Ensemble analysis of adaptive compressed genome sequencing strategies
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Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo M-J, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS: Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nature Biotech. 2011, 29 (10): 915-921. 10.1038/nbt.1966.
Zengler K, Toledo G, Rapp´e M, Elkins J, Mathur EJ, Short JM, Keller M: Cultivating the uncultured. Proc Nat Acad Sci. 2002, 99 (24): 15681-15686. 10.1073/pnas.252630999.
Fitzsimons MS, Novotny M, Lo C-C, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K: Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome research. 2013, 23 (5): 878-888. 10.1101/gr.142208.112.
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J, Antolin M, Artiguenave F, Blottiere H, Borruel N, Bruls T, Casellas F, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Forte M, Friss C, van de Guchte M, Guedon E, Haimet F, Jamet A, Juste C, Kaci G, Kleerebezem M, Knol J, Kristensen M, Layec S, Le Roux K, Leclerc M, Maguin E, Minardi RM, Oozeer R, Rescigno M, Sanchez N, Tims S, Torrejon T, Varela E, de Vos W, Winogradsky Y, Zoetendal E: A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010, 464 (7285): 59-65. 10.1038/nature08821.
Candès EJ, Tao T: Decoding by linear programming. IEEE Transactions on Information Theory. 2005, 51 (12): 4203-4215. 10.1109/TIT.2005.858979.
Candès EJ, Tao T: Near-optimal signal recovery from random projections: Universal encoding strategies?. IEEE Transactions on Information Theory. 2006, 52 (12): 5406-5425.
Donoho DL: Compressed sensing. Information Theory. IEEE Transactions. 2006, 52 (4): 1289-1306.
Haupt J, Castro RM, Nowak R: Distilled sensing: Adaptive sampling for sparse detection and estimation. IEEE Transactions on Information Theory. 2011, 57 (9): 6222-6235.
Wei D, Hero AO: Multistage adaptive estimation of sparse signals. IEEE Statistical Signal Processing Workshop (SSP). 2012, 153-156.
Erlich Y, Gordon A, Brand M, Hannon GJ, Mitra PP: Compressed genotyping. Information Theory. IEEE Transactions. 2010, 56 (2): 706-723.
Stobbe P, Krause A: Learning fourier sparse set functions. Journal of Machine Learning Research - Proceedings Track. 2012, 22: 1125-1133.
Malloy ML, Nowak RD: Near-optimal adaptive compressed sensing. Signals, Systems and Computers (ASILOMAR). 2012, 1935-1939. 2012 Conference Record of the Forty Sixth Asilomar Conference On IEEE
Kane DM, Nelson J, Woodruff DP: Proceedings of the Twenty-ninth ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems. An optimal algorithm for the distinct elements problem. 2010, 41-52. ACM
Efron B, Thisted R: Estimating the number of unseen species: How many words did shakespeare know?. 1976, 63 (3): 435-447.
Taghavi Z, Movahedi NS, Drăghici S, Chitsaz H: Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities. Bioinformatics. 2013, 29 (19): 2395-2401. 10.1093/bioinformatics/btt420.
Movahedi NS, Forouzmand E, Chitsaz H: De novo co-assembly of bacterial genomes from multiple single cells. IEEE Conference on Bioinformatics and Biomedicine. 2012, 561-565.
Compeau PEC, Pevzner PA, Tesler G: How to apply de bruijn graphs to genome assembly. Nature biotechnology. 2011, 29 (11): 987-991. 10.1038/nbt.2023.
Johnson WB, Lindenstrauss J: Extensions of lipschitz mappings into a hilbert space. Contemporary mathematics. 1984, 26 (189-206): 1-
Taghavi Z, Draghici S: MDAsim:A multiple displacement amplification simulator. IEEE Conference on Bioinformatics and Biomedicine. 2012, 575-578.
Motahari AS, Bresler G, Tse DNC: Information theory of DNA shotgun sequencing. Information Theory IEEE Transactions on. 2013, 59 (10): 6273-6289.