Insights from human/mouse genome comparisons (original) (raw)
BS Abrahams GM Mak ML Berry DL Palmquist JR Saionz_et al._ (2002)ArticleTitleNovel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce loci.Genomics80 45–53Occurrence Handle10.1006/geno.2002.6795Occurrence Handle1:CAS:528:DC%2BD38XkslSjsbo%3DOccurrence Handle12079282 ArticleCASPubMed Google Scholar
SF Altschul W Gish W Miller EW Myers DJ Lipman (1990)ArticleTitleBasic local alignment search tool.J Mol Biol215 403–410Occurrence Handle10.1006/jmbi.1990.9999Occurrence Handle1:CAS:528:DyaK3MXitVGmsA%3D%3DOccurrence Handle2231712 ArticleCASPubMed Google Scholar
S Aparicio S Brenner (1997)ArticleTitleHow good a model is the Fugu genome?Nature387 140Occurrence Handle10.1038/387140a0Occurrence Handle1:CAS:528:DyaK2sXjtFyqsrg%3D ArticleCAS Google Scholar
S Aparicio A Morrison A Gould J Gilthorpe C Chaudhuri_et al._ (1995)ArticleTitleDetecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes.Proc Natl Acad Sci USA92 1684–1688Occurrence Handle1:CAS:528:DyaK2MXktFWrs78%3DOccurrence Handle7878040 CASPubMed Google Scholar
S Aparicio J Chapman E Stupka N Putnam JM Chia_et al._ (2002)ArticleTitleWhole-genome shotgun assembly and analysis of the genome of Fugu rubripes.Science297 1301–1310Occurrence Handle10.1126/science.1072104Occurrence Handle1:CAS:528:DC%2BD38Xms1ejtr8%3DOccurrence Handle12142439 ArticleCASPubMed Google Scholar
S Bagheri-Fam C Ferraz J Demaille G Scherer D Pfeifer (2001)ArticleTitleComparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions.Genomics78 73–82Occurrence Handle10.1006/geno.2001.6648Occurrence Handle1:CAS:528:DC%2BD3MXot1Kis78%3DOccurrence Handle11707075 ArticleCASPubMed Google Scholar
JA Bailey Z Gu RA Clark K Reinert RV Samonte_et al._ (2002)ArticleTitleRecent segmental duplications in the human genome.Science297 1003–1007Occurrence Handle10.1126/science.1072047Occurrence Handle1:CAS:528:DC%2BD38Xmt1Cktr4%3DOccurrence Handle12169732 ArticleCASPubMed Google Scholar
MS Boguski (2002)ArticleTitleComparative genomics: the mouse that roared.Nature420 515–516Occurrence Handle10.1038/420515aOccurrence Handle1:CAS:528:DC%2BD38Xpt1Whsrc%3DOccurrence Handle12466847 ArticleCASPubMed Google Scholar
N Bray I Dubchak L Pachter (2003)ArticleTitleAVID: A global alignment program.Genome Res13 97–102Occurrence Handle10.1101/gr.789803Occurrence Handle1:CAS:528:DC%2BD3sXnvFGmuw%3D%3DOccurrence Handle12529311 ArticleCASPubMed Google Scholar
S Brenner G Elgar R Sandford A Macrae B Venkatesh_et al._ (1993)ArticleTitleCharacterization of the pufferfish (Fugu) genome as a compact model vertebrate genome.Nature366 265–268 Google Scholar
O Couronne A Poliakov N Bray T Ishkhanov D Ryaboy_et al._ (2003)ArticleTitleStrategies and tools for whole-genome alignments.Genome Res13 73–80Occurrence Handle10.1101/gr.762503Occurrence Handle1:CAS:528:DC%2BD3sXnvFGmtA%3D%3DOccurrence Handle12529308 ArticleCASPubMed Google Scholar
P Dehal P Predki AS Olsen A Kobayashi P Folta_et al._ (2001)ArticleTitleHuman chromosome 19 and related regions in mouse: conservative and lineage-specific evolution.Science293 104–111Occurrence Handle10.1126/science.1060310Occurrence Handle1:CAS:528:DC%2BD3MXltFCntbw%3DOccurrence Handle11441184 ArticleCASPubMed Google Scholar
