Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE: Metagenomic analysis of the human distal gut microbiome. Science. 2006, 312: 1355-1359. 10.1126/science.1124234.
Article
PubMed Central
PubMed
CAS
Google Scholar
Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan M-S, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DMA, et al: Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002, 419: 498-511. 10.1038/nature01097.
Article
PubMed
CAS
Google Scholar
Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE, Tekaia F, Badcock K, Basham D, Brown D, Chillingworth T, Connor R, Davies R, Devlin K, Feltwell T, Gentles S, Hamlin N, Holroyd S, Hornsby T, Jagels K, Krogh A, McLean J, Moule S, Murphy L, Oliver K, Osborne J, et al: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998, 393: 537-544. 10.1038/31159.
Article
PubMed
CAS
Google Scholar
Campbell PJ, Stephens PJ, Pleasance ED, O’Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PAW, Bignell GR, Stratton MR, Futreal PA: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008, 40: 722-729. 10.1038/ng.128.
Article
PubMed Central
PubMed
CAS
Google Scholar
Ley TJ, Mardis ER, Ding L, Fulton B, Mclellan MD, Chen K, Dooling D, Dunford-shore BH, Mcgrath S, Cook L, Abbott R, Larson DE, Koboldt DC, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Fulton L, Magrini V, Wylie T, Glasscock J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, et al: DNA sequencing of a cytogenetically normal acute myeloid leukemia genome. Nature. 2008, 456: 66-72. 10.1038/nature07485.
Article
PubMed Central
PubMed
CAS
Google Scholar
Atlas TCG: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008, 455: 1061-1068. 10.1038/nature07385.
Article
Google Scholar
Shrestha AMS, Frith MC: An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome. Bioinformatics. 2013, 29: 965-972. 10.1093/bioinformatics/btt073.
Article
PubMed Central
PubMed
CAS
Google Scholar
Hoban S, Bertorelle G, Gaggiotti OE: Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet. 2011, 13: 110-122.
Google Scholar
Huang W, Li L, Myers JR, Marth GT: ART: a next-generation sequencing read simulator. Bioinformatics. 2012, 28: 593-594. 10.1093/bioinformatics/btr708.
Article
PubMed Central
PubMed
Google Scholar
Richter DC, Ott F, Auch AF, Schmid R, Huson DH: MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE. 2008, 3: e3373-10.1371/journal.pone.0003373.
Article
PubMed Central
PubMed
Google Scholar
Edwards TL, Bush WS, Turner SD, Dudek SM, Torstenson ES, Schmidt M, Martin E, Ritchie MD: Generating Linkage Disequilibrium Patterns in Data Simulations Using genomeSIMLA. Evol. Comput. Mach. Learn. Data Min. Bioinforma. Lect. Notes Comput. Sci. 2008, Berlin Heidelberg: Springer, 24-35. 4973
Google Scholar
Li C, Li M: GWAsimulator: a rapid whole-genome simulation program. Bioinformatics. 2008, 24: 140-142. 10.1093/bioinformatics/btm549.
Article
PubMed
CAS
Google Scholar
Hoggart CJ, Chadeau-Hyam M, Clark TG, Lampariello R, Whittaker JC, De Iorio M, Balding DJ: Sequence-level population simulations over large genomic regions. Genetics. 2007, 177: 1725-1731. 10.1534/genetics.106.069088.
Article
PubMed Central
PubMed
CAS
Google Scholar
Liang L, Zöllner S, Abecasis GR: GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics. 2007, 23: 1565-1567. 10.1093/bioinformatics/btm138.
Article
PubMed
CAS
Google Scholar
Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C: ALF–a simulation framework for genome evolution. Mol Biol Evol. 2012, 29: 1115-1123. 10.1093/molbev/msr268.
Article
PubMed Central
PubMed
CAS
Google Scholar
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P: Ensembl variation resources. BMC Genomics. 2010, 11: 293-10.1186/1471-2164-11-293.
Article
PubMed Central
PubMed
Google Scholar
The 1000 Genomes Project Consortium: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038/nature09534.
Article
PubMed Central
Google Scholar
The International HapMap Consortium: The International HapMap Project. Nature. 2003, 426: 789-796. 10.1038/nature02168.
Article
Google Scholar
Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer. 2004, 91: 355-358.
PubMed Central
PubMed
CAS
Google Scholar
Database of Genomic Variation Archive. http://www.ebi.ac.uk/dgva/,
Kudla G, Helwak A, Lipinski L: Gene conversion and GC-content evolution in mammalian Hsp70. Mol Biol Evol. 2004, 21: 1438-1444. 10.1093/molbev/msh146.
Article
PubMed
CAS
Google Scholar
Lercher MJ, Hurst LD: Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 2002, 18: 337-340. 10.1016/S0168-9525(02)02669-0.
Article
PubMed
CAS
Google Scholar
Dean J, Ghemawat S: MapReduce: Simplified Data Processing on Large Clusters. Commun ACM. 2008, 51: 1-13.
Article
Google Scholar
Apache Hadoop. http://hadoop.apache.org/,
Chang F, Dean J, Ghemawat S, Hsieh WC, Wallach DA, Burrows M, Chandra T, Fikes A, Gruber RE: Bigtable: A Distributed Storage System for Structured Data. ACM Trans Comput Syst. 2008, 26 (4): 1–4:26-
Google Scholar
Robinson T, Killcoyne S, Bressler R, Boyle J: SAMQA: error classification and validation of high-throughput sequenced read data. BMC Genomics. 2011, 12: 419-10.1186/1471-2164-12-419.
Article
PubMed Central
PubMed
Google Scholar
Schatz MC: CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics. 2009, 25: 1363-1369. 10.1093/bioinformatics/btp236.
Article
PubMed Central
PubMed
CAS
Google Scholar
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL: Searching for SNPs with cloud computing. Genome Biol. 2009, 10: R134-10.1186/gb-2009-10-11-r134.
Article
PubMed Central
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25: 1754-1760. 10.1093/bioinformatics/btp324.
Article
PubMed Central
PubMed
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25: 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
Smith JS, Perry A, Borell TJ, Lee HK, O’Fallon J, Hosek SM, Kimmel D, Yates A, Burger PC, Scheithauer BW, Jenkins RB: Alterations of chromosome arms 1p and 19q as predictors of survival in oligodendrogliomas, astrocytomas, and mixed oligoastrocytomas. J Clin Oncol. 2000, 18: 636-645.
PubMed
CAS
Google Scholar
Ręcławowicz D, Stempniewicz M, Biernat W, Limon J, Słoniewski P: Loss of genetic material within 1p and 19q chromosomal arms in low grade gliomas of central nervous system. Folia Neuropathol. 2013, 51: 26-32.
PubMed
Google Scholar
Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer. http://cgap.nci.nih.gov/Chromosomes/Mitelman,
Medvedev P, Stanciu M, Brudno M: Computational methods for discovering structural variation with next-generation sequencing. Nat Methods. 2009, 6: S13-S20. 10.1038/nmeth.1374.
Article
PubMed
CAS
Google Scholar