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Mon Jul 31 15:56:19 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
View: Overview   Sorted by first author.

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#LCRNCRNode / Date / Journal / AuthorLCSGCS
11177 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
214269 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
313956 2005 GENOME BIOLOGY 6 (7): Art. No. 115
Aloni R; Lancet D
Conservation anchors in the vertebrate genome
00
4165158 2006 GENES CHROMOSOMES & CANCER 45 (7): 676-691
Angeloni D; ter Elst A; Wei MH; van der Veen AY; Braga EA; et al.
Analysis of a new homozygous deletion in the tumor suppressor region at 3p12.3 reveals two novel intronic noncoding RNA genes
00
512545 2005 DEVELOPMENTAL DYNAMICS 232 (4): 877-882
Antin PB; Konieczka JH
Genomic resources for chicken
12
61347 2005 FEBS JOURNAL 272: 117-117
Antonarakis SE
The mystery of conserved non-genic (CNG) sequences
00
7114171 2005 IMMUNOLOGICAL INVESTIGATIONS 34 (3): 295-323
Appenheimer MM; Chen Q; Girard RA; Wang WC; Evans SS
Impact of fever-range thermal stress on lymphocyte-endothelial adhesion and lymphocyte trafficking
01
815381 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
913380 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
00
101399 2005 ANIMAL GENETICS 36 (5): 401-407
Beaumont C; Roussot O; Feve K; Vignoles F; Leroux S; et al.
A genome scan with AFLP((TM)) markers to detect fearfulness-related QTLs in Japanese quail
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
11144107 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
1211450 2005 GENE 362: 117-124
Benkel BF; Nguyen T; Uno Y; de Leon FAP; Hickey DA
Structural organization and chromosomal location of the chicken alpha-amylase gene family
00
13153177 2006 JOURNAL OF MOLECULAR EVOLUTION 62 (1): 66-U36
Berlin S; Ellegren H
Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds
00
14155178 2006 JOURNAL OF MOLECULAR EVOLUTION 62 (2): 226-U17
Berlin S; Brandstrom M; Backstrom N; Axelsson E; Smith NDC; et al.
Substitution rate heterogeneity and the male mutation bias
00
1513429 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
16112183 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284
Blair JE; Hedges SB
Molecular phylogeny and divergence times of deuterostome animals
07
17164160 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
00
18110162 2006 GENOME RESEARCH 16 (3): 311-313
Bourque G; Tesler G; Pevzner PA
The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction
00
1917062 2005 GENOME RESEARCH 15 (12): 1777-1786
Brent MR
Genome annotation past, present, and future: How to define an ORF at each locus
01
20106061 2005 GENOME RESEARCH 15 (12): 1692-1698
Burt DW
Chicken genome: Current status and future opportunities
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2113354 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
22356167 2006 IMMUNOGENETICS 58 (5-6): 362-373
Cannon JP; Haire RN; Mueller MG; Litman RT; Eason DD; et al.
Ancient divergence of a complex family of immune-type receptor genes
00
23249193 2006 PHYSIOLOGICAL GENOMICS 25 (3): 514-524
Carre W; Wang XF; Porter TE; Nys Y; Tang JS; et al.
Chicken genomics resource: sequencing and annotation of 35,407 ESTs from single and multiple tissue cDNA libraries and CAP3 assembly of a chicken gene index
00
2412196 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
251110131 2006 BMC GENOMICS 7: Art. No. 83
Chakravarti R; Adams JC
Comparative genomics of the syndecans defines an ancestral genomic context associated with matrilins in vertebrates
00
2611799 2005 PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 360 (1459): 1365-1366
Charlesworth B; Keightley P; Visscher P
Introduction: Population genetics, quantitative genetics and animal improvement: papers in honour of William (Bill) Hill
00
27217124 2006 ANIMAL GENETICS 37 (2): 130-138
Chaves LD; Knutson TP; Krueth SB; Reed KM
Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo)
00
28267183 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
2919367 2005 GROWTH FACTORS 23 (4): 263-272
Clump DA; Qazi IH; Sudol M; Flynn DC
c-Yes response to growth factor activation
00
301133119 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
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
3116357 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
3213133 2005 CHROMOSOME RESEARCH 13 (7): 665-673
Coullin P; Bed'Hom B; Candelier JJ; Vettese D; Maucolin S; et al.
Cytogenetic repartition of chicken CR1 sequences evidenced by PRINS in Galliformes and some other birds
00
33126111 2005 REPRODUCTION 130 (2): 157-163
Coward K; Ponting CP; Chang HY; Hibbitt O; Savolainen P; et al.
