Recent advances in computational epigenetics

References

• Bentley DR. Decoding the human genome sequence. Hum Mol Genet. 2000;16:2353–2358.
   Google Scholar
• Lander ES, Linton LM, Birren B, et al; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921.
   PubMed Web of Science ®Google Scholar
• Fusco G, Minelli A. Phenotypic plasticity in development and evolution: facts and concepts. Philos Trans R Soc Lond B Biol Sci. 2010;365(1540):547–556.
   Web of Science ®Google Scholar
• Petronis A. Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature. 2010;465(7299):721–727.
   PubMed Web of Science ®Google Scholar
• Barrett T, Troup DB, Wilhite SE, et al. NCBI GEO: archive for functional genomics data sets—10 years on. Nucleic Acids Res. 2011;39(Database issue):D1005–D1010.
   Google Scholar
• ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57–74.
   PubMed Web of Science ®Google Scholar
• Herrero J, Muffato M, Beal K, et al. Ensembl comparative genomics resources. Database (Oxford). 2016;2016:bav096.
   Google Scholar
• MacArthur J, Bowler E, Cerezo M, et al. The new NHGRI-EBI catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res. 2017;45(Database issue):D896–D901.
   Google Scholar
• NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2017;45(Database issue):D12–D17.
   Google Scholar
• Lee TI, Young RA. Transcriptional regulation and its misregulation in disease. Cell. 2013;152(6):1237–1251.
   PubMed Web of Science ®Google Scholar
• Seki Y, Williams L, Vuguin PM, Charron MJ. Minireview: epigenetic programming of diabetes and obesity: animal models. Endocrinology. 2012;153(3):1031–1038.
   PubMed Web of Science ®Google Scholar
• Suvà ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science. 2013;339(6127):1567–1570.
   PubMed Web of Science ®Google Scholar
• Hu Z, Tee WW. Enhancers and chromatin structures: regulatory hubs in gene expression and diseases. BioSci Rep. 2017;37(2):BSR20160183.
   Web of Science ®Google Scholar
• Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. An operational definition of epigenetics. Genes Dev. 2009;23(7):781–783.
   PubMed Web of Science ®Google Scholar
• Tammen SA, Friso S, Choi SW. Epigenetics: the link between nature and nurture. Mol Aspects Med. 2013;34(4):753–764.
   PubMed Web of Science ®Google Scholar
• Shen H, Laird PW. Interplay between the cancer genome and epigenome. Cell. 2013;153:38–55.
   PubMed Web of Science ®Google Scholar
• Basso M, Sleiman S, Ratan RR. Looking above but not beyond the genome for therapeutics in neurology and psychiatry: epigenetic proteins and RNAs find new focus. Neurotherapeutics. 2013;10(4):551–555.
   Web of Science ®Google Scholar
• Alelú-Paz R, Ashour N, González-Corpas A, Ropero S. DNA methylation, histone modifications, and signal transduction pathways: a close relationship in malignant gliomas pathophysiology. J Signal Transduct. 2012;2012:956–958.
   Google Scholar
• Le Roy G, Dimaggio PA, Chan EY, et al. A quantitative atlas of histone modification signatures from human cancer cells. Epigenetics Chromatin. 2013;6(1):20.
   Google Scholar
• Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015;16(9):519–532.
   PubMed Web of Science ®Google Scholar
• Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009;10(5):295–304.
   PubMed Web of Science ®Google Scholar
• Ioudinkova ES, Barat A, Pichugin A, et al. Distinct distribution of ectopically expressed histone variants H2A.Bbd and macroH2A in open and closed chromatin domains. PLoS One. 2012;7(10):1101–1113.
   Web of Science ®Google Scholar
• Falls JG, Pulford DJ, Wylie AA, Jirtle RL. Genomic imprinting: implications for human disease. Am J Pathol. 1999;154:635–647.
