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complexity","volume":"15","author":"M a Matzke","year":"2014","journal-title":"Nat Rev Genet"},{"key":"pgen.1008370.ref085","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1101\/gad.2037511","article-title":"CpG islands and the regulation of transcription","volume":"25","author":"A Deaton","year":"2011","journal-title":"Genes Dev"},{"key":"pgen.1008370.ref086","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1046\/j.1365-313x.2001.01062.x","article-title":"Gene-associated CpG islands in plants as revealed by analyses of genomic sequences","volume":"26","author":"I Ashikawa","year":"2001","journal-title":"Plant J"},{"key":"pgen.1008370.ref087","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1093\/genetics\/132.4.1141","article-title":"High density molecular linkage maps of the tomato and potato genomes","volume":"132","author":"SD Tanksley","year":"1992","journal-title":"Genetics"},{"key":"pgen.1008370.ref088","doi-asserted-by":"crossref","first-page":"617","DOI":"10.15252\/embj.201695602","article-title":"DNA sequence properties that predict susceptibility to epiallelic switching","volume":"36","author":"M Catoni","year":"2017","journal-title":"EMBO J"},{"key":"pgen.1008370.ref089","first-page":"1","article-title":"DMRcaller: a versatile R\/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts","author":"M Catoni","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pgen.1008370.ref090","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for Computing and Annotating Genomic Ranges","volume":"9","author":"M Lawrence","year":"2013","journal-title":"PLoS Comput 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