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Mon Jul 31 15:49:43 2006

Rat Genome Sequencing Project Consortium
Genome sequence of the Brown Norway rat
yields insights into mammalian evolution
NATURE 428 (6982): 493-521 APR 1 2004
and the citing papers
Nodes: 353, Authors: 2563, Journals: 153, Outer References: 13847, Words: 1363
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Collection span: 2004 - 2006
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#LCRNCRNode / Date / Journal / AuthorLCSGCS
1022666 2004 NATURE 428 (6982): 493-521
Gibbs RA; Weinstock GM; Metzker ML; Muzny DM; Sodergren EJ; et al.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
352352
2316571 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
40201
3224129 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
5156
413785 2004 SCIENCE 304 (5675): 1321-1325
Bejerano G; Pheasant M; Makunin I; Stephen S; Kent WJ; et al.
Ultraconserved elements in the human genome
27124
515769 2004 NATURE 431 (7011): 946-957
Jaillon O; Aury JM; Brunet F; Petit JL; Stange-Thomann N; et al.
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
13122
6337232 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
7113
732886 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
1394
8229249 2005 NUCLEIC ACIDS RESEARCH 33: D447-D453
Hubbard T; Andrews D; Caccamo M; Cameron G; Chen Y; et al.
Ensembl 2005
091
96172235 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
888
10267231 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
11250239 2005 NATURE GENETICS 37 (3): 243-253
Hubner N; Wallace CA; Zimdahl H; Petretto E; Schulz H; et al.
Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease
858
1212788 2004 TRENDS IN GENETICS 20 (11): 563-569
Itoh N; Ornitz DM
Evolution of the Fgf and Fgfr gene families
049
1315629 2004 GENOME BIOLOGY 5 (9): Art. No. R68
Miska EA; Alvarez-Saavedra E; Townsend M; Yoshii A; Sestan N; et al.
Microarray analysis of microRNA expression in the developing mammalian brain
048
14113477 2004 NATURE REVIEWS GENETICS 5 (6): 435-445
Ellegren H
Microsatellites: Simple sequences with complex evolution
140
1518113 2004 CELL 119 (7): 1027-1040
Dorus S; Vallender EJ; Evans PD; Anderson JR; Gilbert SL; et al.
Accelerated evolution of nervous system genes in the origin of Homo sapiens
438
1612368 2004 NATURE 431 (7011): 927-930
She XW; Jiang ZX; Clark RL; Liu G; Cheng Z; et al.
Shotgun sequence assembly and recent segmental duplications within the human genome
437
171192170 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
1811933 2004 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 15-56
Miller W; Makova KD; Nekrutenko A; Hardison RC
Comparative genomics
1131
1914119238 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
429
2013336 2004 GENOME RESEARCH 14 (10B): 2121-2127
Gerhard DS; Wagner L; Feingold EA; Shenmen CM; Grouse LH; et al.
The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)
527
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2121972 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
127
2222870 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
725
2318689 2004 TRENDS IN GENETICS 20 (12): 631-639
Murphy WJ; Pevzner PA; O'Brien SJ
Mammalian phylogenomics comes of age
424
24144234 2005 NATURE 435 (7044): 903-910
Muotri AR; Chu VT; Marchetto MCN; Deng W; Moran JV; et al.
Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition
124
25128164 2005 GENOME RESEARCH 15 (1): 98-110
Bourque G; Zdobnov EM; Bork P; Pevzner PA; Tesler G
Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
123
26234166 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
523
2713479 2004 NUCLEIC ACIDS RESEARCH 32: W273-W279
Frazer KA; Pachter L; Poliakov A; Rubin EM; Dubchak I
VISTA: computational tools for comparative genomics
022
2815183 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (39): 13994-14001
Hwang DG; Green P
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
622
29347265 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
021
30244262 2005 PLOS BIOLOGY 3 (2): Art. No. e42
Keightley PD; Lercher MJ; Eyre-Walker A
Evidence for widespread degradation of gene control regions in hominid genomes
018
#LCRNCRNode / Date / Journal / AuthorLCSGCS
3112731 2004 GENOME RESEARCH 14 (5): 976-987
Eyras E; Caccamo M; Curwen V; Clamp M
ESTGenes: Alternative splicing from ESTs in Ensembl
317
3218534 2004 GENOME RESEARCH 14 (10B): 2001-2009
Brasch MA; Hartley JL; Vidal M
ORFeome cloning and systems biology: Standardized mass production of the parts from the parts-list
016
33559269 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
416
34231279 2005 SCIENCE 309 (5734): 613-617
Murphy WJ; Larkin DM; Everts-van der Wind A; Bourque G; Tesler G; et al.
