The Genom of Homo sapiens.pdf

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IDENTIFYING LIVESTOCK QTN 187Farnir F., Coppieters W., Arranz J.-J., Berzi P., Cambisano N.,Grisart B., Karim L., Marcq F., Moreau L., Mni M., Nezer C.,Simon P., Vanmanshoven P., Wagenaar D., and Georges M.2000. Extensive genome-wide linkage disequilibrium in cattle.Genome Res. 10: 220.Georges M., Nielsen D., Mackinnon M., Mishra A., Okimoto R.,Pasquino A.T., Sargeant L.S., Sorensen A., Steele M.R., ZhaoX., Womack J.E., and Hoeschele I. 1995. Mapping quantitativetrait loci controlling milk production by exploitingprogeny testing. Genetics 139: 907.Giuffra E., Kijas J.M.H., Amarger V., Carlborg Ö., Jeon J.-T.,and Andersson L. 2000. The origin of the domestic pig: Independentdomestication and subsequent introgression. Genetics154: 1785.Glazier A.M., Nadeau J.H., and Aitman T.J. 2002. Finding genesthat underlie complex traits. Science 298: 2345.Grisart B., Coppieters W., Farnir F., Karim L., Ford C., CambisanoN., Mni M., Reid S., Spelman R., Georges M., andSnell R. 2002. 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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.
Page 144 and 145: EVOLUTION OF ZNF GENES 137get gene,
Page 146 and 147: EVOLUTION OF ZNF GENES 139Y., Goodw
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(
Page 184: HUMAN CHROMOSOME 1p IN THE DOG 177l
Page 187 and 188: 180 GEORGES AND ANDERSSON5. There i
Page 189 and 190: 182 GEORGES AND ANDERSSONplied to r
Page 191 and 192: 184 GEORGES AND ANDERSSONbe common
Page 193: 186 GEORGES AND ANDERSSONin humans
Page 197 and 198: 190 GIBBS AND WEINSTOCKBACATLASWGSF
Page 199 and 200: 192 GIBBS AND WEINSTOCKsentation of
Page 201 and 202: 194 GIBBS AND WEINSTOCKCONCLUSIONSE
Page 203 and 204: 196 HAYASHIZAKIFigure 1. Strategy f
Page 205 and 206: 198 HAYASHIZAKIpasses per day. Ther
Page 207 and 208: 200 HAYASHIZAKIto known genes. As s
Page 209 and 210: 202 HAYASHIZAKIaged small amounts o
Page 211 and 212: 204 HAYASHIZAKIanalysis of more tha
Page 213 and 214: 206 ZHANG AND WATERMAN(a)Repeat Rep
Page 215 and 216: 208 ZHANG AND WATERMAN501234301245(
Page 217 and 218: 210 ZHANG AND WATERMANing and Green
Page 219 and 220: 212 ZHANG AND WATERMANACKNOWLEDGMEN
Page 221 and 222: 214 BIRNEY ET AL.Table 1. General I
Page 224 and 225: Prediction, Annotation, and Analysi
Page 226 and 227: ANALYSIS OF HUMAN PROMOTERS 219Inte
Page 228 and 229: ANALYSIS OF HUMAN PROMOTERS 221Figu
Page 230 and 231: ANALYSIS OF HUMAN PROMOTERS 223nacc
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Page 235 and 236: 228 ASHBURNER ET AL.cally meaningfu
Page 237 and 238: 230 ASHBURNER ET AL.man protein ann
Page 239 and 240: 232 ASHBURNER ET AL.associations be
Page 241 and 242: 234 ASHBURNER ET AL.cabulary for th
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The Genome Knowledgebase: A Resourc
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THE GENOME KNOWLEDGEBASE 239Figure
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THE GENOME KNOWLEDGEBASE 241by the
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THE GENOME KNOWLEDGEBASE 243Karp P.
