TY - JOUR AU - Jin, B. AU - Li, Y. AU - Robertson, K. D. PY - 2011 DA - 2011// TI - DNA methylation: superior or subordinate in the epigenetic hierarchy? JO - Genes Cancer VL - 2 UR - https://doi.org/10.1177/1947601910393957 DO - 10.1177/1947601910393957 ID - Jin2011 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 - Medvedeva, Y. A. AU - Khamis, A. M. AU - Kulakovskiy, I. V. AU - Ba-Alawi, W. AU - Bhuyan, M. S. I. AU - Kawaji, H. PY - 2014 DA - 2014// TI - Effects of cytosine methylation on transcription factor binding sites JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-119 DO - 10.1186/1471-2164-15-119 ID - Medvedeva2014 ER - TY - JOUR AU - Szyf, M. PY - 2012 DA - 2012// TI - DNA methylation signatures for breast cancer classification and prognosis JO - Genome Med VL - 4 UR - https://doi.org/10.1186/gm325 DO - 10.1186/gm325 ID - Szyf2012 ER - TY - JOUR AU - Lou, S. AU - Lee, H. -. M. AU - Qin, H. AU - Li, J. -. W. AU - Gao, Z. AU - Liu, X. PY - 2014 DA - 2014// TI - Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0408-0 DO - 10.1186/s13059-014-0408-0 ID - Lou2014 ER - TY - JOUR AU - Jaenisch, R. AU - Bird, A. PY - 2003 DA - 2003// TI - Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals JO - Nat Genet VL - 33 Suppl UR - https://doi.org/10.1038/ng1089 DO - 10.1038/ng1089 ID - Jaenisch2003 ER - TY - JOUR AU - Cotton, A. M. AU - Price, E. M. AU - Jones, M. J. AU - Balaton, B. P. AU - Kobor, M. S. AU - Brown, C. J. PY - 2015 DA - 2015// TI - Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation JO - Hum Mol Genet VL - 24 UR - https://doi.org/10.1093/hmg/ddu564 DO - 10.1093/hmg/ddu564 ID - Cotton2015 ER - TY - JOUR AU - Straussman, R. AU - Nejman, D. AU - Roberts, D. AU - Steinfeld, I. AU - Blum, B. AU - Benvenisty, N. PY - 2009 DA - 2009// TI - Developmental programming of CpG island methylation profiles in the human genome JO - Nat Struct Mol Biol VL - 16 UR - https://doi.org/10.1038/nsmb.1594 DO - 10.1038/nsmb.1594 ID - Straussman2009 ER - TY - JOUR AU - Smith, Z. D. AU - Meissner, A. PY - 2013 DA - 2013// TI - DNA methylation: roles in mammalian development JO - Nat Rev Genet Nature VL - 14 UR - https://doi.org/10.1038/nrg3354 DO - 10.1038/nrg3354 ID - Smith2013 ER - TY - JOUR AU - Rodríguez-Paredes, M. AU - Esteller, M. PY - 2011 DA - 2011// TI - Cancer epigenetics reaches mainstream oncology JO - Nat Med VL - 17 UR - https://doi.org/10.1038/nm.2305 DO - 10.1038/nm.2305 ID - Rodríguez-Paredes2011 ER - TY - JOUR AU - Han, L. AU - Zhao, Z. PY - 2009 DA - 2009// TI - CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-65 DO - 10.1186/1471-2105-10-65 ID - Han2009 ER - TY - STD TI - Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, et al. High resolution detection and analysis of CpG dinucleotides methylation using MBD-seq technology. PLoS One. 2011;6 ID - ref12 ER - TY - JOUR AU - Couldrey, C. AU - Brauning, R. AU - Bracegirdle, J. AU - Maclean, P. AU - Henderson, H. V. AU - McEwan, J. C. PY - 2014 DA - 2014// TI - Genome-wide DNA methylation patterns and transcription analysis in sheep muscle JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0101853 DO - 10.1371/journal.pone.0101853 ID - Couldrey2014 ER - TY - JOUR AU - Su, J. AU - Wang, Y. AU - Xing, X. AU - Liu, J. AU - Zhang, Y. PY - 2014 DA - 2014// TI - Genome-wide analysis of DNA methylation in bovine placentas JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-12 DO - 10.1186/1471-2164-15-12 ID - Su2014 ER - TY - JOUR AU - Yuan, X. -. L. AU - Gao, N. AU - Xing, Y. AU - Zhang, H. -. B. AU - Zhang, A. -. L. AU - Liu, J. PY - 2016 DA - 2016// TI - Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep22138 DO - 10.1038/srep22138 ID - Yuan2016 ER - TY - STD TI - Hu Y, Xu H, Li Z, Zheng X, Jia X, Nie Q, et al. Comparison of the Genome-Wide DNA Methylation Profiles between