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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
View: Overview   Sorted by LCS.

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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
313785 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
415769 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
532886 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
611933 2004 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 15-56
Miller W; Makova KD; Nekrutenko A; Hardison RC
Comparative genomics
1131
76172235 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
8250239 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
922870 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
10337232 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
1125039 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
1215183 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
1313336 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
14224129 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
15234166 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
16424268 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
1718113 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
1813324 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
1916238 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
2012368 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
2118689 2004 TRENDS IN GENETICS 20 (12): 631-639
Murphy WJ; Pevzner PA; O'Brien SJ
Mammalian phylogenomics comes of age
424
2214119238 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
23559269 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
2411158 2004 BIOESSAYS 26 (8): 833-843
Suzuki M; Hayashizaki Y
Mouse-centric comparative transcriptomics of protein coding and non-coding RNAs
314
2512731 2004 GENOME RESEARCH 14 (5): 976-987
Eyras E; Caccamo M; Curwen V; Clamp M
ESTGenes: Alternative splicing from ESTs in Ensembl
317
2613843 2004 GENOMICS 84 (5): 806-813
Smith NGC; Brandstrom M; Ellegren H
Evidence for turnover of functional noncoding DNA in mammalian genome evolution
37
2715949 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
281192170 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
29133192 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
30125203 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
31267231 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
3227740 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
3313941 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
3413347 2004 HYPERTENSION 44 (5): 695-701
Bilusic M; Bataillard A; Tschannen MR; Gao L; Barreto NE; et al.
Mapping the genetic determinants of hypertension, metabolic diseases, and related phenotypes in the lyon hypertensive rat
24
3534873 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
36277128 2005 BRIEFINGS IN BIOINFORMATICS 6 (1): 6-22
Batzoglou S
The many faces of sequence alignment
25
37663169 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
38128193 2005 HYPERTENSION 45 (4): 557-564
Dutil J; Eliopoulos V; Tremblay J; Hamet P; Charron S; et al.
Multiple quantitative trait loci for blood pressure interacting epistatically and additively on Dahl rat chromosome 2
24
39350233 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
40228258 2005 PHYSIOLOGICAL GENOMICS 21 (1): 112-116
Grondin M; Eliopoulos V; Lambert R; Deng YS; Ariyarajah A; et al.
Complete and overlapping congenics proving the existence of a quantitative trait locus for blood pressure on Dahl rat chromosome 17
24
#LCRNCRNode / Date / Journal / AuthorLCSGCS
41337266 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
42231279 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
43130283 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
441327 2004 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 324 (2): 562-568
Tripodi G; Florio M; Ferrandi M; Modica R; Zimdahl H; et al.
Effect of Add1 gene transfer on blood pressure in reciprocal congenic strains of Milan rats
12
452319 2004 BIOESSAYS 26 (10): 1039-1042
Hancock JM
A bigger mouse? The rat genome unveiled
11
46110615 2004 CHEMICO-BIOLOGICAL INTERACTIONS 150 (1): 53-70
Shenton JM; Chen J; Uetrecht JP
Animal models of idiosyncratic drug reactions
18
4715919 2004 EUROPEAN JOURNAL OF NEUROSCIENCE 20 (12): 3244-3258
Koehl A; Schmidt N; Rieger A; Pilgram SM; Letunic I; et al.
Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression
12
4816230 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
4917532 2004 GENOME RESEARCH 14 (8): 1516-1529
Emes RD; Riley MC; Laukaitis CM; Goodstadt L; Karn RC; et al.
Comparative evolutionary genomics of androgen-binding protein genes
14
5012233 2004 GENOME RESEARCH 14 (8): 1610-1616
Ogurtsov AY; Sunyaev S; Kondrashov AS
Indel-based evolutionary distance and mouse-human divergence
16
#LCRNCRNode / Date / Journal / AuthorLCSGCS
5113937 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
5214444 2004 GENOMICS 84 (5): 814-823
Mortlock DP; Portnoy ME; Chandler RL; Green ED
Comparative sequence analysis of the Gdf6 locus reveals a duplicon-mediated chromosomal rearrangement in rodents and rapidly diverging coding and regulatory sequences
13
53113856 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
5421972 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
5511075 2004 NATURE GENETICS 36 (5): 441-442
Wallace CA; Aitman TJ
The rat comes clean
11
56113477 2004 NATURE REVIEWS GENETICS 5 (6): 435-445
Ellegren H
Microsatellites: Simple sequences with complex evolution
140
5715878 2004 NATURE REVIEWS GENETICS 5 (8): 578-U1
Meyers BC; Scalabrin S; Morgante M
Mapping and sequencing complex genomes: Let's get physical!
113
5813580 2004 OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 8 (4): 289-305
Hunt E; Hanlon N; Leader DP; Bryce H; Dominiczak AF
The visual language of synteny
11
5914884 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
60118133 2005 COMPARATIVE GENOMICS 3388: 1-14
Berard S; Bergeron A; Chauve C
Conservation of combinatorial structures in evolution scenarios
12
#LCRNCRNode / Date / Journal / AuthorLCSGCS
61152143 2005 ENDOCRINOLOGY 146 (1): 406-413
Ueta Y; Fujihara H; Serino R; Dayanithi G; Ozawa H; et al.
Transgenic expression of enhanced green fluorescent protein enables direct visualization for physiological studies of vasopressin neurons and isolated nerve terminals of the rat
13
62144156 2005 GENETICS 170 (4): 1887-1896
Smits BMG; Peters TA; Mul JD; Croes HJ; Fransen JAM; et al.
