TY - JOUR AU - Meissner, A. PY - 2008 DA - 2008// TI - Genome-scale DNA methylation maps of pluripotent and differentiated cells JO - Nature VL - 454 UR - https://doi.org/10.1038/nature07107 DO - 10.1038/nature07107 ID - Meissner2008 ER - TY - JOUR AU - Jones, P. A. PY - 2012 DA - 2012// TI - Functions of DNA methylation: islands, start sites, gene bodies and beyond JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3230 DO - 10.1038/nrg3230 ID - Jones2012 ER - TY - JOUR AU - Feinberg, A. P. PY - 2007 DA - 2007// TI - Phenotypic plasticity and the epigenetics of human disease JO - Nature VL - 447 UR - https://doi.org/10.1038/nature05919 DO - 10.1038/nature05919 ID - Feinberg2007 ER - TY - JOUR AU - Hovestadt, V. PY - 2014 DA - 2014// TI - Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing JO - Nature VL - 510 UR - https://doi.org/10.1038/nature13268 DO - 10.1038/nature13268 ID - Hovestadt2014 ER - TY - JOUR AU - Kretzmer, H. PY - 2015 DA - 2015// TI - DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control JO - Nat Genet VL - 47 UR - https://doi.org/10.1038/ng.3413 DO - 10.1038/ng.3413 ID - Kretzmer2015 ER - TY - JOUR AU - Gardiner-Garden, M. AU - Frommer, M. PY - 1987 DA - 1987// TI - CpG islands in vertebrate genomes JO - J Mol Biol VL - 196 UR - https://doi.org/10.1016/0022-2836(87)90689-9 DO - 10.1016/0022-2836(87)90689-9 ID - Gardiner-Garden1987 ER - TY - JOUR AU - Zhu, J. PY - 2008 DA - 2008// TI - On the nature of human housekeeping genes JO - Trends Genet VL - 24 UR - https://doi.org/10.1016/j.tig.2008.08.004 DO - 10.1016/j.tig.2008.08.004 ID - Zhu2008 ER - TY - JOUR AU - Deaton, A. M. AU - Bird, A. PY - 2011 DA - 2011// TI - CpG islands and the regulation of transcription JO - Genes Dev VL - 25 UR - https://doi.org/10.1101/gad.2037511 DO - 10.1101/gad.2037511 ID - Deaton2011 ER - TY - JOUR AU - Feinberg, A. P. AU - Vogelstein, B. PY - 1983 DA - 1983// TI - Hypomethylation distinguishes genes of some human cancers from their normal counterparts JO - Nature VL - 301 UR - https://doi.org/10.1038/301089a0 DO - 10.1038/301089a0 ID - Feinberg1983 ER - TY - JOUR AU - Cheah, M. S. AU - Wallace, C. D. AU - Hoffman, R. M. PY - 1984 DA - 1984// TI - Hypomethylation of DNA in human cancer cells: a site-specific change in the c-myc oncogene JO - J Natl Cancer Inst VL - 73 ID - Cheah1984 ER - TY - JOUR AU - Brunner, A. L. PY - 2009 DA - 2009// TI - Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.088773.108 DO - 10.1101/gr.088773.108 ID - Brunner2009 ER - TY - JOUR AU - Brinkman, A. B. PY - 2010 DA - 2010// TI - Whole-genome DNA methylation profiling using MethylCap-seq JO - Methods VL - 52 UR - https://doi.org/10.1016/j.ymeth.2010.06.012 DO - 10.1016/j.ymeth.2010.06.012 ID - Brinkman2010 ER - TY - JOUR AU - Gu, H. PY - 2010 DA - 2010// TI - Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth.1414 DO - 10.1038/nmeth.1414 ID - Gu2010 ER - TY - JOUR AU - Serre, D. AU - Lee, B. H. AU - Ting, A. H. PY - 2010 DA - 2010// TI - MBD-isolated genome sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkp992 DO - 10.1093/nar/gkp992 ID - Serre2010 ER - TY - JOUR AU - Lister, R. PY - 2009 DA - 2009// TI - Human DNA methylomes at base resolution show widespread epigenomic differences JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08514 DO - 10.1038/nature08514 ID - Lister2009 ER - TY - JOUR AU - Bibikova, M. PY - 2009 DA - 2009// TI - Genome-wide