P Dehal Y Satou RK Campbell J Chapman B Degnan_et al._ (2002)ArticleTitleThe draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.Science298 2157–2167Occurrence Handle10.1126/science.1080049Occurrence Handle1:CAS:528:DC%2BD38XpsVSkt7o%3DOccurrence Handle12481130 ArticleCASPubMed Google Scholar
AL Delcher A Phillippy J Carlton SL Salzberg (2002)ArticleTitleFast algorithms for large-scale genome alignment and comparison.Nucleic Acids Res30 2478–2483Occurrence Handle10.1093/nar/30.11.2478Occurrence Handle12034836 ArticlePubMed Google Scholar
I Dubchak M Brudno GG Loots L Pachter C Mayor_et al._ (2000)ArticleTitleActive conservation of noncoding sequences revealed by three-way species comparisons.Genome Res10 1304–1306Occurrence Handle10.1101/gr.142200Occurrence Handle1:CAS:528:DC%2BD3cXms1yjtLk%3DOccurrence Handle10984448 ArticleCASPubMed Google Scholar
L Duret P Bucher (1997)ArticleTitleSearching for regulatory elements in human noncoding sequences.Curr Opin Struct Biol7 399–406 Google Scholar
G Elgar (1996)ArticleTitleQuality not quantity: the pufferfish genome.Hum Mol Genet5 1437–1442Occurrence Handle1:CAS:528:DyaK28XlsFyltbY%3DOccurrence Handle8875249 CASPubMed Google Scholar
G Elgar R Sandford S Aparicio A Macrae B Venkatesh_et al._ (1996)ArticleTitleSmall is beautiful: comparative genomics with the pufferfish (Fugu rubripes).Trends Genet12 145–150Occurrence Handle10.1016/0168-9525(96)10018-4Occurrence Handle1:CAS:528:DyaK28Xit1ensLY%3DOccurrence Handle8901419 ArticleCASPubMed Google Scholar
K Endo H Yanagi J Araki C Hirano . Yamakawa-Kobayashi (2002)ArticleTitleAssociation found between the promoter region polymorphism in the apolipoprotein A-V gene and the serum triglyceride level in Japanese school children.Hum Genet111 570–572Occurrence Handle10.1007/s00439-002-0825-0Occurrence Handle1:CAS:528:DC%2BD3sXhvFCisL4%3DOccurrence Handle12436249 ArticleCASPubMed Google Scholar
P Gilligan S Brenner B Venkatesh (2002)ArticleTitleFugu and human sequence comparison identifies novel human genes and conserved non-coding sequences.Gene294 35Occurrence Handle10.1016/S0378-1119(02)00793-XOccurrence Handle1:CAS:528:DC%2BD38XmvF2qsbg%3DOccurrence Handle12234665 ArticleCASPubMed Google Scholar
B Gottgens LM Barton JG Gilbert AJ Bench MJ Sanchez_et al._ (2000)ArticleTitleAnalysis of vertebrate SCL loci identifies conserved enhancers.Nat Biotechnol18 181–186Occurrence Handle10.1038/72635Occurrence Handle1:CAS:528:DC%2BD3cXhtVOlsrg%3DOccurrence Handle10657125 ArticleCASPubMed Google Scholar
B Gottgens JG Gilbert LM Barton D Grafham J Rogers_et al._ (2001)ArticleTitleLong-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences.Genome Res11 87–97Occurrence Handle10.1101/gr.153001Occurrence Handle1:CAS:528:DC%2BD3MXmsVCrsw%3D%3DOccurrence Handle11156618 ArticleCASPubMed Google Scholar
B Gottgens LM Barton MA Chapman AM Sinclair B Knudsen_et al._ (2002)ArticleTitleTranscriptional regulation of the stem cell leukemia gene (SCL)–comparative analysis of five vertebrate SCL loci.Genome Res12 749–759Occurrence Handle10.1101/gr.45502Occurrence Handle1:CAS:528:DC%2BD38XjvFSgtL8%3DOccurrence Handle11997341 ArticleCASPubMed Google Scholar
