Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D: Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci. 2002, 99: 16144-16149. 10.1073/pnas.242624799.
Article
CAS
PubMed Central
PubMed
Google Scholar
Herring C, Raghunathan A, Honisch C, Patel T, Applebee M, Joyce A, Albert T, Blattner F, Boom Van Den D, Cantor C, Palsson B: Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet. 2006, 38: 1406-1412. 10.1038/ng1906.
Article
CAS
PubMed
Google Scholar
Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, Kruglyak L: Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science. 2006, 311: 1932-1936. 10.1126/science.1123726.
Article
CAS
PubMed
Google Scholar
Gresham D, Desai M, Tucker C, Jenq H, Pai D, Ward A, Desevo C, Botstein D, Dunham M: The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet. 2008, 4: e1000303-10.1371/journal.pgen.1000303.
Article
PubMed Central
PubMed
Google Scholar
Segre AV, Murray AW, Leu JY: High-resolution mutation mapping reveals parallel experimental evolution in yeast. PLoS Biol. 2006, 4: e256-10.1371/journal.pbio.0040256.
Article
PubMed Central
PubMed
Google Scholar
Blount ZD, Borland CZ, Lenski R: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci. 2008, 105: 7899-7906. 10.1073/pnas.0803151105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kao K, Sherlock G: Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat Genet. 2008, 40: 1499-1504. 10.1038/ng.280.
Article
CAS
PubMed Central
PubMed
Google Scholar
Srivatsan A, Han Y, Peng J, Tehranchi A, Gibbs R, Wang JD, Chen R: High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 2008, 4: e1000139-10.1371/journal.pgen.1000139.
Article
PubMed Central
PubMed
Google Scholar
Lind PA, Andersson DI: Whole-genome mutational biases in bacteria. Proc Natl Acad Sci. 2008, 105: 17878-17883. 10.1073/pnas.0804445105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA, Fraser-Liggett CM, Liggett SB: Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science. 2009, 324: 55-59. 10.1126/science.1165557.
Article
CAS
PubMed Central
PubMed
Google Scholar
Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V: Population genomics of domestic and wild yeasts. Nature. 2009, 458: 337-341. 10.1038/nature07743.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, Thomas WK: A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci. 2008, 105: 9272-9277. 10.1073/pnas.0803466105.
Article
CAS
PubMed Central
PubMed
Google Scholar
Smith DR, Quinlan AR, Peckham HE, Makowsky K: Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res. 2008, 18: 1638-1642. 10.1101/gr.077776.108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Barrick J, Yu D, Yoon S, Jeong H, Oh T, Schneider D, Lenski R, Kim J: Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 2009, 461: 1243-1247. 10.1038/nature08480.
Article
CAS
PubMed
Google Scholar
Wheeler DA, Srinivasan M, Egholm M, Shen , Chen , McGuire , He W, Chen YJ, Makhijani , Roth : The complete genome of an individual by massively parallel DNA sequencing. Nature. 2008, 452: 872-876. 10.1038/nature06884.
Article
CAS
PubMed
Google Scholar
Bentley DR, Balasubramanian S, Swerdlow H, Smith G, Milton J, Brown C, Hall K, Evers D, Barnes C, Bignell H: Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008, 456: 53-59. 10.1038/nature07517.
Article
CAS
PubMed Central
PubMed
Google Scholar
Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Guo Y: The diploid genome sequence of an Asian individual. Nature. 2008, 456: 60-65. 10.1038/nature07484.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ahn SM, Kim T, Lee S, Kim D, Ghang H, Kim D, Kim B, Kim S, Kim W, Kim C: The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Res. 2009, 19: 1622-1629. 10.1101/gr.092197.109.
Article
CAS
PubMed Central
PubMed
Google Scholar
Tarpey PS, Smith R, Pleasance E, Whibley A, Edkins S, Hardy C, O'Meara S, Latimer C, Dicks E, Menzies A: A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nat Genet. 2009, 41: 535-543. 10.1038/ng.367.
Article
CAS
PubMed Central
PubMed
Google Scholar
Turner EH, Lee C, Ng SB, Nickerson DA, Shendure J: Massively parallel exon capture and library-free resequencing across 16 genomes. Nat Meth. 2009, 6: 315-316. 10.1038/nmeth.f.248.
Article
CAS
Google Scholar
Ng SB, Turner EH, Robertson P, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler E: Targeted capture and massively parallel sequencing of 12 human exomes. Nature. 2009, 461: 272-276. 10.1038/nature08250.
Article
CAS
PubMed Central
PubMed
Google Scholar
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA: Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2009, 42: 30-35. 10.1038/ng.499.
Article
PubMed Central
PubMed
Google Scholar
Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18: 1851-1858. 10.1101/gr.078212.108.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bodem J, Dobreva G, Hoffmann-Rohrer U, Iben S, Zentgraf H, Delius H, Vingron M, Grummt I: TIF-IA, the factor mediating growth-dependent control of ribosomal RNA synthesis, is the mammalian homolog of yeast Rrn3p. EMBO Rep. 2000, 1: 171-175. 10.1093/embo-reports/kvd032.
Article
CAS
PubMed Central
PubMed
Google Scholar
Moorefield B, Greene EA, Reeder RH: RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human. Proc Natl Acad Sci. 2000, 97: 4724-4729. 10.1073/pnas.080063997.
Article
CAS
PubMed Central
PubMed
Google Scholar
Mayer C, Zhao J, Yuan X, Grummt I: mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes & Dev. 2004, 18: 423-434.
Article
CAS
Google Scholar
Venkatraman ES, Olshen AB: A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics. 2007, 23: 657-663. 10.1093/bioinformatics/btl646.
Article
CAS
PubMed
Google Scholar
Zerbino DR, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18: 821-829. 10.1101/gr.074492.107.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM: Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 2005, 309: 1728-1732. 10.1126/science.1117389.
Article
CAS
PubMed
Google Scholar
Pepin KM, Wichman HA: Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage phiX174. BMC Evol Biol. 2008, 8: 85-10.1186/1471-2148-8-85.
Article
PubMed Central
PubMed
Google Scholar
Beaumont H, Gallie J, Kost C, Ferguson G: Experimental evolution of bet hedging. Nature. 2009, 462: 90-93. 10.1038/nature08504.
Article
CAS
PubMed
Google Scholar
Haber JE, Debatisse M: Gene amplification: yeast takes a turn. Cell. 2006, 125: 1237-1240. 10.1016/j.cell.2006.06.012.
Article
CAS
PubMed
Google Scholar
Narayanan V, Mieczkowski PA, Kim HM, Petes TD, Lobachev KS: The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. Cell. 2006, 125: 1283-1296. 10.1016/j.cell.2006.04.042.
Article
CAS
PubMed
Google Scholar
Payen C, Koszul R, Dujon B, Fischer G, Haber JE: Segmental Duplications Arise from Pol32-Dependent Repair of Broken Forks through Two Alternative Replication-Based Mechanisms. PLoS Genet. 2008, 4: e1000175-10.1371/journal.pgen.1000175.
Article
PubMed Central
PubMed
Google Scholar
Hegreness M, Kishony R: Analysis of genetic systems using experimental evolution and whole-genome sequencing. Genome Biol. 2007, 8: 201-10.1186/gb-2007-8-9-r201.
Article
PubMed Central
PubMed
Google Scholar
Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ: A large genome center's improvements to the Illumina sequencing system. Nat Meth. 2008, 5: 1005-1010. 10.1038/nmeth.1270.
Article
CAS
Google Scholar