The Diploid Genome Sequence of an Individual Human

1924, The sex chromosomes of man., Am Nat, 58, 506, 10.1086/280002

1956, The chromosome number of man., Hereditas, 42, 1

1961, Chromosomal aberrations in man., Am J Hum Genet, 13, 175

1970, Identification of human chromosomes by DNA-binding fluorescent agents., Chromosoma, 30, 215

1991, Light-directed, spatially addressable parallel chemical synthesis., Science, 251, 767, 10.1126/science.1990438

1998, High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays., Nat Genet, 20, 207, 10.1038/2524

2001, The sequence of the human genome., Science, 291, 1304, 10.1126/science.1058040

2001, Initial sequencing and analysis of the human genome., Nature, 409, 860, 10.1038/35057062

International Human Genome Sequencing Consortium, 2004, Finishing the euchromatic sequence of the human genome., Nature, 431, 931, 10.1038/nature03001

2004, Shotgun sequence assembly and recent segmental duplications within the human genome., Nature, 431, 927, 10.1038/nature03062

2006, Structural variation in the human genome., Nat Rev Genet, 7, 85, 10.1038/nrg1767

2006, Strategies for the detection of copy number and other structural variants in the human genome., Hum Genomics, 2, 403, 10.1186/1479-7364-2-6-403

2006, Copy number variation: New insights in genome diversity., Genome Res, 16, 949, 10.1101/gr.3677206

2006, Structural variants: Changing the landscape of chromosomes and design of disease studies., Hum Mol Genet, 15, R57

2006, Structural variation of the human genome., Annu Rev Genomics Hum Genet, 7, 407, 10.1146/annurev.genom.7.080505.115618

2003, Meta-analysis of indels causing human genetic disease: Mechanisms of mutagenesis and the role of local DNA sequence complexity., Hum Mutat, 21, 28, 10.1002/humu.10146

2005, Microdeletions and microinsertions causing human genetic disease: Common mechanisms of mutagenesis and the role of local DNA sequence complexity., Hum Mutat, 26, 205, 10.1002/humu.20212

2003, Human Gene Mutation Database (HGMD): 2003 update., Hum Mutat, 21, 577

2005, The transcriptional landscape of the mammalian genome., Science, 309, 1559, 10.1126/science.1112014

2006, Tagging mammalian transcription complexity., Trends Genet, 22, 501, 10.1016/j.tig.2006.07.003

2002, Initial sequencing and comparative analysis of the mouse genome., Nature, 420, 520, 10.1038/nature01262

Chimpanzee Sequencing and Analysis Consortium, 2005, Initial sequence of the chimpanzee genome and comparison with the human genome., Nature, 437, 69, 10.1038/nature04072

2007, Evolutionary and biomedical insights from the rhesus macaque genome., Science, 316, 222, 10.1126/science.1139247

2001, Genomic strategies to identify mammalian regulatory sequences., Nat Rev Genet, 2, 100, 10.1038/35052548

2002, rVista for comparative sequence-based discovery of functional transcription factor binding sites., Genome Res, 12, 832, 10.1101/gr.225502

2000, Comparative genomics of the eukaryotes., Science, 287, 2204, 10.1126/science.287.5461.2204

2003, Strategies and tools for whole-genome alignments., Genome Res, 13, 73, 10.1101/gr.762503

2003, Cross-species sequence comparisons: A review of methods and available resources., Genome Res, 13, 1, 10.1101/gr.222003

2002, Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover., Mol Biol Evol, 19, 1114, 10.1093/oxfordjournals.molbev.a004169

2001, Noncoding RNA gene detection using comparative sequence analysis., BMC Bioinformatics, 2, 8, 10.1186/1471-2105-2-8

2004, The microRNA registry., Nucleic Acids Res, 32, D109, 10.1093/nar/gkh023

2006, miRBase: The microRNA sequence database., Methods Mol Biol, 342, 129

2007, miRGen: A database for the study of animal microRNA genomic organization and function., Nucleic Acids Res, 35, D149, 10.1093/nar/gkl904

2007, Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues., Physiol Genomics, 29, 35, 10.1152/physiolgenomics.00081.2006

The International HapMap Consortium, 2005, A haplotype map of the human genome., Nature, 437, 1299, 10.1038/nature04226

2004, Characterization of a common susceptibility locus for asthma-related traits., Science, 304, 300, 10.1126/science.1090010

2005, Complement factor H polymorphism in age-related macular degeneration., Science, 308, 385, 10.1126/science.1109557

