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#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
1	14	119	238 2005 NATURE 438 (7069): 803-819 Lindblad-Toh K; Wade CM; Mikkelsen TS; Karlsson EK; Jaffe DB; et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog	4	29
2	11	92	170 2005 GENOME RESEARCH 15 (8): 1034-1050 Siepel A; Bejerano G; Pedersen JS; Hinrichs AS; Hou MM; et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes	3	33
3	8	74	303 2006 CURRENT OPINION IN NEPHROLOGY AND HYPERTENSION 15 (2): 145-151 McBride MW; Graham D; Delles C; Dominiczak AF Functional genomics in hypertension	0	0
4	6	102	96 2005 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 6: 143-164 Stone EA; Cooper GM; Sidow A Trade-offs in detecting evolutionarily constrained sequence by comparative genomics	0	3
5	6	63	169 2005 GENOME RESEARCH 15 (7): 901-913 Cooper GM; Stone EA; Asimenos G; Green ED; Batzoglou S; et al. Distribution and intensity of constraint in mammalian genomic sequence	2	8
6	6	135	179 2005 GENOME RESEARCH 15 (12): 1717-1728 Lazar J; Moreno C; Jacob HJ; Kwitek AE Impact of genomics on research in the rat	0	0
7	6	172	235 2005 NATURE 437 (7055): 69-87 Mikkelsen TS; Hillier LW; Eichler EE; Zody MC; Jaffe DB; et al. Initial sequence of the chimpanzee genome and comparison with the human genome	8	88
8	6	34	236 2005 NATURE 437 (7058): 551-555 Nusbaum C; Zody MC; Borowsky ML; Kamal M; Kodira CD; et al. DNA sequence and analysis of human chromosome 18	0	3
9	6	36	293 2006 BIOESSAYS 28 (6): 569-573 Lee S; Kasif S The complete genome sequence of a dog: a perspective	0	0
10	6	89	320 2006 HUMAN MOLECULAR GENETICS 15: R31-R43 Temple G; Lamesch P; Milstein S; Hill DE; Wagner L; et al. From genome to proteome: developing expression clone resources for the human genome	0	0
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
11	6	37	321 2006 HUMAN MOLECULAR GENETICS 15: R51-R56 Dewey CN; Pachter L Evolution at the nucleotide level: the problem of multiple whole-genome alignment	0	0
12	6	25	351 2006 TRENDS IN GENETICS 22 (4): 187-193 Margulies EH; Chen CW; Green ED Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons	0	0
13	5	145	94 2005 ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS 77 (4): 627-650 Salzano FM Evolutionary change - patterns and processes	0	0
14	5	117	97 2005 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 6: 381-406 Giallourakis C; Henson C; Reich M; Xie XH; Mootha VK Disease gene discovery through integrative genomics	0	1
15	5	49	123 2005 BMC EVOLUTIONARY BIOLOGY 5: Art. No. 40 Laukaitis CM; Dlouhy SR; Emes RD; Ponting CP; Karn RC Diverse spatial, temporal, and sexual expression of recently duplicated androgen-binding protein genes in Mus musculus	0	0
16	5	61	137 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 628-633 Adams MD Conserved sequences and the evolution of gene regulatory signals	0	0
17	5	59	269 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (16): 5767-5772 Grus WE; Shi P; Zhang YP; Zhang JZ Dramatic variation of the vomeronasal pheromone receptor gene repertoire among five orders of placental and marsupial mammals	4	16
18	5	49	295 2006 BMC BIOINFORMATICS 7: Art. No. 103 Shih ACC; Lee DT; Lin L; Peng CL; Chen SH; et al. SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools	0	0
19	5	21	346 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (8): 2740-2745 Kamal M; Xie XH; Lander ES A large family of ancient repeat elements in the human genome is under strong selection	0	2
