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Items: 32

1.

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 Nov 2. pii: e9443. doi: 10.15252/emmm.201809443. [Epub ahead of print]

2.

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.

PMID:
30341162
3.

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.

PMID:
29633898
4.

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.

5.

Enrichment analysis with EpiAnnotator.

Pageaud Y, Plass C, Assenov Y.

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

6.

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.

7.

Genome-wide genetic and epigenetic analyses of pancreatic acinar cell carcinomas reveal aberrations in genome stability.

Jäkel C, Bergmann F, Toth R, Assenov Y, van der Duin D, Strobel O, Hank T, Klöppel G, Dorrell C, Grompe M, Moss J, Dor Y, Schirmacher P, Plass C, Popanda O, Schmezer P.

Nat Commun. 2017 Nov 6;8(1):1323. doi: 10.1038/s41467-017-01118-x.

8.

Erratum: DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C.

Nat Genet. 2017 Oct 27;49(11):1661. doi: 10.1038/ng1117-1661c.

PMID:
29074949
9.

Circulating cytokines and small molecules follow distinct expression patterns in acute myeloid leukaemia.

Islam M, Mohamed EH, Esa E, Kamaluddin NR, Zain SM, Yusoff YM, Assenov Y, Mohamed Z, Zakaria Z.

Br J Cancer. 2017 Nov 7;117(10):1551-1556. doi: 10.1038/bjc.2017.316. Epub 2017 Sep 12.

10.

Strategies for analyzing bisulfite sequencing data.

Wreczycka K, Gosdschan A, Yusuf D, Grüning B, Assenov Y, Akalin A.

J Biotechnol. 2017 Nov 10;261:105-115. doi: 10.1016/j.jbiotec.2017.08.007. Epub 2017 Aug 16. Review.

11.

Differential Analysis of Genetic, Epigenetic, and Cytogenetic Abnormalities in AML.

Islam M, Mohamed Z, Assenov Y.

Int J Genomics. 2017;2017:2913648. doi: 10.1155/2017/2913648. Epub 2017 Jun 20.

12.

DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.

Brocks D, Schmidt CR, Daskalakis M, Jang HS, Shah NM, Li D, Li J, Zhang B, Hou Y, Laudato S, Lipka DB, Schott J, Bierhoff H, Assenov Y, Helf M, Ressnerova A, Islam MS, Lindroth AM, Haas S, Essers M, Imbusch CD, Brors B, Oehme I, Witt O, Lübbert M, Mallm JP, Rippe K, Will R, Weichenhan D, Stoecklin G, Gerhäuser C, Oakes CC, Wang T, Plass C.

Nat Genet. 2017 Jul;49(7):1052-1060. doi: 10.1038/ng.3889. Epub 2017 Jun 12. Erratum in: Nat Genet. 2017 Oct 27;49(11):1661.

13.

Melanoma-Derived iPCCs Show Differential Tumorigenicity and Therapy Response.

Bernhardt M, Novak D, Assenov Y, Orouji E, Knappe N, Weina K, Reith M, Larribere L, Gebhardt C, Plass C, Umansky V, Utikal J.

Stem Cell Reports. 2017 May 9;8(5):1379-1391. doi: 10.1016/j.stemcr.2017.03.007. Epub 2017 Apr 6.

14.

Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis.

Moran S, Martínez-Cardús A, Sayols S, Musulén E, Balañá C, Estival-Gonzalez A, Moutinho C, Heyn H, Diaz-Lagares A, de Moura MC, Stella GM, Comoglio PM, Ruiz-Miró M, Matias-Guiu X, Pazo-Cid R, Antón A, Lopez-Lopez R, Soler G, Longo F, Guerra I, Fernandez S, Assenov Y, Plass C, Morales R, Carles J, Bowtell D, Mileshkin L, Sia D, Tothill R, Tabernero J, Llovet JM, Esteller M.

Lancet Oncol. 2016 Oct;17(10):1386-1395. doi: 10.1016/S1470-2045(16)30297-2. Epub 2016 Aug 27.

PMID:
27575023
15.

Epigenetic regulation of diacylglycerol kinase alpha promotes radiation-induced fibrosis.

Weigel C, Veldwijk MR, Oakes CC, Seibold P, Slynko A, Liesenfeld DB, Rabionet M, Hanke SA, Wenz F, Sperk E, Benner A, Rösli C, Sandhoff R, Assenov Y, Plass C, Herskind C, Chang-Claude J, Schmezer P, Popanda O.

Nat Commun. 2016 Mar 11;7:10893. doi: 10.1038/ncomms10893.

16.

DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia.

Oakes CC, Seifert M, Assenov Y, Gu L, Przekopowitz M, Ruppert AS, Wang Q, Imbusch CD, Serva A, Koser SD, Brocks D, Lipka DB, Bogatyrova O, Weichenhan D, Brors B, Rassenti L, Kipps TJ, Mertens D, Zapatka M, Lichter P, Döhner H, Küppers R, Zenz T, Stilgenbauer S, Byrd JC, Plass C.

Nat Genet. 2016 Mar;48(3):253-64. doi: 10.1038/ng.3488. Epub 2016 Jan 18.

17.

Pediatric T-cell lymphoblastic leukemia evolves into relapse by clonal selection, acquisition of mutations and promoter hypomethylation.

Kunz JB, Rausch T, Bandapalli OR, Eilers J, Pechanska P, Schuessele S, Assenov Y, Stütz AM, Kirschner-Schwabe R, Hof J, Eckert C, von Stackelberg A, Schrappe M, Stanulla M, Koehler R, Avigad S, Elitzur S, Handgretinger R, Benes V, Weischenfeldt J, Korbel JO, Muckenthaler MU, Kulozik AE.