DL Gumucio DA Shelton W Zhu D Millinoff T Gray_et al._ (1996)ArticleTitleEvolutionary strategies for the elucidation of cis and trans factors that regulate the developmental switching programs of the beta-like globin genes.Mol Phylogenet Evol5 18–32Occurrence Handle10.1006/mpev.1996.0004Occurrence Handle1:CAS:528:DyaK28XitVyrsb4%3DOccurrence Handle8673285 ArticleCASPubMed Google Scholar
RC Hardison (2000)ArticleTitleConserved noncoding sequences are reliable guides to regulatory elements.Trends Genet16 369–372Occurrence Handle1:CAS:528:DC%2BD3cXmtlOnsL0%3DOccurrence Handle10973062 CASPubMed Google Scholar
RC Hardison J Oeltjen W Miller (1997)ArticleTitleLong human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.Genome Res7 959–966Occurrence Handle1:CAS:528:DyaK2sXntFaitrs%3DOccurrence Handle9331366 CASPubMed Google Scholar
SB Hedges S Kumar (2002)ArticleTitleGenomics. Vertebrate genomes compared.Science297 1283–1285Occurrence Handle10.1126/science.1076231Occurrence Handle1:CAS:528:DC%2BD38Xms1Slu7k%3DOccurrence Handle12193771 ArticleCASPubMed Google Scholar
L Hood L Rowen BF Koop (1995)ArticleTitleHuman and mouse T-cell receptor loci: genomics, evolution, diversity, and serendipity.Ann N Y Acad Sci758 390–412Occurrence Handle1:CAS:528:DyaK2MXptVSitr4%3DOccurrence Handle7625706 CASPubMed Google Scholar
GF How B Venkatesh S Brenner (1996)ArticleTitleConserved linkage between the puffer fish (Fugu rubripes) and human genes for platelet-derived growth factor receptor and macrophage colony-stimulating factor receptor.Genome Res6 1185–1191Occurrence Handle1:CAS:528:DyaK2sXkslCkOccurrence Handle8973913 CASPubMed Google Scholar
TJ Hudson DM Church S Greenaway H Nguyen A Cook_et al._ (2001)ArticleTitleA radiation hybrid map of mouse genes.Nat Genet29 201–205Occurrence Handle10.1038/ng1001-201Occurrence Handle1:CAS:528:DC%2BD3MXnsFKgu7k%3DOccurrence Handle11586302 ArticleCASPubMed Google Scholar
N Jareborg R Durbin (2000)ArticleTitleAlfresco—a workbench for comparative genomic sequence analysis.Genome Res10 1148–1157Occurrence Handle10.1101/gr.10.8.1148Occurrence Handle1:CAS:528:DC%2BD3cXmtFelsrk%3DOccurrence Handle10958633 ArticleCASPubMed Google Scholar
G Jimenez KB Gale T Enver (1992)ArticleTitleThe mouse beta-globin locus control region: hypersensitive sites 3 and 4.Nucleic Acids Res20 5797–5803Occurrence Handle1:CAS:528:DyaK3sXit1Kqt7g%3DOccurrence Handle1454540 CASPubMed Google Scholar
WJ Kent CW Sugnet TS Furey KM Roskin TH Pringle_et al._ (2002)ArticleTitleThe human genome browser at UCSC.Genome Res12 996–1006Occurrence Handle1:CAS:528:DC%2BD38Xks12hs7s%3DOccurrence Handle12045153 CASPubMed Google Scholar
C Kimura N Takeda M Suzuki M Oshimura S Aizawa_et al._ (1997)ArticleTitleCis-acting elements conserved between mouse and pufferfish Otx2 genes govern the expression in mesencephalic neural crest cells.Development124 3929–3941Occurrence Handle1:CAS:528:DyaK2sXnt12gs7k%3DOccurrence Handle9374391 CASPubMed Google Scholar
