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Items: 1 to 50 of 118

1.

Appraising the causal relevance of DNA methylation for risk of lung cancer.

Battram T, Richmond RC, Baglietto L, Haycock PC, Perduca V, Bojesen SE, Gaunt TR, Hemani G, Guida F, Carreras-Torres R, Hung R, Amos CI, Freeman JR, Sandanger TM, Nøst TH, Nordestgaard BG, Teschendorff AE, Polidoro S, Vineis P, Severi G, Hodge AM, Giles GG, Grankvist K, Johansson MB, Johansson M, Davey Smith G, Relton CL.

Int J Epidemiol. 2019 Sep 24. pii: dyz190. doi: 10.1093/ije/dyz190. [Epub ahead of print]

PMID:
31549173
2.

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.

Chen W, Morabito SJ, Kessenbrock K, Enver T, Meyer KB, Teschendorff AE.

Commun Biol. 2019 Aug 9;2:306. doi: 10.1038/s42003-019-0554-8. eCollection 2019.

3.

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data.

Breeze CE, Reynolds AP, van Dongen J, Dunham I, Lazar J, Neph S, Vierstra J, Bourque G, Teschendorff AE, Stamatoyannopoulos JA, Beck S.

Bioinformatics. 2019 Jun 4. pii: btz456. doi: 10.1093/bioinformatics/btz456. [Epub ahead of print]

PMID:
31161210
4.

Estimating Differentiation Potency of Single Cells Using Single-Cell Entropy (SCENT).

Chen W, Teschendorff AE.

Methods Mol Biol. 2019;1935:125-139. doi: 10.1007/978-1-4939-9057-3_9.

PMID:
30758824
5.

ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies.

Dong D, Tian Y, Zheng SC, Teschendorff AE.

Bioinformatics. 2019 Sep 15;35(18):3514-3516. doi: 10.1093/bioinformatics/btz073.

6.

Identification of differentially methylated cell types in epigenome-wide association studies.

Zheng SC, Breeze CE, Beck S, Teschendorff AE.

Nat Methods. 2018 Dec;15(12):1059-1066. doi: 10.1038/s41592-018-0213-x. Epub 2018 Nov 30.

7.

Cell and tissue type independent age-associated DNA methylation changes are not rare but common.

Zhu T, Zheng SC, Paul DS, Horvath S, Teschendorff AE.

Aging (Albany NY). 2018 Nov 27;10(11):3541-3557. doi: 10.18632/aging.101666.

8.

Avoiding common pitfalls in machine learning omic data science.

Teschendorff AE.

Nat Mater. 2019 May;18(5):422-427. doi: 10.1038/s41563-018-0241-z. No abstract available.

PMID:
30478452
9.

Detection of epigenetic field defects using a weighted epigenetic distance-based method.

Wang Y, Qian M, Ruan P, Teschendorff AE, Wang S.

Nucleic Acids Res. 2019 Jan 10;47(1):e6. doi: 10.1093/nar/gky882.

10.

Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures.

Shi J, Teschendorff AE, Chen W, Chen L, Li T.

Brief Bioinform. 2018 Oct 5. doi: 10.1093/bib/bby093. [Epub ahead of print]

PMID:
30289442
11.

Epigenetic clocks galore: a new improved clock predicts age-acceleration in Hutchinson Gilford Progeria Syndrome patients.

Teschendorff AE.

Aging (Albany NY). 2018 Aug 21;10(8):1799-1800. doi: 10.18632/aging.101533. No abstract available.

12.

Accounting for differential variability in detecting differentially methylated regions.

Wang Y, Teschendorff AE, Widschwendter M, Wang S.

Brief Bioinform. 2019 Jan 18;20(1):47-57. doi: 10.1093/bib/bbx097.

PMID:
29912290
13.

Tensorial blind source separation for improved analysis of multi-omic data.

Teschendorff AE, Jing H, Paul DS, Virta J, Nordhausen K.

Genome Biol. 2018 Jun 8;19(1):76. doi: 10.1186/s13059-018-1455-8.

14.

DNA Methylation Patterns in Normal Tissue Correlate more Strongly with Breast Cancer Status than Copy-Number Variants.

Gao Y, Widschwendter M, Teschendorff AE.

EBioMedicine. 2018 May;31:243-252. doi: 10.1016/j.ebiom.2018.04.025. Epub 2018 May 4.

15.

A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix.

