Erdogan Taskesen

Postdoctoral researcher
Team Member

CV

• Oct. 2015 – Now: Postdoc at the Ahlzheimers Center, Dept. of Complex Trait Genetics, VU University

• April 2013 – Sep. 2015: Postdoc, Delft Bioinformatics Lab, Delft University of Technology, collaboration with Philips

• March 2011 – June 2011: Visiting researcher, Dept. of Hematology/Oncology, Melnick Lab, Weill Cornell Medical College

• April 2008 – April 2013: PhD, Dept. of Hematology, Erasmus University Medical Center, Rotterdam

• April 2007 – Oct. 2007: Scientific programmer, Dept. of Epidemiology, Erasmus University Medical Center, Rotterdam

• Sep. 2003 – April 2007: Master degree, Media & Knowledge engineering, specialization Bioinformatics, Delft University of Technology

• Sep. 2000 – July 2003: Bachelor degree, Computer Science, Hogeschool Rotterdam (HR&O)

• Sep. 1996 – July 2000: Degree in Electrical Engineering, Differentiation Computer Interface Technique (ROC)

Research focus

My aim is to improve patient characterization and subtyping by employing data and hypothesis driven machine learning and pattern recognition techniques in high-throughput genome-wide data. During my post-doctoral research at the TU-delft I created statistical integrative methodologies to detect prognostic biomarkers associated with WNT signalling, and predictive signatures to improve characterization of Acute Myeloid Leukemia subtypes. My latest work involved development of a novel statistical approach to integratively analyze data from The Cancer Genome Atlas (TCGA), such as gene expression, DNA-methylation, microRNA, and copy number changes to further improve patient disease characterization in a pan-cancer manner. In addition to my main project, I also like to work in various other projects where I can support biologists and colleague bioinformaticians/biostaticians in their data analysis and the interpretation of the data. Pathway, motif, clinical, survival, microarray, NGS, the use of machine learning and pattern recognition techniques is where I am experienced in. I enjoy to crunch big-data for the detection of biological relevant patterns, and to create out-of-the-box solutions. Currently my research focuses on genetic heterogeneity in FTD, ALS, and mental disorders, in which I investigate the genetic variants across biological pathways.

Publications

Taskesen E, Staal FJT and Reinders MJT, An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia. BMC Bioinformatics. 2015 Feb 23

Taskesen E, Babaei S, Reinders MJT and Ridder J, Integration of Gene Expression and DNA-methylation Profiles Improves Molecular Subtype Classification in Acute Myeloid Leukemia. BMC Bioinformatics. 2015 Feb 23

Taskesen E, Havermans M, van Lom K, Sanders MA, van Norden Y, Bindels E, Hoogenboezem R, Reinders MJ, Figueroa ME, Valk PJ, Löwenberg B, Melnick A, Delwel R. Two splice factor mutant leukemia subgroups uncovered at the boundaries of MDS and AML using combined gene expression and DNA-methylation profiling. Blood. 2014 Mar 25.

Taskesen E, Karin Klauke. De ontdekking van twee extra acute myeloïde leukemie subgroepen door gebruik van een combinatie van genexpressie en DNA methylatie profielen. PUR SANG, het MPN-magazine, jaargang 10, nr. 3, 2013.

Taskesen E, Schlenk RF, van Norden Y, Krauter J, Ganser A, Bullinger L, Gaidzik VI, Paschka P, Corbacioglu A, Göhring G, Kündgen A, Held G, Götze K, Vellenga E, Kuball J, Schanz U, Passweg J, Pabst T, Maertens J, Ossenkoppele GJ, Delwel R, Döhner H, Cornelissen JJ, Döhner K, Löwenberg B. The value of allogeneic and autologous hematopoietic stem cell transplantation in prognostically favorable acute myeloid leukemia with double mutant CEBPA. Blood. 2013 Aug 29;122(9):1576-82. doi: 10.1182/blood-2013-05-503847.

Taskesen E, Hoogeboezem R, Delwel R, Reinders MJT. Hypergeometric Analysis of Tiling-array and Sequence Data: Detection and Interpretation of Peaks. Advances and Applications in Bioinformatics and Chemistry. 25;6:55-62. doi:10.2147/AABC.S51271
Taskesen E, Wouters BJ, and Delwel R. HAT: a novel statistical approach to discover functional regions in the genome. Springer Series (book Chapter). doi: 10.1007/978-1-62703-607-8.

