Career

I am currenly working in the department of Translational genomics at Cologne university as a computational biologist. In this role, I am heading a target discovery project and provide computational support for this and other projects, with a heavy focus on genome and transcriptome sequencing.

My strong points include:

  • Experienced biomedical data scientist and programmer in Python and R, responsible for our project's RNA sequencing analysis pipeline, the department's internal R package and a deep learning network to predict certain protein features
  • Effective communicator of scientific results, as demonstrated by 5 accepted first author publications and 2 co-authorships (mean impact factor 7.6). My work was furthermore accepted for presentation at over 10 congresses (>5 international)
  • Strong project management and collaboration skills: currently heading a drug discovery team and previously supervised 3 research professionals and 5 students on several different projects, resulting in continued funding and top 10% marks for the student projects

Details can be found in my resume below:

Projects

Some examples of bioinformatics projects I have been or are involved in:

  • Differential gene expression analysis to find cancer treatment resistance factors (chapter 5 of thesis)
  • Automated image analysis on immunoflurorescence slides (chapter 2 of thesis)
  • Genome structure analysis to stratify patients in responder and non-responder (abstract)
  • Application of deep learning to predict protein features
  • Programming of an interactive user interface in shiny to vizualize multiplex experiments (link)

Thesis

My thesis on microenvironmental signalling in chronic lymphocytic leukemia can be found below:

Scientific journal publications

  • Pascutti MF, Jak M, Tromp JM, Derks IA, Remmerswaal EB, Thijssen R, van Attekum MHA, van Bochove GG, Luijks DM, Pals ST, van Lier RA, Kater AP, van Oers MH, Eldering E. IL-21 and CD40L signals from autologous T cells can induce antigen-independent proliferation of CLL cells. Blood. 2013 Oct 24;122(17):3010-9. Pubmed - Journal - Full text
  • van Attekum MHA, Terpstra S, Reinen E, Kater AP, Eldering E. Macrophage-mediated chronic lymphocytic leukemia cell survival is independent of APRIL signaling. Cell Death Discovery. 2016;2:16020. Pubmed - Journal - Full text
  • van Attekum MHA, Terpstra S, Slinger E, von Lindern M, Kater AP, Eldering E. Macrophages confer survival signals via CCR1-dependent translational MCL-1 induction in chronic lymphocytic leukemia. Oncogene. 2017 Jun 29;36(26):3651-3660 Pubmed - Journal - Full text
  • van Attekum MHA, Eldering E, Kater AP. Chronic lymphocytic leukemia cells are active participants in microenvironmental cross-talk. Haematologica. 2017 Sep;102(9):1469-1476 Pubmed - Journal - Full text
  • van Attekum MHA, Lebre MC, Eldering E, Kater AP. CD40 signaling instructs CLL cells to attract monocytes via the CCR2 axis. Haematologica. 2017 Dec;102(12):2069-2076 Pubmed - Journal - Full text
  • van Attekum MHA, Kater AP, Eldering E. The APRIL paradox in normal versus malignant B cell biology. Cell Death Dis. 2016 Jun 23;7(6):e2276. Pubmed - Journal - Full text
  • Wensveen F, Slinger S, van Attekum MHA, Brink R, Eldering E. Antigen-affinity controls pre-germinal center B cell selection by promoting Mcl-1 induction through BAFF receptor signaling. Sci Rep. 2016 Oct 20;6:35673. Pubmed - Journal - Full text

Press publications

  • For our B cell malignancies consortium: Wetenschapper in de spotlights Link
  • For our B cell malignancies consortium: Een publicatie toegelicht Link

Honors and awards