20	4	39	160 2005 GENOME BIOLOGY 6 (7): Art. No. 115 Aloni R; Lancet D Conservation anchors in the vertebrate genome	0	0
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
21	4	103	171 2005 GENOME RESEARCH 15 (8): 1051-1060 King DC; Taylor J; Elnitski L; Chiaromonte F; Miller W; et al. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences	0	6
22	4	70	180 2005 GENOME RESEARCH 15 (12): 1777-1786 Brent MR Genome annotation past, present, and future: How to define an ORF at each locus	1	1
23	4	44	186 2005 GENOMICS 86 (3): 295-305 Portnoy ME; McDermott KJ; Antonellis A; Margulies EH; Prasad AB; et al. Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer	0	0
24	4	59	187 2005 GENOMICS 86 (3): 306-315 Yang H; Shi P; Zhang YP; Zhang JZ Composition and evolution of the V2r vorneronasal receptor gene repertoire in mice and rats	0	10
25	4	38	196 2005 HYPERTENSION 46 (6): 1300-1308 Charron S; Duong C; Menard A; Roy J; Eliopoulos V; et al. Epistasis, not numbers, regulates functions of clustered Dahl rat quantitative trait loci applicable to human hypertension	0	0
26	4	111	243 2005 NATURE REVIEWS GENETICS 6 (9): 699-708 Gregory TR Synergy between sequence and size in large-scale genomics	0	1
27	4	18	264 2005 PLOS GENETICS 1 (6): 672-675 Pardi F; Goldman N Species choice for comparative genomics: Being greedy works	0	0
28	4	24	268 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (13): 4795-4800 Margulies EH; Vinson JP; Miller W; Jaffe DB; Lindblad-Toh K; et al. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing	5	12
29	4	68	282 2005 TRENDS IN ECOLOGY & EVOLUTION 20 (4): 180-186 Ellegren H The avian genome uncovered	0	3
30	4	67	333 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (3): 675-682 Chen FC; Wang SS; Chen CJ; Li WH; Chuang TJ Alternatively and constitutively spliced exons are subject to different evolutionary forces	0	2
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
31	4	92	352 2006 TRENDS IN GENETICS 22 (4): 232-240 Smits BMG; Cuppen E Rat genetics: the next episode	0	0
32	3	165	71 2004 NATURE 432 (7018): 695-716 Hillier LW; Miller W; Birney E; Warren W; Hardison RC; et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution	40	201
33	3	48	73 2004 NATURE 432 (7020): 988-994 Martin J; Han C; Gordon LA; Terry A; Prabhakar S; et al. The sequence and analysis of duplication-rich human chromosome 16	2	11
34	3	28	86 2004 SCIENCE 306 (5296): 636-640 Feingold EA; Good PJ; Guyer MS; Kamholz S; Liefer L; et al. The ENCODE (ENCyclopedia of DNA elements) Project	13	94
35	3	33	99 2005 AUSTRALIAN JOURNAL OF EXPERIMENTAL AGRICULTURE 45 (7-8): 1011-1016 Dalrymple BP Harnessing the bovine genome sequence for the Australian cattle and sheep industries	0	0
36	3	16	107 2005 BIOFUTUR (254): 24-28 Esnault Y; Jaillon O; Aury JM; Weissenbach J; Crollius HR Tetraodon, fish in the genomic model	0	1
37	3	33	117 2005 BMC BIOINFORMATICS 6: Art. No. 131 Eyras E; Reymond A; Castelo R; Bye JM; Camara F; et al. Gene finding in the chicken genome	0	2
38	3	22	125 2005 BMC GENOMICS 6: Art. No. 70 Wernersson R; Schierup MH; Jorgensen FG; Gorodkin J; Panitz F; et al. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing	0	10
39	3	57	126 2005 BMC GENOMICS 6: Art. No. 139 Otto H; Reche PA; Bazan F; Dittmar K; Haag F; et al. In silico characterization of the family of PARP-like poly(ADP-ribosyl) transferases (pARTs)	0	2
40	3	64	136 2005 CURRENT GENOMICS 6 (8): 589-595 Fedorova L; Fedorov A Puzzles of the human genome: Why do we need our introns?	0	0
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
