第4章

参考文献:第4章 基因组序列比对



Antoniou, P., et al. 2010. A fast and efficient algorithm for mapping short sequences to a reference genome. Adv Exp Med Biol. 680: 399-403. [PubMed]

Campagna, D., et al. 2009. PASS: a program to align short sequences. Bioinformatics. 25(7): 967-968. [PubMed]

Clement, N. L., et al. 2010. The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics. 26(1): 38-45. [PubMed]

Cokus, S. J., et al. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 452(7184): 215-219. [PubMed]

Hamada, M., et al. 2011. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics. 27(22): 3085-3092. [PubMed]

Hoffmann, S., et al. 2009. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol. 5(9): e1000502. [PubMed]

Jiang, H. and W. H. Wong. 2008. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics. 24(20): 2395-2396. [PubMed]

Johnson, D. S., et al. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science. 316(5830): 1497-1502. [PubMed]

Langmead, B., et al. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3): R25. [PubMed]

Li, H., et al. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18(11): 1851-1858. [PubMed]

Li, R., et al. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 25(15): 1966-1967. [PubMed]

Lin, H., et al. 2008. ZOOM! Zillions of oligos mapped. Bioinformatics. 24(21): 2431-2437. [PubMed]

Marguerat, S. and J. Bahler. 2010. RNA-seq: from technology to biology. Cell Mol Life Sci. 67(4): 569-579. [PubMed]

Marioni, J. C., et al. 2008. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18(9): 1509-1517. [PubMed]

Ning, Z., et al. 2001. SSAHA: a fast search method for large DNA databases. Genome Res. 11(10): 1725-1729. [PubMed]

Ondov, B. D., et al. 2008. Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications. Bioinformatics. 24(23): 2776-2777. [PubMed]

Rizk, G. and D. Lavenier. 2010. GASSST: global alignment short sequence search tool. Bioinformatics. 26(20): 2534-2540. [PubMed]

Rumble, S. M., et al. 2009. SHRiMP: accurate mapping of short color-space reads. PLoS Comput Biol. 5(5): e1000386. [PubMed]

Shang, J., et al. 2014. Evaluation and comparison of multiple aligners for next-generation sequencing data analysis. Biomed Res Int. 2014: 309650. [PubMed]

Shendure, J. and H. Ji. 2008. Next-generation DNA sequencing. Nat Biotechnol. 26(10): 1135-1145. [PubMed]

Smith, A. D., et al. 2009. Updates to the RMAP short-read mapping software. Bioinformatics. 25(21): 2841-2842. [PubMed]

Weese, D., et al. 2009. RazerS--fast read mapping with sensitivity control. Genome Res. 19(9): 1646-1654. [PubMed]

Weese, D., et al. 2012. RazerS 3: faster, fully sensitive read mapping. Bioinformatics. 28(20): 2592-2599. [PubMed]

Marguerat, S., et al. 2008. Next-generation sequencing: applications beyond genomes. Biochem Soc Trans. 36(Pt 5): 1091-1096. [PubMed]

Marshall, E. 1982. A cloudburst of yellow rain reports. Science. 218(4578): 1202-1203. [PubMed]