The Genom of Homo sapiens.pdf

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HUMAN VS. CHIMP CHROMOSOME COMPARISON 459Figure 3. Sequence alignment of upstream regions of IFNAR2 gene. Identical bases are shown by *. Nonidentical bases are shownby open gothic, and deleted region is shown by underline. Arrows show possible regulatory elements.this study came from the Ka/Ks study showing that morethan 5% of genes are relatively free from constraint, andsome of them have been positively selected. The numberof genes examined by the present study is too small todraw general conclusions, but there is the suggestion thatsome tissue-specific genes may play a positive role in establishingspecies-specific phenotypes.In summary, the present study revealed a complex setof genetic differences between human and chimpanzee.Further experimental examination is required to say exactlywhat biological differences are caused by these geneticdifferences, but these data suggest that the biologicalconsequences derived from the genetic differencesmay be more complicated than previously speculated.ACKNOWLEDGMENTSWe are grateful to T. Ito, T. Kawagoe, T. Kojima, X.Son, A. Beck, K. Borzym, S. Gelling, V. Gimmel, K.Heitmann, A. Kel, S. Klages, N. Lang, I. Mueller, M.Sontag, R. Yildirimman, Jean Wickings, Cornelia Baumgart,Oliver Mueller, T.T. Liao, H. Tsai, Y. Huang, Y.Liu, and all the technical staffs of the contributinggenome centers. This work was supported in part by aSpecial grant from RIKEN Genomic Sciences Center andGrant-in-Aid for Scientific Research on Priority Areas“Genome Science” from the Ministry of Education, Culture,Sports, Science and Technology, Japan; The Ministryof Education and Research, Germany; The ChineseInternational Science and Technology Cooperation Project,Ministry of Science and Technology, China; TheChinese High-Tech Research and Development Program,Shanghai Commission for Science and Technology; andThe National Research Program for Genomic Medicineof National Science Council, Taiwan.REFERENCESBailey J.A., Yavor A.M., Viggiano L., Misceo D., Horvath J.E.,Archidiacono N., Schwartz S., Rocchi M., and Eichler E.E.2002. Human-specific duplication and mosaic transcripts:The recent paralogous structure of chromosome 22. Am. J.Hum. Genet. 70: 83.Britten R.J. 2002. Divergence between samples of chimpanzeeand human DNA sequences is 5%, counting indels. Proc.Natl. Acad. Sci. 99: 13633.Carrol S.B. 2003. Genetics and making of Homo sapiens. Nature422: 849.Chen F.-C. and Li W.-H. 2001. Genomic divergence betweenhumans and other hominoids and the effective population sizeof the common ancestor of humans and chimpanzees. Am. J.Hum. Genet. 68: 444.Enard W., Khaitovich P., Klose J., Zöllner S., Heissig F., GiavaliscoP., Nieselt-Struwe K., Muchmore E., Varki A., RavidR., Doxiadis G.M., Bontrop R.E., and Pääbo S. 2002. Intraandinterspecific variation in primate gene expression patterns.Science 296: 340.Frazer K.A., Chen X., Hinds D.A., Pant K., Patil N., and Cox
460 SAKAKI ET AL.D.R. 2003. Genomic DNA insertions and deletions occur frequentlybetween humans and nonhuman primates. GenomeRes. 13: 341.Fujiyama A., Watanabe H., Toyoda A., Taylor T.D. Itoh T., TsaiS.-F., Park H.-S., Yaspo M.-L., Lehrach H., Chen Z., Fu G.,Saitou N., Osoegawa K., de Jong P., Suto Y., Hattori M., andSakaki Y. 2002. Construction and analysis of a human-chimpanzeecomparative clone map. Science 295: 131.Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., ParkH.S., Toyoda A., Ishii K., Totoki Y., Choi D.K., Soeda E., OhkiM., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., PolleyA., Menzel U., Delabar J., Kumpf K., Lehmann R., PattersonD., Reichwald K., Rump A., and Schillhabel M., et al. 2000.The DNA sequence of human chromosome 21. The chromosome21 mapping and sequencing consortium. Nature 405: 311.Nei M., and Gojobori T. 1986. Simple methods for estimatingthe numbers of synonymous and nonsynonymous nucleotidesubstitutions. Mol. Biol. Evol. 5: 418.Olson M. and Varki A. 2003. Sequencing the chimpanzeegenome: Insights into human evolution and diseases. Nat.Rev. Genet. 4: 20.Saitou N. 1991. Reconstruction of molecular phylogeny of extanthominoids from DNA sequence data. Am. J. Phys. Anthropol.84: 75.Sibley C.G. and Ahlquist J.E. 1984. The phylogeny of the hominoidprimates, as indicated by DNA-DNA hybridization. J.Mol. Evol. 20: 2.Wildman D.E., Uddin M., Liu G., I. Grossman L.I., and GoodmanM. 2003. The role of natural selection in shaping 99.4%identity between humans and chimpanzees at non-synonymousDNA sites: Implications for enlarging the genus Homo.Proc. Natl. Acad. Sci. 100: 7181.
