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Fri Jul 16 11:16:20 2004

Initial sequencing and comparative analysis of the mouse genome
R.H. Waterston et al.
NATURE
420 (6915): 520-562 DEC 5 2002
and the citing papers

Nodes: 549
Authors: 2932, Journals: 196, Outer References: 18463
Collection span: 2002 - 2004
View: Overview. Sorted by NCR.
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#LCRNCRNodes / Authors / DateLCSGCS
10116772 2003 DEVELOPMENTAL BIOLOGY 264(2):391-406
Elms P; Siggers P; Napper D; Greenfield A; Arkell R
Zic2 is required for neural crest formation and hindbrain patterning during mouse development
02
1021367153 2003 GENOME RESEARCH 13(12):2507-2518
Margulies EH; Blanchette M; Haussler D; Green ED
Identification and characterization of multi-species conserved sequences
79
103267157 2003 GENOME RESEARCH 13(12):2621-2636
Xie T; Rowen L; Aguado B; Ahearn ME; Madan A; Qin SZ; Campbell RD; Hood L
Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse
02
104167294 2003 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100(22):12660-12665
Wang J; Webb G; Cao Y; Steiner DF
Contrasting patterns of expression of transcription factors in pancreatic alpha and beta cells
02
105167435 2004 GENOMICS 83(5):790-801
Pimenta AF; Levitt P
Characterization of the genomic structure of the mouse limbic system-associated membrane protein (Lsamp) gene
00
106167452 2004 JOURNAL OF INHERITED METABOLIC DISEASE 27(3):319-330
Druker R; Whitelaw E
Retrotransposon-derived elements in the mammalian genome: A potential source of disease
00
107367540 2004 TRENDS IN BIOTECHNOLOGY 22(1):23-30
Ruan YJ; Le Ber P; Ng HH; Liu ET
Interrogating the transcriptome
01
108166278 2003 PLANT CELL 15(8):1749-1770
Toledo-Ortiz G; Huq E; Quail PH
The Arabidopsis basic/helix-loop-helix transcription factor family
010
109166288 2003 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100(12):7181-7188
Wildman DE; Uddin M; Liu GZ; Grossman LI; Goodman M
Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo
112
110166473 2004 MOLECULAR BIOLOGY AND EVOLUTION 21(5):828-840
Shiu SH; Li WH
Origins, lineage-specific expansions, and multiple losses of tyrosine kinases in eukaryotes
01
#LCRNCRNodes / Authors / DateLCSGCS
11116512 2003 AMYOTROPHIC LATERAL SCLEROSIS AND OTHER MOTOR NEURON DISORDERS 4(4):249-257
Hafezparast M; Ahmad-Annuar A; Hummerich H; Shah P; Ford M; Baker C; Bowen S; Martin JE; Fisher EMC
Paradigms for the identification of new genes in motor neuron degeneration
00
11216581 2003 DRUG METABOLISM AND DISPOSITION 31(12):1532-1540
Johnson EF
The 2002 Bernard B. Brodie Award Lecture - Deciphering substrate recognition by drug-metabolizing cytochromes P450
01
113165208 2003 MAMMALIAN GENOME 14(8):565-579
Tuggle CK; Green JA; Fitzsimmons C; Woods R; Prather RS; Malchenko S; Soares MB; Kucaba T; Crouch K; Smith C; Tack D; Robinson N; O'Leary B; Scheetz T; Casavant T; Pomp D; Edeal JB; Zhang YD; Rothschild MF; Garwood K; Beavis W
EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human
13
114865343 2004 BMC BIOINFORMATICS 5():-
Pollard DA; Bergman CM; Stoye J; Celniker SE; Eisen MB
Benchmarking tools for the alignment of functional noncoding DNA
01
11516416 2003 BASIC RESEARCH IN CARDIOLOGY 98(4):219-227
McDonald TG; Van Eyk JE
Mitochondrial proteomics - Undercover in the lipid bilayer
01
11626460 2003 CURRENT OPINION IN MOLECULAR THERAPEUTICS 5(3):285-293
Kislinger T; Emili A
Going global: Protein expression profiling using shotgun mass spectrometry
00
11716492 2003 FUNGAL GENETICS AND BIOLOGY 39(3):250-263
Silar P; Barreau C; Debuchy R; Kicka S; Turcq B; Sainsard-Chanet A; Sellem CH; Billault A; Cattolico L; Duprat S; Weissenbach J
Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing
04
118164132 2003 GENOME RESEARCH 13(6B):1273-1289
Carninci P; Waki K; Shiraki T; Konno H; Shibata K; Itoh M; Aizawa K; Arakawa T; Ishii Y; Sasaki D; Bono H; Kondo S; Sugahara Y; Saito R; Osato N; Fukuda S; Sato K; Watahiki A; Hirozane-Kishikawa T; Nakamura M; Shibata Y; Yasunishi A; Kikuchi N; Yoshiki A; Kusakabe M; Gustincich S; Beisel K; Pavan W; Aidinis V; Nakagawara A; Held WA; Iwata H; Kono T; Nakauchi H; Lyons P; Wells C; Hume DA; Fagiolini M; Hensch TK; Brinkmeier M; Camper S; Hirota J; Mombaerts P; Muramatsu M; Okazaki Y; Kawai J; Hayashizaki Y
Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
311
11916310 2003 AMERICAN JOURNAL OF PSYCHIATRY 160(4):646-656
Tecott LH
The genes and brains of mice and men
110
120163189 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(40):39214-39223
Czipri M; Otto JM; Cs-Szabo G; Kamath RV; Vermes C; Firneisz G; Kolman KJ; Watanabe H; Li YF; Roughley PJ; Yamada Y; Olsen BR; Glant TT
Genetic rescue of chondrodysplasia and the perinatal lethal effect of cartilage link protein deficiency
01
#LCRNCRNodes / Authors / DateLCSGCS
121263199 2003 JOURNAL OF MOLECULAR BIOLOGY 333(1):1-20
Giuliodori S; Percudani R; Braglia P; Ferrari R; Guffanti E; Ottonello S; Dieci G
A composite upstream sequence motif potentiates tRNA gene transcription in yeast
00
122163356 2004 DEVELOPMENTAL BIOLOGY 265(2):462-477
Kleinjan DA; Seawright A; Childs AJ; van Heyningen V
Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription
00
12316289 2003 FASEB JOURNAL 17(13):1849-1870
Rhen T; Grissom S; Afshari C; Cidlowski JA
Dexamethasone blocks the rapid biological effects of 17 beta-estradiol in the rat uterus without antagonizing its global genomic actions
00
124262137 2003 GENOME RESEARCH 13(6B):1466-1477
Kawasawa Y; McKenzie LM; Hill DP; Bono H; Yanagisawa M
G protein-coupled receptor genes in the FANTOM2 database
01
125262321 2003 TRENDS IN GENETICS 19(11):640-648
Landry JR; Mager DL; Wilhelm BT
Complex controls: the role of alternative promoters in mammalian genomes
01
126362420 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
00
127162460 2004 JOURNAL OF VIROLOGY 78(2):899-911
Shen CH; Steiner LA
Genome structure and thymic expression of an endogenous retrovirus in zebrafish
00
128462493 2004 NATURE REVIEWS GENETICS 5(1):43-51
Schaffner SF
The X chromosome in population genetics
00
12976153 2003 CURRENT OPINION IN GENETICS & DEVELOPMENT 13(6):611-616
Li H; Wang W
Dissecting the transcription networks of a cell using computational genomics
00
130161359 2004 DIFFERENTIATION 72(2-3):92-102
Calegari F; Marzesco AM; Kittler R; Buchholz F; Huttner WB
Tissue-specific RNA interference in post-implantation mouse embryos using directional electroporation and whole embryo culture
00
#LCRNCRNodes / Authors / DateLCSGCS
13116032 2003 BMC BIOINFORMATICS 4():-
Tatusov RL; Fedorova ND; Jackson JD; Jacobs AR; Kiryutin B; Koonin EV; Krylov DM; Mazumder R; Mekhedov SL; Nikolskaya AN; Rao BS; Smirnov S; Sverdlov AV; Vasudevan S; Wolf YI; Yin JJ; Natale DA
The COG database: an updated version includes eukaryotes
015
132160271 2003 PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 358(1436):1417-1423
Lee JT
Functional intergenic transcription: a case study of the X-inactivation centre
01
133560306 2003 SCIENCE 301(5634):793-797
Eichler EE; Sankoff D
Structural dynamics of eukaryotic chromosome evolution
59
134160319 2003 TRENDS IN GENETICS 19(9):505-513
Steward RE; MacArthur MW; Laskowski RA; Thornton JM
Molecular basis of inherited diseases: a structural perspective
00
135760488 2004 NATURE 429(6990):440-445
Bentley DR
Genomes for medicine
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136360516 2004 NUCLEIC ACIDS RESEARCH 32(5):1774-1782
Shabalina SA; Ogurtsov AY; Rogozin IB; Koonin EV; Lipman DJ
Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals
00
13725957 2003 CURRENT OPINION IN GENETICS & DEVELOPMENT 13(6):651-658
Deininger PL; Moran JV; Batzer MA; Kazazian HH
Mobile elements and mammalian genome evolution
01
13825968 2003 DEVELOPMENT 130(26):6485-6495
Yamada L; Shoguchi E; Wada S; Kobayashi K; Mochizuki Y; Satou Y; Satoh N
Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis
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139359195 2003 JOURNAL OF DENTAL RESEARCH 82(12):944-950
LeClair EE
Four reasons to consider a novel class of innate immune molecules in the oral epithelium
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140259549 2004 VISION RESEARCH 44(16):1857-1867
Schmucker C; Schaeffel F
A paraxial schematic eye model for the growing C57BL/6 mouse
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14115891 2003 FOOD TECHNOLOGY 57(4):60-67
Fogg-Johnson N; Kaput J
Nutrigenomics: An emerging scientific discipline
01
142158196 2003 JOURNAL OF ENDOCRINOLOGY 179(3):335-346
Wiemers D; Ain R; Ohboshi S; Soares MJ
Migratory trophoblast cells express a newly identified member of the prolactin gene family
