Substitution in Two Complete Genomes of Mycobacterium tuberculosis Emerging Infectious Diseases. 8: 1342-1346. PMID 12453367 DOI: 10.3201/Eid0811.020064 |
0.61 |
|
| 2002 |
Hughes AL. Evolution of the human killer cell inhibitory receptor family Molecular Phylogenetics and Evolution. 25: 330-340. PMID 12414314 DOI: 10.1016/S1055-7903(02)00255-5 |
0.306 |
|
| 2002 |
Hughes AL, Verra F. Extensive polymorphism and ancient origin of Plasmodium falciparum Trends in Parasitology. 18: 348-351. PMID 12377283 DOI: 10.1016/S1471-4922(02)02290-0 |
0.366 |
|
| 2002 |
Jongwutiwes S, Putaporntip C, Friedman R, Hughes AL. The Extent of Nucleotide Polymorphism is Highly Variable Across a 3-kb Region on Plasmodium falciparum Chromosome 2 Molecular Biology and Evolution. 19: 1585-1590. PMID 12200485 DOI: 10.1093/Oxfordjournals.Molbev.A004220 |
0.556 |
|
| 2002 |
Hughes AL. Adaptive evolution after gene duplication Trends in Genetics. 18: 433-434. PMID 12175796 DOI: 10.1016/S0168-9525(02)02755-5 |
0.413 |
|
| 2002 |
Lipovich L, Hughes AL, King MC, Abkowitz JL, Quigley JG. 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. 286: 203-13. PMID 11943475 DOI: 10.1016/S0378-1119(02)00457-2 |
0.436 |
|
| 2002 |
Friedman R, Hughes AL. Molecular evolution of the NF-κB signaling system Immunogenetics. 53: 964-974. PMID 11862396 DOI: 10.1007/S00251-001-0399-3 |
0.542 |
|
| 2002 |
Hughes AL. Origin and evolution of viral interleukin-10 and other DNA virus genes with vertebrate homologues Journal of Molecular Evolution. 54: 90-101. PMID 11734902 DOI: 10.1007/S00239-001-0021-1 |
0.413 |
|
| 2001 |
Hughes AL. Evolutionary change of predicted cytotoxic T cell epitopes of dengue virus Infection, Genetics and Evolution. 1: 123-130. PMID 12798027 DOI: 10.1016/S1567-1348(01)00013-2 |
0.318 |
|
| 2001 |
Friedman R, Hughes AL. Pattern and timing of gene duplication in animal genomes Genome Research. 11: 1842-1847. PMID 11691848 DOI: 10.1101/Gr.200601 |
0.63 |
|
| 2001 |
Westover KM, Hughes AL. Molecular evolution of viral fusion and matrix protein genes and phylogenetic relationships among the Paramyxoviridae Molecular Phylogenetics and Evolution. 21: 128-134. PMID 11603943 DOI: 10.1006/Mpev.2001.0999 |
0.344 |
|
| 2001 |
Hughes AL, Verra F. Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum Proceedings of the Royal Society B: Biological Sciences. 268: 1855-1860. PMID 11522206 DOI: 10.1098/Rspb.2001.1759 |
0.314 |
|
| 2001 |
Hughes AL, Westover K, da Silva J, O'Connor DH, Watkins DI. Simultaneous positive and purifying selection on overlapping reading frames of the tat and vpr genes of simian immunodeficiency virus. Journal of Virology. 75: 7966-72. PMID 11483741 DOI: 10.1128/Jvi.75.17.7966-7972.2001 |
0.418 |
|
| 2001 |
Friedman R, Hughes AL. Gene duplication and the structure of eukaryotic genomes [1] Genome Research. 11: 373-381. PMID 11230161 DOI: 10.1101/Gr.155801 |
0.624 |
|
| 2001 |
Hughes AL. Evolution of the integrin α and β protein families Journal of Molecular Evolution. 52: 63-72. PMID 11139295 DOI: 10.1007/S002390010134 |
0.321 |
|
| 2001 |
Zeyl C, Hughes AL. Adaptive Evolution of Genes and Genomes The Journal of Parasitology. 87: 560. DOI: 10.2307/3285093 |
0.31 |
|
| 2001 |
Hughes AL, Silva Jd, Friedman R. Ancient Genome Duplications Did Not Structure the Human Hox-Bearing Chromosomes Genome Research. 11: 771-780. DOI: 10.1101/Gr.160001 |
0.595 |
|
| 2000 |
Hughes AL, Friedman R. Evolutionary diversification of protein-coding genes of hantaviruses. Molecular Biology and Evolution. 17: 1558-68. PMID 11018161 DOI: 10.1093/Oxfordjournals.Molbev.A026254 |
0.612 |
|
| 2000 |
Allen TM, O'Connor DH, Jing P, Dzuris JL, Mothé BR, Vogel TU, Dunphy E, Liebl ME, Emerson C, Wilson N, Kunstman KJ, Wang X, Allison DB, Hughes AL, Desrosiers RC, et al. Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature. 407: 386-90. PMID 11014195 DOI: 10.1038/35030124 |
0.318 |
|
| 2000 |