Zheng SC, Webster AP, Dong D, Feber A, Graham DG, Sullivan R, Jevons S, Lovat LB, Beck S, Widschwendter M, Teschendorff AE.

Epigenomics. 2018 Jul;10(7):925-940. doi: 10.2217/epi-2018-0037. Epub 2018 Apr 25.

16.

Epigenome-based cancer risk prediction: rationale, opportunities and challenges.

Widschwendter M, Jones A, Evans I, Reisel D, Dillner J, Sundström K, Steyerberg EW, Vergouwe Y, Wegwarth O, Rebitschek FG, Siebert U, Sroczynski G, de Beaufort ID, Bolt I, Cibula D, Zikan M, Bjørge L, Colombo N, Harbeck N, Dudbridge F, Tasse AM, Knoppers BM, Joly Y, Teschendorff AE, Pashayan N; FORECEE (4C) Consortium.

Nat Rev Clin Oncol. 2018 May;15(5):292-309. doi: 10.1038/nrclinonc.2018.30. Epub 2018 Feb 27. Review.

17.

Psychosocial adversity and socioeconomic position during childhood and epigenetic age: analysis of two prospective cohort studies.

Lawn RB, Anderson EL, Suderman M, Simpkin AJ, Gaunt TR, Teschendorff AE, Widschwendter M, Hardy R, Kuh D, Relton CL, Howe LD.

Hum Mol Genet. 2018 Apr 1;27(7):1301-1308. doi: 10.1093/hmg/ddy036.

18.

The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer.

Widschwendter M, Zikan M, Wahl B, Lempiäinen H, Paprotka T, Evans I, Jones A, Ghazali S, Reisel D, Eichner J, Rujan T, Yang Z, Teschendorff AE, Ryan A, Cibula D, Menon U, Wittenberger T.

Genome Med. 2017 Dec 22;9(1):116. doi: 10.1186/s13073-017-0500-7.

19.
20.

Statistical and integrative system-level analysis of DNA methylation data.

Teschendorff AE, Relton CL.

Nat Rev Genet. 2018 Mar;19(3):129-147. doi: 10.1038/nrg.2017.86. Epub 2017 Nov 13. Review.

PMID:
29129922
21.

Tumor origin detection with tissue-specific miRNA and DNA methylation markers.

Tang W, Wan S, Yang Z, Teschendorff AE, Zou Q.

Bioinformatics. 2018 Feb 1;34(3):398-406. doi: 10.1093/bioinformatics/btx622.

PMID:
29028927
22.

ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

Tian Y, Morris TJ, Webster AP, Yang Z, Beck S, Feber A, Teschendorff AE.

Bioinformatics. 2017 Dec 15;33(24):3982-3984. doi: 10.1093/bioinformatics/btx513.

23.

Roadmap for investigating epigenome deregulation and environmental origins of cancer.

Herceg Z, Ghantous A, Wild CP, Sklias A, Casati L, Duthie SJ, Fry R, Issa JP, Kellermayer R, Koturbash I, Kondo Y, Lepeule J, Lima SCS, Marsit CJ, Rakyan V, Saffery R, Taylor JA, Teschendorff AE, Ushijima T, Vineis P, Walker CL, Waterland RA, Wiemels J, Ambatipudi S, Degli Esposti D, Hernandez-Vargas H.

Int J Cancer. 2018 Mar 1;142(5):874-882. doi: 10.1002/ijc.31014. Epub 2017 Sep 13. Review.

24.

Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome.

Teschendorff AE, Enver T.

Nat Commun. 2017 Jun 1;8:15599. doi: 10.1038/ncomms15599.

25.

Cell-type deconvolution in epigenome-wide association studies: a review and recommendations.

Teschendorff AE, Zheng SC.

Epigenomics. 2017 May;9(5):757-768. doi: 10.2217/epi-2016-0153. Epub 2017 Mar 14. Review.

26.

DNA methylome analysis reveals distinct epigenetic patterns of ascending aortic dissection and bicuspid aortic valve.

Pan S, Lai H, Shen Y, Breeze C, Beck S, Hong T, Wang C, Teschendorff AE.

Cardiovasc Res. 2017 May 1;113(6):692-704. doi: 10.1093/cvr/cvx050.

PMID:
28444195
27.

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE.

Nat Methods. 2017 Feb 28;14(3):216-217. doi: 10.1038/nmeth.4187. No abstract available.

28.

A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.

Teschendorff AE, Breeze CE, Zheng SC, Beck S.

