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Mon Jul 31 15:56:18 2006

Hillier LW, Miller W, Birney E, et al.
Sequence and comparative analysis of the chicken genome
provide unique perspectives on vertebrate evolution
NATURE 432 (7018): 695-716 DEC 9 2004
and the citing papers
Nodes: 203, Authors: 1483, Journals: 94, Outer References: 8307, Words: 911
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Collection span: 2004 - 2006
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#LCRNCRNode / Date / Journal / AuthorLCSGCS
101652 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
202202
212426 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
5158
3117287 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
490
422691 2005 NATURE GENETICS 37 (5): 495-500
Krek A; Grun D; Poy MN; Wolf R; Rosenberg L; et al.
Combinatorial microRNA target predictions
168
516785 2005 NATURE 434 (7031): 325-337
Ross MT; Grafham DV; Coffey AJ; Scherer S; McLay K; et al.
The DNA sequence of the human X chromosome
360
649258 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
333
7411989 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
329
8137103 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
212
9135105 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (17): 6039-6044
Niimura Y; Nei M
Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods
111
1016444 2005 DEVELOPMENTAL CELL 8 (1): 9-17
Stern CD
The chick: A great model system becomes even greater
310
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1115086 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
310
1213752 2005 GENETICS 170 (1): 313-326
Go Y; Satta Y; Takenaka O; Takahata N
Lineage-specific loss of function of bitter taste receptor genes in humans and nonhuman primates
28
1316357 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
28
14137106 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (24): 8674-8679
Miller MM; Wang C; Parisini E; Coletta RD; Goto RM; et al.
Characterization of two avian MHC-like genes reveals an ancient origin of the CD1 family
18
1514582 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2198-2208
Cusack BP; Wolfe KH
Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
17
16112183 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284
Blair JE; Hedges SB
Molecular phylogeny and divergence times of deuterostome animals
07
1717714 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 191-209
Snel B; Huynen MA; Dutilh BE
Genome trees and the nature of genome evolution
06
1813354 2005 GENOME BIOLOGY 6 (1): Art. No. R6
Caldwell RB; Kierzek AM; Arakawa H; Bezzubov Y; Zaim J; et al.
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis
06
19110359 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
06
20143 2004 NATURE 432 (7019): 799-799
Miller MM
Genome news highlights loss of chicken strains - Future research is already under threat, as budget cuts wipe out irreplaceable lines.
35
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2113041 2005 CYTOGENETIC AND GENOME RESEARCH 111 (2): 118-127
Reed KM; Chaves LD; Hall MK; Knutson TP; Harry DE
A comparative genetic map of the turkey genome
45
221126102 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102: 6550-6557
Edwards SV; Kingan SB; Calkins JD; Balakrishnan CN; Jennings WB; et al.
Speciation in birds: Genes, geography, and sexual selection
05
23131104 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (11): 4057-4062
Nikolaidis N; Makalowska I; Chalkia D; Makalowski W; Klein J; et al.
Origin and evolution of the chicken leukocyte receptor complex
25
24182118 2005 TRENDS IN GENETICS 21 (10): 573-581
Mitreva M; Blaxter ML; Bird DM; McCarter JP
Comparative genomics of nematodes
05
2514920 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
04
2614775 2005 JOURNAL OF IMMUNOLOGY 175 (1): 385-393
Viertlboeck BC; Habermann FA; Schmitt R; Groenen MAM; Du Pasquier L; et al.
The chicken leukocyte receptor complex: A highly diverse multigene family encoding at least six structurally distinct receptor types
24
2716577 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
04
28146120 2005 WORLDS POULTRY SCIENCE JOURNAL 61 (2): 215-226
Hocking PM
Review of QTL mapping results in chickens
14
291328 2005 ANIMAL GENETICS 36 (5): 396-400
Miwa M; Inoue-Murayama M; Kayang BB; Minvielle F; Monvoisin JL; et al.
Mapping of plumage colour and blood protein loci on the microsatellite linkage map of the Japanese quail
13
30110212 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
13
#LCRNCRNode / Date / Journal / AuthorLCSGCS
3114932 2005 CHROMOSOME RESEARCH 13 (6): 601-615
Matsuda Y; Nishida-Umehara C; Tarui H; Kuroiwa A; Yamada K; et al.
Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other
23
3212946 2005 EUROPEAN JOURNAL OF CELL BIOLOGY 84 (6): 623-635
Zimek A; Weber K
Terrestrial vertebrates have two keratin gene clusters; striking differences in teleost fish
13
3312960 2005 GENOME RESEARCH 15 (10): 1373-1378
Keightley PD; Kryukov GV; Sunyaev S; Halligan DL; Gaffney DJ
Evolutionary constraints in conserved nongenic sequences of mammals
03
3415664 2005 GENOMICS 86 (5): 566-580
Zebhauser R; Kammerer R; Eisenried A; McLellan A; Moore T; et al.
Identification of a novel group of evolutionarily conserved members within the rapidly diverging murine Cea family
03
3515979 2005 JOURNAL OF VIROLOGY 79 (16): 10408-10419
Elleder D; Stepanets V; Melder DC; Senigl F; Geryk J; et al.
The receptor for the subgroup C avian sarcoma and leukosis viruses, Tvc, is related to mammalian butyrophilins, members of the immunoglobulin superfamily
03
3623488 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
13
3712196 2005 NUCLEIC ACIDS RESEARCH 33 (6): 1935-1939
Castelo R; Reymond A; Wyss C; Camara F; Parra G; et al.
