Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes by Liam McAllan, Damir Baranasic, Sergio Villicaña, Scarlett Brown, Weihua Zhang, Benjamin Lehne, Marco Adamo, Andrew Jenkinson, Mohamed Elkalaawy, Borzoueh Mohammadi, Majid Hashemi, Nadia Fernandes, Nathalie Lambie, Richard Williams, Colette Christiansen, Youwen Yang, Liudmila Zudina, Vasiliki Lagou, Sili Tan, Juan Castillo-Fernandez, James W. D. King, Richie Soong, Paul Elliott, James Scott, Inga Prokopenko, Inês Cebola, Marie Loh, Boris Lenhard, Rachel L. Batterham, Jordana T. Bell, John C. Chambers, Jaspal S. Kooner, William R. Scott

“…Abstract DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. …”
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Epigenetic Mechanisms of Endocrine-Disrupting Chemicals in Obesity by Immacolata Cristina Nettore, Fabiana Franchini, Giuseppe Palatucci, Paolo Emidio Macchia, Paola Ungaro

“…Specifically, EDCs exposure during early-life development can detrimentally affect individuals via inducing epigenetic modifications that can permanently change the epigenome in the germline, enabling changes to be transmitted to the next generations and predisposing them to a multitude of diseases. …”
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XenoCell: classification of cellular barcodes in single cell experiments from xenograft samples by Stefano Cheloni, Roman Hillje, Lucilla Luzi, Pier Giuseppe Pelicci, Elena Gatti

“…Abstract Background Single-cell sequencing technologies provide unprecedented opportunities to deconvolve the genomic, transcriptomic or epigenomic heterogeneity of complex biological systems. …”
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Emerging Molecular Targets for Anti-Epileptogenic and Epilepsy Modifying Drugs by Katarzyna Łukasiuk, Władysław Lasoń

“…Epileptogenesis triggers a vast array of genomic, epigenomic and transcriptomic changes, which ultimately lead to morphological and functional transformation of specific neuronal circuits resulting in the occurrence of spontaneous convulsive or nonconvulsive seizures. …”
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AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species by Du Zhang, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao

“…Abstract Background Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysis, differential epigenomic analysis or co-expression network analysis. …”
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Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies by Natasja L. de Vries, Natasja L. de Vries, Ahmed Mahfouz, Ahmed Mahfouz, Ahmed Mahfouz, Frits Koning, Noel F. C. C. de Miranda

“…In addition, we discuss the integration of transcriptomic, genomic, epigenomic, proteomic, and spatially-resolved data in the context of human cancers. …”
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Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma by Sabatini, David, Wolfson, Rachel Laura, Efeyan, Alejo

“…Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). …”
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A role for the bacterial GATC methylome in antibiotic stress survival by Ross, Christian A, Belenky, Peter, Li, Hu, Cohen, Nadia, Jain, Saloni R., Gutierrez, Arnaud, Collins, James J., Shapiro, Rebecca

“…We explore the role of the bacterial epigenome in antibiotic stress survival using classical genetic tools and single-molecule real-time sequencing to characterize genomic methylation kinetics. …”
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Integrated genomic analyses of de novo pathways underlying atypical meningiomas by Youngblood, Mark W., Clark, Victoria E., Henegariu, Octavian, Duran, Daniel, Erson-Omay, E. Zeynep, Kaulen, Leon D., Simon, Matthias, Krischek, Boris, Timmer, Marco, Goldbrunner, Roland, Baranoski, Jacob, Bai, Hanwen, Mishra-Gorur, Ketu, Schramm, Johannes, Moliterno, Jennifer, Vortmeyer, Alexander O., Bilg?var, Kaya, Yasuno, Katsuhito, G?nel, Murat, Harmanci, Akdes Serin, Suleyman, Coskun, Omay, S. Bulent, Baran, Burcin, Carrion-Grant, Geneive, Bilguvar, Kaya, Lee, Tong Ihn, Abraham, Brian Joseph, Young, Richard A.