BMC Bioinformatics. 2017 Feb 13;18(1):105. doi: 10.1186/s12859-017-1511-5.

29.

Epigenetic and genetic deregulation in cancer target distinct signaling pathway domains.

Gao Y, Teschendorff AE.

Nucleic Acids Res. 2017 Jan 25;45(2):583-596. doi: 10.1093/nar/gkw1100. Epub 2016 Nov 29.

30.

dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers.

Yang Z, Wu L, Wang A, Tang W, Zhao Y, Zhao H, Teschendorff AE.

Nucleic Acids Res. 2017 Jan 4;45(D1):D812-D818. doi: 10.1093/nar/gkw1079. Epub 2016 Nov 28.

31.

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types.

Paul DS, Teschendorff AE, Dang MA, Lowe R, Hawa MI, Ecker S, Beyan H, Cunningham S, Fouts AR, Ramelius A, Burden F, Farrow S, Rowlston S, Rehnstrom K, Frontini M, Downes K, Busche S, Cheung WA, Ge B, Simon MM, Bujold D, Kwan T, Bourque G, Datta A, Lowy E, Clarke L, Flicek P, Libertini E, Heath S, Gut M, Gut IG, Ouwehand WH, Pastinen T, Soranzo N, Hofer SE, Karges B, Meissner T, Boehm BO, Cilio C, Elding Larsson H, Lernmark Å, Steck AK, Rakyan VK, Beck S, Leslie RD.

Nat Commun. 2016 Nov 29;7:13555. doi: 10.1038/ncomms13555.

32.

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data.

Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S.

Cell Rep. 2016 Nov 15;17(8):2137-2150. doi: 10.1016/j.celrep.2016.10.059.

33.

Correlation of an epigenetic mitotic clock with cancer risk.

Yang Z, Wong A, Kuh D, Paul DS, Rakyan VK, Leslie RD, Zheng SC, Widschwendter M, Beck S, Teschendorff AE.

Genome Biol. 2016 Oct 3;17(1):205.

34.

The lncRNA HOTAIR impacts on mesenchymal stem cells via triple helix formation.

Kalwa M, Hänzelmann S, Otto S, Kuo CC, Franzen J, Joussen S, Fernandez-Rebollo E, Rath B, Koch C, Hofmann A, Lee SH, Teschendorff AE, Denecke B, Lin Q, Widschwendter M, Weinhold E, Costa IG, Wagner W.

Nucleic Acids Res. 2016 Dec 15;44(22):10631-10643. Epub 2016 Sep 14.

35.

The multi-omic landscape of transcription factor inactivation in cancer.

Teschendorff AE, Zheng SC, Feber A, Yang Z, Beck S, Widschwendter M.

Genome Med. 2016 Aug 25;8(1):89. doi: 10.1186/s13073-016-0342-8.

36.

Menopause accelerates biological aging.

Levine ME, Lu AT, Chen BH, Hernandez DG, Singleton AB, Ferrucci L, Bandinelli S, Salfati E, Manson JE, Quach A, Kusters CD, Kuh D, Wong A, Teschendorff AE, Widschwendter M, Ritz BR, Absher D, Assimes TL, Horvath S.

Proc Natl Acad Sci U S A. 2016 Aug 16;113(33):9327-32. doi: 10.1073/pnas.1604558113. Epub 2016 Jul 25.

37.

DNA Methylation Signatures in Vaginal Fluid Samples for Detection of Cervical and Endometrial Cancer.

Doufekas K, Zheng SC, Ghazali S, Wong M, Mohamed Y, Jones A, Reisel D, Mould T, Olaitan A, Macdonald N, Teschendorff AE, Widschwendter M.

Int J Gynecol Cancer. 2016 Jun 2. [Epub ahead of print]

PMID:
27258725
38.

Erratum to: The integrative epigenomic-transcriptomic landscape of ER positive breast cancer.

Gao Y, Jones A, Fasching PA, Ruebner M, Beckmann MW, Widschwendter M, Teschendorff AE.

Clin Epigenetics. 2016 Jun 1;8:63. doi: 10.1186/s13148-016-0231-4. eCollection 2016. No abstract available.

39.

Epigenetic drift, epigenetic clocks and cancer risk.

Zheng SC, Widschwendter M, Teschendorff AE.

Epigenomics. 2016 May;8(5):705-19. doi: 10.2217/epi-2015-0017. Epub 2016 Apr 22. Review.

