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However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor\u2019s motif.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>\n                      SEMplMe is available from\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/Boyle-Lab\/SEMplMe\">https:\/\/github.com\/Boyle-Lab\/SEMplMe<\/jats:ext-link>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-022-04865-x","type":"journal-article","created":{"date-parts":[[2022,8,4]],"date-time":"2022-08-04T05:04:10Z","timestamp":1659589450000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions"],"prefix":"10.1186","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4288-4567","authenticated-orcid":false,"given":"Sierra S.","family":"Nishizaki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2081-1105","authenticated-orcid":false,"given":"Alan P.","family":"Boyle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,8,4]]},"reference":[{"key":"4865_CR1","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1038\/321209a0","volume":"321","author":"AP Bird","year":"1986","unstructured":"Bird AP. 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