DNA methylation profiling using Infinium (R) assay JO - Epigenomics VL - 1 UR - https://doi.org/10.2217/epi.09.14 DO - 10.2217/epi.09.14 ID - Bibikova2009 ER - TY - JOUR AU - Bibikova, M. PY - 2011 DA - 2011// TI - High density DNA methylation array with single CpG site resolution JO - Genomics VL - 98 UR - https://doi.org/10.1016/j.ygeno.2011.07.007 DO - 10.1016/j.ygeno.2011.07.007 ID - Bibikova2011 ER - TY - JOUR AU - Pidsley, R. PY - 2016 DA - 2016// TI - Critical evaluation of the illumina METHYLATIONEPIC BeadChip microarray for whole-genome DNA methylation profiling JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-1066-1 DO - 10.1186/s13059-016-1066-1 ID - Pidsley2016 ER - TY - JOUR AU - Zhou, W. AU - Laird, P. W. AU - Shen, H. PY - 2017 DA - 2017// TI - Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes JO - Nucleic Acids Res VL - 45 ID - Zhou2017 ER - TY - JOUR AU - Suzuki, M. M. AU - Bird, A. PY - 2008 DA - 2008// TI - DNA methylation landscapes: provocative insights from epigenomics JO - Nat Rev Genet VL - 9 UR - https://doi.org/10.1038/nrg2341 DO - 10.1038/nrg2341 ID - Suzuki2008 ER - TY - JOUR AU - Bibikova, M. AU - Fan, J. B. PY - 2010 DA - 2010// TI - Genome-wide DNA methylation profiling JO - Wiley Interdiscip Rev Syst Biol Med VL - 2 UR - https://doi.org/10.1002/wsbm.35 DO - 10.1002/wsbm.35 ID - Bibikova2010 ER - TY - JOUR AU - Laird, P. W. PY - 2010 DA - 2010// TI - Principles and challenges of genomewide DNA methylation analysis JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2732 DO - 10.1038/nrg2732 ID - Laird2010 ER - TY - JOUR AU - Beck, S. PY - 2010 DA - 2010// TI - Taking the measure of the methylome JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt1010-1026 DO - 10.1038/nbt1010-1026 ID - Beck2010 ER - TY - JOUR AU - Bock, C. PY - 2010 DA - 2010// TI - Quantitative comparison of genome-wide DNA methylation mapping technologies JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1681 DO - 10.1038/nbt.1681 ID - Bock2010 ER - TY - JOUR AU - Harris, R. A. PY - 2010 DA - 2010// TI - Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1682 DO - 10.1038/nbt.1682 ID - Harris2010 ER - TY - JOUR AU - Schubeler, D. PY - 2015 DA - 2015// TI - Function and information content of DNA methylation JO - Nature VL - 517 UR - https://doi.org/10.1038/nature14192 DO - 10.1038/nature14192 ID - Schubeler2015 ER - TY - JOUR AU - Ziller, M. J. PY - 2015 DA - 2015// TI - Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3152 DO - 10.1038/nmeth.3152 ID - Ziller2015 ER - TY - JOUR AU - Jensen, T. J. PY - 2015 DA - 2015// TI - Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0645-x DO - 10.1186/s13059-015-0645-x ID - Jensen2015 ER - TY - JOUR AU - Jenkinson, G. PY - 2017 DA - 2017// TI - Potential energy landscapes identify the information-theoretic nature of the epigenome JO - Nat Genet VL - 49 UR - https://doi.org/10.1038/ng.3811 DO - 10.1038/ng.3811 ID - Jenkinson2017 ER - TY - JOUR AU - Kulis, M. PY - 2015 DA - 2015// TI - Whole-genome fingerprint of the DNA methylome during human B cell differentiation JO - Nat Genet VL - 47 UR - https://doi.org/10.1038/ng.3291 DO - 10.1038/ng.3291 ID - Kulis2015 ER - TY - JOUR AU - Durek, P. PY - 2016 DA - 2016// TI - Epigenomic profiling of human CD4 + T cells supports a linear differentiation model and highlights molecular regulators of memory development JO - Immunity VL - 45 UR - https://doi.org/10.1016/j.immuni.2016.10.022 DO - 10.1016/j.immuni.2016.10.022 ID - Durek2016 ER - TY - JOUR AU - Grunau, C. AU - Clark, S. J. AU - Rosenthal, A. PY - 2001 DA - 2001// TI - Bisulfite genomic sequencing: systematic investigation of critical experimental parameters JO - Nucleic Acids Res VL - 29 UR - https://doi.org/10.1093/nar/29.13.e65 DO - 10.1093/nar/29.13.e65 ID - Grunau2001 ER - TY - JOUR AU - Miura, F. PY - 2012 DA - 2012// TI - Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks454 DO - 10.1093/nar/gks454 ID - Miura2012 ER - TY - JOUR AU - Gao, S. PY - 2015 DA - 2015// TI - BS-SNPer: SNP calling in bisulfite-seq data JO - Bioinformatics VL - 31 ID - Gao2015 ER - TY - JOUR AU - McHugh, M. L. PY - 2012 DA - 2012// TI - Interrater reliability: the kappa statistic JO - Biochem Med (Zagreb) VL - 22 UR - https://doi.org/10.11613/BM.2012.031 DO - 10.11613/BM.2012.031 ID - McHugh2012 ER - TY - JOUR AU - Pei, L. PY - 2012 DA - 2012// TI - Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia JO - Epigenetics VL - 7 UR - https://doi.org/10.4161/epi.20237 DO - 10.4161/epi.20237 ID - Pei2012 ER - TY - JOUR AU - Zouridis, H. PY - 2012 DA - 2012// TI - Methylation subtypes and large-scale epigenetic alterations in gastric cancer JO - Sci Transl Med VL - 4 UR - https://doi.org/10.1126/scitranslmed.3004504 DO - 10.1126/scitranslmed.3004504 ID - Zouridis2012 ER - TY - JOUR AU - El Hajj, N. PY - 2017 DA - 2017// TI - DNA methylation signatures in cord blood of ICSI children JO - Hum Reprod VL - 32 UR - https://doi.org/10.1093/humrep/dex209 DO - 10.1093/humrep/dex209 ID - El Hajj2017 ER - TY - JOUR AU - Stirzaker, C. PY - 2014 DA - 2014// TI - Mining cancer methylomes: prospects and challenges JO - Trends Genet VL - 30 UR - https://doi.org/10.1016/j.tig.2013.11.004 DO - 10.1016/j.tig.2013.11.004 ID - Stirzaker2014 ER - TY - STD TI - Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole genome bisulphite sequencing using the illumina Hiseq X system. BioRxiv preprint; 2017. ID - ref40 ER - TY - JOUR AU - Stone, A. PY - 2015 DA - 2015// TI - DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms8758 DO - 10.1038/ncomms8758 ID - Stone2015 ER - TY - JOUR AU - Toouli, C. D. PY - 2002 DA - 2002// TI - Comparison of human mammary epithelial cells immortalized by simian virus 40 T-antigen or by the telomerase catalytic subunit JO - Oncogene VL - 21 UR - https://doi.org/10.1038/sj.onc.1205014 DO - 10.1038/sj.onc.1205014 ID - Toouli2002 ER - TY - JOUR AU - Li, H. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - STD TI - Warnes GR, Bolker B. gplots: various R programming tools for plotting data. R package version 2.6.0, 2012. ID - ref44 ER - TY - JOUR AU - Luu, P. L. PY - 2017 DA - 2017// TI - P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data JO - Bioinformatics VL - 33 ID - Luu2017 ER - TY - STD TI - Pedersen BS, Eyring K, De S, Yang IV, Schwartz DA. Fast and accurate alignment of long bisulfite-seq reads. ArXiv, 2014. 1401.1129v2. ID - ref46 ER - TY - JOUR AU - Okonechnikov, K. AU - Conesa, A. AU - García-Alcalde, F. PY - 2015 DA - 2015// TI - Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data JO - Bioinformatics VL - 32 ID - Okonechnikov2015 ER - TY - JOUR AU - Van der Auwera, G. A. PY - 2013 DA - 2013// TI - From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline JO - Curr Protoc Bioinf VL - 43 ID - Van der Auwera2013 ER -