01
143158300 2003 PROTEIN ENGINEERING 16(12):881-888
Bhaduri A; Sowdhamini R
A genome-wide survey of human tyrosine phosphatases
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144258530 2004 REPRODUCTION FERTILITY AND DEVELOPMENT 16(1-2):79-85
Ko MSH
Embryogenomics of pre-implantation mammalian development: current status
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14525743 2003 CNS SPECTRUMS 8(8):578-+
Tecott LH; Abdallah L
Mouse genetic approaches to feeding regulation: Serotonin 5-HT2C receptor mutant mice
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146157163 2003 GENOMICS 82(4):417-432
Rijnkels M; Elnitski L; Miller W; Rosen JM
Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins
02
147457206 2003 MAMMALIAN GENOME 14(7):429-436
Pennacchio LA
Insights from human/mouse genome comparisons
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148157263 2003 NUCLEIC ACIDS RESEARCH 31(16):4929-4940
Yang N; Zhang L; Zhang Y; Kazazian HH
An important role for RUNX3 in human L1 transcription and retrotransposition
14
149157523 2004 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(6):1748-1753
Hong HK; Chakravarti A; Takahashi JS
The gene for soluble N-ethylmaleimide sensitive factor attachment protein alpha is mutated in hydrocephaly with hop gait (hyh) mice
02
15035654 2003 CURRENT OPINION IN GENETICS & DEVELOPMENT 13(6):617-622
Swanson WJ
Adaptive evolution of genes and gene families
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15115676 2003 DNA AND CELL BIOLOGY 22(7):457-468
Balliet AG; Hollander MC; Fornace AJ; Hoffman B; Liebermann DA
Comparative analysis of the genetic structure and chromosomal mapping of the murine Gadd45g/CR6 gene
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152156190 2003 JOURNAL OF BIOLOGICAL CHEMISTRY 278(44):43178-43187
Prasannan P; Pike S; Peng K; Shane B; Appling DR
Human mitochondrial C-1-tetrahydrofolate synthase - Gene structure, tissue distribution of the mRNA, and immunolocalization in Chinese hamster ovary cells
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153156200 2003 JOURNAL OF MOLECULAR BIOLOGY 333(5):1045-1059
Contreras-Moreira B; Johnsson PF; Bates PA
Structural context of exons in protein domains: Implications for protein modelling and design
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154156277 2003 PIGMENT CELL RESEARCH 16(6):685-692
Regales L; Giraldo P; Garcia-DIaz A; Lavado A; Montoliu L
Identification and functional validation of a 5 ' upstream regulatory sequence in the human tyrosinase gene homologous to the locus control region of the mouse tyrosinase gene
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155156299 2003 PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 270(1522):1331-1340
Fronicke L; Wienberg J; Stone G; Adams L; Stanyon R
Towards the delineation of the ancestral eutherian genome organization: comparative genome maps of human and the African elephant (Loxodonta africana) generated by chromosome painting
01
156156331 2004 AMERICAN JOURNAL OF HUMAN GENETICS 74(2):197-207
Wen G; Mahata SK; Cadman P; Mahata M; Ghosh S; Mahapatra NR; Rao FW; Stridsberg M; Smith DW; Mahboubi P; Schork NJ; O'Connor DT; Hamilton BA
Both rare and common polymorphisms contribute functional variation at CHGA, a regulator of catecholamine physiology
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157156417 2004 GENOME RESEARCH 14(4):766-779
Krzywinski M; Wallis J; Gosele C; Bosdet I; Chiu R; Graves T; Hummel O; Layman D; Mathewson C; Wye N; Zhu B; Albracht D; Asano J; Barber S; Brown-John M; Chan S; Chand S; Cloutier A; Davito J; Fjell C; Gaige T; Ganten D; Girn N; Guggenheimer K; Himmelbauer H; Kreitler T; Leach S; Lee D; Lehrach H; Mayo M; Mead K; Olson T; Pandoh P; Prabhu AL; Shin H; Tanzer S; Thompson J; Tsai M; Walker J; Yang G; Sekhon M; Hillier L; Zimdahl H; Marziali A; Osoegawa K; Zhao S; Siddiqui A; de Jong PJ; Warren W; Mardis E; McPherson JD; Wilson R; Hubner N; Jones S; Marra M; Schein J
Integrated and sequence-ordered BAC and YAC-based physical maps for the rat genome
11
158256457 2004 JOURNAL OF PHYSIOLOGY-LONDON 554(1):56-63
McBride MW; Charchar FJ; Graham D; Miller WH; Strahorn P; Carr FJ; Dominiczak AF
Functional genomics in rodent models of hypertension