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246 CHIAROMONTE ET AL.We make no pa
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248 CHIAROMONTE ET AL.Figure 1. Smo
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250 CHIAROMONTE ET AL.can use this
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252 CHIAROMONTE ET AL.However, we c
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254 CHIAROMONTE ET AL.Ihaka R. and
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256 MARGULIES ET AL.HumanMouseFuguR
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258 MARGULIES ET AL.Base Position 1
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260 MARGULIES ET AL.Figure 4. Gener
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262 MARGULIES ET AL.CONCLUSIONSWith
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Comparative Analysis of Human Chrom
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COMPARATIVE GENOMIC ANALYSIS 267aBa
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COMPARATIVE GENOMIC ANALYSIS 269µg
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COMPARATIVE GENOMIC ANALYSIS 271aHu
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COMPARATIVE GENOMIC ANALYSIS 273___
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Genome-wide Analyses Based on Compa
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WHOLE-GENOME COMPARISONS 277Figure
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WHOLE-GENOME COMPARISONS 279Table 2
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WHOLE-GENOME COMPARISONS 281models
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Comparative Genomic Tools for Explo
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COMPUTATIONAL TOOLS FOR ANALYZING G
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294 ROGOZIN ET AL.BeTs are combined
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296 ROGOZIN ET AL.Dm Hs Ce Sc Sp Ec
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298 ROGOZIN ET AL.Dm Ag Hs Ce Sc Sp
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300 ROGOZIN ET AL.gene lossgene gai
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Human-Mouse Comparative Genomics: S
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HUMAN-MOUSE COMPARATIVE GENOMICS 30
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MOUSE KNOCKOUTS ILLUSTRATE FUNCTION
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MOUSE KNOCKOUTS ILLUSTRATE FUNCTION
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318 LIAN ET AL.0 12 34 5 6 78 9 101
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320 LIAN ET AL.90 minutes and the c
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322 LIAN ET AL.Iyer V.I., Horak C.A
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324 LI ET AL.Figure 1. Array-based
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326 LI ET AL.Figure 4. Test of quan
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328 LI ET AL.Figure 5. Comparison o
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Annotation of Novel Proteins Utiliz
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FUNCTIONAL SHOTGUN SEQUENCING 333Fi
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Global Predictions and Tests of Ery
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PREDICTING GENE REGULATORY REGIONS
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Systems Approaches Applied to the S
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SYSTEMS BIOLOGY IN S. CEREVISIAE AN
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360 MERIKANGASidentification of gen
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362 MERIKANGASDay 1984; Ottman 1990
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364 MERIKANGASPrevention Research G
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366 DRAYNA ET AL.Figure 1. Distribu
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368 DRAYNA ET AL.Table 1. Summary o
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370 DRAYNA ET AL.Figure 5. Predicte
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Genomic Variation in Multigenic Tra
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GENOMIC VARIATION IN MULTIGENIC TRA
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384 PORTEOUS ET AL.of these devasta
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386 PORTEOUS ET AL.Figure 2. The t(
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388 PORTEOUS ET AL.Figure 3. DISC1
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390 PORTEOUS ET AL.cgi-bin/hgGatewa
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392 PORTEOUS ET AL.REFERENCESAshers
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394 PORTEOUS ET AL.Valles V., Van O
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396 GOLDSTEIN, CAVALLERI, AND AHMAD
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Genetics of Quantitative Variation
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HUMAN GENE EXPRESSION VARIATION 405
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HUMAN GENE EXPRESSION VARIATION 407
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410 CHIBA-FALEK AND NUSSBAUMconcent
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412 CHIBA-FALEK AND NUSSBAUMTable 4
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414 CHIBA-FALEK AND NUSSBAUMclein i
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Genomic Perspective and CancerD. BO
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GENOMIC PERSPECTIVE AND CANCER 419F
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GENOMIC PERSPECTIVE AND CANCER 421F
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GENOMIC PERSPECTIVE AND CANCER 423f
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Chromosome 21 and Down Syndrome: Th
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DOWN SYNDROME AND HUMAN CHROMOSOME
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DOWN SYNDROME AND HUMAN CHROMOSOME
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Harvesting the Genome’s Bounty: I
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INTEGRATIVE GENOMICS 433with high-d
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INTEGRATIVE GENOMICS 435497 baits3,
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INTEGRATIVE GENOMICS 437In contrast
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INTEGRATIVE GENOMICS 439Fly19,912Ye
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INTEGRATIVE GENOMICS 441IMPLICATION
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INTEGRATIVE GENOMICS 443gene intera
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446 STANKIEWICZ ET AL.Table 1. Sele
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448 STANKIEWICZ ET AL.al. 2002; Wal
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450 STANKIEWICZ ET AL.ate DNA rearr
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452 STANKIEWICZ ET AL.Figure 5. Sch
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454 STANKIEWICZ ET AL.Legius E. 200
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456 SAKAKI ET AL.determined. We pai
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458 SAKAKI ET AL.Table 2. Base Subs
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460 SAKAKI ET AL.D.R. 2003. Genomic
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462 LIPOVICH AND KINGtions that cre
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464 LIPOVICH AND KINGto-tail antise
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466 LIPOVICH AND KINGFigure 2. Perl
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468 LIPOVICH AND KINGtions. In inte
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470 LIPOVICH AND KINGOlson M.V. and
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472 WALLACE, RUIZ-PESINI, AND MISHM
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480 CLARK ET AL.Table 1. Derivation
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482 CLARK ET AL.Table 3. Biological
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484 CLARK ET AL.be under adaptive e
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Inferring Human History: Clues from
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Y-CHROMOSOME HAPLOTYPES AND GEOGRAP
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496 OLSONTable 1. Talks Grouped by
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498 OLSONbacterial lineages prosper
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500 OLSONwill respond to perturbati
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502 OLSONIn short, much remained to
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