10 Years of Epigenomics: A Journey with the Epigenetic Community Through Exciting Times

Figures & data

Table 1. The ten most cited articles published in Epigenomics.

Title	Study	Year	Citations	Ref.
DNA hypomethylation in cancer cells	M Ehrlich	2009	448	[1]
Genome-wide DNA methylation profiling using Infinium assay	M Bibikova, J Le, B Barnes, S Saedinia-Melnyk, L Zhou, RShen, KL Gunderson	2009	406	[2]
Evaluation of the Infinium Methylation 450K technology	S Dedeurwaerder, M Defrance, E Calonne, H Denis, C Sotiriou, F Fuks	2011	360	[3]
Complete pipeline for Infinium Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation	N Touleimat, J Tost	2012	253	[4]
Effects of arsenic exposure on DNA methylation and epigenetic gene regulation	JF Reichard, A Puga	2010	176	[5]
Epigenetics and lifestyle	JA Alegra-Torres, A Baccarelli, V Bollati	2011	173	[6]
Epigenetic diet: impact on the epigenome and cancer	TM Hardy, TO Tollefsbol	2011	170	[7]
Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences	S Moran, C Arribas, M Esteller	2016	166	[8]
Molecular coupling of DNA methylation and histone methylation	H Hashimoto, P M Vertino, X Cheng	2010	145	[9]
The NIH Roadmap Epigenomics Program data resource	LH Chadwick	2012	133	[10]

Source: https://app.dimensions.ai/discover/publication?and_facet_source_title=jour.1042549&and_facet_source_title=jour.1042549&order=times_cited

Table 2. The 20 most trending articles published in Epigenomics.

Title	Study	Year	Altmetric Attention Score	Ref.
Genome-wide sperm DNA methylation changes after 3 months of exercise training in humans	J Denham, BJ O’Brien, JT Harvey, FJ Charchar	2015	572	[11]
MethylMeter^®: bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples	D McCarthy, W Pulverer, A Weinhaeusel, OR Diago, DJ Hogan, D Ostertag, MM Hanna	2016	512	[12]
Epigenetic regulation of chronic pain	L Liang, BM Lutz, A Bekker, Y-X Tao	2015	108	[13]
Postnatal diet remodels hepatic DNA methylation in metabolic pathways established by a maternal high-fat diet	L Moody, H Chen, Y-X Pan	2017	84	[14]
Genome-wide miRNA methylome analysis in oral cancer: possible biomarkers associated with patient survival	R Roy, A Chatterjee, D Das, A Ray, R Singh, E Chattopadhyay, ND Sarkar, M Eccles, M Pal, A Maitra, B Roy	2019	68	[15]
Role of histone acetylation in gastric cancer: implications of dietetic compounds and clinical perspectives	DQ Calcagno, F Wisnieski, ER da Silva Mota, SBM de Sousa, JMC da Silva, MF Leal, CO Gigek, LC Santos, LT Rasmussen, PP Assumpção, RR Burbano, MAC Smith	2019	63	[16]
Aging, exceptional longevity and comparisons of the Hannum and Horvath epigenetic clocks	NJ Armstrong, KA Mather, A Thalamuthu, MJ Wright, JN Trollor, D Ames, H Brodaty, PR Schofield, PS Sachdev, JB Kwok	2017	45	[17]
Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences	S Moran, C Arribas, M Esteller	2016	44	[18]
DNA hypomethylation in cancer cells	M Ehrlich	2009	34	[1]
Integration of DNA methylation & health scores identifies subtypes in myalgic encephalomyelitis/chronic fatigue syndrome	WC de Vega, L Erdman, SD Vernon, A Goldenberg, PO McGowan	2018	33	[19]
Epigenetic diet: impact on the epigenome and cancer	TM Hardy, TO Tollefsbol	2011	30	[7]
The biological embedding of early-life socioeconomic status and family adversity in children’s genome-wide DNA methylation	NR Bush, RD Edgar, M Park, JL MacIsaac, LM McEwen, NE Adler, MJ Essex, MS Kobor, WT Boyce	2018	29	[20]
Epigenetics and lifestyle	JA Alegría-Torres, A Baccarelli, V Bollati	2011	26	[6]
Evolving role of MeCP2 in Rett syndrome and autism	JM LaSalle, DH Yasui	2009	26	[21]
The epigenetic impacts of social stress: how does social adversity become biologically embedded?	VT Cunliffe	2016	25	[22]
Demethylation and re-expression of epigenetically silenced tumor suppressor genes: sensitization of cancer cells by combination therapy	S Sarkar, S Goldgar, S Byler, S Rosenthal, S Heerboth	2013	20	[23]
Salivary microRNAs identified by small RNA sequencing and machine learning as potential biomarkers of alcohol dependence	AJ Rosato, X Chen, Y Tanaka, LA Farrer, HR Kranzler, YZ Nunez, DC Henderson, J Gelernter, H Zhang	2019	20	[24]
scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups	A Chatterjee, PA Stockwell, EJ Rodger, MF Parry, MR Eccles	2016	20	[25]
Frailty phenotype: a clinical marker of age acceleration in the older HIV-infected population	M Sánchez-Conde, J Rodriguez-Centeno, F Dronda, JC López, Z Jiménez, J Berenguer, MJ Pérez-Elías, S Moreno, B Rodés, F Brañas	2019	19	[26]
Sex-specific epigenetic mediators between early life social disadvantage and adulthood BMI	SH Chu, EB Loucks, KT Kelsey, SE Gilman, G Agha, CB Eaton, SL Buka, Y-T Huang	2018	19	[27]