41	3	65	211 2005 JOURNAL OF LIPID RESEARCH 46 (10): 2151-2167 Sabol SL; Brewer HB; Santamarina-Fojo S The human ABCG1 gene: identification of LXR response elements that modulate expression in macrophages and liver	0	4
42	3	121	228 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284 Blair JE; Hedges SB Molecular phylogeny and divergence times of deuterostome animals	0	7
43	3	37	232 2005 NATURE 434 (7031): 338-345 Xie XH; Lu J; Kulbokas EJ; Golub TR; Mootha V; et al. Systematic discovery of regulatory motifs in human promoters and 3 ' UTRs by comparison of several mammals	7	113
44	3	50	233 2005 NATURE 434 (7034): 724-731 Hillier LW; Graves TA; Fulton RS; Fulton LA; Pepin KH; et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4	2	10
45	3	34	242 2005 NATURE REVIEWS GENETICS 6 (8): 643-649 Hitte C; Madeoy J; Kirkness EF; Priat C; Lorentzen TD; et al. Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping	1	3
46	3	38	261 2005 PLANT PHYSIOLOGY 138 (3): 1301-1309 Schoof H; Spannagl M; Yang L; Ernst R; Gundlach H; et al. Munich Information Center for Protein Sequences plant genome resources. A framework for integrative and comparative analyses	0	0
47	3	47	265 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (7): 2454-2459 Washietl S; Hofacker IL; Stadler PF Fast and reliable prediction of noncoding RNAs	0	21
48	3	37	266 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (9): 3354-3359 Margulies EH; Maduro VVB; Thomas PJ; Tomkins JP; Amemiya CT; et al. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes	2	12
49	3	18	270 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (19): 6639-6640 Rodriguez I Remarkable diversity of mammalian pheromone receptor repertoires	0	0
50	3	133	284 2005 TRENDS IN GENETICS 21 (12): 673-682 Coghlan A; Eichler EE; Oliver SG; Paterson AH; Stein L Chromosome evolution in eukaryotes: a multi-kingdom perspective	0	1
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
51	3	49	296 2006 BMC BIOINFORMATICS 7: Art. No. 136 Chen FC; Chen CJ; Ho JY; Chuang TJ Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat	0	0
52	3	91	298 2006 BMC GENOMICS 7: Art. No. 20 Steinke D; Salzburger W; Braasch I; Meyer A Many genes in fish have species-specific asymmetric rates of molecular evolution	0	0
53	3	54	299 2006 BULLETIN OF MATHEMATICAL BIOLOGY 68 (1): 179-196 Wendl MC Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing	0	0
54	3	59	301 2006 CHROMOSOME RESEARCH 14 (2): 187-202 Kuraku S; Ishijima J; Nishida-Umehara C; Agata K; Kuratani S; et al. cDNA-based gene mapping and GC(3) profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids	0	0
55	3	42	309 2006 GENE 365: 130-136 Noda AO; Ikeo K; Gojobori T Comparative genome analyses of nervous system-specific genes	0	0
56	3	64	313 2006 GENOME BIOLOGY 7 (5): Art. No. R43 Blomme T; Vandepoele K; De Bodt S; Simillion C; Maere S; et al. The gain and loss of genes during 600 million years of vertebrate evolution	0	0
57	3	30	314 2006 GENOME RESEARCH 16 (2): 173-181 Wilson GM; Flibotte S; Missirlis PI; Marra MA; Jones S; et al. Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla	0	1
58	3	64	315 2006 GENOME RESEARCH 16 (7): 922-933 Sun M; Hurst LD; Carmichael GG; Chen J Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcription and organismic complexity	0	0
59	3	38	319 2006 GENOMICS 88 (1): 34-43 Wang XX; Zhang JZ Remarkable expansions of an X-linked reproductive homeobox gene cluster in rodent evolution	0	0
60	3	99	324 2006 JOURNAL OF BIOMEDICAL INFORMATICS 39 (1): 51-61 Kosiol C; Bofkin L; Whelan S Phylogenetics by likelihood: Evolutionary modeling as a tool for understanding the genome	0	1
