Chromatin Immunoprecipitation Sequencing    ◾    251

REFERENCES

1. Bernstein BE, Meissner A, Lander ES: The mammalian epigenome. Cell 2007, 128(4):669–681.

2. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers

RM, Brown M, Li W et al: Model-based Analysis of ChIP-Seq (MACS). Genome Biol 2008,

9(9):R137.

3. Narlikar L, Jothi R: ChIP-Seq data analysis: identification of protein-DNA binding sites with

SISSRs peak-finder. Methods Mol Biol 2012, 802:305–322.

4. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass

CK: Simple combinations of lineage-determining transcription factors prime cis-regulatory

elements required for macrophage and B cell identities. Mol Cell 2010, 38(4):576–589.

5. Ibrahim MM, Lacadie SA, Ohler U: JAMM: a peak finder for joint analysis of NGS replicates.

Bioinformatics 2015, 31(1):48–55.

6. Feng J, Liu T, Qin B, Zhang Y, Liu XS: Identifying ChIP-seq enrichment using MACS. Nat

Protoc 2012, 7(9):1728–1740.

7. Feng J, Liu T, Zhang Y: Using MACS to identify peaks from ChIP-Seq data. Curr Prot Bioinfor

2011, Chapter 2:Unit2 14–12.14.

8. Freese NH, Norris DC, Loraine AE: Integrated genome browser: visual analytics platform for

genomics. Bioinformatics 2016, 32(14):2089–2095.

9. Yu G, Wang LG, He QY: ChIPseeker: an R/Bioconductor package for ChIP peak annotation,

comparison and visualization. Bioinformatics 2015, 31(14):2382–2383.

10. Yu G, Wang LG, Han Y, He QY: clusterProfiler: an R package for comparing biological themes

among gene clusters. Omics 2012, 16(5):284–287.

11. Bailey TL, Gribskov M: Combining evidence using p-values: application to sequence homol-

ogy searches. Bioinformatics 1998, 14(1):48–54.