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
216
35229237 2005 NATURE 437 (7062): 1149-1152
Andolfatto P
Adaptive evolution of non-coding DNA in Drosophila
015
36230241 2005 NATURE METHODS 2 (2): 105-111
Ng P; Wei CL; Sung WK; Chiu KP; Lipovich L; et al.
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
015
3711158 2004 BIOESSAYS 26 (8): 833-843
Suzuki M; Hayashizaki Y
Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs
314
3816611 2004 BMC GENOMICS 5: Art. No. 62
Balciunas D; Davidson AE; Sivasubbu S; Hermanson SB; Welle Z; et al.
Enhancer trapping in zebrafish using the Sleeping Beauty transposon
014
3915878 2004 NATURE REVIEWS GENETICS 5 (8): 578-U1
Meyers BC; Scalabrin S; Morgante M
Mapping and sequencing complex genomes: Let's get physical!
113
40130230 2005 NATURE 433 (7026): 633-638
Jordan IK; Kondrashov FA; Adzhubei IA; Wolf YI; Koonin EV; et al.
A universal trend of amino acid gain and loss in protein evolution
013
#LCRNCRNode / Date / Journal / AuthorLCSGCS
4111734 2004 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 443-477
Borevitz JO; Ecker JR
Plant genomics: The third wave
012
421486 2004 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 321 (3): 707-715
Boutros PC; Moffat ID; Franc MA; Tijet N; Tuomisto J; et al.
Dioxin-responsive AHRE-II gene battery: identification by phylogenetic footprinting
012
4316230 2004 GENOME RESEARCH 14 (5): 802-811
Castillo-Davis CI; Kondrashov FA; Hartl DL; Kulathinal RJ
The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
112
4413937 2004 GENOME RESEARCH 14 (10B): 2128-2135
Rual JF; Hirozane-Kishikawa T; Hao T; Bertin N; Li SM; et al.
Human ORFeome version 1.1: A platform for reverse proteomics
112
4515949 2004 IMMUNOGENETICS 56 (5): 343-354
Hao L; Nei M
Genomic organization and evolutionary analysis of Ly49 genes encoding the rodent natural killer cell receptors: rapid evolution by repeated gene duplication
312
4616859 2004 JOURNAL OF NEUROSCIENCE 24 (23): 5410-5419
Cirelli C; Tononi G
Locus ceruleus control of state-dependent gene expression
012
47135224 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (4): 1147-1155
Zhang JZ; He XL
Significant impact of protein dispensability on the instantaneous rate of protein evolution
012
48133240 2005 NATURE IMMUNOLOGY 6 (7): 689-697
Saveanu L; Carroll O; Lindo V; Del Val M; Lopez D; et al.
Concerted peptide trimming by human ERAP1 and ERAP2 aminopeptidase complexes in the endoplasmic reticulum
012
49337266 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
50424268 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
512
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5114710 2004 BMC EVOLUTIONARY BIOLOGY 4: Art. No. 17
Pereira SL; Baker AJ
Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics
011
5227740 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
211
5318163 2004 MOLECULAR BIOLOGY AND EVOLUTION 21 (10): 1923-1937
Bertrand W; Brunet FG; Escriva H; Parmentier G; Laudet V; et al.
Evolutionary genomics of nuclear receptors: From twenty-five ancestral genes to derived endocrine systems
011
5416065 2004 MOLECULAR THERAPY 10 (2): 344-354
Nicol CG; Graham D; Miller WH; White SJ; Smith TAG; et al.