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ForewordIn 2001, as we considered t
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The Finished Genome Sequence of Hom
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4 ROGERSFigure 2. Accumulation of h
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6 ROGERSFigure 4. Sequencing center
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8 ROGERSabcFigure 5. Ensembl view o
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10 ROGERS2000. Analysis of vertebra
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The Human Genome: Genes, Pseudogene
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VARIATION ON CHROMOSOME 7 15rived f
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VARIATION ON CHROMOSOME 7 17DNAs an
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VARIATION ON CHROMOSOME 7 19expecte
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VARIATION ON CHROMOSOME 7 21Drosoph
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Mutational Profiling in the Human G
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HUMAN MUTATIONAL PROFILING 25Anothe
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HUMAN MUTATIONAL PROFILING 27Figure
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HUMAN MUTATIONAL PROFILING 29Rieder
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32 SCHMUTZ ET AL.algorithm itself,
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34 SCHMUTZ ET AL.Figure 2. Genomic
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36 SCHMUTZ ET AL.compared. Some of
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Human Subtelomeric DNAH. RIETHMAN,
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HUMAN SUBTELOMERIC SEQUENCES 41The
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HUMAN SUBTELOMERIC SEQUENCES 43cate
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HUMAN SUBTELOMERIC SEQUENCES 45Figu
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HUMAN SUBTELOMERIC SEQUENCES 47pres
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50 COLLINSand expand the genomics r
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52 COLLINSFigure 2. A public-sector
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54 COLLINSdefine all the parts of t
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56 BENTLEYmon over many generations
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58 BENTLEYTable 1. Genetic Disease
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60 BENTLEY(Clark et al. 1998; Reich
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62 BENTLEYACKNOWLEDGMENTSThe author
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SNP Genotyping and Molecular Haplot
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GENETIC ANALYSIS OF DNA POOLS 67gen
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70 FAN ET AL.matrix is then mated t
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72 FAN ET AL.Figure 3. Views of gen
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74 FAN ET AL.including 32 duplicate
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76 FAN ET AL.Figure 7. Allele-speci
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78 FAN ET AL.microsphere-based assa
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80 BERTRANPETIT ET AL.function, may
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82 BERTRANPETIT ET AL.diversity in
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84 BERTRANPETIT ET AL.gree of block
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86 BERTRANPETIT ET AL.Figure 1. Dec
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88 BERTRANPETIT ET AL.1999. Populat
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90 WINDEMUTH ET AL.Expression data.
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92 WINDEMUTH ET AL.Table 1. A Summa
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94 WINDEMUTH ET AL.Table 2. Signifi
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96 WINDEMUTH ET AL.Table 3. Summary
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98 WINDEMUTH ET AL.Table 6. List of
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100 WINDEMUTH ET AL.Table 6. (Conti
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102 WINDEMUTH ET AL.Table 6. (Conti
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104 WINDEMUTH ET AL.much of a surpr
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106 WINDEMUTH ET AL.Given our resul
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Genetic Variation and the Control o
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GENETIC CONTROL OF TRANSCRIPTION 11
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GENETIC CONTROL OF TRANSCRIPTION 11
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Genome-wide Detection and Analysis
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RECENT SEGMENTAL DUPLICATIONS 117Fi
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RECENT SEGMENTAL DUPLICATIONS 119St
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RECENT SEGMENTAL DUPLICATIONS 121Co
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RECENT SEGMENTAL DUPLICATIONS 123Ho
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The Effects of Evolutionary Distanc
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EVOLUTIONARY DISTANCE AND GENE PRED
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EVOLUTIONARY DISTANCE AND GENE PRED
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Lineage-specific Expansion of KRAB
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EVOLUTION OF ZNF GENES 133Figure 2.
