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. Multimodal and multiscale circuit-, network-, and graph-based fusion of multi-omics, clinical, imaging, and perturbation data across studies of patients, etiologies and model systems of complex human disease, including cancer, infectious, neurologic and immune-mediated diseases (http://portals.broadinstitute.org/pochetlab/amaretto.html)

  3. Trinity and Trinity CTAT
  4. 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 (https://github.com/NCIP/Trinity_CTAT/wiki)

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

  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 (tutorial: https://ftp.esat.kuleuven.be/sista/npochet/tutorial.pdf, web service previously at: http://www.esat.kuleuven.be/MACBETH)