Source: https://www.altmetric.com/explorer/outputs?journal_id%5B%5D=4f6fa6163cf058f6100072c9

Figure 1. Evolution of Epigenomics over the last years.

(A) Performance of the impact factor (left y axis) as well as the journal impact factor percentiles (right y axis) allowing cross journal comparison for Epigenomics. Data from InCites Journal Citation Reports dataset updated 20 September 2019. (B) Evolution of accepted submissions in Epigenomics showing the strong increase in primary research articles over the last 4 years. The commentary category also includes editorials, conference reports and interviews with leading experts in the field.

JIF: Journal impact factor.

Ehrlich M . DNA hypomethylation in cancer cells. Epigenomics1(2), 239–259 (2009).

 PubMed Web of Science ®Google Scholar

Bibikova M , LeJ , BarnesBet al. Genome-wide DNA methylation profiling using Infinium® assay. Epigenomics1(1), 177–200 (2009).

 PubMed Web of Science ®Google Scholar

Dedeurwaerder S , DefranceM , CalonneE , DenisH , SotiriouC , FuksF. Evaluation of the Infinium Methylation 450K technology. Epigenomics3(6), 771–784 (2011).

 PubMed Web of Science ®Google Scholar

Touleimat N , TostJ. Complete pipeline for Infinium® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics4(3), 325–341 (2012).

 PubMed Web of Science ®Google Scholar

Reichard JF , PugaA. Effects of arsenic exposure on DNA methylation and epigenetic gene regulation. Epigenomics2(1), 87–104 (2010).

 PubMed Web of Science ®Google Scholar

Alegría-Torres JA , BaccarelliA , BollatiV. Epigenetics and lifestyle. Epigenomics3(3), 267–277 (2011).

 PubMed Web of Science ®Google Scholar

Hardy TM , TollefsbolTO. Epigenetic diet: impact on the epigenome and cancer. Epigenomics3(4), 503–518 (2011).

 PubMed Web of Science ®Google Scholar

Moran S , ArribasC , EstellerM. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics8(3), 389–399 (2016).

 PubMed Web of Science ®Google Scholar

Hashimoto H , VertinoPM , ChengX. Molecular coupling of DNA methylation and histone methylation. Epigenomics2(5), 657–669 (2010).

 PubMed Web of Science ®Google Scholar

Chadwick LH . The NIH Roadmap Epigenomics Program data resource. Epigenomics4(3), 317–324 (2012).