Bindels EM, Havermans M, Lugthart S, Erpelinck C, Wocjtowicz E, Krivtsov AV, Rombouts E, Armstrong SA, Taskesen E, Haanstra JR, Beverloo HB, Döhner H, Hudson WA, Kersey JH, Delwel R, Kumar AR. EVI1 is critical for the pathogenesis of a subset of MLL-AF9-rearranged AMLs. Blood

Zebisch A, Wölfler A, Fried I, Wolf O, Lind K, Bodner C, Haller M, Drasche A, Pirkebner D, Matallanas D, Rath O, Blyth K, Delwel R, Taskesen E, Quehenberger F, Kolch W, Troppmair J, Sill H. Frequent loss of RAF kinase inhibitor protein expression in acute myeloid leukemia. Leukemia

Horos R, Ijspeert H, Pospisilova D, Sendtner R, Andrieu-Soler C, Taskesen E, Nieradka A, Cmejla R, Sendtner M, Touw IP, von Lindern M. Ribosomal deficiencies in Diamond-Blackfan anemia impair translation of transcripts essential for differentiation of murine and human erythroblasts. Blood

Erdogan Taskesen, Roberto Avellino, Jeroen de Ridder, Claudia A.J. Erpelinck, Bas J. Wouters, Marcel J.T. Reinders, Ruud Delwel. Improved identification of C/EBPα target genes, transcriptional-modules and networks by integrative ChIP-on-Chip and gene expression analyses.

Erdogan Taskesen, Roberto Avellino, Meritxell AlberichJorda, Daniel G. Tenen, Jeroen Ridder de, Peter Valk, Bas Wouters, Claudia Erpelinck, Marcel Reinders and Ruud Delwel. C/EBPα Is a Transcriptional Repressor of T-Cell Related Genes Explaining the Myeloid/T-Lymphoid Features of C/EBPα -Silenced AML.

Beekman R, Valkhof M, Erkeland SJ, Taskesen E, Rockova V, Peeters JK, Valk PJ, Löwenberg B, Touw IP. Retroviral integration mutagenesis in mice and comparative analysis in human AML identify reduced PTP4A3 expression as a prognostic indicator. PLoS One

Meenhuis A, van Veelen PA, de Looper H, van Boxtel N, van den Berge IJ, Sun SM, Taskesen E, Stern P, de Ru AH, van Adrichem AJ, Demmers J, Jongen-Lavrencic M, Löwenberg B, Touw IP, Sharp PA, Erkeland SJ. MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1-regulated pathways in mice. Blood

Smith LL, Yeung J, Zeisig BB, Popov N, Huijbers I, Barnes J, Wilson AJ, Taskesen E, Delwel R, Gil J, Van Lohuizen M, So CW. Functional crosstalk between Bmi1 and MLL/Hoxa9 axis in establishment of normal hematopoietic and leukemic stem cells. Cell Stem Cell.

Taskesen E, Bullinger L, Corbacioglu A, Sanders MA, Erpelinck CA, Wouters BJ, van der Poel-van de Luytgaarde SC, Damm F, Krauter J, Ganser A, Schlenk RF, Löwenberg B, Delwel R, Döhner H, Valk PJ, Döhner K. Prognostic impact, concurrent genetic mutations, and gene expression features of AML with CEBPA mutations in a cohort of 1182 cytogenetically normal AML patients: further evidence for CEBPA double mutant AML as a distinctive disease entity. Blood

Taskesen E, Beekman R, de Ridder J, Wouters BJ, Peeters JK, Touw IP, Reinders MJ, Delwel R. HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. BMC Bioinformatics

Taskesen E, Wessels LFA, van Vliet M, and Reinders MJT, Novel approaches for cross-species subtype identification. M.Sc. Thesis, pp. 26, Delft University of Technology, March 23 2007.

Contact info

Address:

De Boelelaan 1085, 1081 HV, Amsterdam, Netherlands
FALW, room B-651

Telephone:

+31 20 598 3343

E-mail:e.taskesen@vu.nl