The Genom of Homo sapiens.pdf

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EVOLUTION OF ZNF GENES 139Y., Goodwin G., Neiman P.E., Collins S.J., and LobanenkovV.V. 1996. An exceptionally conserved transcriptional repressor,CTCF, employs different combinations of zinc fingersto bind diverged promoter sequences of avian and mammalianc-myc oncogenes. Mol. Cell. Biol. 16: 2802.Friedman R. and Hughes A.L. 2003. The temporal distributionof gene duplication events in a set of highly conserved humangene families. Mol. Biol. Evol. 20: 154.Gaudieri S., Kulski J.K., Dawkins R.L., and Gojobori T. 1999.Different evolutionary histories in two subgenomic regions ofthe major histocompatibility complex. Genome Res. 9: 541.Gilad Y., Man O., Paabo S., and Lancet D. 2003. Human specificloss of olfactory receptor genes. Proc. Natl. Acad. Sci. 100:3324.Hennemann H., Vassen L., Geisen C., Eilers M., and Moroy T.2003. Identification of a novel Kruppel-associated box domainprotein, Krim-1, that interacts with c-Myc and inhibitsits oncogenic activity. J. Biol. 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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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Page 99 and 100: 92 WINDEMUTH ET AL.Table 1. A Summa
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Page 103 and 104: 96 WINDEMUTH ET AL.Table 3. Summary
Page 105 and 106: 98 WINDEMUTH ET AL.Table 6. List of
Page 107 and 108: 100 WINDEMUTH ET AL.Table 6. (Conti
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Page 111 and 112: 104 WINDEMUTH ET AL.much of a surpr
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Page 116 and 117: Genetic Variation and the Control o
Page 118 and 119: GENETIC CONTROL OF TRANSCRIPTION 11
Page 120 and 121: GENETIC CONTROL OF TRANSCRIPTION 11
Page 122 and 123: Genome-wide Detection and Analysis
Page 124 and 125: RECENT SEGMENTAL DUPLICATIONS 117Fi
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Page 130 and 131: RECENT SEGMENTAL DUPLICATIONS 123Ho
Page 132 and 133: The Effects of Evolutionary Distanc
Page 134 and 135: EVOLUTIONARY DISTANCE AND GENE PRED
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Page 138 and 139: Lineage-specific Expansion of KRAB
Page 140 and 141: EVOLUTION OF ZNF GENES 133Figure 2.
Page 142 and 143: EVOLUTION OF ZNF GENES 135Figure 4.
Page 144 and 145: EVOLUTION OF ZNF GENES 137get gene,
Page 148 and 149: Sequence Organization and Functiona
Page 150 and 151: CENTROMERE ANNOTATION 143THE CENTRO
Page 152 and 153: CENTROMERE ANNOTATION 145Figure 4.
Page 154 and 155: CENTROMERE ANNOTATION 147CONCLUSION
Page 156: CENTROMERE ANNOTATION 149Schueler M
Page 159 and 160: 152 PARKHILL AND THOMSONFigure 1. T
Page 161 and 162: 154 PARKHILL AND THOMSONshow very h
Page 163 and 164: 156 PARKHILL AND THOMSONGene Loss a
Page 165 and 166: 158 PARKHILL AND THOMSONYersinia ad
Page 167 and 168: 160 MCKAY ET AL.Choosing Candidate
Page 169 and 170: 162 MCKAY ET AL.new comparative too
Page 171 and 172: 164 MCKAY ET AL.rich. Based on a th
Page 173 and 174: 166 MCKAY ET AL.Embryonic Muscle an
Page 175 and 176: 168 MCKAY ET AL.native polyadenylat
Page 178 and 179: Building Comparative Maps Using 1.5
Page 180 and 181: HUMAN CHROMOSOME 1p IN THE DOG 1731
Page 182 and 183: HUMAN CHROMOSOME 1p IN THE DOG 175(
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Page 187 and 188: 180 GEORGES AND ANDERSSON5. There i
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Page 191 and 192: 184 GEORGES AND ANDERSSONbe common
Page 193 and 194: 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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Regulation of α-Synuclein Expressi
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α-SYNUCLEIN EXPRESSION AND PD 411T
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1. The levels of α-synuclein prote
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α-SYNUCLEIN EXPRESSION AND PD 415g
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418 BOTSTEINFigure 1. (A) Blectron
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420 BOTSTEINFigure 3. Cluster diagr
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422 BOTSTEINFigure 6. Kaplan-Meier
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424 BOTSTEINGarber M.E., Troyanskay
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426 ANTONARAKIS ET AL.1316192225283
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428 ANTONARAKIS ET AL.Figure 5. Sam
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430 ANTONARAKIS ET AL.POPULATION VA
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432 JORGENSEN ET AL.tive small mole
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434 JORGENSEN ET AL.FLAG-tagged pro
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436 JORGENSEN ET AL.visualization t
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438 JORGENSEN ET AL.AArp2/3 Complex
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Pathway40S440 JORGENSEN ET AL.ANutr
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442 JORGENSEN ET AL.Giaever G., Chu
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Genomic Disorders: Genome Architect
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GENOME ARCHITECTURE AND GENOMIC DIS
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Human Versus Chimpanzee Chromosome-
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HUMAN VS. CHIMP CHROMOSOME COMPARIS
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HUMAN VS. CHIMP CHROMOSOME COMPARIS
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Novel Transcriptional Units and Unc
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TRANSCRIPTIONAL UNITS AND GENE PAIR
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mtDNA Variation, Climatic Adaptatio
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mtDNA VARIATION 473Figure 3. Region
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ANALYSIS OF ADAPTIVE SELECTION FORR
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mtDNA VARIATION 477Figure 8. Temper
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Positive Selection in the Human Gen
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HUMAN-SPECIFIC EVOLUTIONARY CHANGES
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488 UNDERHILLorigin episodes, each
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490 UNDERHILLhaplogroups C through
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492 UNDERHILLO (Fig. 2e) that share
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The New Quantitative BiologyM.V. OL
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NEW QUANTITATIVE BIOLOGY 497alone.
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NEW QUANTITATIVE BIOLOGY 499There w
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NEW QUANTITATIVE BIOLOGY 501ceded,
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