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Robert FriedmanAssistant Professor of Biological Sciences
Ph.D., 2002, University of South Carolina
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Robert FriedmanAssistant Professor of Biological Sciences
Ph.D., 2002, University of South Carolina
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Gene duplication is an important topic. Presumably, the first living organisms had smaller genomes, and, over time, gene duplication provided the raw material for new proteins. These duplicated genes were then molded by the processes of natural selection, mutation, recombination and genetic drift. These forces provided the opportunity for an organism, and its underlying genes, to adapt to new environments. I believe that much of life's complexity can be studied by phylogenetic analysis of duplicated genes and quantifying the evolutionary forces that acted upon them.
Another interest of mine is the methods of bioinformatics. There are many evolutionary methods, many not so well tested, which are used in the analysis of genetic sequence data. One common type of analysis is to find the relationship among different species by constructing a gene tree. For instance, a gene tree can reveal instances of gene transfer between species, an especially contentious and debated phenomenon. Much controversy surrounds the application of the use of different phylogenetic methods and its accompanying models of sequence evolution. Further work is needed to clarify the applicability and practical usage of these methods.
Lastly, I have studied the evolution of animal genomes, particularly that of vertebrates. There is a widely cited hypothesis that vertebrates, including humans, acquired their complexity from two genome doublings in early vertebrate evolution. Austin Hughes and I showed this to be false. But this area remains controversial and has opened up an area of inquiry as to the quantity and timing of the duplication and movement of large genomic regions in vertebrates. Fortunately, this issue may be further addressed by analysis of upcoming sequences from different chordate genomes.
Friedman R, Hughes AL (2003) The Temporal Distribution of Gene Duplication Events in a Set of Highly Conserved Human Gene Families. Mol Biol Evol 20:154-61.
Friedman R, Hughes AL (2004) Two Patterns of Genome Organization in Mammals: The Chromosomal Distribution of Duplicate Genes in Human and Mouse. Mol Biol Evol 21:1008-13.
Friedman R, Ekollu V, Rose JR, Hughes AL (2004) Dblox: a genome-wide test for ancient segmental duplication. Bioinformatics 20:2834-5.
Friedman R, Drake JW, Hughes AL (2004) Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of Thermophiles. Genetics 167:1507-12.
Huang SW, Friedman R, Yu N, Yu A, Li WH (2005) How Strong is the Mutagenicity of Recombination in Mammals? Mol Biol Evol 22:426-31.
Hughes AL, Friedman R (2005) Variation in the Pattern of Synonymous and Nonsynonymous Difference between Two Fungal Genomes. Mol Biol Evol 22:1320-4.
Friedman R, Hughes AL (2005) Codon Volatility as an Indicator of Positive Selection: Data from Eukaryotic Genome Comparisons. Mol Biol Evol 22:542-6.
Hughes AL, Ekollu V, Friedman R, Rose JR (2005) Gene Family Content-Based Phylogeny of Prokaryotes: The Effect of Criteria for Inferring Homology. Syst Biol 54:268-76.
Friedman R, Hughes AL (2005) The Pattern of Nucleotide Difference at Individual Codons among Mouse, Rat, and Human. Mol Biol Evol 22:1285-9.
Rooney AP, Swezey JL, Friedman R, Hecht DW, Maddox CW (2006) Evolutionary Analysis of the Core Genome Reveals Cryptic Lineages of Clostridium perfringens. Genetics 172:2081-92.
Friedman R, Hughes AL (2006) Pattern of gene duplication in the Cotesia congregata Bracovirus. Infect Genet Evol 6:315-22.