 PubMed Web of Science ®Google Scholar

Denham J , O’BrienBJ , HarveyJT , CharcharFJ. Genome-wide sperm DNA methylation changes after 3 months of exercise training in humans. Epigenomics7(5), 717–731 (2015).

 PubMed Web of Science ®Google Scholar

McCarthy D , PulvererW , WeinhaeuselAet al. MethylMeter®: bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples. Epigenomics8(6), 747–765 (2016).

 PubMed Web of Science ®Google Scholar

Liang L , LutzBM , BekkerA , TaoY-X. Epigenetic regulation of chronic pain. Epigenomics7(2), 235–245 (2015).

 PubMed Web of Science ®Google Scholar

Moody L , ChenH , PanYX. Postnatal diet remodels hepatic DNA methylation in metabolic pathways established by a maternal high-fat diet. Epigenomics9(11), 1387–1402 (2017).

 PubMed Web of Science ®Google Scholar

Roy R , ChatterjeeA , DasDet al. Genome-wide miRNA methylome analysis in oral cancer: possible biomarkers associated with patient survival. Epigenomics11(5), 473–487 (2019).

 PubMed Web of Science ®Google Scholar

Calcagno DQ , WisnieskiF , DaSilva Mota ERet al. Role of histone acetylation in gastric cancer: implications of dietetic compounds and clinical perspectives. Epigenomics11(3), 349–362 (2019).

 PubMed Web of Science ®Google Scholar

Armstrong NJ , MatherKA , ThalamuthuAet al. Aging, exceptional longevity and comparisons of the Hannum and Horvath epigenetic clocks. Epigenomics9(5), 689–700 (2017).

 PubMed Web of Science ®Google Scholar

Moran S , ArribasC , EstellerM. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics8(3), 389–399 (2016).

 PubMed Web of Science ®Google Scholar

De Vega WC , ErdmanL , VernonSD , GoldenbergA , McGowanPO. Integration of DNA methylation & health scores identifies subtypes in myalgic encephalomyelitis/chronic fatigue syndrome. Epigenomics10(5), 539–557 (2018).

 PubMed Web of Science ®Google Scholar

Bush NR , EdgarRD , ParkMet al. The biological embedding of early-life socioeconomic status and family adversity in children’s genome-wide DNA methylation. Epigenomics10(11), 1445–1461 (2018).

 PubMed Web of Science ®Google Scholar

LaSalle JM , YasuiDH. Evolving role of MeCP2 in Rett syndrome and autism. Epigenomics1(1), 119–130 (2009).

 PubMed Web of Science ®Google Scholar

Cunliffe VT . The epigenetic impacts of social stress: how does social adversity become biologically embedded?Epigenomics8(12), 1653–1669 (2016).

 PubMed Web of Science ®Google Scholar

Sarkar S , GoldgarS , BylerS , RosenthalS , HeerbothS. Demethylation and re-expression of epigenetically silenced tumor suppressor genes: sensitization of cancer cells by combination therapy. Epigenomics5(1), 87–94 (2013).

 PubMed Web of Science ®Google Scholar

Rosato AJ , ChenX , TanakaYet al. Salivary microRNAs identified by small RNA sequencing and machine learning as potential biomarkers of alcohol dependence. Epigenomics11(7), 739–749 (2019).

 PubMed Web of Science ®Google Scholar

Chatterjee A , StockwellPA , RodgerEJ , ParryMF , EcclesMR. Scan-tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups. Epigenomics8(10), 1315–1330 (2016).

 PubMed Web of Science ®Google Scholar

Sánchez-Conde M , Rodriguez-CentenoJ , DrondaFet al. Frailty phenotype: a clinical marker of age acceleration in the older HIV-infected population. Epigenomics11(5), 501–509 (2019).

 PubMed Web of Science ®Google Scholar

Chu SH , LoucksEB , KelseyKTet al. Sex-specific epigenetic mediators between early life social disadvantage and adulthood BMI. Epigenomics10(6), 707–722 (2018).

 PubMed Web of Science ®Google Scholar