TY - JOUR AU - Baer, C. F. AU - Miyamoto, M. M. AU - Denver, D. R. PY - 2007 DA - 2007// TI - Mutation rate variation in multicellular eukaryotes: causes and consequences JO - Nat Rev Genet VL - 8 UR - https://doi.org/10.1038/nrg2158 DO - 10.1038/nrg2158 ID - Baer2007 ER - TY - JOUR AU - Chuang, J. H. AU - Li, H. PY - 2004 DA - 2004// TI - Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020029 DO - 10.1371/journal.pbio.0020029 ID - Chuang2004 ER - TY - JOUR AU - Lercher, M. J. AU - Williams, E. J. AU - Hurst, L. D. PY - 2001 DA - 2001// TI - Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: implications for understanding the mechanistic basis of the male mutation bias JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003744 DO - 10.1093/oxfordjournals.molbev.a003744 ID - Lercher2001 ER - TY - JOUR AU - Liu, G. E. AU - Matukumalli, L. K. AU - Sonstegard, T. S. AU - Shade, L. L. AU - Van Tassell, C. P. PY - 2006 DA - 2006// TI - Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences JO - BMC Genomics VL - 7 UR - https://doi.org/10.1186/1471-2164-7-140 DO - 10.1186/1471-2164-7-140 ID - Liu2006 ER - TY - JOUR AU - Malcom, C. M. AU - Wyckoff, G. J. AU - Lahn, B. T. PY - 2003 DA - 2003// TI - Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity JO - Mol Biol Evol VL - 20 UR - https://doi.org/10.1093/molbev/msg178 DO - 10.1093/molbev/msg178 ID - Malcom2003 ER - TY - JOUR AU - Matassi, G. AU - Sharp, P. M. AU - Gautier, C. PY - 1999 DA - 1999// TI - Chromosomal location effects on gene sequence evolution in mammals JO - Curr Biol VL - 9 UR - https://doi.org/10.1016/S0960-9822(99)80361-3 DO - 10.1016/S0960-9822(99)80361-3 ID - Matassi1999 ER - TY - JOUR AU - Wolfe, K. H. AU - Sharp, P. M. AU - Li, W. H. PY - 1989 DA - 1989// TI - Mutation rates differ among regions of the mammalian genome JO - Nature VL - 337 UR - https://doi.org/10.1038/337283a0 DO - 10.1038/337283a0 ID - Wolfe1989 ER - TY - JOUR AU - Gaffney, D. J. AU - Keightley, P. D. PY - 2005 DA - 2005// TI - The scale of mutational variation in the murid genome JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3895005 DO - 10.1101/gr.3895005 ID - Gaffney2005 ER - TY - JOUR AU - Chin, C. S. AU - Chuang, J. H. AU - Li, H. PY - 2005 DA - 2005// TI - Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.3243305 DO - 10.1101/gr.3243305 ID - Chin2005 ER - TY - JOUR AU - Pheasant, M. AU - Mattick, J. S. PY - 2007 DA - 2007// TI - Raising the estimate of functional human sequences JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6406307 DO - 10.1101/gr.6406307 ID - Pheasant2007 ER - TY - JOUR AU - Hardison, R. C. AU - Roskin, K. M. AU - Yang, S. AU - Diekhans, M. AU - Kent, W. J. AU - Weber, R. AU - Elnitski, L. AU - Li, J. AU - O'Connor, M. AU - Kolbe, D. AU - Schwartz, S. AU - Furey, T. S. AU - Whelan, S. AU - Goldman, N. AU - Smit, A. AU - Miller, W. AU - Chiaromonte, F. AU - Haussler, D. PY - 2003 DA - 2003// TI - Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.844103 DO - 10.1101/gr.844103 ID - Hardison2003 ER - TY - CHAP AU - Graur, D. AU - Li, W. H. PY - 2000 DA - 2000// BT - Fundamentals of molecular evolution PB - Sunderland, Mass. CY - Sinauer ID - Graur2000 ER - TY - JOUR AU - Chamary, J. V. AU - Parmley, J. L. AU - Hurst, L. D. PY - 2006 DA - 2006// TI - Hearing silence: non-neutral evolution at synonymous sites in mammals JO - Nat Rev Genet VL - 7 UR - https://doi.org/10.1038/nrg1770 DO - 10.1038/nrg1770 ID - Chamary2006 ER - TY - JOUR AU - Fitzpatrick, D. AU - Logue, M. AU - Stajich, J. AU - Butler, G. PY - 2006 DA - 2006// TI - A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis JO - BMC Evolutionary Biology VL - 6 UR - https://doi.org/10.1186/1471-2148-6-99 DO - 10.1186/1471-2148-6-99 ID - Fitzpatrick2006 ER - TY - JOUR AU - Murphy, W. J. AU - Pringle, T. H. AU - Crider, T. A. AU - Springer, M. S. AU - Miller, W. PY - 2007 DA - 2007// TI - Using genomic data to unravel the root of the placental mammal phylogeny JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5918807 DO - 10.1101/gr.5918807 ID - Murphy2007 ER - TY - JOUR AU - Nikolaev, S. AU - Montoya-Burgos, J. I. AU - Margulies, E. H. AU - Rougemont, J. AU - Nyffeler, B. AU - Antonarakis, S. E. PY - 2007 DA - 2007// TI - Early history of mammals is elucidated with the ENCODE multiple species sequencing data JO - PLoS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030002 DO - 10.1371/journal.pgen.0030002 ID - Nikolaev2007 ER - TY - STD TI - Broad-Institute: Candida albicans Sequencing Project, Broad Institute of Harvard and MIT. [http://www.broad.mit.edu] UR - http://www.broad.mit.edu ID - ref17 ER - TY - JOUR AU - Yokogawa, T. AU - Suzuki, T. AU - Ueda, T. AU - Mori, M. AU - Ohama, T. AU - Kuchino, Y. AU - Yoshinari, S. AU - Motoki, I. AU - Nishikawa, K. AU - Osawa, S. PY - 1992 DA - 1992// TI - Serine tRNA complementary to the nonuniversal serine codon CUG in Candida cylindracea: evolutionary implications JO - Proc Natl Acad Sci U S A VL - 89 UR - https://doi.org/10.1073/pnas.89.16.7408 DO - 10.1073/pnas.89.16.7408 ID - Yokogawa1992 ER - TY - JOUR AU - Sharp, P. M. AU - Li, W. H. PY - 1987 DA - 1987// TI - The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications JO - Nucleic Acids Res VL - 15 UR - https://doi.org/10.1093/nar/15.3.1281 DO - 10.1093/nar/15.3.1281 ID - Sharp1987 ER - TY - JOUR AU - Lunter, G. AU - Ponting, C. P. AU - Hein, J. PY - 2006 DA - 2006// TI - Genome-wide identification of human functional DNA using a neutral indel model JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020005 DO - 10.1371/journal.pcbi.0020005 ID - Lunter2006 ER - TY - JOUR AU - Singh, N. D. AU - Arndt, P. F. AU - Petrov, D. A. PY - 2005 DA - 2005// TI - Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster JO - Genetics VL - 169 UR - https://doi.org/10.1534/genetics.104.032250 DO - 10.1534/genetics.104.032250 ID - Singh2005 ER - TY - JOUR AU - Chuang, J. AU - Li, H. PY - 2007 DA - 2007// TI - Similarity of Synonymous Substitution Rates Across Mammalian Genomes JO - Journal of Molecular Evolution VL - 65 UR - https://doi.org/10.1007/s00239-007-9008-x DO - 10.1007/s00239-007-9008-x ID - Chuang2007 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. AU - Davis, A. P. AU - Dolinski, K. AU - Dwight, S. S. AU - Eppig, J. T. AU - Harris, M. A. AU - Hill, D. P. AU - Issel-Tarver, L. AU - Kasarskis, A. AU - Lewis, S. AU - Matese, J. C. AU - Richardson, J. E. AU - Ringwald, M. AU - Rubin, G. M. AU - Sherlock, G. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology. The Gene Ontology Consortium JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Bejerano, G. AU - Pheasant, M. AU - Makunin, I. AU - Stephen, S. AU - Kent, W. J. AU - Mattick, J. S. AU - Haussler, D. PY - 2004 DA - 2004// TI - Ultraconserved Elements in the Human Genome JO - Science VL - 304 UR - https://doi.org/10.1126/science.1098119 DO - 10.1126/science.1098119 ID - Bejerano2004 ER - TY - JOUR AU - Jones, T. AU - Federspiel, N. A. AU - Chibana, H. AU - Dungan, J. AU - Kalman, S. AU - Magee, B. B. AU - Newport, G. AU - Thorstenson, Y. R. AU - Agabian, N. AU - Magee, P. T. AU - Davis, R. W. AU - Scherer, S. PY - 2004 DA - 2004// TI - The diploid genome sequence of Candida albicans JO - Proceedings of the National Academy of Sciences VL - 101 UR - https://doi.org/10.1073/pnas.0401648101 DO - 10.1073/pnas.0401648101 ID - Jones2004 ER - TY - JOUR AU - Lott, T. J. AU - Fundyga, R. E. AU - Kuykendall, R. J. AU - Arnold, J. PY - 2005 DA - 2005// TI - The human commensal yeast, Candida albicans, has an ancient origin JO - Fungal Genet Biol VL - 42 UR - https://doi.org/10.1016/j.fgb.2005.01.012 DO - 10.1016/j.fgb.2005.01.012 ID - Lott2005 ER - TY - JOUR AU - Selker, E. U. PY - 1990 DA - 1990// TI - Premeiotic instability of repeated sequences in Neurospora crassa JO - Annu Rev Genet VL - 24 UR - https://doi.org/10.1146/annurev.ge.24.120190.003051 DO - 10.1146/annurev.ge.24.120190.003051 ID - Selker1990 ER - TY - JOUR AU - Vyas, M. AU - Kasbekar, D. P. PY - 2005 DA - 2005// TI - Collateral damage: spread of repeat-induced point mutation from a duplicated DNA sequence into an adjoining single-copy gene in Neurospora crassa JO - J Biosci VL - 30 UR - https://doi.org/10.1007/BF02705146 DO - 10.1007/BF02705146 ID - Vyas2005 ER - TY - JOUR AU - Cox, E. C. PY - 1972 DA - 1972// TI - On the organization of higher chromosomes JO - Nat New Biol VL - 239 UR - https://doi.org/10.1038/newbio239133a0 DO - 10.1038/newbio239133a0 ID - Cox1972 ER - TY - JOUR AU - Schattner, P. AU - Diekhans, M. PY - 2006 DA - 2006// TI - Regions of extreme synonymous codon selection in mammalian genes JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl095 DO - 10.1093/nar/gkl095 ID - Schattner2006 ER - TY - JOUR AU - Tuch, B. B. AU - Galgoczy, D. J. AU - Hernday, A. D. AU - Li, H. AU - Johnson, A. D. PY - 2008 DA - 2008// TI - The Evolution of Combinatorial Gene Regulation in Fungi JO - PLoS Biology VL - 6 UR - https://doi.org/10.1371/journal.pbio.0060038 DO - 10.1371/journal.pbio.0060038 ID - Tuch2008 ER - TY - JOUR AU - Ikemura, T. PY - 1985 DA - 1985// TI - Codon usage and tRNA content in unicellular and multicellular organisms JO - Mol Biol Evol VL - 2 ID - Ikemura1985 ER -