Haematologica. 2015 Nov;100(11):1442-50. doi: 10.3324/haematol.2015.129692. Epub 2015 Aug 20.

18.

Mutational dynamics between primary and relapse neuroblastomas.

Schramm A, Köster J, Assenov Y, Althoff K, Peifer M, Mahlow E, Odersky A, Beisser D, Ernst C, Henssen AG, Stephan H, Schröder C, Heukamp L, Engesser A, Kahlert Y, Theissen J, Hero B, Roels F, Altmüller J, Nürnberg P, Astrahantseff K, Gloeckner C, De Preter K, Plass C, Lee S, Lode HN, Henrich KO, Gartlgruber M, Speleman F, Schmezer P, Westermann F, Rahmann S, Fischer M, Eggert A, Schulte JH.

Nat Genet. 2015 Aug;47(8):872-7. doi: 10.1038/ng.3349. Epub 2015 Jun 29.

PMID:
26121086
19.

Comprehensive analysis of DNA methylation data with RnBeads.

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

Nat Methods. 2014 Nov;11(11):1138-1140. doi: 10.1038/nmeth.3115. Epub 2014 Sep 28.

20.

Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer.

Brocks D, Assenov Y, Minner S, Bogatyrova O, Simon R, Koop C, Oakes C, Zucknick M, Lipka DB, Weischenfeldt J, Feuerbach L, Cowper-Sal Lari R, Lupien M, Brors B, Korbel J, Schlomm T, Tanay A, Sauter G, Gerhäuser C, Plass C; ICGC Early Onset Prostate Cancer Project.

Cell Rep. 2014 Aug 7;8(3):798-806. doi: 10.1016/j.celrep.2014.06.053. Epub 2014 Jul 24.

21.

Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia.

Oakes CC, Claus R, Gu L, Assenov Y, Hüllein J, Zucknick M, Bieg M, Brocks D, Bogatyrova O, Schmidt CR, Rassenti L, Kipps TJ, Mertens D, Lichter P, Döhner H, Stilgenbauer S, Byrd JC, Zenz T, Plass C.

Cancer Discov. 2014 Mar;4(3):348-61. doi: 10.1158/2159-8290.CD-13-0349. Epub 2013 Dec 19.

22.

A prognostic DNA methylation signature for stage I non-small-cell lung cancer.

Sandoval J, Mendez-Gonzalez J, Nadal E, Chen G, Carmona FJ, Sayols S, Moran S, Heyn H, Vizoso M, Gomez A, Sanchez-Cespedes M, Assenov Y, Müller F, Bock C, Taron M, Mora J, Muscarella LA, Liloglou T, Davies M, Pollan M, Pajares MJ, Torre W, Montuenga LM, Brambilla E, Field JK, Roz L, Lo Iacono M, Scagliotti GV, Rosell R, Beer DG, Esteller M.

J Clin Oncol. 2013 Nov 10;31(32):4140-7. doi: 10.1200/JCO.2012.48.5516. Epub 2013 Sep 30.

23.

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues.

Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG.

Epigenetics. 2012 Dec 1;7(12):1355-67. doi: 10.4161/epi.22562. Epub 2012 Oct 18.

24.

Topological analysis and interactive visualization of biological networks and protein structures.

Doncheva NT, Assenov Y, Domingues FS, Albrecht M.

Nat Protoc. 2012 Mar 15;7(4):670-85. doi: 10.1038/nprot.2012.004.

PMID:
22422314
25.

Analyzing epigenome data in context of genome evolution and human diseases.

Feuerbach L, Halachev K, Assenov Y, Müller F, Bock C, Lengauer T.

Methods Mol Biol. 2012;856:431-67. doi: 10.1007/978-1-61779-585-5_18.

PMID:
22399470
26.

A promoter DNA demethylation landscape of human hematopoietic differentiation.

Calvanese V, Fernández AF, Urdinguio RG, Suárez-Alvarez B, Mangas C, Pérez-García V, Bueno C, Montes R, Ramos-Mejía V, Martínez-Camblor P, Ferrero C, Assenov Y, Bock C, Menendez P, Carrera AC, Lopez-Larrea C, Fraga MF.

Nucleic Acids Res. 2012 Jan;40(1):116-31. doi: 10.1093/nar/gkr685. Epub 2011 Sep 12.

27.

A DNA methylation fingerprint of 1628 human samples.

Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Graña O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M.

Genome Res. 2012 Feb;22(2):407-19. doi: 10.1101/gr.119867.110. Epub 2011 May 25.

28.

Computing topological parameters of biological networks.

Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht M.

Bioinformatics. 2008 Jan 15;24(2):282-4. Epub 2007 Nov 15.

PMID:
18006545
29.

Computational analysis of human protein interaction networks.

Ramírez F, Schlicker A, Assenov Y, Lengauer T, Albrecht M.

Proteomics. 2007 Aug;7(15):2541-52.

PMID:
17647236
30.

The implications of alternative splicing in the ENCODE protein complement.

Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500. Epub 2007 Mar 19.

31.

A network-based analysis of polyanion-binding proteins utilizing human protein arrays.

Salamat-Miller N, Fang J, Seidel CW, Assenov Y, Albrecht M, Middaugh CR.

J Biol Chem. 2007 Apr 6;282(14):10153-63. Epub 2007 Feb 2.

32.

A network-based analysis of polyanion-binding proteins utilizing yeast protein arrays.

Salamat-Miller N, Fang J, Seidel CW, Smalter AM, Assenov Y, Albrecht M, Middaugh CR.

Mol Cell Proteomics. 2006 Dec;5(12):2263-78. Epub 2006 Sep 18.

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