BF Koop L Hood (1994)ArticleTitleStriking sequence similarity over almost 100 kilobases of human and mouse T-cell receptor DNA.Nat Genet7 48–53Occurrence Handle1:CAS:528:DyaK2cXksFWitrk%3DOccurrence Handle8075639 CASPubMed Google Scholar
ES Lander LM Linton B Birren C Nusbaum MC Zody_et al._ (2001)ArticleTitleInitial sequencing and analysis of the human genome.Nature409 860–921Occurrence Handle1:CAS:528:DC%2BD3MXhsFCjtLc%3DOccurrence Handle11237011 CASPubMed Google Scholar
G Lennon C Auffray M Polymeropoulos MB Soares (1996)ArticleTitleThe I.M.A.G.E. Consortium: an integrated molecular analysis of genomes and their expression.Genomics33 151–152Occurrence Handle1:CAS:528:DyaK28XisFSmsbc%3DOccurrence Handle8617505 CASPubMed Google Scholar
WH Li DL Ellsworth J Krushkal BH Chang D Hewett-Emmett (1996)ArticleTitleRates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis.Mol Phylogenet Evol5 182–187Occurrence Handle1:CAS:528:DyaK28XitVyrsbo%3DOccurrence Handle8673286 CASPubMed Google Scholar
GG Loots RM Locksley CM Blankespoor ZE Wang W Miller_et al._ (2000)ArticleTitleIdentification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons.Science288 136–140 Google Scholar
JB Margot GW Demers RC Hardison (1989)ArticleTitleComplete nucleotide sequence of the rabbit beta-like globin gene cluster. Analysis of intergenic sequences and comparison with the human beta-like globin gene cluster.J Mol Biol205 15–40Occurrence Handle1:CAS:528:DyaL1MXhsV2js7g%3DOccurrence Handle2486295 CASPubMed Google Scholar
C Mayor M Brudno JR Schwartz A Poliakov EM Rubin_et al._ (2000)ArticleTitleVISTA: visualizing global DNA sequence alignments of arbitrary length.Bioinformatics16 1046–1047Occurrence Handle10.1093/bioinformatics/16.11.1046Occurrence Handle1:CAS:528:DC%2BD3MXptlOltw%3D%3DOccurrence Handle11159318 ArticleCASPubMed Google Scholar
T Nabika S Nasreen S Kobayashi J Masuda (2002)ArticleTitleThe genetic effect of the apolipoprotein AV gene on the serum triglyceride level in Japanese.Atherosclerosis165 201–204Occurrence Handle10.1016/S0021-9150(02)00252-6Occurrence Handle1:CAS:528:DC%2BD38Xotl2msLw%3DOccurrence Handle12417270 ArticleCASPubMed Google Scholar
JH Nadeau BA Taylor (1984)ArticleTitleLengths of chromosomal segments conserved since divergence of man and mouse.Proc Natl Acad Sci USA81 814–818Occurrence Handle1:CAS:528:DyaL2cXhsFWrurk%3DOccurrence Handle6583681 CASPubMed Google Scholar
K Osoegawa M Tateno PY Woon E Frengen AG Mammoser_et al._ (2000)ArticleTitleBacterial artificial chromosome libraries for mouse sequencing and functional analysis.Genome Res10 116–128Occurrence Handle1:CAS:528:DC%2BD3cXpsl2jtQ%3D%3DOccurrence Handle10645956 CASPubMed Google Scholar
K Osoegawa AG Mammoser C Wu E Frengen C Zeng_et al._ (2001)ArticleTitleA bacterial artificial chromosome library for sequencing the complete human genome.Genome Res11 483–496Occurrence Handle10.1101/gr.169601Occurrence Handle1:CAS:528:DC%2BD3MXhvVOntrY%3DOccurrence Handle11230172 ArticleCASPubMed Google Scholar
LA Pennacchio EM Rubin (2001)ArticleTitleGenomic strategies to identify mammalian regulatory sequences.Nat Rev Genet2 100–109Occurrence Handle10.1038/35052548Occurrence Handle1:CAS:528:DC%2BD3MXisVGjtbg%3DOccurrence Handle11253049 ArticleCASPubMed Google Scholar