   PubMed Web of Science ®Google Scholar
• Bjornsson HT, Brown LJ, Fallin MD, et al. Epigenetic specificity of loss of imprinting of the IGF2 gene in Wilms tumors. J Natl Cancer Inst. 2007;99(16):1270–1273.
   PubMedGoogle Scholar
• Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A. 2010;107 Suppl 1:1757–1764.
   Google Scholar
• Burggren W. Epigenetic inheritance and its role in evolutionary biology: re-evaluation and new perspectives. Biology (Basel). 2016;5(2):24–46.
   Google Scholar
• Van Dijk SJ, Tellam RL, Morrison JL, Muhlhausler BS, Molloy PL. Recent developments on the role of epigenetics in obesity and metabolic disease. Clin Epigenetics. 2015;7:66.
   PubMed Web of Science ®Google Scholar
• Archer T, Oscar-Berman M, Blum K, Gold MS. Epigenetic modulation of mood disorders. J Genet Syndr Gene Ther. 2013;4(120):1000120.
   Google Scholar
• Roth TL, Sweatt JD. Annual research review: epigenetic mechanisms and environmental shaping of the brain during sensitive periods of development. J Child Psychol Psychiatry. 2010;52(4):398–408.
   Web of Science ®Google Scholar
• Bakulski KM, Halladay A, Hu VW, Mill J, Fallin MD. Epigenetic research in neuropsychiatric disorders: the “Tissue Issue”. Curr Behav Neurosci Rep. 2016;3(3):264–274.
   PubMedGoogle Scholar
• Cao Y, Lu L, Liu M, et al. Impact of epigenetics in the management of cardiovascular disease: a review. Eur Rev Med Pharmacol Sci. 2014; 18(20):3097–3104.
   Web of Science ®Google Scholar
• Berezin A. Epigenetics in heart failure phenotypes. BBA Clin. 2016;6:31–37.
   PubMedGoogle Scholar
• Feinberg AP, Koldobskiy MA, Göndör A. Epigenetic modulators, modifiers and mediators in cancer aetiology and progression. Nat Rev Genet. 2016;17(5):284–299.
   PubMed Web of Science ®Google Scholar
• Hannum G, Guinney J, Zhao L, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013;49(2):359–367.
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, West J, Beck S. Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum Mol Genet. 2013;22(R1):R7–R15.
   Google Scholar
• Benayoun BA, Pollina EA, Brunet A. Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol. 2015;16(10):593–610.
   PubMed Web of Science ®Google Scholar
• Swaminathan V, Reddy BA, Ruthrotha Selvi B, Sukanya MS, Kundu TK. Small molecule modulators in epigenetics: implications in gene expression and therapeutics. Subcell Biochem. 2007;41:397–428.
   PubMedGoogle Scholar
• Balaur I, Saqi M, Barat A, et al. EpiGeNet: a graph database of interdependencies between genetic and epigenetic events in colorectal cancer. J Comput Biol. 2016;23:1–12.
   Google Scholar
• Romanoski CE, Glass CK, Stunnenberg HG, Wilson L, Almouzni G. Epigenomics: roadmap for regulation. Nature. 2015;518(7539):314–316.
   PubMed Web of Science ®Google Scholar
• Halsberger A, Varger F, Karlic H. A model for epigenetic mechanisms in cancer development. Med Hypotheses. 2006;67(6):1448–1454.
   Web of Science ®Google Scholar
• Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012;13(7):R61.
   PubMed Web of Science ®Google Scholar
• Anink-Groenen LC, Maarlerveld TR, Verschure PJ, Bruggeman FJ. Mechanistic stochastic model of histone modification pattern formation. Epigenetics Chromatin. 2014;7(1):30.
   Google Scholar
• Capra JA, Kostka D. Modeling DNA methylation dynamics with approaches from Phylogenetics. Bioinformatics. 2014;30(17):i408–i414.
   Web of Science ®Google Scholar
• Erdel F, Greene EC. Generalized nucleation and looping model for epigenetic memory of histone modifications. Proc Natl Acad Sci U S A. 2016;113(29):E4180–E4189.
