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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
313041 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
4117287 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
5143 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
616444 2005 DEVELOPMENTAL CELL 8 (1): 9-17
Stern CD
The chick: A great model system becomes even greater
310
749258 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
816785 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
915086 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
10411989 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1114932 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
12137140 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
1313752 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
1416357 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
1514775 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
1612196 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
17137103 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
18131104 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
191124109 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
20168115 2005 TRENDS IN ECOLOGY & EVOLUTION 20 (4): 180-186
Ellegren H
The avian genome uncovered
23
#LCRNCRNode / Date / Journal / AuthorLCSGCS
211328 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
22110212 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
2312828 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
2413429 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
2512030 2005 CHROMOSOME RESEARCH 13 (2): 215-222
Romanov MN; Daniels LM; Dodgson JB; Delany ME
Integration of the cytogenetic and physical maps of chicken chromosome 17
11
2614242 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
2712545 2005 DEVELOPMENTAL DYNAMICS 232 (4): 877-882
Antin PB; Konieczka JH
Genomic resources for chicken
12
2812946 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
2915048 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
3015151 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
3115381 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
3214582 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
3323488 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
3422691 2005 NATURE GENETICS 37 (5): 495-500
Krek A; Grun D; Poy MN; Wolf R; Rosenberg L; et al.
Combinatorial microRNA target predictions
168
35135105 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
36137106 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
37144107 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
38125117 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
39146120 2005 WORLDS POULTRY SCIENCE JOURNAL 61 (2): 215-226
Hocking PM
Review of QTL mapping results in chickens
14
401181 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4111594 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
4211455 2005 ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS 77 (4): 627-650
Salzano FM
Evolutionary change - patterns and processes
00
432106 2005 ANIMAL BIOTECHNOLOGY 16 (2): 81-102
Reed KM; Knutson TP; Krueth SB; Sullivan LR; Chaves LD
In silco mapping of ESTs from the Turkey (Meleagris gallopavo)
00
441177 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
451399 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
461410 2005 ANIMAL GENETICS 36 (5): 438-443
Reed KM
In silico comparative mapping of 278 genomic survey sequences from the turkey (Meleagris gallopavo)
00
4714211 2005 ANIMAL GENETICS 36 (6): 468-476
Rabie TSKM; Crooijmans RPMA; Bovenhuis H; Vereijken ALJ; Veenendaal T; et al.
Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome
00
48211713 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
4917714 2005 ANNUAL REVIEW OF MICROBIOLOGY 59: 191-209
Snel B; Huynen MA; Dutilh BE
Genome trees and the nature of genome evolution
06
5018615 2005 AUSTRALIAN JOURNAL OF EXPERIMENTAL AGRICULTURE 45 (7-8): 749-756
Moore RJ; Doran TJ; Wise TG; Riddell S; Granger K; et al.
Chicken functional genomics: an overview
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5113316 2005 AVIAN PATHOLOGY 34 (4): 324-331
Zhang HM; Bacon LD; Cheng HH; Hunt HD
Development and validation of a PCR-RFLP assay to evaluate TVB haplotypes coding receptors for subgroup B and subgroup E avian leukosis viruses in White Leghorns
00
5212317 2005 BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS 1734 (2): 136-142
Matsuyama H; Sato K; Nakamura Y; Suzuki K; Akiba Y
Modulation of regulatory factors involved in cholesterol metabolism in response to feeding of pravastatin-or cholesterol-supplemented diet in chickens
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
5514920 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
5614921 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
5715522 2005 BMC EVOLUTIONARY BIOLOGY 5: Art. No. 54
Winter EE; Ponting CP
Mammalian BEX, WEX and GASP genes: Coding and non-coding chimaerism sustained by gene conversion events
00
5814823 2005 BMC GENOMICS 6: Art. No. 41
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
01
5915724 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
6033825 2005 BMC GENOMICS 6: Art. No. 167
Kaiserman D; Bird PI
Analysis of vertebrate genomes suggests a new model for clade B serpin evolution
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
61122327 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
6234831 2005 CHROMOSOME RESEARCH 13 (6): 581-591
Rodrigue KL; May BP; Famula TR; Delany ME
Meiotic instability of chicken ultra-long telomeres and mapping of a 2.8 megabase array to the W-sex chromosome
00
6313133 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
6413434 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
6522335 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
66212836 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
6714337 2005 CURRENT GENOMICS 6 (2): 75-80
Smith EJ; Kamara D; Pimentel G; Geng T; Guan X; et al.
Avian genomes: Important resources for understanding vertebrate biology
00
6814238 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
6934739 2005 CURRENT OPINION IN GENETICS & DEVELOPMENT 15 (6): 645-651
Fraser JA; Heitman J
Chromosomal sex-determining regions in animals, plants and fungi
02
7014243 2005 DEVELOPMENTAL BIOLOGY 286 (2): 601-617
Matsumata M; Uchikawa M; Kamachi Y; Kondoh H
Multiple N-cadherin enhancers identified by systematic functional screening indicate its Group B1SOX-dependent regulation in neural and placodal development
01
#LCRNCRNode / Date / Journal / AuthorLCSGCS
711347 2005 FEBS JOURNAL 272: 117-117
Antonarakis SE
The mystery of conserved non-genic (CNG) sequences
00
7217749 2005 GENE 359: 1-17
Edelstein LC; Collins T
The SCAN domain family of zinc finger transcription
00
7311450 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
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
7513354 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
7611555 2005 GENOME BIOLOGY 6 (2): Art. No. 207
Furlong RF
Insights into vertebrate evolution from the chicken genome sequence
00
7713956 2005 GENOME BIOLOGY 6 (7): Art. No. 115
Aloni R; Lancet D
Conservation anchors in the vertebrate genome
00
78110359 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
7912960 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
80106061 2005 GENOME RESEARCH 15 (12): 1692-1698
Burt DW
Chicken genome: Current status and future opportunities
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
8117062 2005 GENOME RESEARCH 15 (12): 1777-1786
Brent MR
Genome annotation past, present, and future: How to define an ORF at each locus
01
8216063 2005 GENOME RESEARCH 15 (12): 1787-1797
Webber C; Ponting CP
Hotspots of mutation and breakage in dog and human chromosomes
00
8315664 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
8416765 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
8511166 2005 GENOMICS 86 (6): 767-770
Haig D
The complex history of distal human chromosome 1q
02
8619367 2005 GROWTH FACTORS 23 (4): 263-272
Clump DA; Qazi IH; Sudol M; Flynn DC
c-Yes response to growth factor activation
00
871568 2005 HEREDITY 94 (6): 567-568
Jensen P
Genomics - The chicken genome sequence
00
8814269 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
8926370 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
90114171 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
9114172 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
9213273 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
9314974 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
9414476 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
9516577 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
9616878 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
9715979 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
9813380 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
99112183 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284
Blair JE; Hedges SB
Molecular phylogeny and divergence times of deuterostome animals
07
1001184 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)
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