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Items: 1 to 20 of 42

1.

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software.

Decamps C, Privé F, Bacher R, Jost D, Waguet A; HADACA consortium, Houseman EA, Lurie E, Lutsik P, Milosavljevic A, Scherer M, Blum MGB, Richard M.

BMC Bioinformatics. 2020 Jan 13;21(1):16. doi: 10.1186/s12859-019-3307-2.

2.

Random forest-based modelling to detect biomarkers for prostate cancer progression.

Toth R, Schiffmann H, Hube-Magg C, Büscheck F, Höflmayer D, Weidemann S, Lebok P, Fraune C, Minner S, Schlomm T, Sauter G, Plass C, Assenov Y, Simon R, Meiners J, Gerhäuser C.

Clin Epigenetics. 2019 Oct 22;11(1):148. doi: 10.1186/s13148-019-0736-8.

3.

Transcriptome Profiling of Adipose Tissue Reveals Depot-Specific Metabolic Alterations Among Patients with Colorectal Cancer.

Haffa M, Holowatyj AN, Kratz M, Toth R, Benner A, Gigic B, Habermann N, Schrotz-King P, Böhm J, Brenner H, Schneider M, Ulrich A, Herpel E, Schirmacher P, Straub BK, Nattenmüller J, Kauczor HU, Lin T, Ball CR, Ulrich CM, Glimm H, Scherer D.

J Clin Endocrinol Metab. 2019 Nov 1;104(11):5225-5237. doi: 10.1210/jc.2019-00461.

PMID:
31225875
4.

Histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target.

Orouji E, Federico A, Larribère L, Novak D, Lipka DB, Assenov Y, Sachindra S, Hüser L, Granados K, Gebhardt C, Plass C, Umansky V, Utikal J.

Int J Cancer. 2019 Dec 15;145(12):3462-3477. doi: 10.1002/ijc.32432. Epub 2019 Jun 9.

PMID:
31131878
5.

DNA methylation signatures of monozygotic twins clinically discordant for multiple sclerosis.

Souren NY, Gerdes LA, Lutsik P, Gasparoni G, Beltrán E, Salhab A, Kümpfel T, Weichenhan D, Plass C, Hohlfeld R, Walter J.

Nat Commun. 2019 May 7;10(1):2094. doi: 10.1038/s41467-019-09984-3.

6.

DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer.

Weigel C, Chaisaingmongkol J, Assenov Y, Kuhmann C, Winkler V, Santi I, Bogatyrova O, Kaucher S, Bermejo JL, Leung SY, Chan TL, Lasitschka F, Bohrer MH, Marx A, Haußen RH, Herold-Mende C, Dyckhoff G, Boukamp P, Delank KW, Hörmann K, Lippert BM, Baier G, Dietz A, Oakes CC, Plass C, Becher H, Schmezer P, Ramroth H, Popanda O.

Clin Epigenetics. 2019 May 3;11(1):67. doi: 10.1186/s13148-019-0666-5.

7.

RnBeads 2.0: comprehensive analysis of DNA methylation data.

Müller F, Scherer M, Assenov Y, Lutsik P, Walter J, Lengauer T, Bock C.

Genome Biol. 2019 Mar 14;20(1):55. doi: 10.1186/s13059-019-1664-9.

8.

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands.

Haller F, Bieg M, Will R, Körner C, Weichenhan D, Bott A, Ishaque N, Lutsik P, Moskalev EA, Mueller SK, Bähr M, Woerner A, Kaiser B, Scherl C, Haderlein M, Kleinheinz K, Fietkau R, Iro H, Eils R, Hartmann A, Plass C, Wiemann S, Agaimy A.

Nat Commun. 2019 Jan 21;10(1):368. doi: 10.1038/s41467-018-08069-x.

9.

Integrative Analysis Defines Distinct Prognostic Subgroups of Intrahepatic Cholangiocarcinoma.

Goeppert B, Toth R, Singer S, Albrecht T, Lipka DB, Lutsik P, Brocks D, Baehr M, Muecke O, Assenov Y, Gu L, Endris V, Stenzinger A, Mehrabi A, Schirmacher P, Plass C, Weichenhan D, Roessler S.

Hepatology. 2019 May;69(5):2091-2106. doi: 10.1002/hep.30493. Epub 2019 Feb 28.

10.

Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood Cells.

Thier MC, Hommerding O, Panten J, Pinna R, García-González D, Berger T, Wörsdörfer P, Assenov Y, Scognamiglio R, Przybylla A, Kaschutnig P, Becker L, Milsom MD, Jauch A, Utikal J, Herrmann C, Monyer H, Edenhofer F, Trumpp A.

Cell Stem Cell. 2019 Jan 3;24(1):166-182.e13. doi: 10.1016/j.stem.2018.11.015. Epub 2018 Dec 20.

11.

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories.

Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L, Assenov Y, Heckmann D, Sidiropoulos N, Waszak SM, Hübschmann D, Urbanucci A, Girma EG, Kuryshev V, Klimczak LJ, Saini N, Stütz AM, Weichenhan D, Böttcher LM, Toth R, Hendriksen JD, Koop C, Lutsik P, Matzk S, Warnatz HJ, Amstislavskiy V, Feuerstein C, Raeder B, Bogatyrova O, Schmitz EM, Hube-Magg C, Kluth M, Huland H, Graefen M, Lawerenz C, Henry GH, Yamaguchi TN, Malewska A, Meiners J, Schilling D, Reisinger E, Eils R, Schlesner M, Strand DW, Bristow RG, Boutros PC, von Kalle C, Gordenin D, Sültmann H, Brors B, Sauter G, Plass C, Yaspo ML, Korbel JO, Schlomm T, Weischenfeldt J.

Cancer Cell. 2018 Dec 10;34(6):996-1011.e8. doi: 10.1016/j.ccell.2018.10.016.

12.

From Basic Knowledge to Effective Therapies.

Lipka DB, Lutsik P, Plass C.

Cancer Cell. 2018 Dec 10;34(6):871-873. doi: 10.1016/j.ccell.2018.11.013.

13.

PDX models recapitulate the genetic and epigenetic landscape of pediatric T-cell leukemia.

Richter-Pechańska P, Kunz JB, Bornhauser B, von Knebel Doeberitz C, Rausch T, Erarslan-Uysal B, Assenov Y, Frismantas V, Marovca B, Waszak SM, Zimmermann M, Seemann J, Happich M, Stanulla M, Schrappe M, Cario G, Escherich G, Bakharevich K, Kirschner-Schwabe R, Eckert C, Muckenthaler MU, Korbel JO, Bourquin JP, Kulozik AE.

EMBO Mol Med. 2018 Dec;10(12). pii: e9443. doi: 10.15252/emmm.201809443.

14.

Maftools: efficient and comprehensive analysis of somatic variants in cancer.

Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP.

Genome Res. 2018 Nov;28(11):1747-1756. doi: 10.1101/gr.239244.118. Epub 2018 Oct 19.

15.

DNA methylation analysis on purified neurons and glia dissects age and Alzheimer's disease-specific changes in the human cortex.

Gasparoni G, Bultmann S, Lutsik P, Kraus TFJ, Sordon S, Vlcek J, Dietinger V, Steinmaurer M, Haider M, Mulholland CB, Arzberger T, Roeber S, Riemenschneider M, Kretzschmar HA, Giese A, Leonhardt H, Walter J.

Epigenetics Chromatin. 2018 Jul 25;11(1):41. doi: 10.1186/s13072-018-0211-3.

16.

Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles.

Klett H, Balavarca Y, Toth R, Gigic B, Habermann N, Scherer D, Schrotz-King P, Ulrich A, Schirmacher P, Herpel E, Brenner H, Ulrich CM, Michels KB, Busch H, Boerries M.

Epigenetics. 2018;13(4):386-397. doi: 10.1080/15592294.2018.1460034. Epub 2018 May 3.

17.

Reactivation of endogenous retroviral elements via treatment with DNMT- and HDAC-inhibitors.

Daskalakis M, Brocks D, Sheng YH, Islam MS, Ressnerova A, Assenov Y, Milde T, Oehme I, Witt O, Goyal A, Kühn A, Hartmann M, Weichenhan D, Jung M, Plass C.

Cell Cycle. 2018;17(7):811-822. doi: 10.1080/15384101.2018.1442623. Epub 2018 Apr 30. Review.

18.

Intratumor heterogeneity in epigenetic patterns.

Assenov Y, Brocks D, Gerhäuser C.

Semin Cancer Biol. 2018 Aug;51:12-21. doi: 10.1016/j.semcancer.2018.01.010. Epub 2018 Jan 31. Review.

19.

Enrichment analysis with EpiAnnotator.

Pageaud Y, Plass C, Assenov Y.

Bioinformatics. 2018 May 15;34(10):1781-1783. doi: 10.1093/bioinformatics/bty007.

20.

RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia.

Lipka DB, Witte T, Toth R, Yang J, Wiesenfarth M, Nöllke P, Fischer A, Brocks D, Gu Z, Park J, Strahm B, Wlodarski M, Yoshimi A, Claus R, Lübbert M, Busch H, Boerries M, Hartmann M, Schönung M, Kilik U, Langstein J, Wierzbinska JA, Pabst C, Garg S, Catalá A, De Moerloose B, Dworzak M, Hasle H, Locatelli F, Masetti R, Schmugge M, Smith O, Stary J, Ussowicz M, van den Heuvel-Eibrink MM, Assenov Y, Schlesner M, Niemeyer C, Flotho C, Plass C.

Nat Commun. 2017 Dec 19;8(1):2126. doi: 10.1038/s41467-017-02177-w.

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