   Web of Science ®Google Scholar
• Raghavan K, Ruskin HJ, Perrin D, Goasmat F, Burns J. Computational micromodel for epigenetic mechanisms. PLoS One. 2010;5(11):e14031.
   Web of Science ®Google Scholar
• Sneppen K, Dodd IB. A simple histone code opens many paths to epigenetics. PLoS Comput Biol. 2012;8(8):e1002643.
   Web of Science ®Google Scholar
• Ruskin HJ, Perrin D. Computational methods in epigenetic research. In: Wells RD, Bond JS, Klinman J, Siler Masters BS, Bell E, editors. Molecular Life Sciences: An Encyclopedic Reference. New York: Springer; 2014;1–8.
   Google Scholar
• Bannister AJ, Kouzarides T. Regulation of chromatin by histone modifications. Cell Res. 2011;21(3):381–395.
   PubMed Web of Science ®Google Scholar
• Rose NR, Klose RJ. Understanding the relationship between DNA methylation and histone lysine methylation. Biochim Biophys Acta. 2014;1839(12):1362–1372.
   PubMed Web of Science ®Google Scholar
• Ushijima T, Sasako M. Focus on gastric cancer. Cancer Cell. 2004;5(2):121–125.
   PubMed Web of Science ®Google Scholar
• Perrin D, Ruskin HJ, Niwa T. Cell type-dependent, infection-induced, aberrant DNA methylation in gastric cancer. J Theor Biol. 2010;264(2):570–577.
   PubMed Web of Science ®Google Scholar
• Harrison LG. The Shaping of Life. The Generation of Biological Pattern. Cambridge: Cambridge University Press; 2011.
   Google Scholar
• Raghavan K, Ruskin HJ. Modelling DNA methylation dynamics. In: Tatarinova T, editor. DNA Methylation – From Genomics to Technology. InTech; 2012.
   Google Scholar
• McGovern AP, Powell BE, Chevassut TJT. A dynamic multi-compartmental model of DNA methylation with demonstrative predictive value in hematological malignancies. J Theor Biol. 2012;310:14–20.
   Web of Science ®Google Scholar
• Karmaus W, Ziyab AH, Everson T, Holloway JW. Epigenetic models and mechanisms in the origins of asthma. Curr Opin Allergy Clin Immunol. 2013;13(1):63–69.
   Web of Science ®Google Scholar
• Bush WS, Moore JH. Genome-wide association studies. PLoS Comput Biol. 2012;8(12):e1002822.
   PubMed Web of Science ®Google Scholar
• Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011;12(8):529–541.
   PubMed Web of Science ®Google Scholar
• Flanagan JM. Epigenome-wide association studies (EWAS): past, present, and future. Methods Mol Biol. 2015;1238:51–63.
   PubMedGoogle Scholar
• Roznovat IA, Ruskin HJ. Theoretical cross-comparative analysis on dynamics of small intestine and colon crypts during cancer initiation. IET Syst Biol. 2015;9(6):259–267.
   Web of Science ®Google Scholar
• Ku WL, Girvan M, Yuan GC, Sorrentino F, Ott E. Modeling the dynamics of bivalent histone modifications. PLoS One. 2013;8(11): e77944.
   Web of Science ®Google Scholar
• Rohlf T, Steiner L, Przybilla J, Prohaska S, Binder H, Galle J. Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics. 2012;4(2):205–219.
   PubMed Web of Science ®Google Scholar
• Bronner C, Chataigneau T, Schini-Kerth VB, Landry Y. The “Epigenetic Code Machinery”, ECREM: a promising drugable target of the epigenetic cell memory. Curr Med Chem. 2007;14(25):2629–2641.
   Web of Science ®Google Scholar
• Peschansky VJ, Wahlestedt C. Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics. 2014;9(1):3–12.