PMID:
27104983
40.

Stochastic epigenetic outliers can define field defects in cancer.

Teschendorff AE, Jones A, Widschwendter M.

BMC Bioinformatics. 2016 Apr 22;17:178. doi: 10.1186/s12859-016-1056-z.

41.

Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer.

Chen Y, Breeze CE, Zhen S, Beck S, Teschendorff AE.

Epigenetics Chromatin. 2016 Mar 8;9:10. doi: 10.1186/s13072-016-0058-4. eCollection 2016.

42.

DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer.

Teschendorff AE, Gao Y, Jones A, Ruebner M, Beckmann MW, Wachter DL, Fasching PA, Widschwendter M.

Nat Commun. 2016 Jan 29;7:10478. doi: 10.1038/ncomms10478.

43.

The integrative epigenomic-transcriptomic landscape of ER positive breast cancer.

Gao Y, Jones A, Fasching PA, Ruebner M, Beckmann MW, Widschwendter M, Teschendorff AE.

Clin Epigenetics. 2015 Dec 9;7:126. doi: 10.1186/s13148-015-0159-0. eCollection 2015. Erratum in: Clin Epigenetics. 2016;8:63.

44.

Glioblastoma Stem Cells Respond to Differentiation Cues but Fail to Undergo Commitment and Terminal Cell-Cycle Arrest.

Carén H, Stricker SH, Bulstrode H, Gagrica S, Johnstone E, Bartlett TE, Feber A, Wilson G, Teschendorff AE, Bertone P, Beck S, Pollard SM.

Stem Cell Reports. 2015 Nov 10;5(5):829-842. doi: 10.1016/j.stemcr.2015.09.014.

45.

HOTAIR and its surrogate DNA methylation signature indicate carboplatin resistance in ovarian cancer.

Teschendorff AE, Lee SH, Jones A, Fiegl H, Kalwa M, Wagner W, Chindera K, Evans I, Dubeau L, Orjalo A, Horlings HM, Niederreiter L, Kaser A, Yang W, Goode EL, Fridley BL, Jenner RG, Berns EM, Wik E, Salvesen HB, Wisman GB, van der Zee AG, Davidson B, Trope CG, Lambrechts S, Vergote I, Calvert H, Jacobs IJ, Widschwendter M.

Genome Med. 2015 Oct 24;7:108. doi: 10.1186/s13073-015-0233-4.

46.

Variational Bayesian Matrix Factorization for Bounded Support Data.

Ma Z, Teschendorff AE, Leijon A, Qiao Y, Zhang H, Guo J.

IEEE Trans Pattern Anal Mach Intell. 2015 Apr;37(4):876-89. doi: 10.1109/TPAMI.2014.2353639.

PMID:
26353300
47.

Expression profiling of nuclear receptors in breast cancer identifies TLX as a mediator of growth and invasion in triple-negative breast cancer.

Lin ML, Patel H, Remenyi J, Banerji CR, Lai CF, Periyasamy M, Lombardo Y, Busonero C, Ottaviani S, Passey A, Quinlan PR, Purdie CA, Jordan LB, Thompson AM, Finn RS, Rueda OM, Caldas C, Gil J, Coombes RC, Fuller-Pace FV, Teschendorff AE, Buluwela L, Ali S.

Oncotarget. 2015 Aug 28;6(25):21685-703.

48.

Correlation of Smoking-Associated DNA Methylation Changes in Buccal Cells With DNA Methylation Changes in Epithelial Cancer.

Teschendorff AE, Yang Z, Wong A, Pipinikas CP, Jiao Y, Jones A, Anjum S, Hardy R, Salvesen HB, Thirlwell C, Janes SM, Kuh D, Widschwendter M.

JAMA Oncol. 2015 Jul;1(4):476-85. doi: 10.1001/jamaoncol.2015.1053. Erratum in: JAMA Oncol. 2015 Jul;1(4):544.

PMID:
26181258
49.

An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer.

Yang Z, Jones A, Widschwendter M, Teschendorff AE.

Genome Biol. 2015 Jul 14;16:140. doi: 10.1186/s13059-015-0699-9.

50.

Increased signaling entropy in cancer requires the scale-free property of protein interaction networks.

Teschendorff AE, Banerji CR, Severini S, Kuehn R, Sollich P.

Sci Rep. 2015 Apr 28;5:9646. doi: 10.1038/srep09646.

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