Effect of adenovirus serotype 5 fiber and penton modifications on in vivo tropism in rats
011
5534873 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
211
561441 2004 ACTA PHYSIOLOGICA SCANDINAVICA 181 (4): 585-592
Cowley AW; Liang M; Roman RJ; Greene AS; Jacob HJ
Consomic rat model systems for physiological genomics
010
5713324 2004 GENE 340 (2): 303-312
Grus WE; Zhang JZ
Rapid turnover and species-specificity of vomeronasal pheromone receptor genes in mice and rats
410
5825039 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
610
59322125 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
010
60459187 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
010
#LCRNCRNode / Date / Journal / AuthorLCSGCS
61350233 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
210
62130283 2005 TRENDS IN GENETICS 21 (2): 77-81
Eisenberg E; Nemzer S; Kinar Y; Sorek R; Rechavi G; et al.
Is abundant A-to-I RNA editing primate-specific?
210
6314928 2004 GENOME BIOLOGY 5 (7): Art. No. R47
Huang H; Winter EE; Wang HJ; Weinstock KG; Xing HM; et al.
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes
09
6416238 2004 GENOME RESEARCH 14 (10A): 1851-1860
Zhao SY; Shetty J; Hou LH; Delcher A; Zhu BL; et al.
Human, mouse, and rat genome large-scale rearrangements: Stability versus speciation
49
6512962 2004 MECHANISMS OF DEVELOPMENT 121 (7-8): 903-913
Khorasani MZ; Hennig S; Imre G; Asakawa S; Palczewski S; et al.
A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing
09
66259161 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
09
67176209 2005 JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 304B (1): 75-85
Tanzer A; Amemiya CT; Kim CB; Stadler PF
Evolution of microRNAs located within Hox gene clusters
09
681107244 2005 NATURE REVIEWS MOLECULAR CELL BIOLOGY 6 (9): 702-714
Yates JR; Gilchrist A; Howell KE; Bergeron JJM
Proteomics of organelles and large cellular structures
09
69110615 2004 CHEMICO-BIOLOGICAL INTERACTIONS 150 (1): 53-70
Shenton JM; Chen J; Uetrecht JP
Animal models of idiosyncratic drug reactions
18
70663169 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
71236177 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
08
72133192 2005 HYPERTENSION 45 (3): 451-459
Garrett MR; Meng HJ; Rapp JP; Joe B
Locating a blood pressure quantitative trait locus within 117 kb on the rat genome - Substitution mapping and renal expression analysis
38
73149278 2005 REPRODUCTION 129 (1): 1-7
Wrobel G; Primig M
Mammalian male germ cells are fertile ground for expression profiling of sexual reproduction
08
7413843 2004 GENOMICS 84 (5): 806-813
Smith NGC; Brandstrom M; Ellegren H
Evidence for turnover of functional noncoding DNA in mammalian genome evolution
37
7513981 2004 PHYSIOLOGICAL GENOMICS 19 (1): 1-10
Wallace KJ; Wallis RH; Collins SC; Argoud K; Kaisaki PJ; et al.
Quantitative trait locus dissection in congenic strains of the Goto-Kakizaki rat identifies a region conserved with diabetes loci in human chromosome 1q
07
76279130 2005 CHEMICAL RESEARCH IN TOXICOLOGY 18 (3): 403-414
Hayes KR; Bradfield RA
Advances in toxicogenomics
07
77121173 2005 GENOME RESEARCH 15 (8): 1127-1135
Vinson JP; Jaffe DB; O'Neill K; Karlsson EK; Stange-Thomann N; et al.