   PubMed Web of Science ®Google Scholar
• Hansen KD, Timp W, Bravo HC, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43(8):768–775.
   PubMed Web of Science ®Google Scholar
• Dinalankara W, Bravo HC. Gene expression signatures based on variability can robustly predict tumor progression and prognosis. Cancer Inform. 2015;14:71–81.
   Google Scholar
• Kanz C, Aldebert P, Althorpe N, et al. The EMBL nucleotide sequence database. Nucleic Acids Res. 2005;33(Database issue):D29–D33.
   Google Scholar
• Liu L, Li Y, Li S, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012;2012:251364.
   PubMedGoogle Scholar
• Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333–351.
   PubMed Web of Science ®Google Scholar
• Lowe R, Shirley N, Bleackley M, Dolan S, Shafee T. Transcriptomics technologies. PLoS Comput Biol. 2017;13(5):e1005457.
   PubMed Web of Science ®Google Scholar
• Bock C, Lengauer T. Computational epigenetics. Bioinformatics. 2008;24(1):1–10.
   PubMed Web of Science ®Google Scholar
• Lim SJ, Tan TW, Tong JC. Computational epigenetics: the new scientific paradigm. Bioinformation. 2010;4(7):331–337.
   Google Scholar
• Epigenie. Epigenetic databases, tools and resources. Available from: http://epigenie.com/epigenetic-tools-and-databases/. Accessed June 20, 2017.
   Google Scholar
• Fingerman IM, Zhang X, Ratzat W, Husain N, Cohen RF, Schuler DG. NCBI epigenomics: whats new for 2013. Nucleic Acids Res. 2013;41:D221–D225.
   Web of Science ®Google Scholar
• Medvedeva YA, Lennartsson A, Ehsani R, et al. EpiFactors: a comprehensive database of human epigenetic factors and complexes. Database (Oxford). 2015;2015:bav067.
   Web of Science ®Google Scholar
• Barat A, Ruskin HJ. A manually curated novel management system for genetic and epigenetic molecular determinants of colon cancer. Open Colorectal Cancer J. 2010;3:36–46.
   Google Scholar
• He X, Chang S, Zhang J, et al. MethyCancer: the database of human DNA methylation and cancer. Nucleic Acids Res. 2008;36(Database issue):D836–D841.
   PubMedGoogle Scholar
• Forbes SA, Beare D, Gunasekaran P, et al. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2015;43(Database issue):D805–D811.
   PubMed Web of Science ®Google Scholar
• Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W. PubMeth: a cancer methylation database combining text mining and expert annotation. Nucleic Acids Res. 2008;36(Database issue):D842–D846.
   PubMedGoogle Scholar
• Fang YC, Lai PT, Dai HJ, Hsu WL. MethInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature. BMC Bioinformatics. 2011;12:471.
   Web of Science ®Google Scholar
• Grunau C, Renault E, Rosenthal A, Roizes G. MethDB—a public database for DNA methylation data. Nucleic Acids Res. 2001;29(1):270–274.
   Web of Science ®Google Scholar
• Zou D, Sun S, Li R, Liu J, Zhang J, Zhang Z. MethBank: a database integrating next-generation sequencing single-base resolution DNA methylation programming data. Nucleic Acids Res. 2015;43(Database issue):D54–D58.
   Google Scholar
• Li LC, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics. 2002;18(11):1427–1431.
   PubMed Web of Science ®Google Scholar
• Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2015;43(Database issue):D298–D299.
   PubMedGoogle Scholar
• Mariño-Ramírez L, Levine KM, Morales M, et al. The Histone Database: an integrated resource for histones and histone fold-containing proteins. Database (Oxford). 2011;2011:bar048.
   Web of Science ®Google Scholar
• Khare SP, Habib F, Sharma R, Gadewal N, Gupta S, Galande S. HIstome—a relational knowledgebase of human histone proteins and histone modifying enzymes. Nucleic Acids Res. 2012;40(Database issue):D337–D342.
