The Genom of Homo sapiens.pdf

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GENE EXPRESSION PROFILING IN C. ELEGANS 167or fewer tags per library). Tags corresponding to the gutspecificGATA-type zinc-finger factor elt-2 (Hawkinsand McGhee 1995; Fukushige et al. 1998) are present atthe highest level of any recognizable transcription factorin the gut library. The library provides an intriguing list ofa dozen or more transcription factors that, by the level oftranscript enrichment, are judged to be gut-specific, andyet nothing is yet known about them.Perhaps the most intriguing finding in either tissuespecificlibrary is the presence of experimentally unverifiedgene models derived from computational analysis forwhich there is no functional annotation. These genespromise much new territory to explore. As many of thesepredicted genes have human homologs, they are of particularrelevance to the themes of this symposium.Throughout the life cycle of any organism there are dynamicchanges in the expression profile of the genome.Tracking and displaying these changes in a way that leadsto further understanding of individual gene function andoverall gene regulation is one of the most significant challengesof 21st-century biology. We are exploring howbest to mine the SAGE data for information pertaining togene regulation and gene pathways and also to explorehow best to present the data for exploitation by others.The following are three examples of how one mighttrack and display a large gene family through development(Fig. 6). In the first example, we examined the largezinc-finger gene family. WormBase identifies 785 potentialzinc-finger-encoding transcripts. From our studies ofall developmental stages, we identified 1,299 specificSAGE tags corresponding to 625 genes. Their expressionprofile is illustrated in Figure 6A. We have done a similarstudy of cuticle collagens (SAGE identifies 167 of 206potential collagen genes annotated in WormBase, Fig.6B) and kinases (SAGE identifies 652 of 734 potential kinase-encodinggenes annotated in WormBase, Fig. 6B).In each of these large families, we were able to track atleast two-thirds of the genes. Although this is already asignificant achievement, we should be able to detect evenmore members of these large families if we use enrichedtissues.Tracking known genes is an important use of expressionprofiling data, but SAGE also enables gene discovery.In the embryonic SAGE and longSAGE libraries, atotal of 1,070 14-bp tags and 2,730 21-bp tags map tounique locations in the genomic DNA but do not map toany known nuclear, mitochondrial, or rRNA transcript.The larger number of unambiguous long tags demonstratesthe resolving power of longSAGE, which resolvedthe ambiguity of one-third of the ambiguous 14-bp tags inthis class. The SAGE protocol involves DNase treatmentof an RNA sample, so tags that map to genomic DNA butnot to predicted transcripts can be used to infer noveltranscribed sequences, or undocumented alternativesplice variants, or UTRs of known genes. For example,Jones et al. (2001) identified two novel transcribed sequencespossessing telomeric repeat-like sequences andno obvious open reading frame that are present at highabundance in dauer larvae but not in other life stages.Among the 14-bp “genomic” tags, 445 map to introns ofknown genes; this could be explained in large part by previouslyunknown exons or, more rarely, by small genesnested entirely within the intron. The remaining 625 genomictags map to regions for which there are no annotatedtranscribed sequences, and likely represent noveltranscription units or, if they are near known genes, alter-AExploiting the SAGE Data Sets: DevelopmentalProfiling and Gene DiscoveryBCKinasesFigure 6. Venn diagrams showing transcription profiles for sixstages of C. elegans development. Only specific SAGE tagswere considered. Transcripts are counted by virtue of presenceor absence rather than relative abundance. Putative alternativesplice variants identified by different SAGE tags for the samegene are counted separately. The criterion for presence of a transcriptis the observation of at least one tag of high-quality sequence(phred40). Regions of overlap indicate the number oftranscripts common to all affected stages. Numbers in black,red, blue, and green correspond to the count of transcripts observedin one, two, three, or all developmental stages. (A) Zincfingergenes. (B) Collagen genes. (C) Kinase genes.