Identification of a rat model for usher syndrome type 1B by N-ethyl-N-nitrosourea mutagenesis-driven forward genetics
11
63128164 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
64152174 2005 GENOME RESEARCH 15 (8): 1136-1144
Harada JN; Bower KE; Orth AP; Callaway S; Nelson CG; et al.
Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis
13
65470180 2005 GENOME RESEARCH 15 (12): 1777-1786
Brent MR
Genome annotation past, present, and future: How to define an ORF at each locus
11
66150183 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
67133185 2005 GENOMICS 86 (3): 271-279
Tsuji AB; Sugyo A; Ogiu T; Sagara M; Kimura T; et al.
Fine mapping of radiation susceptibility and gene expression analysis of LEC congenic rat lines
13
68135194 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
69152213 2005 JOURNAL OF MOLECULAR EVOLUTION 60 (5): 566-576
Shi P; Bielawski JP; Yang H; Zhang YP
Adaptive diversification of vomeronasal receptor 1 genes in rodents
14
70150217 2005 KIDNEY INTERNATIONAL 68 (6): 2462-2472
Van Dijk SJ; Specht PAC; Lutz MM; Lazar J; Jacob HJ; et al.
Interaction between Rf-1 and Rf-4 quantitative trait loci increases susceptibility to renal damage in double congenic rats
11
#LCRNCRNode / Date / Journal / AuthorLCSGCS
71143225 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (7): 1546-1554
Gogolevskaya IK; Koval AP; Kramerov DA
Evolutionary history of 4.5SH RNA
11
72144226 2005 MOLECULAR BIOLOGY AND EVOLUTION 22 (9): 1845-1852
Podlaha O; Webb DM; Tucker PK; Zhang JZ
Positive selection for indel substitutions in the rodent sperm protein Catsper1
14
73144234 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
74334242 2005 NATURE REVIEWS GENETICS 6 (8): 643-649
Hitte C; Madeoy J; Kirkness EF; Priat C; Lorentzen TD; et al.
Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping
13
75119260 2005 PHYSIOLOGICAL GENOMICS 23 (2): 246-256
Twigger SN; Pasko D; Nie J; Shimoyama M; Bromberg S; et al.
Tools and strategies for physiological genomics: the Rat Genome Database
13
76121271 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (22): 7900-7905
McAuliffe JD; Jordan MI; Pachter L
Subtree power analysis and species selection for comparative genomics
11
77135273 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
78222274 2005 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (51): 18526-18531
Everts-van der Wind A; Larkin DM; Green CA; Elliott JS; Olmstead CA; et al.
A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution
12
79230340 2006 NATURE GENETICS 38 (2): 234-239
Malek RL; Wang HY; Kwitek AE; Greene AS; Bhagabati N; et al.
Physiogenomic resources for rat models of heart, lung and blood disorders
12
801441 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
#LCRNCRNode / Date / Journal / AuthorLCSGCS
811472 2004 ALCOHOLISM-CLINICAL AND EXPERIMENTAL RESEARCH 28 (11): 1622-1628
Liang TB; Habegger K; Spence JP; Foroud T; Ellison JA; et al.
Glutathione S-transferase 8-8 expression is lower in alcohol-preferring than in alcohol-nonpreferring rats
02
8211734 2004 ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS 5: 443-477
Borevitz JO; Ecker JR
Plant genomics: The third wave
012
831185 2004 ARBOR-CIENCIA PENSAMIENTO Y CULTURA 177 (698): 285-310
Martinez JMR
Genome sequencing
00
841486 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
8514710 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
8616611 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
8715612 2004 CANADIAN JOURNAL OF PHYSIOLOGY AND PHARMACOLOGY 82 (12): 1053-1060
Hunter AL; Cruz RP; Cheyne BM; McManus BM; Granville DJ
Cytochrome p450 enzymes and cardiovascular disease
02
8815714 2004 CELL COMMUNICATION AND ADHESION 11 (5-6): 155-171
Cruciani V; Heintz KM; Husoy T; Hovig E; Warren DJ; et al.
The detection of hamster connexins: A comparison of expression profiles with wild-type mouse and the cancer-prone Min mouse
01
89111116 2004 COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING 7 (4): 345-359
Bazylak G; Nagels LJ; Geise HJ
Potentiometric quasi-array employing calixarene derivatives for the high-throughput similarity/diversity screening of beta-adrenergic and beta-blocking chiral drugs by HPLC
00
9014417 2004 CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT 7 (5): 658-664
Aparicio SAJR; Powell J
Genetic approaches to unraveling G protein-coupled receptor biology
00
#LCRNCRNode / Date / Journal / AuthorLCSGCS
911418 2004 EJSO 30 (8): 905-906
Rew DA
The sequencing of the rat genone
00
9219720 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
9318121 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
9414322 2004 FEBS LETTERS 573 (1-3): 214-218
Suzuki H; Okunishi R; Hashizume W; Katayama S; Ninomiya N; et al.
Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR
01
95117123 2004 FOLIA BIOLOGICA 50 (2): 43-57
Seda O
Comparative gene map of hypertriglyceridaemia
03
9612625 2004 GENE 343 (2): 239-244
Leeb T; Muller M
Comparative human-mouse-rat sequence analysis of the ICAM gene cluster on HSA 19p13.2 and a 185-kb porcine region from SSC 2q
02
9711926 2004 GENETICS 168 (2): 1077-1080
Robertson HM
Genes encoding vitamin-K epoxide reductase are present in Drosophila and trypanosomatid protists
02
981827 2004 GENOME BIOLOGY 5 (5): Art. No. 221
Mullins LJ; Mullins JJ
Insights from the rat genome sequence
04
9914928 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
10015629 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

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