   Google Scholar
• Gendler K, Paulsen T, Napoli C. CHROMDB: the chromatin database. Nucleic Acids Res. 2008;36(Database issue):D298–D302.
   Google Scholar
• Shipra A, Chetan K, Rao MR. CREMOFAC—a database of chromatin remodelling factors. Bioinformatics. 2006;22(23):2940–2944.
   Web of Science ®Google Scholar
• Wang Q, Huang J, Sun H, et al. CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Res. 2014;42(Database issue):D450–D458.
   Google Scholar
• GigaOM. Twitter open-sources the home of its social graph. Available from: http://gigaom.com/2010/04/12/twitter-open-sources-the-home-of-its-social-graph. Accessed February 8, 2017.
   Google Scholar
• AllegroGraph. AllegroGraph RDFStore Web 30s database. Available from: http://franz.com/agraph/allegrograph. Accessed February 4, 2017.
   Google Scholar
• Neo4j. Neo4j world’s leading graph database. Available from: http://neo4j.com. Accessed January 20, 2017.
   Google Scholar
• Johnson D, Connor AJ, McKeever S, et al. Semantically linking in silico cancer models. Cancer Inform. 2014;13 Suppl 1:133–143.
   Google Scholar
• Henkel R, Wolkenhauer O, Waltemath D. Combining computational models, semantic annotations and simulation experiments in a graph database. Database(Oxford). 2015;2015:bau130.
   Google Scholar
• Chelliah V, Juty N, Ajmera I, et al. BioModels: ten-year anniversary. Nucleic Acids Res. 2015;43(D1):D542–D548.
   Web of Science ®Google Scholar
• Low Y, Gonzalez J, Kyrola A, Bickson D, Guestrin C, Hellerstein JM. Distributed Graphlab: a framework for machine learning and data mining in the cloud. Proc VLDB Endowment. 2012;5(8):716–727.
   Google Scholar
• Corbellini A, Mateos C, Godoy D, Zunino A, Schiaffino S. An architecture and platform for developing distributed recommendation algorithms on large-scale social networks. J Inf Sci. 2015;41(5):686–704.
   Web of Science ®Google Scholar
• Michels KB, Binder AM, Dedeurwaerder S, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013;10(10):949–955.
   PubMed Web of Science ®Google Scholar
• Birney E, Smith GD, Greally JM. Epigenome-wide association studies and the interpretation of disease-omics. PLoS Genet. 2016;12(6):e1006105.
   PubMed Web of Science ®Google Scholar
• Scacheri PC, Crawford GE, Davis S. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol. 2006;411:270–282.
   Web of Science ®Google Scholar
• Krueger F, Kreck B, Franke A, Andrews SR. DNA methylome analysis using short bisulfite sequencing data. Nat Methods. 2012;9(2):145–151.
   PubMed Web of Science ®Google Scholar
• Pedersen BS, Eyring K, De S, Yang IV, Schwartz DA. Fast and accurate alignment of long bisulfite-seq reads. Bioinformatics. 2014:1–2.
   Google Scholar
• Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–1572.
   PubMed Web of Science ®Google Scholar
• Sun D, Xi Y, Rodriguez B, et al. MOABS: model based analysis of bisulfite sequencing data. Genome Biol. 2014;15:R38.
   PubMed Web of Science ®Google Scholar
• Dolzhenko E, Smith AD. Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. BMC Bioinformatics. 2014;15:215.
   PubMed Web of Science ®Google Scholar
• Lea AJ, Tung J, Zhou X. A flexible, efficient binomial mixed model for identifying differential dna methylation in bisulfite sequencing data. PLoS Genet. 2015;11(11):e1005650.
   PubMed Web of Science ®Google Scholar
• Gao S, Zou D, Mao L, et al. BS-SNPer: SNP calling in bisulfite-seq data. Bioinformatics. 2015;31(24):4006–4008.
   PubMed Web of Science ®Google Scholar
• Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ, Timp W. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods. 2017;14(4):407–410.
