Software Tools & Resources

Selected contributions to the development and dissemination of algorithms and software tools that have helped advance and overcome challenges in biomedical research for better understanding, diagnosis and treatment of human disease:

  2. Multiscale and multimodal inference of regulatory networks to identify cell circuits and their drivers shared and distinct across biological systems of human disease (see The *AMARETTO framework)

  3. GenomeSpace
  4. A platform for integrative genomic analysis by interoperation of bioinformatics tools (http://www.genomespace.org)

  5. Trinity
  6. De novo transcriptome assembly from RNA sequencing for studying non-model organisms (http://trinityrnaseq.github.io)
    Trinity Cancer Transcriptome Analysis Toolkit (CTAT) for deciphering genetic, epigenetic and functional heterogeneity from de novo assembled cancer transcriptomes (http://trinityrnaseq.github.io)

  7. SERV
  8. A nonlinear model to study the role of variation in tandem repeat sequences from yeast evolution to human disease (http://www.igs.cnrs-mrs.fr/SERV)
    Multi-species database (http://www.igs.cnrs-mrs.fr/TandemRepeat)

  9. M@CBETH
  10. A tool for optimal use of clinical microarray data classification to support clinical management decisions (http://www.esat.kuleuven.be/MACBETH)