Biology Reference
In-Depth Information
58. Brudno M, Morgenstern B. (2002) Fast and sensitive alignment of large
genomic sequences.
Proc IEEE Comput Soc Bioinform Conf
1
: 138-47.
59. Delcher AL, Kasif S, Fleischmann RD
et al
. (1999) Alignment of whole
genomes.
Nucleic Acids Res
27
(11): 2369-76.
60. Schwartz S, Kent WJ, Smit A
et al
. (2003) Human-mouse alignments with
BLASTZ.
Genome Res
13
(1): 103-7.
61. Sinha AU, Meller J. (2007) Cinteny: flexible analysis and visualization of
synteny and genome rearrangements in multiple organisms.
BMC Bioinformatics
8
: 82.
62. Brudno M, Do CB, Cooper GM
et al
. (2003) LAGAN and Multi-LAGAN:
efficient tools for large-scale multiple alignment of genomic DNA.
Genome Res
13
(4): 721-31.
63. Wang J, Keightley PD, Johnson T. (2006) MCALIGN2: faster, accurate global
pairwise alignment of non-coding DNA sequences based on explicit models of
indel evolution.
BMC Bioinformatics
7
: 292.
64. Scannell DR, Byrne KP, Gordon JL
et al
. (2006) Multiple rounds of speciation
associated with reciprocal gene loss in polyploid yeasts.
Nature
440
(7082):
341-5.
65. Aury JM, Jaillon O, Duret L
et al
. (2006) Global trends of whole-genome dupli-
cations revealed by the ciliate
Paramecium tetraurelia
.
Nature
444
(7116):
171-8.
66. Vastenhouw NL, Plasterk RH. (2004) RNAi protects the
Caenorhabditis
elegans
germline against transposition.
Trends Genet
20
(7): 314-9.
67. Bestor TH. (2003) Cytosine methylation mediates sexual conflict.
Trends Genet
19
(4): 185-90.
68. Lynch M. (2007)
The Origins of Genome Architecture
. Sunderland, MA: Sinauer
Associates.
69. Zdobnov EM, Campillos M, Harrington ED
et al
. (2005) Protein coding
potential of retroviruses and other transposable elements in vertebrate genomes.
Nucleic Acids Res
33
(3): 946-54.
70. Dooner HK, Weil CF. (2007) Give-and-take: interactions between DNA trans-
posons and their host plant genomes.
Curr Opin Genet Dev
17
(6): 486-92.
71. Kazazian Jr HH. (2004) Mobile elements: drivers of genome evolution.
Science
303
(5664): 1626-32.
72. Christley S, Lobo NF, Madey G. (2008) Multiple organism algorithm for find-
ing ultraconserved elements.
BMC Bioinformatics
9
: 15.
73. Lowe TM, Eddy SR. (1997) tRNAscan-SE: a program for improved detection
of transfer RNA genes in genomic sequence.
Nucleic Acids Res
25
(5): 955-64.
74. Eddy SR. (2006) Computational analysis of RNAs.
Cold Spring Harb Symp
Quant Biol
71
: 117-28.
75. Ambros V. (2004) The functions of animal microRNAs.
Nature
431
(7006):
350-5.