   PubMed Web of Science ®Google Scholar
• Rand AC, Jain M, Eizenga JM, et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat Methods. 2017;14(4):411–413.
   PubMed Web of Science ®Google Scholar
• Houseman EA, Christensen BC, Yeh RF, et al. Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics. 2008;9:365.
   PubMed Web of Science ®Google Scholar
• Wang B, Mezlini AM, Demir F, et al. Similarity network fusion for aggregating data types on a genomic scale. Nat Methods. 2014;11(3):333–337.
   PubMed Web of Science ®Google Scholar
• Sánchez A, Fernández-Real J, Vegas E, et al. Multivariate methods for the integration and visualization of omics data. In: Freitas AT, Navarro A, editors. Bioinformatics for Personalized Medicine. Lecture Notes in Computer Science. Berlin, Heidelberg: Springer; 2012: 6620.
   Google Scholar
• Zhang L, Lin X. Multivariate statistical methods in bioinformatics research. In: Jiang R, Zhang X, Zhang M, editors. Basics of Bioinformatics. Berlin, Heidelberg: Springer; 2013:63–231.
   Google Scholar
• Teschendorff AE, Zheng SC. Cell-type deconvolution in epigenome-wide association studies: a review and recommendations. Epigenomics. 2017;9(5):757–768.
   PubMed Web of Science ®Google Scholar
• Zheng SC, Beck S, Jaffe AE, et al. Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses. Nat Methods. 2017;14(3):216–217.
   PubMed Web of Science ®Google Scholar
• Jones MJ, Islam SA, Edgar RD, Kobor MS. Adjusting for cell type composition in DNA methylation data using a regression-based approach. Methods Mol Biol. 2017;1589:99–106.
   PubMedGoogle Scholar
• König IR, Auerbach J, Gola D, et al. Machine Learning and data mining in complex genomic data – a review on the lessons learned in Genetic Analysis Workshop 19. BMC Genet. 2016;17 Suppl 2:1.
   Google Scholar
• Dutkowski J, Kramer M, Surma MA, et al. A gene ontology inferred from molecular networks. Nat Biotechnol. 2013;31(1):38–45.
   Web of Science ®Google Scholar
• Raja K, Patrick M, Gao Y, Madu D, Yang Y, Tsoil LC. A review of recent advancement in integrating omics data with literature mining towards biomedical discoveries. Int J Genomics. 2017;2017:6213474.
   PubMed Web of Science ®Google Scholar
• Leslie R, O’Donnell CJ, Johnson AD. GRASP: analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics. 2014;30(12):i185–i194.
   Web of Science ®Google Scholar
• Banerji CRS, Miranda-Saavedra D, Severini S, et al. Cellular network entropy as the energy potential in Waddington’s differentiation landscape. Sci Rep. 2013;3:3039.
   Web of Science ®Google Scholar
• Teschendorff AE, Banerji CRS, Severini S, Kuehn R, Sollich P. Increased signaling entropy in cancer requires the scale-free property of protein interaction networks. Sci Rep. 2015;5:9646.
   Web of Science ®Google Scholar
• Eason K, Sandanandam A. Molecular or metabolic reprogramming: what triggers tumor subtypes? Cancer Res. 2016;76(18):5195–5200.
   Google Scholar
• Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet. 2006;7(1):21–33.
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, Jones A, Fiegl H, et al. Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. Genome Med. 2012;4(3):24.
   PubMedGoogle Scholar
• Timp W, Feinberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer. 2013;13(7):497–510.
   PubMed Web of Science ®Google Scholar
• Plass C, Pfister SM, Lindroth AM, Bogatyrova O, Claus R, Lichter P. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nat Rev Genet. 2013;14:765–780.
   PubMed Web of Science ®Google Scholar
• Barat A, Ruskin HJ. Comparative correlation structure of colon cancer locus specific methylation: characterization of patient profiles and potential markers across 3 array-based datasets. J Cancer. 2015;6(8):795–811.
