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@ARTICLE{ij:125420,
      author       = {T. Äijö and Y. Huang and H. Mannerström and L.
                      Chavez$^*$ and A. Tsagaratou and A. Rao and H. Lähdesmäki},
      title        = {{A} probabilistic generative model for quantification of
                      {DNA} modifications enables analysis of demethylation
                      pathways.},
      journal      = {Genome biology},
      volume       = {17},
      number       = {1},
      issn         = {1474-760X},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {DKFZ-2017-01550},
      pages        = {49},
      year         = {2016},
      abstract     = {We present a generative model, Lux, to quantify DNA
                      methylation modifications from any combination of bisulfite
                      sequencing approaches, including reduced, oxidative,
                      TET-assisted, chemical-modification assisted, and
                      methylase-assisted bisulfite sequencing data. Lux models all
                      cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC)
                      simultaneously together with experimental parameters,
                      including bisulfite conversion and oxidation efficiencies,
                      as well as various chemical labeling and protection steps.
                      We show that Lux improves the quantification and comparison
                      of cytosine modification levels and that Lux can process any
                      oxidized methylcytosine sequencing data sets to quantify all
                      cytosine modifications. Analysis of targeted data from
                      Tet2-knockdown embryonic stem cells and T cells during
                      development demonstrates DNA modification quantification at
                      unprecedented detail, quantifies active demethylation
                      pathways and reveals 5hmC localization in putative
                      regulatory regions.},
      keywords     = {DNA-Binding Proteins (NLM Chemicals) / 5-Methylcytosine
                      (NLM Chemicals) / Cytosine (NLM Chemicals) / DNA (NLM
                      Chemicals)},
      cin          = {B062},
      ddc          = {570},
      cid          = {I:(DE-He78)B062-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:26975309},
      pmc          = {pmc:PMC4792102},
      doi          = {10.1186/s13059-016-0911-6},
      url          = {https://inrepo02.dkfz.de/record/125420},
}