Ensemble analysis of adaptive compressed genome sequencing strategies

Article, Preprint English OPEN
Taghavi, Zeinab;
(2013)
  • Publisher: Springer Nature
  • Journal: BMC Bioinformatics,volume 15,issue Suppl 9,pagesS13-S13 (issn: 1471-2105, eissn: 1471-2105)
  • Publisher copyright policies & self-archiving
  • Related identifiers: doi: 10.1186/1471-2105-15-s9-s13, pmc: PMC4221792
  • Subject: Molecular Biology | single-cell sequencing | microbial community | compressed sensing | Biochemistry | Quantitative Biology - Genomics | Computer Science Applications | co-assembly | sparsity | Proceedings | compressive genomics | adaptive sensing
Background Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue is that deep sequen... View more
  • References (21)
    21 references, page 1 of 3

    1. 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.

    2. 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.

    3. Fitzsimons MS, Novotny M, Lo C-C, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, et al: Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome research 2013, 23(5):878-888.

    4. 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.

    5. Candès EJ, Tao T: Decoding by linear programming. IEEE Transactions on Information Theory 2005, 51(12):4203-4215.

    6. Candès EJ, Tao T: Near-optimal signal recovery from random projections: Universal encoding strategies? IEEE Transactions on Information Theory 2006, 52(12):5406-5425.

    7. Donoho DL: Compressed sensing. Information Theory. IEEE Transactions 2006, 52(4):1289-1306.

    8. 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.

    9. Wei D, Hero AO: Multistage adaptive estimation of sparse signals. IEEE Statistical Signal Processing Workshop (SSP) 2012, 153-156.

    10. Erlich Y, Gordon A, Brand M, Hannon GJ, Mitra PP: Compressed genotyping. Information Theory. IEEE Transactions 2010, 56(2):706-723.

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