Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921.
Article
CAS
PubMed
Google Scholar
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA: The sequence of the human genome. Science. 2001, 291: 1304-1351.
Article
CAS
PubMed
Google Scholar
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE: Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004, 428: 493-521.
Article
CAS
PubMed
Google Scholar
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P: Initial sequencing and comparative analysis of the mouse genome. Nature. 2002, 420: 520-562.
Article
CAS
PubMed
Google Scholar
Finishing the euchromatic sequence of the human genome. Nature. 2004, 431: 931-945.
Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, Bult CJ, Agarwala R, Cherry JL, DiCuccio M: Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol. 2009, 7: e1000112-
Article
PubMed Central
PubMed
Google Scholar
Cordaux R, Batzer MA: The impact of retrotransposons on human genome evolution. Nat Rev Genet. 2009, 10: 691-703.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D: Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med. 2011, 365: 709-717.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dimalanta ET, Lim A, Runnheim R, Lamers C, Churas C, Forrest DK, de Pablo JJ, Graham MD, Coppersmith SN, Goldstein S: A microfluidic system for large DNA molecule arrays. Anal Chem. 2004, 76: 5293-5301.
Article
CAS
PubMed
Google Scholar
Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM: High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A. 2010, 107: 10848-10853.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhou S, Wei F, Nguyen J, Bechner M, Potamousis K, Goldstein S, Pape L, Mehan MR, Churas C, Pasternak S: A single molecule scaffold for the maize genome. PLoS Genet. 2009, 5: e1000711-
Article
PubMed Central
PubMed
Google Scholar
Ajay SS, Parker SC, Ozel Abaan H, Fuentes Fajardo KV, Margulies EH: Accurate and comprehensive sequencing of personal genomes. Genome Res. 2011, 21: 1498-1505.
Article
PubMed Central
PubMed
Google Scholar
Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L: Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007, 318: 420-426.
Article
PubMed Central
CAS
PubMed
Google Scholar
Treangen TJ, Salzberg SL: Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet. 2012, 13: 36-46.
CAS
Google Scholar
Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L: CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods. 2011, 8: 652-654.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S: High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 2011, 108: 1513-1518.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L: Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res. 2011, 21: 665-675.
Article
PubMed Central
CAS
PubMed
Google Scholar
Peng Z, Zhao Z, Nath N, Froula JL, Clum A, Zhang T, Cheng JF, Copeland AC, Pennacchio LA, Chen F: Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS One. 2012, 7: e29437-
Article
PubMed Central
CAS
PubMed
Google Scholar
Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J: Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010, 463: 943-947.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hampton OA, Miller CA, Koriabine M, Li J, Den Hollander P, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ: Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines. Cancer Genet. 2011, 204: 447-457.
Article
PubMed Central
CAS
PubMed
Google Scholar
Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK: Paired-end sequencing of Fosmid libraries by Illumina. Genome Res. 2012, 22: 2241-2249.
Article
PubMed Central
CAS
PubMed
Google Scholar
Herschleb J, Ananiev G, Schwartz DC: Pulsed-field gel electrophoresis. Nat Protoc. 2007, 2: 677-684.
Article
CAS
PubMed
Google Scholar
Schwartz DC, Cantor CR: Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell. 1984, 37: 67-75.
Article
CAS
PubMed
Google Scholar
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S: Ensembl 2012. Nucleic Acids Res. 2012, 40 (Database issue): D84-90.
Article
PubMed Central
CAS
PubMed
Google Scholar
Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W: Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 2011, 27: 578-579.
Article
CAS
PubMed
Google Scholar
Sarkar D, Goldstein S, Schwartz DC, Newton MA: Statistical significance of optical map alignments. J Comput Biol. 2012, 19: 478-492.
Article
PubMed Central
CAS
PubMed
Google Scholar
Valouev A, Schwartz DC, Zhou S, Waterman MS: An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc Natl Acad Sci U S A. 2006, 103: 15770-15775.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K: De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010, 20: 265-272.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ye L, Hillier LW, Minx P, Thane N, Locke DP, Martin JC, Chen L, Mitreva M, Miller JR, Haub KV: A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol. 2011, 12: R31-
Article
PubMed Central
CAS
PubMed
Google Scholar
Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping. Nat Rev Genet. 2011, 12: 363-376.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kloosterman WP, Guryev V, van Roosmalen M, Duran KJ, de Bruijn E, Bakker SC, Letteboer T, van Nesselrooij B, Hochstenbach R, Poot M: Chromothripsis as a mechanism driving complex de novo structural rearrangements in the germline. Hum Mol Genet. 2011, 20: 1916-1924.
Article
CAS
PubMed
Google Scholar
Kloosterman WP, Hoogstraat M, Paling O, Tavakoli-Yaraki M, Renkens I, Vermaat JS, van Roosmalen MJ, van Lieshout S, Nijman IJ, Roessingh W: Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biol. 2011, 12: R103-
Article
PubMed Central
CAS
PubMed
Google Scholar
Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA: Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011, 144: 27-40.
Article
PubMed Central
CAS
PubMed
Google Scholar
Molenaar JJ, Koster J, Zwijnenburg DA, van Sluis P, Valentijn LJ, van der Ploeg I, Hamdi M, van Nes J, Westerman BA, van Arkel J: Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature. 2012, 483: 589-593.
Article
CAS
PubMed
Google Scholar
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F: Mapping and sequencing of structural variation from eight human genomes. Nature. 2008, 453: 56-64.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G: Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods. 2010, 7: 365-371.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760.
Article
PubMed Central
CAS
PubMed
Google Scholar