Phospholipase C zeta, the trigger of egg activation in mammals, is present in a non-mammalian species
01
341105135 2006 CELLULAR AND MOLECULAR LIFE SCIENCES 63 (10): 1125-1140
Cruciani V; Mikalsen SO
The vertebrate connexin family
00
3514582 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
3614242 2005 DEVELOPMENTAL BIOLOGY 285 (1): 80-90
Dai FP; Yusuf F; Farjah GH; Brand-Saberi B
RNAi-induced targeted silencing of developmental control genes during chicken embryogenesis
11
37130127 2006 BMC EVOLUTIONARY BIOLOGY 6: Art. No. 5
Danchin EGJ; Gouret P; Pontarotti P
Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
00
38238144 2006 DEVELOPMENTAL BIOLOGY 294 (2): 554-563
Das RM; Van Hateren NJ; Howell GR; Farrell ER; Bangs FK; et al.
A robust system for RNA interference in the chicken using a modified microRNA operon
00
39141157 2006 GENES & DEVELOPMENT 20 (10): 1365-1377
Davey MG; Paton IR; Yin Y; Schmidt M; Bangs FK; et al.
The chicken talpid(3) gene encodes a novel protein essential for Hedgehog signaling
00
402140187 2006 MOLECULAR ECOLOGY 15 (5): 1299-1320
Dawson DA; Burke T; Hansson B; Pandhal J; Hale MC; et al.
A predicted microsatellite map of the passerine genome based on chicken-passerine sequence similarity
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4112828 2005 CHROMOSOMA 114 (5): 338-343
de Oliveira EHC; Habermann FA; Lacerda O; Sbalqueiro IJ; Wienberg J; et al.
Chromosome reshuffling in birds of prey: the karyotype of the world's largest eagle (Harpy eagle, Harpia harpyja) compared to that of the chicken (Gallus gallus)
11
42216195 2006 POULTRY SCIENCE 85 (2): 223-226
Delany ME
Avian genetic stocks: The high and low points from an academia researcher
00
43124155 2006 GENE 372: 26-32
Diaz-Gil G; Gomez-Esquer F; Agudo D; Delcan J; Martinez-Arribas F; et al.
Characterization of a human Bid homologue protein from Gallus gallus
00
44170116 2005 TRENDS IN ENDOCRINOLOGY AND METABOLISM 16 (9): 414-419
Dougherty DC; Sanders MM
Estrogen action: revitalization of the chick oviduct model
01
451190 2005 NATURE BIOTECHNOLOGY 23 (3): 283-285
Dove AW
Clone on the range: What animal biotech is bringing to the table
02
46125117 2005 TRENDS IN GENETICS 21 (9): 488-492
Dunzinger U; Nanda I; Schmid M; Haaf T; Zechner U
Chicken orthologues of mammalian imprinted genes are clustered on macrochromosomes and replicate asynchronously
11
4717749 2005 GENE 359: 1-17
Edelstein LC; Collins T
The SCAN domain family of zinc finger transcription
00
481126102 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
491124109 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
5015979 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
51168115 2005 TRENDS IN ECOLOGY & EVOLUTION 20 (4): 180-186
Ellegren H
The avian genome uncovered
23
52262192 2006 PHYSIOLOGICAL GENOMICS 25 (3): 414-425
Ellestad LE; Carre W; Muchow M; Jenkins SA; Wang XF; et al.
Gene expression profiling during cellular differentiation in the embryonic pituitary gland using cDNA microarrays
00
5311618 2005 BIOFUTUR (254): 24-28
Esnault Y; Jaillon O; Aury JM; Weissenbach J; Crollius HR
Tetraodon, fish in the genomic model
01
5413319 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
5513434 2005 CHROMOSOME RESEARCH 13 (8): 785-793
Federico C; Cantarella CD; Scavo C; Saccone S; Bed'Hom B; et al.
Avian genomes: different karyotypes but a similar distribution of the GC-richest chromosome regions at interphase
01
5614397 2005 NUCLEIC ACIDS RESEARCH 33 (14): 4563-4577
Flannick J; Batzoglou S
Using multiple alignments to improve seeded local alignment algorithms
01
57122327 2005 CHROMOSOMA 114 (4): 212-229
Foster HA; Bridger JM
The genome and the nucleus: a marriage made by evolution - Genome organisation and nuclear architecture
01
5834739 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 645-651
Fraser JA; Heitman J
Chromosomal sex-determining regions in animals, plants and fungi
02
59329161 2006 GENOME RESEARCH 16 (3): 306-310
Froenicke L; Caldes MG; Graphodatsky A; Muller S; Lyons LA; et al.
Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
01
60144168 2006 IMMUNOGENETICS 58 (5-6): 407-421
Fulton JE; Juul-Madsen HR; Ashwell CM; McCarron AM; Arthur JA; et al.