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes
23
38168115 2005 TRENDS IN ECOLOGY & EVOLUTION 20 (4): 180-186
Ellegren H
The avian genome uncovered
23
391181 2004 BMC GENOMICS 5: Art. No. 98
Wahl MB; Caldwell RB; Kierzek AM; Arakawa H; Eyras E; et al.
Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
02
4013319 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
02
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4115724 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)
02
4213429 2005 CHROMOSOME RESEARCH 13 (2): 205-214
Bisoni L; Batlle-Morera L; Bird AP; Suzuki M; McQueen HA
Female-specific hyperacetylation of histone H4 in the chicken Z chromosome
12
4314238 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (3): 294-300
Lettice LA; Hill RE
Preaxial polydactyly: a model for defective long-range regulation in congenital abnormalities
02
4434739 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 645-651
Fraser JA; Heitman J
Chromosomal sex-determining regions in animals, plants and fungi
02
45137140 2005 CYTOGENETIC AND GENOME RESEARCH 109 (4): 415-479
Schmid M; Nanda I; Hoehn H; Schartl M; Haaf T; et al.
Second report on chicken genes and chromosomes 2005
22
4612545 2005 DEVELOPMENTAL DYNAMICS 232 (4): 877-882
Antin PB; Konieczka JH
Genomic resources for chicken
12
4715048 2005 FEBS LETTERS 579 (15): 3355-3361
Zdobnov EM; von Mering C; Letunic I; Bork P
Consistency of genome-based methods in measuring Metazoan evolution
12
4815151 2005 GENETICAL RESEARCH 86 (2): 115-125
Jacobsson L; Park HB; Wahlberg P; Fredriksson R; Perez-Enciso M; et al.
Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens
12
4911166 2005 GENOMICS 86 (6): 767-770
Haig D
The complex history of distal human chromosome 1q
02
5014269 2005 HUMAN MOLECULAR GENETICS 14 (20): 3057-3063
Ahituv N; Prabhakar S; Rubin EM; Couronne O
Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
02
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5113273 2005 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (39): 33506-33515
Karakas E; Wilson HL; Graf TN; Xiang S; Jaramillo-Buswuets S; et al.
Structural insights into sulfite oxidase deficiency
02
5215381 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (10): 1992-1999
Backstrom N; Ceplitis H; Berlin S; Ellegren H
Gene conversion drives the evolution of HINTW, an ampliconic gene on the female-specific avian W chromosome
12
531190 2005 NATURE BIOTECHNOLOGY 23 (3): 283-285
Dove AW
Clone on the range: What animal biotech is bringing to the table
02
54210395 2005 NEURON 48 (3): 455-464
Scott K
Taste recognition: Food for thought
02
55144107 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (32): 11367-11372
Benarafa C; Remold-O'Donnell E
The ovalbumin serpins revisited: Perspective from the chicken genome of clade B serpin evolution in vertebrates
12
56139108 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (43): 15518-15522
Signorovitch AY; Dellaporta SL; Buss LW
Molecular signatures for sex in the Placozoa
02
571124109 2005 PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 272 (1567): 979-992
Edwards SV; Jennings WB; Shedlock AM
Phylogenetics of modern birds in the era of genomics
22
58151137 2006 COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY 144 (3): 345-350
Yoshimura T
Molecular mechanism of the photoperiodic response of gonads in birds and mammals
02
59250164 2006 GENOMICS 87 (1): 181-190
Luo MZ; Yu YS; Kim HR; Kudrna D; Itoh Y; et al.
Utilization of a zebra finch BAC library to determine the structure of an avian androgen receptor genomic region
02
60267183 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
02
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61321198 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
02
6211594 2005 ADVANCES IN PARASITOLOGY, VOL 60 60: 285-330
Shirley MW; Smith AL; Tomley FM
The biology of avian Eimeria with an emphasis on their control by vaccination
01
631177 2005 ANIMAL GENETICS 36 (3): 216-222
Aerts JA; Veenendaal T; van der Poel JJ; Crooijmans RPMA; Groenen MAM
Chromosomal assignment of chicken clone contigs by extending the consensus linkage map
01
64211713 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
01
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Tetraodon, fish in the genomic model
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Niskanen EA; Hytonen VP; Grapputo A; Nordlund HR; Kulomaa MS; et al.
Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family
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The genome and the nucleus: a marriage made by evolution - Genome organisation and nuclear architecture
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Integration of the cytogenetic and physical maps of chicken chromosome 17
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RNAi-induced targeted silencing of developmental control genes during chicken embryogenesis
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Multiple N-cadherin enhancers identified by systematic functional screening indicate its Group B1SOX-dependent regulation in neural and placodal development
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Genome annotation past, present, and future: How to define an ORF at each locus
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Impact of fever-range thermal stress on lymphocyte-endothelial adhesion and lymphocyte trafficking
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Enhanced gene expression in the forebrain of hatchling and juvenile male zebra finches
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Synergy between sequence and size in large-scale genomics
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Using multiple alignments to improve seeded local alignment algorithms
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Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
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Estrogen action: revitalization of the chick oviduct model
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Gene discovery for dental anomalies - A primer for the dental professional
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Olinski RP; Lundin LG; Hallbook F
Conserved synteny between the Ciona genome and human paralogons identifies large duplication events in the molecular evolution of the insulin-relaxin gene family
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A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum
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DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
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Marek's disease virus: from miasma to model
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Weil JE; Beemon KL
A 3 ' UTR sequence stabilizes termination codons in the unspliced RNA of Rous sarcoma virus
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Salzano FM
Evolutionary change - patterns and processes
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In silco mapping of ESTs from the Turkey (Meleagris gallopavo)
00

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