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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. Among authors: song js. 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.
Microarray blob-defect removal improves array analysis.
Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X. Song JS, et al. Bioinformatics. 2007 Apr 15;23(8):966-71. doi: 10.1093/bioinformatics/btm043. Epub 2007 Mar 1. Bioinformatics. 2007. PMID: 17332024
Normalization, bias correction, and peak calling for ChIP-seq.
Diaz A, Park K, Lim DA, Song JS. Diaz A, et al. Among authors: song js. Stat Appl Genet Mol Biol. 2012 Mar 31;11(3):Article 9. doi: 10.1515/1544-6115.1750. Stat Appl Genet Mol Biol. 2012. PMID: 22499706 Free PMC article.
Chromatin structure analyses identify miRNA promoters.
Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. Ozsolak F, et al. Among authors: song js. Genes Dev. 2008 Nov 15;22(22):3172-83. doi: 10.1101/gad.1706508. Genes Dev. 2008. PMID: 19056895 Free PMC article.
1,217 results