Yassen Assenov

Yassen Assenov

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Yassen Assenov

Yassen Assenov

Publications by authors named "Yassen Assenov"

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RnBeads 2.0: comprehensive analysis of DNA methylation data.

Genome Biol 2019 03 14;20(1):55. Epub 2019 Mar 14.

Max Planck Institute for Informatics, Saarland Informatics Campus, 66123, Saarbrücken, Germany.

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http://dx.doi.org/10.1186/s13059-019-1664-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419383PMC
March 2019

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

Cell Stem Cell 2019 01 20;24(1):166-182.e13. Epub 2018 Dec 20.

Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.11.015DOI Listing
January 2019

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

Cancer Cell 2018 12;34(6):996-1011.e8

Finsen Laboratory, Rigshospitalet, DK-2200, Copenhagen, Denmark; Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK-2200, Copenhagen, Denmark; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69120 Heidelberg, Germany; Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.10.016DOI Listing
December 2018

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

Genome Res 2018 11 19;28(11):1747-1756. Epub 2018 Oct 19.

Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.239244.118
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http://dx.doi.org/10.1101/gr.239244.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211645PMC
November 2018

Intratumor heterogeneity in epigenetic patterns.

Semin Cancer Biol 2018 08 31;51:12-21. Epub 2018 Jan 31.

Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.semcancer.2018.01.010DOI Listing
August 2018

Enrichment analysis with EpiAnnotator.

Bioinformatics 2018 05;34(10):1781-1783

Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1093/bioinformatics/bty007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946894PMC
May 2018

Strategies for analyzing bisulfite sequencing data.

J Biotechnol 2017 Nov 16;261:105-115. Epub 2017 Aug 16.

Bioinformatics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.jbiotec.2017.08.007DOI Listing
November 2017

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

Br J Cancer 2017 Nov 12;117(10):1551-1556. Epub 2017 Sep 12.

Haematology Unit, Cancer Research Centre, Institute for Medical Research, Jalan Pahang, Kuala Lumpur 50588, Malaysia.

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http://dx.doi.org/10.1038/bjc.2017.316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680464PMC
November 2017

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

Int J Genomics 2017 20;2017:2913648. Epub 2017 Jun 20.

Computational Epigenomics Group, Division of Epigenomics and Cancer Risk Factor, German Cancer Research Center, Heidelberg, Germany.

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http://dx.doi.org/10.1155/2017/2913648DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5496127PMC
June 2017

Melanoma-Derived iPCCs Show Differential Tumorigenicity and Therapy Response.

Stem Cell Reports 2017 05 6;8(5):1379-1391. Epub 2017 Apr 6.

Skin Cancer Unit (G300), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, 68167 Mannheim, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2017.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425615PMC
May 2017

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

Lancet Oncol 2016 Oct 27;17(10):1386-1395. Epub 2016 Aug 27.

Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain; School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain. Electronic address:

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http://dx.doi.org/10.1016/S1470-2045(16)30297-2DOI Listing
October 2016

Mutational dynamics between primary and relapse neuroblastomas.

Nat Genet 2015 Aug 29;47(8):872-7. Epub 2015 Jun 29.

1] Pediatric Oncology and Hematology, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany. [2] Pediatric Oncology and Hematology, Charité University Medicine, Berlin, Germany. [3] German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.

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http://search.proquest.com/openview/bef3fe020af3cd6708016aba
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http://dx.doi.org/10.1038/ng.3349DOI Listing
August 2015

Comprehensive analysis of DNA methylation data with RnBeads.

Nat Methods 2014 Nov 28;11(11):1138-1140. Epub 2014 Sep 28.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/nmeth.3115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216143PMC
November 2014

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

Cell Rep 2014 Aug 24;8(3):798-806. Epub 2014 Jul 24.

Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany; The German Cancer Consortium, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.06.053DOI Listing
August 2014

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

Cancer Discov 2014 Mar 19;4(3):348-61. Epub 2013 Dec 19.

Divisions of 1Epigenomics and Cancer Risk Factors, 2Theoretical Bioinformatics, 3Biostatistics, and 4Molecular Genetics; 5Department of Translational Oncology, National Center for Tumor Diseases (NCT), The German Cancer Research Center (DKFZ); 6Department of Medicine V, University of Heidelberg, Heidelberg; 7Department of Medicine, University of Freiburg Medical Center, Freiburg; 8Department of Internal Medicine III, University of Ulm, Ulm; 9The German Cancer Consortium, Germany; 10Department of Medicine, University of California at San Diego Moores Cancer Center, La Jolla, California; and 11Division of Hematology, The Ohio State University, Columbus, Ohio.

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http://dx.doi.org/10.1158/2159-8290.CD-13-0349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4134522PMC
March 2014

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

J Clin Oncol 2013 Nov 30;31(32):4140-7. Epub 2013 Sep 30.

Juan Sandoval, Jesus Mendez-Gonzalez, F. Javier Carmona, Sergi Sayols, Sebastian Moran, Holger Heyn, Miguel Vizoso, Antonio Gomez, Montse Sanchez-Cespedes, and Manel Esteller, Bellvitge Biomedical Research Institute; Josefina Mora, Hospital de la Santa Creu i Sant Pau; Manel Esteller, University of Barcelona and Institucio Catalana de Recerca i Estudis Avançats, Barcelona; Miquel Taron and Rafael Rosell, Catalan Institute of Oncology, Badalona, Catalonia; Marina Pollan, Instituto de Salud Carlos III, Madrid; Maria J. Pajares and Luis M. Montuenga, University of Navarra; Wenceslao Torre, Clínica University de Navarra, Pamplona, Spain; Ernest Nadal, Guoan Chen, and David G. Beer, University of Michigan Medical School, Ann Arbor, MI; Yassen Assenov and Fabian Müller, Max Planck Institute, Saarbrücken, Germany; Christoph Bock, Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Lucia A. Muscarella, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy; Triantafillos Liloglou, Michael Davies, and John K. Field, The University of Liverpool Cancer Research Centre, Liverpool, United Kingdom; Elisabeth Brambilla, Centre Hospitalier Universitaire A Michallon, Grenoble, France; Luca Roz, IRCCS Foundation National Cancer Institute, Milan; Marco Lo Iacono and Giorgio V. Scagliotti, University of Torino, Orbassano (Torino), Italy.

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http://dx.doi.org/10.1200/JCO.2012.48.5516DOI Listing
November 2013

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

Epigenetics 2012 Dec 18;7(12):1355-67. Epub 2012 Oct 18.

Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.

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http://dx.doi.org/10.4161/epi.22562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528691PMC
December 2012

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

Nat Protoc 2012 Mar 15;7(4):670-85. Epub 2012 Mar 15.

Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1038/nprot.2012.004DOI Listing
March 2012

Computing topological parameters of biological networks.

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

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btm554DOI Listing
January 2008

Computational analysis of human protein interaction networks.

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

Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany.

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http://dx.doi.org/10.1002/pmic.200600924DOI Listing
August 2007

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

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

Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA.

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http://dx.doi.org/10.1074/jbc.M610957200DOI Listing
April 2007

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

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

Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, USA.

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http://dx.doi.org/10.1074/mcp.M600240-MCP200DOI Listing
December 2006