“…On the basis of comprehensive genomic, transcriptomic and epigenomic analyses, we compared benign meningiomas to atypical ones. …”
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Meta-analyses identify DNA methylation associated with kidney function and damage by Schlosser, Pascal, Tin, Adrienne, Matias-Garcia, Pamela R., Thio, Chris H. L., Joehanes, Roby, Liu, Hongbo, Weihs, Antoine, Yu, Zhi, Hoppmann, Anselm, Grundner-Culemann, Franziska, Min, Josine L., Adeyemo, Adebowale A., Agyemang, Charles, Ärnlöv, Johan, Aziz, Nasir A., Baccarelli, Andrea, Bochud, Murielle, Brenner, Hermann, Breteler, Monique M. B., Carmeli, Cristian, Chaker, Layal, Chambers, John C., Cole, Shelley A., Coresh, Josef, Corre, Tanguy, Correa, Adolfo, Cox, Simon R., de Klein, Niek, Delgado, Graciela E., Domingo-Relloso, Arce, Eckardt, Kai-Uwe, Ekici, Arif B., Endlich, Karlhans, Evans, Kathryn L., Floyd, James S., Fornage, Myriam, Franke, Lude, Fraszczyk, Eliza, Gao, Xu, Gào, Xīn, Ghanbari, Mohsen, Ghasemi, Sahar, Gieger, Christian, Greenland, Philip, Grove, Megan L., Harris, Sarah E., Hemani, Gibran, Henneman, Peter, Herder, Christian, Horvath, Steve, Hou, Lifang, Hurme, Mikko A., Hwang, Shih-Jen, Jarvelin, Marjo-Riitta, Kardia, Sharon L. R., Kasela, Silva, Kleber, Marcus E., Koenig, Wolfgang, Kooner, Jaspal S., Kramer, Holly, Kronenberg, Florian, Kühnel, Brigitte, Lehtimäki, Terho, Lind, Lars, Liu, Dan, Liu, Yongmei, Lloyd-Jones, Donald M., Lohman, Kurt, Lorkowski, Stefan, Lu, Ake T., Marioni, Riccardo E., März, Winfried, McCartney, Daniel L., Meeks, Karlijn A. C., Milani, Lili, Mishra, Pashupati P., Nauck, Matthias, Navas-Acien, Ana, Nowak, Christoph, Peters, Annette, Prokisch, Holger, Psaty, Bruce M., Raitakari, Olli T., Ratliff, Scott M., Reiner, Alex P., Rosas, Sylvia E., Schöttker, Ben, Schwartz, Joel, Sedaghat, Sanaz, Smith, Jennifer A., Sotoodehnia, Nona, Stocker, Hannah R., Stringhini, Silvia, Sundström, Johan, Swenson, Brenton R., Tellez-Plaza, Maria, van Meurs, Joyce B. J., van Vliet-Ostaptchouk, Jana V., Venema, Andrea, Verweij, Niek, Walker, Rosie M., Wielscher, Matthias, Winkelmann, Juliane, Wolffenbuttel, Bruce H. R., Zhao, Wei, Zheng, Yinan, Milani, Lili, Esko, Tõnu, Metspalu, Andres, Mägi, Reedik, Nelis, Mari, Min, Josine L., Hemani, Gibran, Loh, Marie, Snieder, Harold, Levy, Daniel, Waldenberger, Melanie, Susztak, Katalin, Köttgen, Anna, Teumer, Alexander

“…To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. …”
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Genome-wide DNA methylation profiling in blood reveals epigenetic signature of incident acute coronary syndrome by Long, P, Si, J, Zhu, Z, Jiang, Y, Wang, Y, Jiang, Q, Li, W, Xu, X, You, Y, Qu, M, Wang, H, Mo, T, Liu, K, Jiang, J, Wang, Q, Yu, C, Guo, Y, Millwood, IY, Walters, RG, He, X, Yuan, Y, Wang, H, Zhang, X, He, M, Chen, Z

“…Here, we conduct a prospective epigenome-wide association study of incident ACS in two Chinese cohorts (discovery: 751 nested case-control pairs; replication: 476 nested case-control pairs). …”

Extensive DNA methylome rearrangement during early lamprey embryogenesis by Angeloni, A, Fissette, S, Kaya, D, Hammond, JM, Gamaarachchi, H, Deveson, IW, Klose, RJ, Li, W, Zhang, X, Bogdanovic, O