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
07
783121228 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (11): 2275-2284
Blair JE; Hedges SB
Molecular phylogeny and divergence times of deuterostome animals
07
79135273 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (40): 14302-14307
Ryu BY; Kubota H; Avarbock MR; Brinster RL
Conservation of spermatogonial stem cell self-renewal signaling between mouse and rat
17
8019720 2004 EUROPEAN JOURNAL OF PHARMACOLOGY 500 (1-3): 385-398
Vercauteren FGG; Bergeron JJM; Vandesande F; Arckens L; Quirion R
Proteomic approaches in brain research and neuropharmacology
06
#LCRNCRNode / Date / Journal / AuthorLCSGCS
8118121 2004 EXPERT OPINION ON THERAPEUTIC TARGETS 8 (6): 587-596
Orth AP; Batalov S; Perrone M; Chanda SK
The promise of genomics to identify novel therapeutic targets
06
8212233 2004 GENOME RESEARCH 14 (8): 1610-1616
Ogurtsov AY; Sunyaev S; Kondrashov AS
Indel-based evolutionary distance and mouse-human divergence
16
8311345 2004 GENOMICS 84 (5): 867-875
Yamashita T; Honda M; Takatori H; Nishino R; Hoshino N; et al.
Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes
06
8412676 2004 NATURE NEUROSCIENCE 7 (11): 1175-1179
Crabbe JC; Morris RGM
Festina lente: Late-night thoughts on high-throughput screening of mouse behavior
06
8514884 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (47): 16543-16548
Ain R; Dai GL; Dunmore JH; Godwin AR; Soares MJ
A prolactin family paralog regulates reproductive adaptations to a physiological stressor
16
8618493 2005 AMERICAN JOURNAL OF PHARMACOGENOMICS 5 (1): 53-62
Penny MA; McHale D
Pharmacogenomics and the drug discovery pipeline - When should it be implemented?
06
874103171 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
88150183 2005 GENOMICS 85 (2): 208-220
Cho S; Beintema JJ; Zhang JZ
The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories
16
89245223 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
06
9013941 2004 GENOME RESEARCH 14 (12): 2439-2447
Abe K; Noguchi H; Tagawa K; Yuzuriha M; Toyoda A; et al.
Contribution of Asian mouse subspecies Mus musculus molossinus to genomic constitution of strain C57BL/6J, as defined by BAC-end sequence-SKIP analysis
25
#LCRNCRNode / Date / Journal / AuthorLCSGCS
91113856 2004 JOURNAL OF COMPARATIVE NEUROLOGY 476 (2): 186-201
Schoenfeld TA; Knott TK
Evidence for the disproportionate mapping of olfactory airspace onto the main olfactory bulb of the hamster
15
9212567 2004 NATURE 429 (6991): 558-562
Bazykin GA; Kondrashov FA; Ogurtsov AY; Sunyaev S; Kondrashov AS
Positive selection at sites of multiple amino acid replacements since rat-mouse divergence
05
9314792 2005 AMERICAN JOURNAL OF PATHOLOGY 166 (5): 1427-1439
Sebbane F; Gardner D; Long D; Gowen BB; Hinnebusch BJ
Kinetics of disease progression and host response in a rat model of bubonic plague
05
94277128 2005 BRIEFINGS IN BIOINFORMATICS 6 (1): 6-22
Batzoglou S
The many faces of sequence alignment
25
95196134 2005 COMPUTATIONAL BIOLOGY AND CHEMISTRY 29 (1): 1-12
Makalowska I; Lin CF; Makalowski W
Overlapping genes in vertebrate genomes
05
96243144 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
05
97115149 2005 GENE 346: 23-28
Niimura Y; Nei M
Evolutionary changes of the number of olfactory receptor genes in the human and mouse lineages
05
98135194 2005 HYPERTENSION 45 (4): 786-792
McBride MW; Brosnan MJ; Mathers J; McLellan LI; Miller WH; et al.
Reduction of Gstm1 expression in the stroke-prone spontaneously hypertension rat contributes to increased oxidative stress
15
99125203 2005 JOURNAL OF APPLIED PHYSIOLOGY 98 (1): 371-379
Mashimo T; Voigt B; Kuramoto T; Serikawa T
Rat Phenome Project: The untapped potential of existing rat strains
35
100154206 2005 JOURNAL OF BIOLOGICAL CHEMISTRY 280 (13): 12721-12731
Hoodbhoy T; Joshi S; Boja ES; Williams SA; Stanley P; et al.
Human sperm do not bind to rat zonae pellucidae despite the presence of four homologous glycoproteins
05

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