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159456478 2004 MOLECULAR CELL 14(2):221-231
Sorek R; Lev-Maor G; Reznik M; Dagan T; Belinky F; Graur D; Ast G
Minimal conditions for exonization of intronic sequences: 5 ' splice site formation in Alu exons
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16015514 2003 ANTIVIRAL RESEARCH 59(3):181-191
Moreau JM; Dyer KD; Bonville CA; Nitto T; Vasquez NL; Easton AJ; Domachowske JB; Rosenberg HF
Diminished expression of an antiviral ribonuclease in response to pneumovirus infection in vivo
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16115571 2003 DEVELOPMENTAL BIOLOGY 258(2):432-442
Moss EG; Tang LJ
Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites
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162355128 2003 GENOME RESEARCH 13(5):838-844
Subramanian S; Kumar S
Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes
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163155156 2003 GENOME RESEARCH 13(12):2609-2620
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Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection
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164155185 2003 JOURNAL OF APPLIED PHYSIOLOGY 94(6):2502-2509
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Genetic models in applied physiology - Invited review: Functional genomics in the mouse: Powerful techniques for unraveling the basis of human development and disease
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165155197 2003 JOURNAL OF IMMUNOLOGY 171(8):4219-4226
Wilhelm BT; Landry JR; Takei F; Mager DL
Transcriptional control of murine CD94 gene: Differential usage of dual promoters by lymphoid cell types
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166154101 2003 GENES & DEVELOPMENT 17(17):2094-2107
Reynolds PA; Smolen GA; Palmer RE; Sgroi D; Yajnik V; Gerald WL; Haber DA
Identification of a DNA-binding site and transcriptional target for the EWS-WT1(+KTS) oncoprotein
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167354471 2004 MOLECULAR BIOLOGY AND EVOLUTION 21(2):410-417
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A gradient of silent substitution rate in the human pseudoautosomal region
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168154480 2004 MOLECULAR PHARMACOLOGY 65(5):1148-1158
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Cloning, expression, and characterization of three new mouse cytochrome P450 enzymes and partial characterization of their fatty acid oxidation activities
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169253160 2003 GENOME RESEARCH 13(12):2747-2753
Clark MS; Edwards YJK; Peterson D; Clifton SW; Thompson AJ; Sasaki M; Suzuki Y; Kikuchi K; Watabe S; Kawakami K; Sugano S; Elgar G; Johnson SL
Fugu ESTs: New resources for transcription analysis and genome annotation
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170153358 2004 DEVELOPMENTAL BIOLOGY 269(1):276-285
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RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos
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171152216 2003 MOLECULAR & CELLULAR PROTEOMICS 2(2):96-106
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PRISM, a generic large scale proteomic investigation strategy for mammals
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172352519 2004 PHARMACOGENETICS 14(1):1-18
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Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
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17315163 2003 CURRENT OPINION IN STRUCTURAL BIOLOGY 13(3):344-352
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Genome comparisons and analysis
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From subgenome analysis to protein structure
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175151149 2003 GENOME RESEARCH 13(9):2069-2081
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A general approach for identifying distant regulatory elements applied to the Gdf6 gene
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An engineered 800 kilobase deletion of Uchl3 and Lmo7 on mouse chromosome 14 causes defects in viability, postnatal growth and degeneration of muscle and retina
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177151205 2003 MAMMALIAN GENOME 14(5):302-313