LA Pennacchio M Olivier JA Hubacek JC Cohen DR Cox_et al._ (2001)ArticleTitleAn apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing.Science294 169–173 Google Scholar
LA Pennacchio M Olivier JA Hubacek RM Krauss EM Rubin_et al._ (2002)ArticleTitleTwo independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels.Hum Mol Genet11 3031–3038Occurrence Handle10.1093/hmg/11.24.3031Occurrence Handle1:CAS:528:DC%2BD38XosFOgs7c%3DOccurrence Handle12417524 ArticleCASPubMed Google Scholar
J Ribalta L Figuera J Fernandez-Ballart E Vilella M Castro Cabezas_et al._ (2002)ArticleTitleNewly identified apolipoprotein AV gene predisposes to high plasma triglycerides in familial combined hyperlipidemia.Clin Chem48 1597–1600Occurrence Handle1:CAS:528:DC%2BD38XmslSqu7Y%3DOccurrence Handle12194944 CASPubMed Google Scholar
DH Rowitch Y Echelard PS Danielian K Gellner S Brenner (1998)ArticleTitleIdentification of an evolutionarily conserved 110 base-pair cis-acting regulatory sequence that governs Wnt-1 expression in the murine neural plate.Development125 2735–2746Occurrence Handle1:CAS:528:DyaK1cXlsV2mu7c%3DOccurrence Handle9636087 CASPubMed Google Scholar
S Schwartz Z Zhang KA Frazer A Smit C Riemer_et al._ (2000)ArticleTitlePipMaker—a web server for aligning two genomic DNA sequences.Genome Res10 577–586Occurrence Handle1:CAS:528:DC%2BD3cXjtVKrsLg%3DOccurrence Handle10779500 CASPubMed Google Scholar
S Schwartz WJ Kent A Smit Z Zhang R Baertsch_et al._ (2003)ArticleTitleHuman-mouse alignments with BLASTZ.Genome Res13 103–107Occurrence Handle10.1101/gr.809403Occurrence Handle1:CAS:528:DC%2BD3sXnvFGlsg%3D%3DOccurrence Handle12529312 ArticleCASPubMed Google Scholar
PJ Talmud E Hawe S Martin M Olivier GJ Miller_et al._ (2002)ArticleTitleRelative contribution of variation within the APOC3/A4/A5 gene cluster in determining plasma triglycerides.Hum Mol Genet11 3039–3046Occurrence Handle10.1093/hmg/11.24.3039Occurrence Handle1:CAS:528:DC%2BD38XosFOgsL4%3DOccurrence Handle12417525 ArticleCASPubMed Google Scholar
B Venkatesh SL Si-Hoe D Murphy S Brenner (1997)ArticleTitleTransgenic rats reveal functional conservation of regulatory controls between the Fugu isotocin and rat oxytocin genes.Proc Natl Acad Sci USA94 12462–12466Occurrence Handle10.1073/pnas.94.23.12462Occurrence Handle1:CAS:528:DyaK2sXns1ylsbY%3DOccurrence Handle9356472 ArticleCASPubMed Google Scholar
B Venkatesh P Gilligan S Brenner (2000)ArticleTitleFugu: a compact vertebrate reference genome.FEBS Lett476 3–7Occurrence Handle10.1016/S0014-5793(00)01659-8Occurrence Handle1:CAS:528:DC%2BD3cXktlKqsLo%3DOccurrence Handle10878239 ArticleCASPubMed Google Scholar
JC Venter MD Adams EW Myers PW Li RJ Mural_et al._ (2001)ArticleTitleThe sequence of the human genome.Science291 1304–1351Occurrence Handle1:CAS:528:DC%2BD3MXhtlSgsbo%3DOccurrence Handle11181995 CASPubMed Google Scholar
RH Waterston K Lindblad-Toh E Birney J Rogers JF Abril_et al._ (2002)ArticleTitleInitial sequencing and comparative analysis of the mouse genome.Nature420 520–562Occurrence Handle10.1038/nature01262Occurrence Handle12466850 ArticlePubMed Google Scholar