[1] Schuster SC. Next-generation sequencing transforms today’s biology. Nat Methods, 2008, 5(1): 16-18.
[2] Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol, 2008, 26(10): 1135-1145.
[3] Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet, 2009, 11(1): 31-46.
[4] Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet, 2008, 24(3): 133-141.
[5] Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet, 2009, 10(10): 669-680.
[6] Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet, 2009, 10(1): 57-63.
[7] Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods, 2008, 5(1): 19-21.
[8] Fouse SD, Nagarajan RP, Costello JF. Genome-scale DNA methylation analysis. Epigenomics, 2010, 2(1): 105-117.
[9] Carey MF, Peterson CL, Smale ST. Chromatin immunoprecipitation (ChIP). Cold Spring Harbor Protocols, 2009, 2009(9): pdb. prot5279.
[10] Sun JM, Chen HY, Davie JR. Differential distribution of unmodified and phosphorylated histone deacetylase 2 in chromatin. J Biol Chem, 2007, 282(45): 33227.
[11] Massie CE, Mills IG. ChIPping away at gene regulation. EMBO Reports, 2008, 9(4): 337-343.
[12] Cosseau C, Azzi A, Smith K, Freitag M, Mitta G, Grunau C. Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni. Critical experimental parameters. Mol Biochem Parasitol, 2009, 166(1): 70-76.
[13] Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol, 2008, 26(12): 1351-1359.
[14] Yamaguchi-Shinozaki K, Shinozaki K. Organization of cis-acting regulatory elements in osmotic-and cold-stress- responsive promoters. Trends Plant Sci, 2005, 10(2): 88-94.
[15] Laird PW. Cancer epigenetics. Hum Mol Genet, 2005, 14(Suppl 1): R65-R76.
[16] Barski A, Zhao KJ. Genomic location analysis by ChIP-Seq. J Cell Biochem, 2009, 107(1): 11-18.
[17] Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science, 2007, 316(5830): 1497-1502.
[18] Schoenherr CJ, Anderson DJ. The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science, 1995, 267(5202): 1360-1363.
[19] Kim CS, Hwang CK, Choi HS, Song KY, Law PY, Wei LN, Loh HH. Neuron-restrictive silencer factor (NRSF) functions as a repressor in neuronal cells to regulate the μ opioid receptor gene. J Biol Chem, 2004, 279(45): 46464-46473.
[20] Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng ZP, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell, 2008, 132(2): 311-322.
[21] Qin ZS, Yu JJ, Shen JC, Maher CA, Hu M, Kalyana- Sundaram S, Yu JD, Chinnaiyan AM. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics, 2010, 11(1): 369.
[22] Wallerman O, Motallebipour M, Enroth S, Patra K, Bysani MSR, Komorowski J, Wadelius C. Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing. Nucleic Acids Res, 2009, 37(22): 7498-7508.
[23] Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo L. A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics, 2009, 10(1): 618.
[24] Mikkelsen TS, Ku MC, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O’Donovan A, Presser A, Russ C, Xie XH, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Geno