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
61	3	48	330 2006 MAMMALIAN GENOME 17 (6): 480-489 Petretto E; Mangion J; Pravanec M; Hubner N; Aitman TJ Integrated gene expression profiling and linkage analysis in the rat	0	0
62	3	65	334 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (5): 927-940 Ezawa K; OOta S; Saitou N Genome-wide search of gene conversions in duplicated genes of mouse and rat	0	0
63	3	28	336 2006 NATURE 440 (7083): 497-500 Taylor TD; Noguchi H; Totoki Y; Toyoda A; Kuroki Y; et al. Human chromosome 11 DNA sequence and analysis including novel gene identification	0	0
64	3	43	338 2006 NATURE 441 (7097): 1103-1108 Patterson N; Richter DJ; Gnerre S; Lander ES; Reich D Genetic evidence for complex speciation of humans and chimpanzees	0	0
65	3	15	339 2006 NATURE GENETICS 38 (2): 140-141 Hubner N Expressing physiology	0	0
66	2	31	9 2004 BIOESSAYS 26 (10): 1039-1042 Hancock JM A bigger mouse? The rat genome unveiled	1	1
67	2	50	39 2004 GENOME RESEARCH 14 (11): 2235-2244 Blakesley RW; Hansen NF; Mullikin JC; Thomas PJ; McDowell JC; et al. An intermediate grade of finished genomic sequence suitable for comparative analyses	6	10
68	2	77	40 2004 GENOME RESEARCH 14 (12): 2412-2423 Blanchette M; Green ED; Miller W; Haussler D Reconstructing large regions of an ancestral mammalian genome in silico	2	11
69	2	28	70 2004 NATURE 431 (7011): 988-993 Nobrega MA; Zhu YW; Plajzer-Frick I; Afzal V; Rubin EM Megabase deletions of gene deserts result in viable mice	7	25
70	2	19	72 2004 NATURE 432 (7018): 761-764 Wallis JW; Aerts J; Groenen MAM; Crooijmans RPMA; Layman D; et al. A physical map of the chicken genome	1	27
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
71	2	22	91 2005 ALGORITHMS IN BIOINFORMATICS, PROCEEDINGS 3692: 228-238 Berard S; Bergeron A; Chauve C; Paul C Perfect sorting by reversals is not always difficult (extended abstract)	0	0
72	2	36	110 2005 BIOINFORMATICS 21 (6): 703-710 Zheng XH; Lu F; Wang ZY; Hoover J; Mural R Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs	0	3
73	2	49	120 2005 BMC BIOLOGY 3: Art. No. 2 Jorgensen FG; Hobolth A; Hornshoj H; Bendixen C; Fredholm M; et al. Comparative analysis of protein coding sequences from human, mouse and the domesticated pig	0	4
74	2	38	127 2005 BMC GENOMICS 6: Art. No. 170 Smits BMG; Guryev V; Zeegers D; Wedekind D; Hedrich HJ; et al. Efficient single nucleotide polymorphism discovery in laboratory rat strains using wild rat-derived SNP candidates	0	0
75	2	77	128 2005 BRIEFINGS IN BIOINFORMATICS 6 (1): 6-22 Batzoglou S The many faces of sequence alignment	2	5
76	2	24	129 2005 CELL 120 (1): 15-20 Lewis BP; Burge CB; Bartel DP Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets	5	156
77	2	79	130 2005 CHEMICAL RESEARCH IN TOXICOLOGY 18 (3): 403-414 Hayes KR; Bradfield RA Advances in toxicogenomics	0	7
78	2	46	138 2005 CURRENT OPINION IN LIPIDOLOGY 16 (2): 179-191 Herrera VLM; Ruiz-Opazo N Genetic studies in rat models: insights into cardiovascular disease	0	1
79	2	43	144 2005 EUROPEAN JOURNAL OF IMMUNOLOGY 35 (1): 261-272 Nylenna O; Naper C; Vaage JT; Woon PY; Gauguier D; et al. The genes and gene organization of the Ly49 region of the rat natural killer cell gene complex	0	5
80	2	77	151 2005 GENE 359: 1-17 Edelstein LC; Collins T The SCAN domain family of zinc finger transcription	0	0
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
