Research

Department of Haematology

The research department is part of the Erasmus MC Cancer Institute.

Research programs

There are currently five different areas of research active in the hematology department. Research on:

  1. Acute leukemia
  2. Bone marrow failure
  3. Hematopoiesis/transplantation
  4. Hemostasis and thrombosis
  5. Multi myeloma

More information on these research projects can be found below:

Read more

Developed Software

1. HAT

Hypergeometric Analysis of Tiling-arrays

Abstract:

We have demonstrated that HAT has increased specificity for analysis of tiling-array data in comparison with alternative methods, and that it accurately detected regions-of-interest in different applications of tiling-arrays. HAT has several advantages over previous methods: i) as there is no single cut-off level for probe-intensity, HAT can detect regions-of-interest at various thresholds, ii) it can detect regions-of-interest of any size, iii) it is independent of probe-resolution across the genome, and across tiling-array platforms, iv) it employs a single user defined parameter: the significance level. Regions-of-interest are detected by computing the hypergeometric-probability, while controlling the Family Wise Error. Furthermore, the model does not require experimental replicates, common regions-of-interest are indicated, a sequence-of-interest can be examined for every detected region-of-interest, and flanking genes can be reported.

Publication:

BMC Bioinformatics 2010, 11:275

Published on 21st May 2010

Contact:

e.taskesen@erasmusmc.nl, h.delwel@erasmusmc.nl

Please use the HATSEQ download section below

2. HATSEQ

Hypergeometric analysis of tiling-array and sequence data

Abstract:

We have build a method to analyze your ChIP-array or ChIP-Seq data. The method can accurately detect peak boundaries among different types of experimental data, such as Protein-DNA interactions, Histone modifications, methylated fragments and more! This tool does not require any knowledge about scripting languages because of the friendly graphic user interface (GUI). Install HATSEQ on your PC, MACbook or Unix, select the files to-be-analyzed, and hit the run button. If you also want to know whether motifs or pathways are enriched for the detected regions in your data, simply check the boxes in the GUI. After pressing the Run button in the GUI, we do the job for you! You can grab a cup of coffee.

Publication:

Adv Appl Bioinform Chem. 2013 Oct 25;6:55-62.

Published in Oct 2013

Contact:

e.taskesen@erasmusmc.nl, h.delwel@erasmusmc.nl


3. SNPExpress

Abstract:

SNPExpress is a tool which can combine visualization of gene expression, DNA copy number and genotype data.

Contact:

m.a.sanders@erasmusmc.nl


4. MADEX

Hypergeometric analysis of tiling-array and sequence data

Abstract:

MADEx is a microarray database system that allows you to dynamically browse and analyze microarraydata. It includes Heatmapper an easy-to-use program that draws heatmaps and displays clinical data next to the heatmap. HeatMapper also has the ability to save the heatmap and clinical data as a picture. To use it, you need a (Omniviz) heatmap correlation file and a clinical data file with matching sample id's. Tab-delimited and comma-separated file formats are accepted.

To access data from MADEx please use the contact details below. To use HeatMapper use the download link.

BMC Bioinformatics., 7 (2006), p. 337.

Published in July 2006

Contact:

m.a.sanders@erasmusmc.nl


Quick download links developed software