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Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Johnson DS, et al. Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7. Genome Res. 2008. PMID: 18258921 Free PMC article.
Model-based analysis of two-color arrays (MA2C).
Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Song JS, et al. Genome Biol. 2007;8(8):R178. doi: 10.1186/gb-2007-8-8-r178. Genome Biol. 2007. PMID: 17727723 Free PMC article.
Getting started in tiling microarray analysis.
Liu XS. Liu XS. PLoS Comput Biol. 2007 Oct;3(10):1842-4. doi: 10.1371/journal.pcbi.0030183. PLoS Comput Biol. 2007. PMID: 17967045 Free PMC article. Review. No abstract available.
xMAN: extreme MApping of OligoNucleotides.
Li W, Carroll JS, Brown M, Liu xS. Li W, et al. BMC Genomics. 2008;9 Suppl 1(Suppl 1):S20. doi: 10.1186/1471-2164-9-S1-S20. BMC Genomics. 2008. PMID: 18366610 Free PMC article.