Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE: Recent segmental duplications in the human genome. Science. 2002, 297 (5583): 1003-1007. 10.1126/science.1072047.
Article
PubMed
CAS
Google Scholar
Cheung J, Estivill X, Khaja R, MacDonald JR, Lau K, Tsui LC, Scherer SW: Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence. Genome Biol. 2003, 4 (4): R25-10.1186/gb-2003-4-4-r25.
Article
PubMed
PubMed Central
Google Scholar
Hillier LDW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, VanBrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK: The DNA sequence of human chromosome 7. Nature. 2003, 424 (6945): 157-164. 10.1038/nature01782.
Article
PubMed
CAS
Google Scholar
Eichler EE: Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends Genet. 2001, 17 (11): 661-669. 10.1016/S0168-9525(01)02492-1.
Article
PubMed
CAS
Google Scholar
Ohno S: Evolution by Gene Duplication. 1970, New York , Springer
Chapter
Google Scholar
Walsh B: Population-genetic models of the fates of duplicate genes. Genetica. 2003, 118 (2-3): 279-294. 10.1023/A:1024194802441.
Article
PubMed
CAS
Google Scholar
Lynch M, Conery JS: The Evolutionary Fate and Consequences of Duplicate Genes. Science. 2000, 290 (5494): 1151-1155. 10.1126/science.290.5494.1151.
Article
PubMed
CAS
Google Scholar
Lynch M, Conery JS: The Evolutionary Demography of Duplicate Genes. J Struct Funct Genomics. 2003, 3 (1-4): 35-44. 10.1023/A:1022696612931.
Article
PubMed
CAS
Google Scholar
Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH: Extent of Gene Duplication in the Genomes of Drosophila, Nematode, and Yeast. Mol Biol Evol. 2002, 19 (3): 256-262.
Article
PubMed
CAS
Google Scholar
Li WH: Molecular Evolution. 1999, Sunderland, MA , Sinauer Assocs.
Google Scholar
Zhang J: Evolution by gene duplication: an update. Trends Eco Evol. 2003, 18 (6): 292-298. 10.1016/S0169-5347(03)00033-8.
Article
Google Scholar
Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y: Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates. PNAS. 2004, 101 (6): 1638-1643. 10.1073/pnas.0307968100.
Article
PubMed
CAS
PubMed Central
Google Scholar
Nadeau JH, Sankoff D: Comparable Rates of Gene Loss and Functional Divergence After Genome Duplications Early in Vertebrate Evolution. Genetics. 1997, 147 (3): 1259-1266.
PubMed
CAS
PubMed Central
Google Scholar
Ferris SD, Whitt GS: Evolution of the differential regulation of duplicate genes after polyploidization. J Mol Evol. 1979, 12 (4): 267-317. 10.1007/BF01732026.
Article
PubMed
CAS
Google Scholar
Force A, Lynch MF, Pickett B, Amores A, Yan Y, Postlethwait J: Preservation of Duplicate Genes by Complementary, Degenerative Mutations. Genetics. 1999, 151 (4): 1531-1545.
PubMed
CAS
PubMed Central
Google Scholar
Lynch M, Force A: The Probability of Duplicate Gene Preservation by Subfunctionalization. Genetics. 2000, 154 (1): 459-473.
PubMed
CAS
PubMed Central
Google Scholar
Ohta T: Simulating Evolution by Gene Duplication. Genetics. 1987, 115 (1): 207-213.
PubMed
CAS
PubMed Central
Google Scholar
Torrents D, Suyama M, Zdobnov E, Bork P: A Genome-Wide Survey of Human Pseudogenes. Genome Res. 2003, 13 (12): 2559-2567. 10.1101/gr.1455503.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhang Z, Harrison PM, Liu Y, Gerstein M: Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome. Genome Res. 2003, 13 (12): 2541-2558. 10.1101/gr.1429003.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lynch M: Genomics. Gene duplication and evolution. Science. 2002, 297 (5583): 945-947. 10.1126/science.1075472.
Article
PubMed
CAS
Google Scholar
Kellis M, Birren BW, Lander ES: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004, 428 (6983): 617-624. 10.1038/nature02424.
Article
PubMed
CAS
Google Scholar
van Geel M, Eichler EE, Beck AF, Shan Z, Haaf T, van der Maarel SM, Frants RR, de Jong PJ: A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes. Am J Hum Genet. 2002, 70 (1): 269-278. 10.1086/338307.
Article
PubMed
CAS
PubMed Central
Google Scholar
Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HHQ, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GAP, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJT, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Dohner H, Dohner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC: Human Chromosome 7: DNA Sequence and Biology. Science. 2003, 300 (5620): 767-772. 10.1126/science.1083423.
Article
PubMed
CAS
PubMed Central
Google Scholar
Altshul SF, Gish WR, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410. 10.1006/jmbi.1990.9999.