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EVOLUTION OF ZNF GENES 135Figure 4.
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EVOLUTION OF ZNF GENES 137get gene,
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EVOLUTION OF ZNF GENES 139Y., Goodw
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Sequence Organization and Functiona
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CENTROMERE ANNOTATION 143THE CENTRO
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CENTROMERE ANNOTATION 145Figure 4.
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CENTROMERE ANNOTATION 147CONCLUSION
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CENTROMERE ANNOTATION 149Schueler M
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152 PARKHILL AND THOMSONFigure 1. T
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154 PARKHILL AND THOMSONshow very h
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156 PARKHILL AND THOMSONGene Loss a
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158 PARKHILL AND THOMSONYersinia ad
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160 MCKAY ET AL.Choosing Candidate
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162 MCKAY ET AL.new comparative too
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164 MCKAY ET AL.rich. Based on a th
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166 MCKAY ET AL.Embryonic Muscle an
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168 MCKAY ET AL.native polyadenylat
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Building Comparative Maps Using 1.5
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HUMAN CHROMOSOME 1p IN THE DOG 1731
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HUMAN CHROMOSOME 1p IN THE DOG 175(
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HUMAN CHROMOSOME 1p IN THE DOG 177l
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180 GEORGES AND ANDERSSON5. There i
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182 GEORGES AND ANDERSSONplied to r
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184 GEORGES AND ANDERSSONbe common
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186 GEORGES AND ANDERSSONin humans
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Evolving Methods for the Assembly o
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ASSEMBLING LARGE GENOMES 191Figure
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ASSEMBLING LARGE GENOMES 193tant ad
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Mouse Genome Encyclopedia ProjectY.
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MOUSE GENOME ENCYCLOPEDIA PROJECT 1
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DNA Sequence Assembly and Multiple
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EULERIAN ASSEMBLY AND MULTIPLE ALIG
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Ensembl: A Genome InfrastructureE.
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ENSEMBL 215projects often submit th
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218 ZHANGthe majority of these are
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220 ZHANGFigure 2. Demonstration of
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222 ZHANG(G.X. Chen et al., in prep
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224 ZHANGWe are waiting for experim
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Ontologies for Biologists: A Commun
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ONTOLOGIES FOR BIOLOGISTS 229al. 20
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ONTOLOGIES FOR BIOLOGISTS 231TOPIC
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ONTOLOGIES FOR BIOLOGISTS 233a.b.Fi
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ONTOLOGIES FOR BIOLOGISTS 2352003.
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238 JOSHI-TOPE ET AL.Figure 1. The
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240 JOSHI-TOPE ET AL.state of knowl
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242 JOSHI-TOPE ET AL.and co-immunop
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The Share of Human Genomic DNA unde
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DNA UNDER SELECTION FROM HUMAN-MOUS
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Detecting Highly Conserved Regions
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DETECTING MULTISPECIES CONSERVED SE
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266 ROE ET AL.noncoding regions. On
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268 ROE ET AL.a48 hpf embryos in Mi
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270 ROE ET AL.aNovel gene KIAA0819[
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272 ROE ET AL.aMouseRatAP00354.2 Hu
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274 ROE ET AL.Tautz D. and Pfeifle
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276 JAILLON ET AL.Detection of Evol
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278 JAILLON ET AL.Table 1. Distribu
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280 JAILLON ET AL.Table 3. Distribu
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282 JAILLON ET AL.ecotig is a resul
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284 OVCHARENKO AND LOOTSdivergent r
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286 OVCHARENKO AND LOOTSmodulation
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288 OVCHARENKO AND LOOTSsequencing
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290 OVCHARENKO AND LOOTSments of cl
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Evolution of Eukaryotic Gene Repert