Molecular genotype identification of the Gallus gallus major histocompatibility complex
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
6111555 2005 GENOME BIOLOGY 6 (2): Art. No. 207
Furlong RF
Insights into vertebrate evolution from the chicken genome sequence
00
62136147 2006 FEBS JOURNAL 273 (8): 1637-1648
Gao F; Zhang CT
Isochore structures in the chicken genome
00
63211713 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
6413752 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
65339184 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (5): 964-972
Go Y
Lineage-specific expansions and contractions of the bitter taste receptor gene repertoire in vertebrates
00
66111194 2005 NATURE REVIEWS GENETICS 6 (9): 699-708
Gregory TR
Synergy between sequence and size in large-scale genomics
01
67161171 2006 JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 54 (11): 3901-3910
Guerin-Dubiard C; Pasco M; Molle D; Desert C; Croguennec T; et al.
Proteomic analysis of hen egg white
00
681493 2005 NATURE REVIEWS GENETICS 6 (1): 4-5
Gunter C
Genomics - Pecking away at evolution
00
6911166 2005 GENOMICS 86 (6): 767-770
Haig D
The complex history of distal human chromosome 1q
02
70284110 2005 PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 272 (1578): 2289-2298
Hansson B; Akesson M; Slate J; Pemberton JM
Linkage mapping reveals sex-dimorphic map distances in a passerine bird
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
7122335 2005 COMPARATIVE AND FUNCTIONAL GENOMICS 6 (5-6): 301-306
Hartman S; Touchton G; Wynn J; Geng T; Chong NW; et al.
Characterization of expressed sequence tags from a Gallus gallus pineal gland cDNA library
00
72142170 2006 INFECTION AND IMMUNITY 74 (6): 3375-3380
Hasenstein JR; Zhang GL; Lamont SJ
Analyses of five gallinacin genes and the Salmonella enterica serovar Enteritidis response in poultry
00
73137165 2006 GENOMICS 87 (6): 801-808
Hawkins RD; Helms CA; Winston JB; Warchol ME; Lovett M
Applying genomics to the avian inner ear: Development of subtractive cDNA resources for exploring sensory function and hair cell regeneration
00
7413653 2005 GENETICS 171 (3): 1173-1181
Heifetz EM; Fulton JE; O'Sullivan N; Zhao H; Dekkers JCM; et al.
Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations
00
7501652 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
7615086 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
77146120 2005 WORLDS POULTRY SCIENCE JOURNAL 61 (2): 215-226
Hocking PM
Review of QTL mapping results in chickens
14
78122152 2006 GENE 365: 83-87
Hokii Y; Kubo A; Ogasawara T; Nogi Y; Taneda A; et al.
Twelve novel C-elegans RNA candidates isolated by two-dimensional polyacrylamide gel electrophoresis
00
7921492 2005 NATURE GENETICS 37 (10): 1041-1043
Itoh T; Toyoda A; Taylor TD; Sakaki Y; Hattori M
Identification of large ancient duplications associated with human gene deserts
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8015151 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
811568 2005 HEREDITY 94 (6): 567-568
Jensen P
Genomics - The chicken genome sequence
00
82157112 2005 RETROVIROLOGY 2: Art. No. 50
Jern P; Sperber GO; Blomberg J
Use of Endogenous Retroviral Sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy
01
8314920 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
8411898 2005 PERIODICUM BIOLOGORUM 107 (4): 379-383
Juretic D; Lucic B; Trinajstic N
Why focusing on bioinformatics?
00
8533825 2005 BMC GENOMICS 6: Art. No. 167
Kaiserman D; Bird PI
Analysis of vertebrate genomes suggests a new model for clade B serpin evolution
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86321198 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
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Karakas E; Wilson HL; Graf TN; Xiang S; Jaramillo-Buswuets S; et al.
Structural insights into sulfite oxidase deficiency
02
881184175 2006 JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 306B (3): 295-316
Kawasaki K; Weiss KM
Evolutionary genetics of vertebrate tissue mineralization: The origin secretory calcium-binding and evolution of the phosphoprotein family
01
8912960 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
90212836 2005 CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY 40 (6): 313-330
Khil PR; Camerini-Otero RD
Molecular features and functional constraints in the evolution of the mammalian X chromosome
00
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91110359 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
92139174 2006 JOURNAL OF ELECTRON MICROSCOPY 55 (1): 31-40
Kobori T; Kodama M; Hizume K; Yoshimura SH; Ohtani T; et al.
Comparative structural biology of the genome: nano-scale imaging of single nucleus from different kingdoms reveals the common physicochemical property of chromatin with a 40 nm structural unit
00
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Kohn M; Hgell J; Vogel W; Minich P; Kehrer-Sawatzki H; et al.
Reconstruction of a 450-My-old ancestral vertebrate protokaryotype
00
94199173 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
01
9522691 2005 NATURE GENETICS 37 (5): 495-500
Krek A; Grun D; Poy MN; Wolf R; Rosenberg L; et al.
Combinatorial microRNA target predictions
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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
00
9714921 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
00
9814238 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
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Lewis BP; Burge CB; Bartel DP
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
5158
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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

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