“…We employed 5mC quantification in lamprey embryos and tissues, and discovered large-scale maternal-to-paternal epigenome remodeling that affects ~30% of the embryonic genome and is predominantly associated with partially methylated domains. …”

Investigation of a possible extended risk haplotype in the IL23R region associated with ankylosing spondylitis by Roberts, A, Vecellio, M, Cortes, A, Knight, J, Cohen, C, Wordsworth, B

“…We used publicly available epigenomic information and historical genetic association data to identify a potential regulatory element (PRE) in the intergenic region between IL23R and IL12RB2, which includes two single-nucleotide polymorphisms (SNPs) independently associated with AS —rs924080 (P=2×10− 3) and rs11578380 (P=2×10− 4). …”

The complement system drives local inflammatory tissue priming by metabolic reprogramming of synovial fibroblasts by Friščić, J, Böttcher, M, Reinwald, C, Bruns, H, Wirth, B, Popp, S-J, Walker, KI, Ackermann, JA, Chen, X, Turner, J, Zhu, H, Seyler, L, Euler, M, Kirchner, P, Krüger, R, Ekici, AB, Major, T, Aust, O, Wiedner, D, Fischer, A, Andes, FT, Stanojevic, Z, Trajkovic, V, Herrmann, M, Korb-Pap, A, Wank, I, Hess, A, Winter, J, Wixler, V, Distler, J, Steiner, G, Kiener, HP, Frey, B, Kling, L, Raza, K, Frey, S, Kleyer, A, Bäuerle, T, Hughes, TR, Grüneboom, A, Steffen, U, Krönke, G, Croft, AP, Filer, A, Köhl, J, Klein, K, Buckley, CD, Schett, G, Mougiakakos, D, Hoffmann, MH

“…Transcriptomic and epigenomic analyses as well as genetic and pharmacological targeting demonstrated that inflammatory tissue priming relies on intracellular complement C3- and C3a receptor-activation and downstream mammalian target of rapamycin- and hypoxia-inducible factor 1α-mediated metabolic SF invigoration that prevents activation-induced senescence, enhances NLRP3 inflammasome activity, and in consequence sensitizes tissue for inflammation. …”

Epigenetic biomarkers in rheumatology – the future? by Caroline Ospelt

“…As in the cancer genome atlas (TCGA), the rheumatology research community should aim to map molecular pathways that drive rheumatic diseases and connect changes in the genome, the epigenome, transcription, protein expression and clinical outcomes. …”
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Systems biology of diet-induced hepatic insulin resistance by Soltis, Anthony Robert

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CHD7 in CHARGE: the implications of neural crest specific regulation of chromatin remodeller CHD7 in CHARGE syndrome by Taylor, Ö

“…Additionally, CRISPRCas9 based genome- and epigenome- editing tools were generated to test the novel enhancer placement within the network.…”

Methylome-wide association study provides evidence of particulate matter air pollution-associated DNA methylation by Rahul Gondalia, Antoine Baldassari, Katelyn M. Holliday, Anne E. Justice, Raúl Méndez-Giráldez, James D. Stewart, Duanping Liao, Jeff D. Yanosky, Kasey J.M. Brennan, Stephanie M. Engel, Kristina M. Jordahl, Elizabeth Kennedy, Cavin K. Ward-Caviness, Kathrin Wolf, Melanie Waldenberger, Josef Cyrys, Annette Peters, Parveen Bhatti, Steve Horvath, Themistocles L. Assimes, James S. Pankow, Ellen W. Demerath, Weihua Guan, Myriam Fornage, Jan Bressler, Kari E. North, Karen N. Conneely, Yun Li, Lifang Hou, Andrea A. Baccarelli, Eric A. Whitsel

“…Further investigation is warranted to uncover mechanisms through which PM-induced epigenomic changes may cause disease. Keywords: Particulate matter, DNA methylation, Epigenetics, Air pollution, Epigenome-wide association study…”
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ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. by Christopher A Miller, Oliver Hampton, Cristian Coarfa, Aleksandar Milosavljevic

“…We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. …”
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Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal by Suhui Zhao, Athe Tsibris

“…High-throughput single-cell technologies that characterize and quantify changes to the epigenome, transcriptome, and proteome continue to rapidly evolve. …”
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