• Breast cancer cells (programmed cell death)
    Annie Cavanagh / Wellcome Images
  • From temporal expression
    to regulatory mechanisms.
    Joana Gonçalves

Algorithmic & Learning Data Science

for molecular understanding and treatment of complex disease

Delft University of Technology

Currently hiring!

  • PhD position on learning algorithms for therapeutic target prediction. Details and application here. Deadline: 9 February 2020.
  • Two postdoc positions on single-cell discovery of biomarkers for targeted proton therapy (computational position with me at TU Delft, experimental position with Miao-Ping Chien at Erasmus MC). Details and application here. Deadline: recruiting until the positions are filled.

Postdoctoral fellowship opportunities

Are you an ambitious researcher with a PhD in computer science (or related)? Would you like to pursue original ideas in our lab?
Please check the eligibility requirements and get in touch:

Research Interests

We design algorithms to understand gene regulation and disruptions in disease, and discover therapeutic targets.

more research

Computer Science

  • Algorithms
  • Machine learning
  • Data mining
Special interests:
  • combinatorial algorithms
  • n-way clustering
  • time course analysis
  • domain-driven data integration

Molecular biology

  • Transcriptional regulation
  • Epigenetic regulation
  • DNA damage and repair
Examples of data we analyse:
  • Gene expression (RNA-seq)
  • TF binding (ChIP-seq)
  • Epi modifications (ChIP-seq)
  • Chromatin compaction (Hi-C)
  • Genome editing (CRISPR/Cas9)

Biomedicine (cancer)

We focus on changes to entire pathways rather than single elements. Pathways are not static (e.g. KEGG), they are captured by our algorithms.

  • Discovery of novel therapeutic targets as major regulatory elements of disrupted pathways
  • Identification of regulatory mechanisms involved in drug resistance

Short Bio

In Aug 2017, I started as an Assistant Professor at the Delft University of Technology (TUDelft). I am also a Guest Researcher at the Netherlands Cancer Institute (NKI). My lab will focus on computational approaches to understand gene regulation, uncover disruptions involved in complex disease (especially cancer), and predict novel targets for therapy. Previously, I was a postdoc in computational cancer biology with Lodewyk Wessels at the TUDelft and the NKI. Before that, I was a Marie Curie/ERCIM fellow in algorithmic computational biology with Gunnar Klau at the Netherlands Research Centre for Mathematics and Informatics. I did a PhD in computer science with Sara Madeira at the Technical University of Lisbon, and spent just over a year in the bioinformatics lab of Yves Moreau at the University of Leuven.




in Computer Science
Tecnical University of Lisbon


Diploma (5-year)

in Computer Science
University of Beira Interior



Assistant Professor

Delft University of Technology
Guest at Netherlands Cancer Institute (NL)

Postdoctoral Researcher

Delft University of Technology
Netherlands Cancer Institute (NL)

Marie Curie/ERCIM Fellow

Centre for Math & Informatics (NL)

Research Assistant

Imperial College London (UK)

Visiting Scholar

University of Leuven (BE)

Doctoral Researcher

Technical University of Lisbon and INESC-ID (PT)