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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
View: Overview   Sorted by journal name.

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#LCRNCRNode / Date / Journal / AuthorLCSGCS
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Webber C; Ponting CP
Hotspots of mutation and breakage in dog and human chromosomes
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Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?
01
103110162 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
104256163 2006 GENOME RESEARCH 16 (7): 864-874
Nishihara H; Smit AFA; Okada N
Functional noncoding sequences derived from SINEs in the mammalian genome
00
10515664 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
10616765 2005 GENOMICS 86 (6): 731-738
Liu WS; Eyer K; Yasue H; Roelofs B; Hiraiwa H; et al.
A 12,000-rad porcine radiation hybrid (IMNpRH2) panel refines the conserved synteny between SSC12 and HSA17
00
10711166 2005 GENOMICS 86 (6): 767-770
Haig D
The complex history of distal human chromosome 1q
02
108250164 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
109137165 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
11019367 2005 GROWTH FACTORS 23 (4): 263-272
Clump DA; Qazi IH; Sudol M; Flynn DC
c-Yes response to growth factor activation
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1111568 2005 HEREDITY 94 (6): 567-568
Jensen P
Genomics - The chicken genome sequence
00
11214269 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
11326370 2005 IMMUNOGENETICS 57 (8): 590-600
Maruoka T; Tanabe H; Chiba M; Kasahara M
Chicken CD1 genes are located in the MHC: CD1 and endothelial protein C receptor genes constitute a distinct subfamily of class-I-like genes that predates the emergence of mammals
00
114240166 2006 IMMUNOGENETICS 58 (2-3): 180-190
Viertlboeck BC; Schmitt R; Gobel TW
The chicken immunoregulatory receptor families SIRP, TREM, and CMRF35/CD300L
00
115356167 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
116144168 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
117139169 2006 IMMUNOGENETICS 58 (5-6): 422-432
Santos MD; Yasuike M; Hirono I; Aoki T
The granulocyte colony-stimulating factors (CSF3s) of fish and chicken
00
118114171 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
119142170 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
12014172 2005 INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 49 (2-3): 231-235
Nakamura H; Watanabe Y
Isthmus organizer and regionalization of the mesencephalon and metencephalon
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
121161171 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
12213273 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
123181172 2006 JOURNAL OF BIOLOGICAL CHEMISTRY 281 (3): 1698-1713
Odom EW; Vasta GR
Characterization of a binary tandem domain F-type lectin from striped bass (Morone saxatilis)
01
124199173 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
125139174 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
1261184175 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
12714974 2005 JOURNAL OF IMMUNOLOGY 174 (8): 4998-5006
Lynch NJ; Khan SUH; Stover CM; Sandrini SM; Marston D; et al.
Composition of the lectin pathway of complement in Gallus gallus: Absence of mannan-binding lectin-associated serine protease-1 in birds
01
12814775 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
12914476 2005 JOURNAL OF IMMUNOLOGY 175 (3): 1724-1734
Oshiumi H; Shida K; Goitsuka R; Kimura Y; Katoh J; et al.
Regulator of complement activation (RCA) locus in chicken: Identification of chicken RCA gene cluster and functional RCA proteins
00
130115176 2006 JOURNAL OF IMMUNOLOGY 176 (1): 365-371
Saribasak H; Saribasak NN; Ipek FM; Ellwart JW; Arakawa H; et al.
Uracil DNA glycosylase disruption blocks Ig gene conversion and induces transition mutations
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
13116577 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
132153177 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
133155178 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
134192179 2006 JOURNAL OF MOLECULAR EVOLUTION 62 (5): 630-644
Piskurek O; Austin CC; Okada N
Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes
00
13516878 2005 JOURNAL OF NEUROBIOLOGY 64 (2): 224-238
Wade J; Tang YP; Peabody C; Tempelman RJ
Enhanced gene expression in the forebrain of hatchling and juvenile male zebra finches
01
136158180 2006 JOURNAL OF THE AMERICAN DENTAL ASSOCIATION 137 (6): 743-752
Pemberton TJ; Gee J; Patel PI
Gene discovery for dental anomalies - A primer for the dental professional
01
13715979 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
13813380 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
139163181 2006 MARINE BIOLOGY 149 (1): 107-115
Watanabe H; Iguchi T
Using ecotoxicogenomics to evaluate the impact of chemicals on aquatic organisms
00
14015381 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
14114582 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
142112183 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284
Blair JE; Hedges SB
Molecular phylogeny and divergence times of deuterostome animals
07
143161182 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (1): 10-22
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
01
144267183 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
145339184 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
146175185 2006 MOLECULAR BIOLOGY AND EVOLUTION 23 (6): 1203-1216
Webster MT; Axelsson E; Ellegren H
Strong regional biases in nucleotide substitution in the chicken genome
00
147164186 2006 MOLECULAR ECOLOGY 15 (5): 1263-1273
Wang ZS; Farmer K; Hill GE; Edwards SV
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
01
1482140187 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
14901652 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
150143 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
1511184 2005 NATURE 433 (7027): 777-777
[Anon]
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution (vol 432, pg 695, 2004)
00
15216785 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
15315086 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
154117287 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
15523488 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
156411989 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
157327188 2006 NATURE 440 (7087): 1045-1049
Zody MC; Garber M; Adams DJ; Sharpe T; Harrow J; et al.
