The Genom of Homo sapiens.pdf

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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
Page 126 and 127: RECENT SEGMENTAL DUPLICATIONS 119St
Page 128 and 129: RECENT SEGMENTAL DUPLICATIONS 121Co
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
Page 136 and 137: EVOLUTIONARY DISTANCE AND GENE PRED
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 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: 168 MCKAY ET AL.native polyadenylat
Page 179 and 180: 172 GUYON ET AL.Table 1. Map Statis
Page 181 and 182: 174 GUYON ET AL.only in one of the
Page 183 and 184: 176 GUYON ET AL.million reads (mean
Page 186 and 187: Positional Identification of Struct
Page 188 and 189: IDENTIFYING LIVESTOCK QTN 181initia
Page 190 and 191: IDENTIFYING LIVESTOCK QTN 183tation
Page 192 and 193: IDENTIFYING LIVESTOCK QTN 185The fa
Page 194: IDENTIFYING LIVESTOCK QTN 187Farnir
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
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ANALYSIS OF HUMAN PROMOTERS 219Inte
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ANALYSIS OF HUMAN PROMOTERS 221Figu
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ANALYSIS OF HUMAN PROMOTERS 223nacc
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ANALYSIS OF HUMAN PROMOTERS 225E2F
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228 ASHBURNER ET AL.cally meaningfu
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230 ASHBURNER ET AL.man protein ann
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232 ASHBURNER ET AL.associations be
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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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