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EVOLUTION OF EUKARYOTIC GENES AND I
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304 PENNACCHIO, BAROUKH, AND RUBINA
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306 PENNACCHIO, BAROUKH, AND RUBINh
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308 PENNACCHIO, BAROUKH, AND RUBINA
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High-Throughput Mouse Knockouts Pro
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314 FRIDDLE ET AL.screen to lines o
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Identification of Novel Functional
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100 bp ladder68G1168G1168H1168H6100
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FUNCTIONAL ELEMENTS IN HUMAN DNA 32
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High-resolution Human Genome Scanni
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HUMAN GENOME SCANNING 325false-posi
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HUMAN GENOME SCANNING 327affecting
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HUMAN GENOME SCANNING 329methods fo
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332 MALEK ET AL.Figure 1. The bacte
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334 MALEK ET AL.J., Vincent S., and
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336 HARDISON ET AL.reflect blocks o
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338 HARDISON ET AL.plain the region
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340 HARDISON ET AL.CALIBRATION OF T
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342 HARDISON ET AL.PositionRP2.3noE
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344 HARDISON ET AL.cific chromosoma
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346 WESTON ET AL.these differences
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348 WESTON ET AL.els controlled by
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350 WESTON ET AL.ures prominently i
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352 WESTON ET AL.nal and Bop, which
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354 WESTON ET AL.ablp 1466 bopbcrtB
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356 WESTON ET AL.like fold (Fig. 6)
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Implications of Genomics for Public
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GENETIC EPIDEMIOLOGY 361lytic epide
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GENETIC EPIDEMIOLOGY 363curate risk
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A Model System for Identifying Gene
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PTC TASTE GENETICS 367Figure 2. Hap
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PTC TASTE GENETICS 369Table 2. Hapl
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PTC TASTE GENETICS 371the emergence
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374 MCCALLION ET AL.Figure 1. Schem
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376 MCCALLION ET AL.lier (Carrasqui
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378 MCCALLION ET AL.Table 3. HSCR A
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380 MCCALLION ET AL.Figure 3. Trans
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Genetics of Schizophrenia and Bipol
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SCHIZOPHRENIA AND BIPOLAR AFFECTIVE
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The Genetics of Common Diseases: 10
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GENETICS OF COMMON DISEASES 397with
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GENETICS OF COMMON DISEASES 399SELE
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GENETICS OF COMMON DISEASES 401F.,
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404 CHEUNG ET AL.netic analysis. Ex
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406 CHEUNG ET AL.Figure 3. The expr
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Page 422: α-SYNUCLEIN EXPRESSION AND PD 415g
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Page 429 and 430: 422 BOTSTEINFigure 6. Kaplan-Meier
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Page 433 and 434: 426 ANTONARAKIS ET AL.1316192225283
Page 435 and 436: 428 ANTONARAKIS ET AL.Figure 5. Sam
Page 437 and 438: 430 ANTONARAKIS ET AL.POPULATION VA
Page 439 and 440: 432 JORGENSEN ET AL.tive small mole
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Page 449 and 450: 442 JORGENSEN ET AL.Giaever G., Chu
Page 452 and 453: Genomic Disorders: Genome Architect
Page 454 and 455: GENOME ARCHITECTURE AND GENOMIC DIS
Page 462 and 463: Human Versus Chimpanzee Chromosome-
Page 464 and 465: HUMAN VS. CHIMP CHROMOSOME COMPARIS
Page 468 and 469: Novel Transcriptional Units and Unc
Page 470 and 471: TRANSCRIPTIONAL UNITS AND GENE PAIR
Page 478 and 479: mtDNA Variation, Climatic Adaptatio
Page 480 and 481: mtDNA VARIATION 473Figure 3. Region
Page 482 and 483: ANALYSIS OF ADAPTIVE SELECTION FORR
Page 484 and 485: mtDNA VARIATION 477Figure 8. Temper
Page 486 and 487: Positive Selection in the Human Gen
Page 488 and 489: HUMAN-SPECIFIC EVOLUTIONARY CHANGES
Page 490 and 491: HUMAN-SPECIFIC EVOLUTIONARY CHANGES
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Page 495 and 496: 488 UNDERHILLorigin episodes, each
Page 497 and 498: 490 UNDERHILLhaplogroups C through
Page 499 and 500: 492 UNDERHILLO (Fig. 2e) that share
Page 502 and 503: The New Quantitative BiologyM.V. OL
Page 504 and 505: NEW QUANTITATIVE BIOLOGY 497alone.
Page 506 and 507: NEW QUANTITATIVE BIOLOGY 499There w
Page 508 and 509: NEW QUANTITATIVE BIOLOGY 501ceded,
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