168 MCKAY ET AL.native polyadenylation signals or UTRs not fully representedby ESTs. The improved resolution of longSAGEallowed us to identify 1,257 tags that map within intronsof known genes and 1,473 that occur in intergenic regions.Many of the novel tags overlap with regions of sequencesimilarity in orthologous regions of the genome ofthe related nematode C. briggsae, suggesting conservedregions may have functional significance. Comparativegenomics and directed RT-PCR experiments will be requiredto characterize the novel transcribed sequenceswhose presence we infer with genomic SAGE tags.CONCLUSIONS1. The C. elegans and human genomes are estimated tohave at least 4,300 orthologous gene pairs.2. The function of many of these genes is unknown ineither organism, but the simplicity of nematodeanatomy coupled with powerful genetic tools shouldcontribute to the understanding of their function.3. There are temporal and tissue-specific promoters, butfew or no single-cell promoters. Individual cell identitywithin a tissue would then appear to result fromcombinatorial overlaps.4. SAGE technology confirms the expression of at least14,600 genes in the nematode. This number will increaseas the technology is refined.5. SAGE reveals multiple different tags for half of thegenes in C. elegans, suggesting that alternative splicingof genes is common in this organism.6. Many of the SAGE tags map to unannotated regions ofthe nematode genome and thus may identify newgenes.7. The studies outlined here using promoter::GFP constructsand SAGE will lead to the establishment of agene expression database that can be interrogated tounderstand temporal and spatial patterning during development.8. We have established the minimum number of genesrequired for nematode embryogenesis, 7,000, and thenumber of genes required to determine and maintainthe function of a specific tissue, about 5,000.ACKNOWLEDGMENTSWe thank David Miller III and his colleagues at Vanderbiltfor providing us with their protocol for fragmentingembryos. Funding for this project was provided byGenome British Columbia and Genome Canada toD.L.B., S.J.M.J., M.M., and D.G.M. J.T. is the recipientof an International Prize Travelling Research Fellowshipfrom the Wellcome Trust. S.J. and M.M. are MichaelSmith Foundation Health Research Scholars. Additionalfunding was provided by National Institutes of Health operatinggrants AG-12689 and GM-60151 to D.L.R. and aCanadian Institute of Health Research grant to J.M.REFERENCESBeanan M.J. and Strome S. 1992. Characterization of a germ-lineproliferation mutation in C. elegans. Development 116: 755.Blumenthal T. 1995. Trans-splicing and polycistronic transcriptionin Caenorhabditis elegans. Trends Genet. 11: 132.Blumenthal T., Evans D., Link C.D., Guffanti A., Lawson D.,Thierry-Mieg J., Thierry-Mieg D., Chiu W.L., Duke K., KiralyM., and Kim S.K. 2002. A global analysis of Caenorhabditiselegans operons. Nature 417: 851.Bürglin T.R. 2000. A two-channel four-dimensional imagerecording and viewing system with automatic drift correction.J. Microsc. 200: 75.Cassata G., Kagoshima H., Pretot R.F., Aspock G., Niklaus G.,and Bürglin T.R. 1998. Rapid expression screening ofCaenorhabditis elegans homeobox open reading frames usinga two-step polymerase chain reaction promoter-gfp reporterconstruction technique. Gene 212: 127.C. elegans Sequencing Consortium. 1998. Genome sequence ofthe nematode C. elegans: A platform for investigating biology.Science 282: 2012.Chalfie M. 1995. Green fluorescent protein. Photochem. Photobiol.62: 651.Chalfie M., Tu Y., Euskirchen G., Ward W.W., and Prasher D.C.1994. Green fluorescent protein as a marker for gene expression.Science 263: 802.Christensen M., Estevez A., Yin X., Fox R., Morrison R., Mc-Donnell M., Gleason C., Miller D.M., III, and Strange K.2002. A primary culture system for functional analysis of C.elegans neurons and muscle cells. Neuron 33: 503.Clark D.V., Johnsen R.C., McKim K.S., and Baillie D.L. 1990.Analysis of lethal mutations induced in a mutator strain thatactivates transposable elements in Caehorhabditis elegans.Genome 33: 109.Ellis H.M. and Horvitz H.R. 1986. Genetic control of programmedcell death in the nematode C. elegans. Cell 44: 817.Epstein H.F., Casey D.L., and Ortiz I. 1993. Myosin andparamyosin of Caenorhabditis elegans embryos assembleinto nascent structures distinct from thick filaments and multifilamentassemblages. J. Cell Biol. 122: 845.Ewing B. and Green P. 1998. Base-calling of automated sequencertraces using phred. II. Error probabilities. GenomeRes. 8: 186.Fire A. 1994. A four dimensional digital archiving system forcell lineage tracing and retrospective embryology. Comput.Appl. Biosci. 10: 443.Fukushige T., Hawkins M.G., and McGhee J.D. 1998. TheGATA-factor elt-2 is essential for formation of theCaenorhabditis elegans intestine. Dev. Biol. 198: 286.Harris T.W., Lee R., Schwarz E., Bradnam K., Lawson D., ChenW., Blasier D., Kenny E., Cunningham F., Kishore R., ChanJ., Muller H.M., Petcherski A., Thorisson G., Day A., Bieri T.,Rogers A., Chen C.K., Spieth J., Sternberg P., Durbin R., andStein L.D. 2003. WormBase: A cross-species database forcomparative genomics. Nucleic Acids Res. 31: 133.Hawkins M.G. and McGhee J.D. 1995. elt-2, a second Gata factorfrom the nematode Caenorhabditis elegans. J. Biol. Chem.270: 14666.Hedgecock E.M., Sulston J.E., and Thomson J.N. 1983. Mutationsaffecting programmed cell deaths in the nematodeCaenorhabditis elegans. Science 220: 1277.Hill A.A., Hunter C.P., Tsung B.T., Tucker-Kellogg G., andBrown E.L. 2000. Genomic analysis of gene expression in C.elegans. Science 290: 809.Hobert O. 2002. PCR fusion-based approach to create reportergene constructs for expression analysis in transgenic C. elegans.Biotechniques 32: 728.Holt S.J. and Riddle D.L. 2003. SAGE surveys C. elegans carbohydratemetabolism: Evidence for an anaerobic shift in thelong-lived dauer larva. Mech. Ageing Dev. 124: 779.Hope I.A. 1991. “Promoter trapping” in Caenorhabditis elegans.Development 113: 399.Jones S.J.M., Riddle D.L., Pouzyrev A.T., Velculescu V.E.,Hillier L., Eddy S.R., Stricklin S.L., Baillie D.L., WaterstonR., and Marra M.A. 2001. Changes in gene expression associatedwith developmental arrest and longevity in Caenorhabditiselegans. Genome Res. 11: 1346.Kelly W.G., Xu S., Montgomery M.K., and Fire A. 1997. Dis-
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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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Page 144 and 145: EVOLUTION OF ZNF GENES 137get gene,
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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
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Page 163 and 164: 156 PARKHILL AND THOMSONGene Loss a
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Page 169 and 170: 162 MCKAY ET AL.new comparative too
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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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