Fast-Growing and Slow-Growing Broilers. PLoS One. 2013;8 ID - ref16 ER - TY - JOUR AU - Lee, J. -. R. AU - Hong, C. P. AU - Moon, J. -. W. AU - Jung, Y. -. D. AU - Kim, D. -. S. AU - Kim, T. -. H. PY - 2014 DA - 2014// TI - Genome-wide analysis of DNA methylation patterns in horse JO - BMC Genomics VL - 15 UR - https://doi.org/10.1186/1471-2164-15-598 DO - 10.1186/1471-2164-15-598 ID - Lee2014 ER - TY - JOUR AU - Ibeagha-Awemu, E. M. AU - Zhao, X. PY - 2015 DA - 2015// TI - Epigenetic marks: Regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs JO - Front Genet VL - 6 UR - https://doi.org/10.3389/fgene.2015.00302 DO - 10.3389/fgene.2015.00302 ID - Ibeagha-Awemu2015 ER - TY - STD TI - Bird A. DNA methylation patterns and epigenetic memory DNA methylation patterns and epigenetic memory. Genes Dev. 2002:6–21. ID - ref19 ER - TY - JOUR AU - Xu, T. AU - Guo, X. AU - Wang, H. AU - Hao, F. AU - Du, X. AU - Gao, X. PY - 2013 DA - 2013// TI - Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence JO - Gene VL - 520 UR - https://doi.org/10.1016/j.gene.2013.01.068 DO - 10.1016/j.gene.2013.01.068 ID - Xu2013 ER - TY - STD TI - FAO. The Second Report on the State of the World’s Animal Genetic Resources for Food and Agriculture. Edited by Scherf B.D. and Pilling D. Rome: FAO Commission on genetic resources for food and agriculture assessments; 2015. p. 29-30. ID - ref21 ER - TY - JOUR AU - Maffucci, J. A. AU - Gore, A. C. PY - 2009 DA - 2009// TI - Chapter 2 Hypothalamic Neural Systems Controlling the Female Reproductive Life Cycle. Gonadotropin-Releasing Hormone, Glutamate, and GABA JO - Int Rev Cell Mol. Biol VL - 274 UR - https://doi.org/10.1016/S1937-6448(08)02002-9 DO - 10.1016/S1937-6448(08)02002-9 ID - Maffucci2009 ER - TY - JOUR AU - Lomniczi, A. AU - Loche, A. AU - Castellano, J. M. AU - Ronnekleiv, O. K. AU - Bosch, M. AU - Kaidar, G. PY - 2013 DA - 2013// TI - Epigenetic control of female puberty JO - Nat Neurosci VL - 16 UR - https://doi.org/10.1038/nn.3319 DO - 10.1038/nn.3319 ID - Lomniczi2013 ER - TY - JOUR AU - Laurent, L. AU - Wong, E. AU - Li, G. AU - Huynh, T. AU - Tsirigos, A. AU - Ong, C. T. PY - 2010 DA - 2010// TI - Dynamic changes in the human methylome during differentiation JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.101907.109 DO - 10.1101/gr.101907.109 ID - Laurent2010 ER - TY - JOUR AU - Sati, S. AU - Tanwar, V. S. AU - Kumar, K. A. AU - Patowary, A. AU - Jain, V. AU - Ghosh, S. PY - 2012 DA - 2012// TI - High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0031621 DO - 10.1371/journal.pone.0031621 ID - Sati2012 ER - TY - JOUR AU - Klose, R. J. AU - Bird, A. P. PY - 2006 DA - 2006// TI - Genomic DNA methylation: The mark and its mediators JO - Trends Biochem Sci VL - 31 UR - https://doi.org/10.1016/j.tibs.2005.12.008 DO - 10.1016/j.tibs.2005.12.008 ID - Klose2006 ER - TY - JOUR AU - Yang, C. AU - Ye, J. AU - Li, X. AU - Gao, X. AU - Zhang, K. AU - Luo, L. PY - 2016 DA - 2016// TI - DNA Methylation Patterns in the Hypothalamus of Female Pubertal Goats JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0165327 DO - 10.1371/journal.pone.0165327 ID - Yang2016 ER - TY - JOUR AU - Sharp, A. AU - Stathaki, E. PY - 2011 DA - 2011// TI - E M, M B, Sb M, Y D, et al. DNA methylation profiles of human active and inactive X chromosomes JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.112680.110 DO - 10.1101/gr.112680.110 ID - Sharp2011 ER - TY - JOUR AU - Barakat, T. S. AU - Gribnau, J. PY - 2012 DA - 2012// TI - X chromosome inactivation in the cycle of life JO - Development VL - 139 UR - https://doi.org/10.1242/dev.069328 DO - 10.1242/dev.069328 ID - Barakat2012 ER - TY - JOUR AU - Deaton, A. 