   Web of Science ®Google Scholar
• Guinney J, Dienstmann R, Wang X, et al. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015;21:1350–1356.
   PubMed Web of Science ®Google Scholar
• Forough F, Iman R, D’agnillo M, Porter L, Rueda L, Ngom A. An integrative approach for identifying network biomarkers of breast cancer subtypes using genome, interactome and transcriptome data. J Comput Biol. 2017;24(8):756–766.
   Web of Science ®Google Scholar
• Lanigan F, Brien GL, Fan Y, et al. Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients. FEBS J. 2015;282(18):3455–3473.
   Web of Science ®Google Scholar
• Barat A, Ruskin HJ, Byrne AT, Prehn JH. Integrating colon cancer microarray data: associating locus-specific methylation groups to gene expression-based classifications. Microarrays (Basel). 2015;4(4):630–646.
   Google Scholar
• Sadanandam A, Lyssiotis CA, Homicsko K, et al. A colorectal cancer classification system that associates cellular phenotype and responses to therapy. Nat Med. 2013;19:619–625.
   PubMed Web of Science ®Google Scholar
• Marisa L, de Reyniès A, Duval A, et al. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 2013;10:e1001453.
   PubMed Web of Science ®Google Scholar
• Isella C, Terrasi A, Bellomo SE, et al. Stromal contribution to the colorectal cancer transcriptome. Nat Genet. 2015;47(4):312–319.
   PubMed Web of Science ®Google Scholar
• Munchel S, Hoang Y, Zhao Y, et al. Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics. Oncotarget. 2015;6(28):25943–25961.
   Google Scholar
• Moran B, Das S, Smeets D, et al. Assessment of concordance between fresh-frozen and formalin-fixed paraffin embedded tumor DNA methylation using a targeted sequencing approach. Oncotarget. 2017;8(29):48126–48137.
   PubMedGoogle Scholar
• Lim AM, Wong NC, Pidsley R, et al. Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas. Clin Epigenetics. 2016;8:74.
   Web of Science ®Google Scholar
• Florath I, Butterbach K, Müller H, Bewerunge-Hudler M, Brenner H. Cross-sectional and longitudinal changes in DNA methylation with age: an epigenome-wide analysis revealing over 60 novel age-associated CpG sites. Hum Mol Genet. 2014;23(5):1186–1201.
   PubMed Web of Science ®Google Scholar
• Yuan T, Jiao Y, de Jong S, Ophoff RA, Beck S, Teschendorff AE. An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet. 2015;11(2):e1004996.
   PubMed Web of Science ®Google Scholar
• Salam MT. Asthma epigenetics. Adv Exp Med Biol. 2014;795:183–199.
   Web of Science ®Google Scholar
• Nugent NR, Goldberg A, Uddin M. Topical review: the emerging field of epigenetics: informing models of pediatric trauma and physical health. J Pediatr Psychol. 2016;41(1):55–64.
   Web of Science ®Google Scholar
• Roth TL. Epigenetic mechanisms in the development of behavior: advances, challenges, and future promises of a new field. Dev Psychopathol. 2013;25(4 Pt 2):1279–1291.
   Web of Science ®Google Scholar
• Champagne FA. Epigenetics of mammalian parenting. In: Narvaez D, Valentino K, Fuentes A, McKenna JJ, Gray P, editors. Ancestral Landscapes in Human Evolution: Culture, Childrearing and Social Wellbeing. Oxford School; 2014.
   Google Scholar
• Raymond JG, Steele JD, Seriès P. Modeling trait anxiety: from computational processes to personality. Front Psychiatry. 2017;8:1.
   Web of Science ®Google Scholar
• Mukherjee K, Twyman RM, Vilcinskas A. Insects as models to study the epigenetic basis of disease. Prog Biophys Mol Biol. 2015;118(1–2):69–78.
   Web of Science ®Google Scholar