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A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers.

Yang Y, Zhao L, Huang B, Hou G, Zhou B, Qian J, Yuan S, Xiao H, Li M, Zhou W.

Sci Rep. 2017 Apr 18;7:46533. doi: 10.1038/srep46533.


Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas.

Degli Esposti D, Sklias A, Lima SC, Beghelli-de la Forest Divonne S, Cahais V, Fernandez-Jimenez N, Cros MP, Ecsedi S, Cuenin C, Bouaoun L, Byrnes G, Accardi R, Sudaka A, Giordanengo V, Hernandez-Vargas H, Pinto LF, Van Obberghen-Schilling E, Herceg Z.

Genome Med. 2017 Apr 5;9(1):33. doi: 10.1186/s13073-017-0419-z.


Septin 9_i2 is downregulated in tumors, impairs cancer cell migration and alters subnuclear actin filaments.

Verdier-Pinard P, Salaun D, Bouguenina H, Shimada S, Pophillat M, Audebert S, Agavnian E, Coslet S, Charafe-Jauffret E, Tachibana T, Badache A.

Sci Rep. 2017 Mar 24;7:44976. doi: 10.1038/srep44976.


Three-dimensional culture system identifies a new mode of cetuximab resistance and disease-relevant genes in colorectal cancer.

Li C, Singh B, Graves-Deal R, Ma H, Starchenko A, Fry WH, Lu Y, Wang Y, Bogatcheva G, Khan MP, Milne GL, Zhao S, Ayers GD, Li N, Hu H, Washington MK, Yeatman TJ, McDonald OG, Liu Q, Coffey RJ.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2852-E2861. doi: 10.1073/pnas.1618297114. Epub 2017 Mar 20.


Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA.

Guo S, Diep D, Plongthongkum N, Fung HL, Zhang K, Zhang K.

Nat Genet. 2017 Apr;49(4):635-642. doi: 10.1038/ng.3805. Epub 2017 Mar 6.


The Ageing Brain: Effects on DNA Repair and DNA Methylation in Mice.

Langie SA, Cameron KM, Ficz G, Oxley D, Tomaszewski B, Gorniak JP, Maas LM, Godschalk RW, van Schooten FJ, Reik W, von Zglinicki T, Mathers JC.

Genes (Basel). 2017 Feb 17;8(2). pii: E75. doi: 10.3390/genes8020075.


CpG Island Hypermethylation Mediated by DNMT3A Is a Consequence of AML Progression.

Spencer DH, Russler-Germain DA, Ketkar S, Helton NM, Lamprecht TL, Fulton RS, Fronick CC, O'Laughlin M, Heath SE, Shinawi M, Westervelt P, Payton JE, Wartman LD, Welch JS, Wilson RK, Walter MJ, Link DC, DiPersio JF, Ley TJ.

Cell. 2017 Feb 23;168(5):801-816.e13. doi: 10.1016/j.cell.2017.01.021. Epub 2017 Feb 16.


An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs.

Edgar RD, Jones MJ, Robinson WP, Kobor MS.

Clin Epigenetics. 2017 Feb 2;9:11. doi: 10.1186/s13148-017-0320-z. eCollection 2017.


Altered methylation of specific DNA loci in the liver of Bhmt-null mice results in repression of Iqgap2 and F2rl2 and is associated with development of preneoplastic foci.

Lupu DS, Orozco LD, Wang Y, Cullen JM, Pellegrini M, Zeisel SH.

FASEB J. 2017 May;31(5):2090-2103. doi: 10.1096/fj.201601169R. Epub 2017 Feb 8.


Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.

Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A; BLUEPRINT Consortium., Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS.

Genome Biol. 2017 Jan 26;18(1):18. doi: 10.1186/s13059-017-1156-8.


Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies.

Zheng X, Zhang N, Wu HJ, Wu H.

Genome Biol. 2017 Jan 25;18(1):17. doi: 10.1186/s13059-016-1143-5.


GSAR: Bioconductor package for Gene Set analysis in R.

Rahmatallah Y, Zybailov B, Emmert-Streib F, Glazko G.

BMC Bioinformatics. 2017 Jan 24;18(1):61. doi: 10.1186/s12859-017-1482-6.


A methodological study of genome-wide DNA methylation analyses using matched archival formalin-fixed paraffin embedded and fresh frozen breast tumors.

Espinal AC, Wang D, Yan L, Liu S, Tang L, Hu Q, Morrison CD, Ambrosone CB, Higgins MJ, Sucheston-Campbell LE.

Oncotarget. 2017 Feb 28;8(9):14821-14829. doi: 10.18632/oncotarget.14739.


Parenclitic Network Analysis of Methylation Data for Cancer Identification.

Karsakov A, Bartlett T, Ryblov A, Meyerov I, Ivanchenko M, Zaikin A.

PLoS One. 2017 Jan 20;12(1):e0169661. doi: 10.1371/journal.pone.0169661. eCollection 2017.


Mutual regulation of microRNAs and DNA methylation in human cancers.

Wang S, Wu W, Claret FX.

Epigenetics. 2017 Mar 4;12(3):187-197. doi: 10.1080/15592294.2016.1273308. Epub 2017 Jan 6. Review.


Dental Pulp Stem Cells Model Early Life and Imprinted DNA Methylation Patterns.

Dunaway K, Goorha S, Matelski L, Urraca N, Lein PJ, Korf I, Reiter LT, LaSalle JM.

Stem Cells. 2017 Apr;35(4):981-988. doi: 10.1002/stem.2563. Epub 2017 Jan 19.


The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.

Jordà M, Díez-Villanueva A, Mallona I, Martín B, Lois S, Barrera V, Esteller M, Vavouri T, Peinado MA.

Genome Res. 2017 Jan;27(1):118-132. doi: 10.1101/gr.207522.116. Epub 2016 Dec 20.


Endogenous retroviral promoter exaptation in human cancer.

Babaian A, Mager DL.

Mob DNA. 2016 Dec 1;7:24. eCollection 2016. Review.


"Gap hunting" to characterize clustered probe signals in Illumina methylation array data.

Andrews SV, Ladd-Acosta C, Feinberg AP, Hansen KD, Fallin MD.

Epigenetics Chromatin. 2016 Dec 7;9:56. eCollection 2016.


Integrating Epigenomics into the Understanding of Biomedical Insight.

Han Y, He X.

Bioinform Biol Insights. 2016 Dec 4;10:267-289. eCollection 2016. Review.

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