| Year |
Citation |
Score |
| 2017 |
Feng B, Lin Y, Zhou L, Guo Y, Friedman R, Xia R, Hu F, Liu C, Tang J. Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data. Scientific Reports. 7: 15209. PMID 29123238 DOI: 10.1038/S41598-017-15484-5 |
0.447 |
|
| 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 |
0.563 |
|
| 2014 |
Gabriel MW, Matsui GY, Friedman R, Lovell CR. Optimization of multilocus sequence analysis for identification of species in the genus Vibrio. Applied and Environmental Microbiology. 80: 5359-65. PMID 24951781 DOI: 10.1128/Aem.01206-14 |
0.488 |
|
| 2013 |
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, Yee-Greenbaum J, Badger JH, Tesler G, Nurk S, Lesin V, Brami D, Hall AP, Edlund A, Allen LZ, Durkin S, Reed S, ... ... Friedman R, et al. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research. 23: 867-77. PMID 23564253 DOI: 10.1101/Gr.150433.112 |
0.303 |
|
| 2012 |
Friedman R, Ely B. Codon usage methods for horizontal gene transfer detection generate an abundance of false positive and false negative results. Current Microbiology. 65: 639-42. PMID 23010940 DOI: 10.1007/S00284-012-0205-5 |
0.469 |
|
| 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 |
0.704 |
|
| 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 |
0.569 |
|
| 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 |
0.482 |
|
| 2011 |
Friedman R. Genomic organization of the glutathione S-transferase family in insects. Molecular Phylogenetics and Evolution. 61: 924-32. PMID 21930223 DOI: 10.1016/J.Ympev.2011.08.027 |
0.538 |
|
| 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 |
0.77 |
|
| 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 |
0.734 |
|
| 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 |
0.542 |
|
| 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 |
0.522 |
|
| 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 |
0.715 |
|
| 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 |
0.778 |
|
| 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 |
0.58 |
|
| 2009 |
Luo H, Sun Z, Arndt W, Shi J, Friedman R, Tang J. Gene order phylogeny and the evolution of methanogens. Plos One. 4: e6069. PMID 19562076 DOI: 10.1371/Journal.Pone.0006069 |
0.594 |
|
| 2009 |
Vogt RG, Miller NE, Litvack R, Fandino RA, Sparks J, Staples J, Friedman R, Dickens JC. The insect SNMP gene family. Insect Biochemistry and Molecular Biology. 39: 448-56. PMID 19364529 DOI: 10.1016/J.Ibmb.2009.03.007 |
0.52 |
|
| 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 |
0.591 |
|
| 2008 |
Luo H, Shi J, Arndt W, Tang J, Friedman R. Gene order phylogeny of the genus Prochlorococcus. Plos One. 3: e3837. PMID 19050756 DOI: 10.1371/Journal.Pone.0003837 |
0.606 |
|
| 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 |
0.67 |
|
| 2008 |
Townsend JP, López-Giráldez F, Friedman R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. Journal of Molecular Evolution. 67: 437-47. PMID 18696029 DOI: 10.1007/S00239-008-9142-0 |
0.431 |
|
| 2008 |
Ivars-Martinez E, Martin-Cuadrado AB, D'Auria G, Mira A, Ferriera S, Johnson J, Friedman R, Rodriguez-Valera F. Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter. The Isme Journal. 2: 1194-212. PMID 18670397 DOI: 10.1038/ismej.2008.74 |
0.309 |
|
| 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 |
0.772 |
|
| 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 |
0.523 |
|
| 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 |
0.613 |
|
| 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 |
0.537 |
|
| 2007 |
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, ... ... Friedman R, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. Plos Biology. 5: e77. PMID 17355176 DOI: 10.1371/Journal.Pbio.0050077 |
0.365 |
|
| 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 |
0.504 |
|
| 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 |
0.597 |
|
| 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 |
0.6 |
|
| 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 |
0.531 |
|
| 2006 |
Rooney AP, Swezey JL, Friedman R, Hecht DW, Maddox CW. Analysis of core housekeeping and virulence genes reveals cryptic lineages of Clostridium perfringens that are associated with distinct disease presentations. Genetics. 172: 2081-92. PMID 16489222 DOI: 10.1534/Genetics.105.054601 |
0.31 |
|
| 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 |
0.57 |
|
| 2006 |
Hughes AL, Friedman R, Glenn NL. The future of data analysis in evolutionary genomics Current Genomics. 7: 227-234. DOI: 10.2174/138920206778426942 |
0.361 |
|
| 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 |
0.551 |
|
| 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 |
0.667 |
|
| 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 |
0.565 |
|
| 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 |
0.684 |
|
| 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 |
0.656 |
|
| 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 |
0.576 |
|
| 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 |
0.498 |
|
| 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 |
0.68 |
|
| 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 |
0.544 |
|
| 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 |
0.617 |
|
| 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 |
0.619 |
|
| 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 |
0.671 |
|
| 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 |
0.66 |
|
| 2004 |
Huang SW, Friedman R, Yu N, Yu A, Li WH. How strong is the mutagenicity of recombination in mammals? Molecular Biology and Evolution. 22: 426-31. PMID 15496551 DOI: 10.1093/Molbev/Msi025 |
0.361 |
|
| 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 |
0.625 |
|
| 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 |
0.61 |
|
| 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 |
0.633 |
|
| 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 |
0.656 |
|
| 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 |
0.604 |
|
| 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 |
0.645 |
|
| 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 |
0.605 |
|
| 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 |
0.61 |
|
| 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 |
0.671 |
|
| 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 |
0.644 |
|
| 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 |
0.633 |
|
| 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 |
0.643 |
|
| 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 |
0.681 |
|
| 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 |
0.592 |
|
| 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 |
0.588 |
|
| 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 |
0.51 |
|
| 2002 |
Szalai G, Duester G, Friedman R, Jia H, Lin S, Roe BA, Felder MR. Organization of six functional mouse alcohol dehydrogenase genes on two overlapping bacterial artificial chromosomes. European Journal of Biochemistry / Febs. 269: 224-32. PMID 11784316 DOI: 10.1046/J.0014-2956.2001.02642.X |
0.461 |
|
| 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 |
0.662 |
|
| 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 |
0.648 |
|
| 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 |
0.611 |
|
| 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 |
0.595 |
|
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