Hughes AL, Pontarotti P. Gene duplication and MHC origins. Immunogenetics. 51: 982-3. PMID 11003392 DOI: 10.1007/S002510000224 |
0.393 |
|
| 2000 |
Hughes AL. Evolution of introns and exons of class II major histocompatibility complex genes of vertebrates Immunogenetics. 51: 473-486. PMID 10866114 DOI: 10.1007/s002510050646 |
0.316 |
|
| 2000 |
Hughes AL, Green JA, Garbayo JM, Roberts RM. 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. 97: 3319-23. PMID 10725351 DOI: 10.1073/pnas.050002797 |
0.337 |
|
| 1999 |
Hughes AL. Concerted evolution of exons and introns in the MHC-linked tenascin-X gene of mammals Molecular Biology and Evolution. 16: 1558-1567. PMID 10555287 DOI: 10.1093/OXFORDJOURNALS.MOLBEV.A026068 |
0.304 |
|
| 1999 |
Yeager M, Hughes AL. Evolution of the mammalian MHC: natural selection, recombination, and convergent evolution. Immunological Reviews. 167: 45-58. PMID 10319250 DOI: 10.1111/j.1600-065X.1999.tb01381.x |
0.329 |
|
| 1999 |
Hughes AL. Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history Journal of Molecular Evolution. 48: 565-576. PMID 10198122 DOI: 10.1007/PL00006499 |
0.31 |
|
| 1998 |
Hughes AL, Yeager M. Natural selection and the evolutionary history of major histocompatibility complex loci Frontiers in Bioscience : a Journal and Virtual Library. 3. PMID 9601106 DOI: 10.2741/A298 |
0.34 |
|
| 1997 |
Hughes AL. Evolution of the proteasome components Immunogenetics. 46: 82-92. PMID 9162093 DOI: 10.1007/s002510050245 |
0.353 |
|
| 1996 |
Milewicz DM, Byers PH, Reveille J, Hughes AL, Duvic M. A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific. Journal of Molecular Evolution. 42: 117-23. PMID 8919863 DOI: 10.1007/Bf02198836 |
0.349 |
|
| 1994 |
Hughes AL. The evolution of functionally novel proteins after gene duplication Proceedings of the Royal Society B: Biological Sciences. 256: 119-124. PMID 8029240 DOI: 10.1098/rspb.1994.0058 |
0.307 |
|
| 1994 |
Hughes AL, Hughes MK, Howell CY, 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. 346: 359-66; discussion 3. PMID 7708830 DOI: 10.1098/Rstb.1994.0153 |
0.491 |
|
| 1994 |
Hughes AL. Evolution of Cysteine Proteinases in Eukaryotes Molecular Phylogenetics and Evolution. 3: 310-321. PMID 7697189 DOI: 10.1006/mpev.1994.1038 |
0.34 |
|
| 1993 |
Hughes AL, Nei M. Evolutionary relationships of the classes of major histocompatibility complex genes. Immunogenetics. 37: 337-46. PMID 8428767 DOI: 10.1007/BF00216798 |
0.451 |
|
| 1992 |
Hughes AL, Nei M. Maintenance of MHC polymorphism. Nature. 355: 402-3. PMID 1734277 DOI: 10.1038/355402b0 |
0.442 |
|
| 1992 |
Hughes AL, Nei M. Models of host-parasite interaction and MHC polymorphism. Genetics. 132: 863-4. PMID 1468636 |
0.438 |
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| 1990 |
Hughes AL, 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. 7: 515-24. PMID 2283951 DOI: 10.1093/Oxfordjournals.Molbev.A040626 |
0.486 |
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| 1990 |
Hughes AL, Nei M. Evolutionary relationships of class II major-histocompatibility-complex genes in mammals. Molecular Biology and Evolution. 7: 491-514. PMID 2126590 DOI: 10.1093/Oxfordjournals.Molbev.A040622 |
0.547 |
|
| 1989 |
Hughes AL, Nei M. Ancient interlocus exon exchange in the history of the HLA-A locus. Genetics. 122: 681-6. PMID 2759423 |
0.538 |
|
| 1989 |
Hughes AL, 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. 86: 958-62. PMID 2492668 DOI: 10.1073/Pnas.86.3.958 |
0.503 |
|
| 1989 |
Hughes AL, Nei M. Evolution of the major histocompatibility complex: independent origin of nonclassical class I genes in different groups of mammals. Molecular Biology and Evolution. 6: 559-79. PMID 2484936 DOI: 10.1093/Oxfordjournals.Molbev.A040573 |
0.592 |
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| 1988 |
Hughes AL, Nei M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature. 335: 167-70. PMID 3412472 DOI: 10.1038/335167a0 |
0.551 |
|
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