title: MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation.
abstract: BACKGROUND
  The two major epigenetic modifications of cytosines, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC), coexist with each other in a range of mammalian cell populations. Increasing evidence points to important roles of 5-hmC in demethylation of 5-mC and epigenomic regulation in development. Recently developed experimental methods allow direct single-base profiling of either 5-hmC or 5-mC. Meaningful analyses seem to require combining these experiments with bisulfite sequencing, but doing so naively produces inconsistent estimates of 5-mC or 5-hmC levels.
  
  
  RESULTS
  We present a method to jointly model read counts from bisulfite sequencing, oxidative bisulfite sequencing and Tet-Assisted Bisulfite sequencing, providing simultaneous estimates of 5-hmC and 5-mC levels that are consistent across experiment types.
  
  
  BACKGROUND
  http://smithlab.usc.edu/software/mlml
authors: Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
authors: Jianghan
authors: J
authors: Qu
authors: Meng
authors: M
authors: Zhou
authors: Qiang
authors: Q
authors: Song
authors: Elizabeth E
authors: EE
authors: Hong
authors: Andrew D
authors: AD
authors: Smith
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis* / Q000378:metabolism / Q000031:analogs & derivatives; D000818:Animals; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis / Q000378:metabolism; D004247:DNA / Q000032:analysis* / Q000378:metabolism; D019175:DNA Methylation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA
references: Science. 2009 May 15;324(5929):929-30
references: 19372393
references: Cell. 2012 Jun 8;149(6):1368-80
references: 22608086
references: Nature. 2010 Aug 26;466(7310):1129-33
references: 20639862
references: Cell Rep. 2013 Feb 21;3(2):567-76
references: 23352666
references: J Biol Chem. 2011 Jul 15;286(28):24685-93
references: 21610077
references: PLoS One. 2010 Jan 26;5(1):e8888
references: 20126651
references: Science. 2009 May 15;324(5929):930-5
references: 19372391
references: Proc Natl Acad Sci U S A. 2011 Mar 1;108(9):3642-7
references: 21321204
references: Mol Biol Evol. 2013 May;30(5):1145-58
references: 23364324
references: Science. 2012 May 18;336(6083):934-7
references: 22539555
references: PLoS One. 2010 Dec 23;5(12):e15367
references: 21203455
references: Science. 2011 Sep 2;333(6047):1300-3
references: 21778364