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 - Panchin, A. Y. AU - Makeev, V. J. AU - Medvedeva, Y. A. PY - 2016 DA - 2016// TI - Preservation of methylated CpG dinucleotides in human CpG islands JO - Biol Direct VL - 11 UR - https://doi.org/10.1186/s13062-016-0113-x DO - 10.1186/s13062-016-0113-x ID - Panchin2016 ER - TY - JOUR AU - Nair, S. S. AU - Coolen, M. W. AU - Stirzaker, C. AU - Song, J. Z. AU - Statham, A. L. AU - Strbenac, D. PY - 2011 DA - 2011// TI - Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias JO - Epigenetics VL - 6 UR - https://doi.org/10.4161/epi.6.1.13313 DO - 10.4161/epi.6.1.13313 ID - Nair2011 ER - TY - JOUR AU - Moore, L. D. AU - Le, T. AU - Fan, G. PY - 2013 DA - 2013// TI - DNA methylation and its basic function JO - Neuropsychopharmacology VL - 38 UR - https://doi.org/10.1038/npp.2012.112 DO - 10.1038/npp.2012.112 ID - Moore2013 ER - TY - JOUR AU - Wan, J. AU - Oliver, V. F. AU - Wang, G. AU - Zhu, H. AU - Zack, D. J. AU - Merbs, S. L. PY - 2015 DA - 2015// TI - Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation JO - BMC Genomics VL - 16 UR - https://doi.org/10.1186/s12864-015-1271-4 DO - 10.1186/s12864-015-1271-4 ID - Wan2015 ER - TY - JOUR AU - Zhou, Y. AU - Xu, L. AU - Bickhart, D. M. AU - Abdel Hay, E. H. AU - Schroeder, S. G. AU - Connor, E. E. PY - 2016 DA - 2016// TI - Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-016-3116-1 DO - 10.1186/s12864-016-3116-1 ID - Zhou2016 ER - TY - JOUR AU - Aran, D. AU - Toperoff, G. AU - Rosenberg, M. AU - Hellman, A. PY - 2011 DA - 2011// TI - Replication timing-related and gene body-specific methylation of active human genes JO - Hum Mol Genet VL - 20 UR - https://doi.org/10.1093/hmg/ddq513 DO - 10.1093/hmg/ddq513 ID - Aran2011 ER - TY - JOUR AU - Evans, G. A. PY - 1990 DA - 1990// TI - Molecular cloning: A laboratory manual. Second edition. Volumes 1, 2, and 3. Current protocols in molecular biology. Volumes 1 and 2 JO - Cell Elsevier VL - 61 ID - Evans1990 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2010 DA - 2010// TI - Fast and accurate long-read alignment with Burrows-Wheeler transform JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp698 DO - 10.1093/bioinformatics/btp698 ID - Li2010 ER - TY - JOUR AU - Giannopoulou, E. G. AU - Elemento, O. PY - 2011 DA - 2011// TI - An integrated ChIP-seq analysis platform with customizable workflows JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-277 DO - 10.1186/1471-2105-12-277 ID - Giannopoulou2011 ER - TY - JOUR AU - Hackenberg, M. AU - Previti, C. AU - Luque-Escamilla, P. L. AU - Carpena, P. AU - Martínez-Aroza, J. AU - Oliver, J. L. PY - 2006 DA - 2006// TI - CpGcluster: a distance-based algorithm for CpG-island detection JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-446 DO - 10.1186/1471-2105-7-446 ID - Hackenberg2006 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic. a flexible trimmer for Illumina sequence data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: Ultrafast universal RNA-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Anders, S. AU - Pyl, P. T. AU - Huber, W. PY - 2015 DA - 2015// TI - HTSeq-A Python framework to work with high-throughput sequencing data JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu638 DO - 10.1093/bioinformatics/btu638 ID - Anders2015 ER - TY - JOUR AU - Robinson, M. D. AU - McCarthy, D. J. AU - Smyth, G. K. PY - 2009 DA - 2009// TI - edgeR: A Bioconductor package for differential expression analysis of digital gene expression data JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp616 DO - 10.1093/bioinformatics/btp616 ID - Robinson2009 ER - TY - JOUR AU - Szklarczyk, D. AU - Franceschini, A. AU - Wyder, S. AU - Forslund, K. AU - Heller, D. AU - Huerta-Cepas, J. PY - 2015 DA - 2015// TI - STRING v10: Protein-protein interaction networks, integrated over the tree of life JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1003 DO - 10.1093/nar/gku1003 ID - Szklarczyk2015 ER -