2007, A genome-wide association study identifies novel risk loci for type 2 diabetes., Nature, 445, 881, 10.1038/nature05616

2005, Genome-wide association studies for common diseases and complex traits., Nat Rev Genet, 6, 95, 10.1038/nrg1521

2004, Whole-genome shotgun assembly and comparison of human genome assemblies., Proc Natl Acad Sci U S A, 101, 1916, 10.1073/pnas.0307971100

2000, Human BAC ends quality assessment and sequence analyses., Genomics, 63, 321, 10.1006/geno.1999.6082

2005, A tool for analyzing mate pairs in assemblies (TAMPA)., J Comput Biol, 12, 497, 10.1089/cmb.2005.12.497

1977, Is the most frequent allele the oldest?, Theor Popul Biol, 11, 141, 10.1016/0040-5809(77)90023-5

2005, Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes., Hum Mol Genet, 14, 59, 10.1093/hmg/ddi006

2004, Pattern of sequence variation across 213 environmental response genes., Genome Res, 14, 1821, 10.1101/gr.2730004

1999, Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis., Nat Genet, 22, 239, 10.1038/10297

1999, Characterization of single-nucleotide polymorphisms in coding regions of human genes., Nat Genet, 22, 231, 10.1038/10290

1999, Tandem repeats finder: A program to analyze DNA sequences., Nucleic Acids Res, 27, 573, 10.1093/nar/27.2.573

Encode Project Consortium, 2004, The ENCODE (ENCyclopedia Of DNA Elements) Project., Science, 306, 636, 10.1126/science.1105136

2002, Human diallelic insertion/deletion polymorphisms., Am J Hum Genet, 71, 854, 10.1086/342727

2006, Automating resequencing-based detection of insertion-deletion polymorphisms., Nat Genet, 38, 1457, 10.1038/ng1925

2002, Alu repeats and human genomic diversity., Nat Rev Genet, 3, 370, 10.1038/nrg798

2006, Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms., Gene, 365, 11, 10.1016/j.gene.2005.09.031

2006, dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans., Hum Mutat, 27, 323, 10.1002/humu.20307

2006, An initial map of insertion and deletion (INDEL) variation in the human genome., Genome Res, 16, 1182, 10.1101/gr.4565806

2006, A high-resolution survey of deletion polymorphism in the human genome., Nat Genet, 38, 75, 10.1038/ng1697

2006, Common deletion polymorphisms in the human genome., Nat Genet, 38, 86, 10.1038/ng1696

2006, Common deletions and SNPs are in linkage disequilibrium in the human genome., Nat Genet, 38, 82, 10.1038/ng1695

2006, Genome assembly comparison identifies structural variants in the human genome., Nat Genet, 38, 1413, 10.1038/ng1921

2002, Recent segmental duplications in the human genome., Science, 297, 1003, 10.1126/science.1072047

2003, Genome-wide detection of segmental duplications and potential assembly errors in the human genome sequence., Genome Biol, 4, R25, 10.1186/gb-2003-4-4-r25

2006, Global variation in copy number in the human genome., Nature, 444, 444, 10.1038/nature05329

2004, Detection of large-scale variation in the human genome., Nat Genet, 36, 949, 10.1038/ng1416

2004, Large-scale copy number polymorphism in the human genome., Science, 305, 525, 10.1126/science.1098918

2005, Positional identification of TNFSF4, encoding OX40 ligand, as a gene that influences atherosclerosis susceptibility., Nat Genet, 37, 365, 10.1038/ng1524

2001, High-resolution haplotype structure in the human genome., Nat Genet, 29, 229, 10.1038/ng1001-229

2001, Haplotype variation and linkage disequilibrium in 313 human genes., Science, 293, 489, 10.1126/science.1059431

1999, Prospects for whole-genome linkage disequilibrium mapping of common disease genes., Nat Genet, 22, 139, 10.1038/9642

2004, Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium., Am J Hum Genet, 74, 106, 10.1086/381000

2002, Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem., Brief Bioinform, 3, 23, 10.1093/bib/3.1.23

2005, Polynomial and APX-hard cases of individual haplotyping problems., Theor Comp Sci, 335, 109, 10.1016/j.tcs.2004.12.017

2002, The structure of haplotype blocks in the human genome., Science, 296, 2225, 10.1126/science.1069424

2007, Mendelian Inheritance in Man and its online version, OMIM., Am J Hum Genet, 80, 588, 10.1086/514346