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
01
1581190 2005 NATURE BIOTECHNOLOGY 23 (3): 283-285
Dove AW
Clone on the range: What animal biotech is bringing to the table
02
15922691 2005 NATURE GENETICS 37 (5): 495-500
Krek A; Grun D; Poy MN; Wolf R; Rosenberg L; et al.
Combinatorial microRNA target predictions
168
16021492 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
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1611493 2005 NATURE REVIEWS GENETICS 6 (1): 4-5
Gunter C
Genomics - Pecking away at evolution
00
162111194 2005 NATURE REVIEWS GENETICS 6 (9): 699-708
Gregory TR
Synergy between sequence and size in large-scale genomics
01
1631135189 2006 NATURE REVIEWS MICROBIOLOGY 4 (4): 283-294
Osterrieder N; Kamil JP; Schumacher D; Tischer BK; Trapp S
Marek's disease virus: from miasma to model
01
164210395 2005 NEURON 48 (3): 455-464
Scott K
Taste recognition: Food for thought
02
16512196 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
16614397 2005 NUCLEIC ACIDS RESEARCH 33 (14): 4563-4577
Flannick J; Batzoglou S
Using multiple alignments to improve seeded local alignment algorithms
01
167655190 2006 NUCLEIC ACIDS RESEARCH 34 (9): Art. No. e65
Tran T; Havlak P; Miller J
MicroRNA enrichment among short 'ultraconserved' sequences in insects
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16811898 2005 PERIODICUM BIOLOGORUM 107 (4): 379-383
Juretic D; Lucic B; Trinajstic N
Why focusing on bioinformatics?
00
16911799 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
170226191 2006 PHYSIOLOGICAL GENOMICS 25 (2): 216-223
Park HB; Jacobsson L; Wahlberg P; Siegel PB; Andersson L
QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth
00
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171262192 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
172249193 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
173138100 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
00
174153101 2005 POULTRY SCIENCE 84 (11): 1678-1688
McElroy JP; Dekkers JCM; Fulton JE; O'Sullivan NP; Soller M; et al.
Microsatellite markers associated with resistance to Marek's disease in commercial layer chickens
00
17528194 2006 POULTRY SCIENCE 85 (2): 198-199
Qureshi MA
Ancillary scientists symposium: Conservation of avian genetic resources: Current opportunities and challenges - Introduction
00
176216195 2006 POULTRY SCIENCE 85 (2): 223-226
Delany ME
Avian genetic stocks: The high and low points from an academia researcher
00
177158196 2006 POULTRY SCIENCE 85 (4): 593-605
McElroy JP; Kim JJ; Harry DE; Brown SR; Dekkers JCM; et al.
Identification of trait loci affecting white meat percentage and other growth and carcass traits in commercial broiler chickens
00
1781126102 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
179137103 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
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Nikolaidis N; Makalowska I; Chalkia D; Makalowski W; Klein J; et al.
Origin and evolution of the chicken leukocyte receptor complex
25
#LCRNCRNode / Date / Journal / AuthorLCSGCS
181135105 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
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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
183144107 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
184139108 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
185144197 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (5): 1434-1439
Wallny HJ; Avila D; Hunt LG; Powell TJ; Riegert P; et al.
Peptide motifs of the single dominantly expressed class I molecule explain the striking MHC-determined response to Rous sarcoma virus in chickens
00
186321198 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
1871124109 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
188284110 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
189168199 2006 PROTEOMICS 6 (9): 2759-2771
McCarthy FM; Cooksey AM; Wang N; Bridges SM; Pharr GT; et al.
Modeling a whole organ using proteomics: The avian bursa of Fabricius
00
190126111 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
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191157112 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
192156200 2006 RNA-A PUBLICATION OF THE RNA SOCIETY 12 (1): 102-110
Weil JE; Beemon KL
A 3 ' UTR sequence stabilizes termination codons in the unspliced RNA of Rous sarcoma virus
01
193153113 2005 RUSSIAN JOURNAL OF GENETICS 41 (5): 461-467
Sazanov AA; Romanov MN; Smirnov AF
Libraries of large-insert genomic clones as a tool for molecular cytogenetic analysis of avian genome
00
194117201 2006 TISSUE ANTIGENS 68 (1): 13-18
Zola H; Mavrangelos C; Millard DJ; Nicholson IC
Conservation of leukocyte cell surface proteins: implications for the generation of monoclonal antibodies against newly identified leukocyte cell surface proteins
00
195114114 2005 TRENDS IN BIOTECHNOLOGY 23 (6): 269-271
Taylor J
Clues to function in gene deserts
00
196168115 2005 TRENDS IN ECOLOGY & EVOLUTION 20 (4): 180-186
Ellegren H
The avian genome uncovered
23
197170116 2005 TRENDS IN ENDOCRINOLOGY AND METABOLISM 16 (9): 414-419
Dougherty DC; Sanders MM
Estrogen action: revitalization of the chick oviduct model
01
198125117 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
199182118 2005 TRENDS IN GENETICS 21 (10): 573-581
Mitreva M; Blaxter ML; Bird DM; McCarter JP
Comparative genomics of nematodes
05
2001133119 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

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