Article
Google Scholar
Tatusova TA, Madden TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett. 1999, 174 (2): 247-50. 10.1111/j.1574-6968.1999.tb13575.x.
Article
PubMed
CAS
Google Scholar
Dubchak I, Brudno M, Loots GG, Pachter L, Mayor C, Rubin EM, Frazer KA: Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons. Genome Res. 2000, 10 (9): 1304-1306. 10.1101/gr.142200.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bray N, Dubchak I, Pachter L: AVID: A Global Alignment Program. Genome Res. 2003, 13 (1): 97-102. 10.1101/gr.789803.
Article
PubMed
CAS
PubMed Central
Google Scholar
Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I: VISTA : visualizing global DNA sequence alignments of arbitrary length. Bioinformatics. 2000, 16 (11): 1046-1047. 10.1093/bioinformatics/16.11.1046.
Article
PubMed
CAS
Google Scholar
Kent WJ: BLAT---The BLAST-Like Alignment Tool. Genome Res. 2002, 12 (4): 656-664. 10.1101/gr.229202. Article published online before March 2002.
Article
PubMed
CAS
PubMed Central
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22 (22): 4673-4680.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kumar S, Tamura K, Jakobsen IB, Nei M: MEGA2: molecular evolutionary genetics analysis software. Bioinformatics. 2001, 17 (12): 1244-1245. 10.1093/bioinformatics/17.12.1244.
Article
PubMed
CAS
Google Scholar
Kumar S, Hedges SB: A molecular timescale for vertebrate evolution. Nature. 1998, 392 (6679): 917-920. 10.1038/31927.
Article
PubMed
CAS
Google Scholar
Honigberg L, Kenyon C: Establishment of left/right asymmetry in neuroblast migration by UNC-40/DCC, UNC-73/Trio and DPY-19 proteins in C. elegans. Development. 2000, 127 (21): 4655-4668.
PubMed
CAS
Google Scholar
Schultz J, Milpetz F, Bork P, Ponting CP: SMART, a simple modular architecture research tool: Identification of signaling domains. PNAS. 1998, 95 (11): 5857-5864. 10.1073/pnas.95.11.5857.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, Studholme DJ, Yeats C, Eddy SR: The Pfam protein families database. Nucl Acids Res. 2004, 32 (90001): D138-141. 10.1093/nar/gkh121.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bailey TL, Elkan C: Fitting a mixture model by expectation maximization to discover motifs in biopolymers: Menlo Park, California.1994, AAAI Press, 28-36.
Google Scholar
Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ: Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature. 2001, 409 (6822): 953-958. 10.1038/35057192.
Article
PubMed
CAS
Google Scholar
Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE: Shuffling of Genes Within Low-Copy Repeats on 22q11 (LCR22) by Alu-Mediated Recombination Events During Evolution. Genome Res. 2003, 13 (12): 2519-2532. 10.1101/gr.1549503.
Article
PubMed
CAS
PubMed Central
Google Scholar
Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR: Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res. 2004, 14 (11): 2209-2220. 10.1101/gr.2746604.
Article
PubMed
CAS
PubMed Central
Google Scholar
Inoue K, Lupski JR: Molecular Mechanisms for Genomic Disorders. Annu Rev Genomics Hum Genet. 2002, 3 (): 199-242. 10.1146/annurev.genom.3.032802.120023.
Article
PubMed
CAS
Google Scholar
Taylor JS, Van de Peer Y, Meyer A: Genome duplication, divergent resolution and speciation. Trends in Genetics. 2001, 17 (6): 299-301. 10.1016/S0168-9525(01)02318-6.
Article
PubMed
CAS
Google Scholar
Nachman MW, Crowell SL: Estimate of the Mutation Rate per Nucleotide in Humans. Genetics. 2000, 156 (1): 297-304.
PubMed
CAS
PubMed Central
Google Scholar
Zhao Z, Jin L, Fu YX, Ramsay M, Jenkins T, Leskinen E, Pamilo P, Trexler M, Patthy L, Jorde LB, Ramos-Onsins S, Yu N, Li WH: Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. PNAS. 2000, 97 (21): 11354-11358. 10.1073/pnas.200348197.
Article
PubMed
CAS
PubMed Central
Google Scholar
NCBI ORF Finder. [http://www.ncbi.nlm.nih.gov/gorf/gorf.html]
Swofford DL: PAUP*:Pjylogenetic Analysis Using Parsimory (* and other methods), Version 4.0b10. Sunderland: Sinauer Associates; 2003
UCSC Genome Bioinformatics. [http://genome.ucsc.edu]
Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992, 8 (3): 275-282.
PubMed
CAS
Google Scholar
Nei M, Gojobori T: Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotides substitutions. Mol Biol Evol. 1986, 3 (5): 418-426.
PubMed
CAS
Google Scholar