1997, The likelihood of being affected with Huntington disease by a particular age, for a specific CAG size., Am J Hum Genet, 60, 1202

2005, Association between a functional variant of the KLOTHO gene and high-density lipoprotein cholesterol, blood pressure, stroke, and longevity., Circ Res, 96, 412, 10.1161/01.RES.0000157171.04054.30

2003, Matrix metalloproteinase-3 genotype contributes to age-related aortic stiffening through modulation of gene and protein expression., Circ Res, 92, 1254, 10.1161/01.RES.0000076891.24317.CA

1991, The human glutathione S-transferases: A case-control study of the incidence of the GST1 0 phenotype in patients with adenocarcinoma., Carcinogenesis, 12, 25, 10.1093/carcin/12.1.25

1992, Increased cytogenetic damage in smokers deficient in glutathione S-transferase isozyme mu., Carcinogenesis, 13, 303, 10.1093/carcin/13.2.303

2004, Effect of glutathione-S-transferase M1 and P1 genotypes on xenobiotic enhancement of allergic responses: Randomised, placebo-controlled crossover study., Lancet, 363, 119, 10.1016/S0140-6736(03)15262-2

1996, Molecular characterization of the human peroxisomal branched-chain acyl-CoA oxidase: cDNA cloning, chromosomal assignment, tissue distribution, and evidence for the absence of the protein in Zellweger syndrome., Proc Natl Acad Sci U S A, 93, 13748, 10.1073/pnas.93.24.13748

2002, Identification of a variant associated with adult-type hypolactasia., Nat Genet, 30, 233, 10.1038/ng826

2006, Genomes for all., Sci Am, 294, 46, 10.1038/scientificamerican0106-46

2007, The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern tropical Pacific., PLoS Biol, 5

2005, Genome sequencing in microfabricated high-density picolitre reactors., Nature, 437, 376, 10.1038/nature03959

2005, Emerging technologies in DNA sequencing., Genome Res, 15, 1767, 10.1101/gr.3770505

2005, Accurate multiplex polony sequencing of an evolved bacterial genome., Science, 309, 1728, 10.1126/science.1117389

2004, Analysis of the centromeric regions of the human genome assembly., Trends Genet, 20, 529, 10.1016/j.tig.2004.08.008

1998, Base-calling of automated sequencer traces using phred. I. Accuracy assessment., Genome Res, 8, 175, 10.1101/gr.8.3.175

SambrookJFritschEManiatisT 1989 Molecular cloning. A laboratory manual Cold Spring Harbor (New York) Cold Spring Laboratory Press 999

1977, DNA sequencing with chain-terminating inhibitors., Proc Natl Acad Sci U S A, 74, 5463, 10.1073/pnas.74.12.5463

2000, A whole-genome assembly of Drosophila., Science, 287, 2196, 10.1126/science.287.5461.2196

2003, Whole-genome sequence assembly for mammalian genomes: Arachne 2., Genome Res, 13, 91, 10.1101/gr.828403

2004, ThurGood: Evaluating assembly-to-assembly mapping., J Comput Biol, 11, 800, 10.1089/cmb.2004.11.800

2005, Finding anchors for genomic sequence comparison., J Comput Biol, 12, 762, 10.1089/cmb.2005.12.762

2004, Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations., Am J Hum Genet, 74, 610, 10.1086/382227

2003, Large-scale genotyping of complex DNA., Nat Biotechnol, 21, 1233, 10.1038/nbt869

LiCWongWH 2003 DNA-Chip Analyzer (dChip). In: ParmigianiGGarrettESIrizarryRZegerSL The analysis of gene expression data: methods and software New York Springer 504

2005, A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays., Cancer Res, 65, 6071, 10.1158/0008-5472.CAN-05-0465

2006, Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays., Genome Res, 16, 1575, 10.1101/gr.5629106

2005, Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis., Cancer Res, 65, 5561, 10.1158/0008-5472.CAN-04-4603

2007, QuantiSNP: An Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data., Nucleic Acids Res, 35, 2013, 10.1093/nar/gkm076

2005, Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH., Genes Chromosomes Cancer, 44, 305, 10.1002/gcc.20243

2006, Accurate and reliable high-throughput detection of copy number variation in the human genome., Genome Res, 16, 1566, 10.1101/gr.5630906

2003, Human chromosome 7: DNA sequence and biology., Science, 300, 767, 10.1126/science.1083423

2002, A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome., Science, 296, 1661, 10.1126/science.1069193

2007, Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi., Genome Res, 17, 1101, 10.1101/gr.5894107