| [1] Zhang LG, Kasif S, Cantor CR, Broude NE. GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci USA, 2004, 101(48): 16855-16860.[2] Glazko GV, Koonin EV, Rogozin IB, Shabalina SA. A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet, 2003, 19(3): 119-124.[3] Borsch T, Quandt D, Koch M. Molecular evolution and phylogenetic utility of non-coding DNA: applications from species to deep level questions. Plant Syst Evol, 2009, 282(3-4): 107- 108.[4] Ishibashi M, Noda AO, Sakate R, Imanishi T. Evolutionary growth process of highly conserved sequences in vertebrate genomes. Gene, 2012, 504(1): 1-5.[5] Vavouri T, Lehner B. Conserved noncoding elements and the evolution of animal body plans. Bioessays, 2009, 31(7): 727-735.[6] Beaster-Jones L. Cis-regulation and conserved non-coding elements in amphioxus. Brief Funct Genomics, 2012, 11(2): 118-130.[7] King DC, Taylor J, Elnitski L, Chiaromonte F, Miller W, Hardison RC. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res, 2005, 15(8): 1051-1060.[8] Su J, Teichmann SA, Down TA. Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol, 2010, 6(12): e1001020.[9] Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W, Edwards YJK, Cooke JE, Elgar G. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol, 2005, 3(1): e7.[10] Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VVB, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED. Comparative analyses of multi-species sequences from targeted genomic regions. Nature, 2003, 424(6950): 788-793.[11] Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou MM, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res, 2005, 15(8): 1034-1050.[12] Drake JA, Bird C, Nemesh J, Thomas DJ, Newton-Cheh C, Reymond A, Excoffier L, Attar H, Antonarakis SE, Dermitzakis ET, Hirschhorn JN. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet, 2005, 38(2): 223-227.[13] Frazer KA, Sheehan JB, Stokowski RP, Chen XY, Hosseini R, Cheng JF, Fodor SPA, Cox DR, Patil N. Evolutionarily conserved sequences on human chromosome 21. Genome Res, 2001, 11(10): 1651- 1659.[14] Margulies EH, Blanchette M, NISC Comparative Sequencing Program, Haussler D, Green ED. Identification and characterization of multi-species conserved sequences. Genome Res, 2003, 13(12): 2507-2518.[15] Haeussler M, Joly JS. When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol, 2011, 350(2): 239-254.[16] Moghadam HK, Ferguson MM, Danzmann RG. Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow tro |