81	2	42	152 2005 GENE 363: 51-60 Makarova JA; Kramerov DA Noncoding RNA of U87 host gene is associated with ribosomes and is relatively resistant to nonsense-mediated decay	0	1
82	2	26	153 2005 GENE 364: 45-52 Fujii Y; Itoh T; Sakate R; Koyanagi KO; Matsuya A; et al. A web tool for comparative genomics: G-compass	0	0
83	2	15	158 2005 GENOME BIOLOGY 6 (2): Art. No. 207 Furlong RF Insights into vertebrate evolution from the chicken genome sequence	0	0
84	2	23	159 2005 GENOME BIOLOGY 6 (4): Art. No. 216 DeCerbo J; Carmichael GG SINEs point to abundant editing in the human genome	0	0
85	2	59	161 2005 GENOME BIOLOGY 6 (8): Art. No. r67 Haddrill PR; Charlesworth B; Halligan DL; Andolfatto P Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content	0	9
86	2	34	166 2005 GENOME RESEARCH 15 (1): 137-145 Ovcharenko I; Loots GG; Nobrega MA; Hardison RC; Miller W; et al. Evolution and functional classification of vertebrate gene deserts	5	23
87	2	49	172 2005 GENOME RESEARCH 15 (8): 1086-1094 Gaffney DJ; Keightley PD The scale of mutational variation in the murid genome	0	2
88	2	36	177 2005 GENOME RESEARCH 15 (9): 1307-1314 Woods IG; Wilson C; Friedlander B; Chang P; Reyes DK; et al. The zebrafish gene map defines ancestral vertebrate chromosomes	0	8
89	2	51	178 2005 GENOME RESEARCH 15 (11): 1519-1534 Smith AV; Thomas DJ; Munro HM; Abecasis GR Sequence features in regions of weak and strong linkage disequilibrium	0	1
90	2	60	181 2005 GENOME RESEARCH 15 (12): 1787-1797 Webber C; Ponting CP Hotspots of mutation and breakage in dog and human chromosomes	0	0
#	LCR	NCR	Node / Date / Journal / Author	LCS	GCS
91	2	80	182 2005 GENOME RESEARCH 15 (12): 1809-1819 Pollinger JP; Bustamante CD; Fledel-Alon A; Schmutz S; Gray MM; et al. Selective sweep mapping of genes with large phenotypic effects	0	0
92	2	59	188 2005 GENOMICS 86 (6): 638-647 Puente XS; Gutierrez-Fernandez A; Ordonez GR; Hillier LDW; Lopez-Otin C Comparative genomic analysis of human and chimpanzee proteases	0	1
93	2	21	189 2005 GENOMICS 86 (6): 759-766 Raymond CK; Subramanian S; Paddock M; Qiu RL; Deodato C; et al. Targeted, haplotype-resolved resequencing of long segments of the human genome	0	1
94	2	41	191 2005 HUMAN MOLECULAR GENETICS 14 (15): 2221-2229 Kryukov GV; Schmidt S; Sunyaev S Small fitness effect of mutations in highly conserved non-coding regions	0	4
95	2	296	200 2005 INTERNATIONAL REVIEW OF CYTOLOGY - A SURVEY OF CELL BIOLOGY, VOL 247 247: 165-+ Kramerov DA; Vassetzky NS Short retroposons in eukaryotic genomes	0	3
96	2	33	215 2005 JOURNAL OF VIROLOGY 79 (18): 12035-12044 Barr SD; Leipzig J; Shinn P; Ecker JR; Bushman FD Integration targeting by avian sarcoma-leukosis virus and human immunodeficiency virus in the chicken genome	0	0
97	2	52	218 2005 MAMMALIAN GENOME 16 (6): 442-459 Chantry-Darmon U; Urien C; Hayes H; Bertaud M; Chadi-Taourit S; et al. Construction of a cytogenetically anchored microsatellite map in rabbit	0	0
98	2	35	219 2005 MAMMALIAN GENOME 16 (12): 934-941 Wen GP; Ramser J; Taudien S; Gausmann U; Blechschmidt K; et al. Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus	0	0
99	2	34	222 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (2): 360-366 Misceo D; Cardone MF; Carbone L; D'Addabbo P; de Jong PJ; et al. Evolutionary history of chromosome 20	0	1
100	2	45	223 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (4): 1044-1052 Good JM; Nachman MW Rates of protein evolution are positively correlated with developmental timing of expression during mouse spermatogenesis	0	6

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