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Loci on Chromosomes 2, 4, 9, and 16 for body weight, body length, and adiposity identified in a genome scan of an F-2 intercross between the 129P3/J and C57BU6ByJ mouse strains
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178351335 2004 ANNUAL REVIEW OF MEDICINE 55():1-13
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The impact of the completed human genome sequence on the development of novel therapeutics for human disease
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179851419 2004 GENOME RESEARCH 14(5):789-801
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Analysis of segmental duplications and genome assembly in the mouse
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18015073 2003 DEVELOPMENTAL BRAIN RESEARCH 144(2):159-168
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The oligodendrocyte-myelin glycoprotein gene is highly expressed during the late stages of myelination in the rat central nervous system
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181150202 2003 JOURNAL OF NEUROSCIENCE 23(32):10214-10223
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A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes
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Overlapping deletions spanning the proximal two-thirds of the mouse t complex
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183150218 2003 MOLECULAR AND CELLULAR BIOLOGY 23(21):7648-7657
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Miz1 is required for early embryonic development during gastrulation
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Sequencing and comparison of yeast species to identify genes and regulatory elements
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The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
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186150332 2004 AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY 286(3):F590-F596
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Serial determination of glomerular filtration rate in conscious mice using FITC-inulin clearance
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Molecular cloning of mouse amino acid transport system B-0, a neutral amino acid transporter related to Hartnup disorder
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188150517 2004 NUCLEIC ACIDS RESEARCH 32(9):2912-2924
Osipovich AB; White-Grindley EK; Hicks GG; Roshon MJ; Shaffer C; Moore JH; Ruley HE
Activation of cryptic 3 ' splice sites within introns of cellular genes following gene entrapment
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Genetic aspects of susceptibility to air pollution
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Human-mouse gene identification by comparative evidence integration and evolutionary analysis
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The DNA sequence of human chromosome 7
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Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
17
194149363 2004 EUROPEAN JOURNAL OF HUMAN GENETICS 12(2):139-149
Kaufmann D; Kenner O; Nurnberg P; Vogel W; Bartelt B
InNF1, CFTR, PER3, CARS and SYT7, alternatively included exons show higher conservation of surrounding intron sequences than constitutive exons
00
195149428 2004 GENOMICS 83(1):106-118
Naumann F; Remus R; Schmitz B; Doerfler W
Gene structure and expression of the 5 '-(CGG)(n)-3 '-binding protein (CGGBP1)
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19614824 2003 BIOCHEMICAL JOURNAL 376():135-145
Denecke B; Graber S; Schafer C; Heiss A; Woltje M; Jahnen-Dechent W
Tissue distribution and activity testing suggest a similar but not identical function of fetuin-B and fetuin-A
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197148105 2003 GENETICAL RESEARCH 82(1):1-18
Silva JC; Shabalina SA; Harris DG; Spouge JL; Kondrashov AS
Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR-and L2-derived sequences within the mouse and human genomes
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198248179 2003 HUMAN MOLECULAR GENETICS 12(24):3325-3330
Sunyaev S; Kondrashov FA; Bork P; Ramensky V
Impact of selection, mutation rate and genetic drift on human genetic variation
00
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