Computational systems biology

Developing predictive models for precision medicine

Publications

  1. Matteo Manica, Philippe Chouvarine, Roland Mathis, Ulrich Wagner, Kathrin Oehl, Karim Saba, Laura De Vargas Roditi, Arati N Pati, Maria Rodriguez-Martinez, Peter J Wild,
    Inferring clonal composition from multiple tumor biopsies,”
    arXiv preprint arXiv:1701.07940, 2017.
  2. Manuel Le Gallo, Abu Sebastian, Roland Mathis, Matteo Manica, Tomas Tuma, Costas Bekas, Alessandro Curioni, Evangelos Eleftheriou,
    Mixed-Precision Memcomputing,”
    arXiv preprint arXiv:1701.04279, 2017.

Interviews & press articles

  1. Nouvelles thérapies contre le cancer, 36.9° Magasin Santé 17 Feb 2017.
  2. Watson, übernehmen Sie! Genug Input macht Computer vielseitig einsetzbar, 3Sat, 9 Aug 2017.
  3. Il pianeta dei robot, RAI3 (Italian TV), 5 Sep 2016. Note: Login needed to access the video.
  4. Precise Project to Construct Computational Models to Improve Prostate Cancer Treatment, Care, Genome Web, 17 Mar 2016.

Presentations

  1. Roland Mathis, Matteo Manica, María Rodríguez Martínez,
    DeepGRN: Deciphering gene deregulation in cancer development using deep learning,”
    PrECISE Project Meeting, Prague, Czech Republic, July 21-25, 2017.
  2. Malamati Koletou, Maria Gabrani, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rudolf Aebersold, Peter Wild, María Rodríguez Martínez, 
    A computational framework for systems pathology of prostate cancer,” 
    Intelligent Systems for Molecular Biology (ISMB) and the 16th European Conference on Computational Biology (ECCB), Prague, Czech Republic, July 21-25, 2017.
  3. Matteo Manica, Philippe Chouvarine, Roland Mathis, Ulrich Wagner, Kathrin Oehl, Karim Saba, Laura De Vargas Roditi, Arati N Pati, María Rodríguez Martínez, Peter J Wild,
    Inferring clonal composition from multiple tumor biopsies,”
    Intelligent Systems for Molecular Biology (ISMB) and the 16th European Conference on Computational Biology (ECCB), Prague, Czech Republic, July 21-25, 2017.
  4. Jelena Čuklina, Yibo Wu, Evan G. Williams, María Rodríguez Martínez, Ruedi Aebersold
    “Selection of stable biomarker signature for prediction of metabolic phenotypes,”
    Intelligent Systems for Molecular Biology (ISMB) and the 16th European Conference on Computational Biology (ECCB), Prague, Czech Republic, July 21-25, 2017 (F1000 Research best poster award).
  5. Roland Mathis, Matteo Manica, María Rodríguez-Martínez,
    “Prostate Cancer Interactome,”
    14th Annual Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, Colorado, USA, December 8-10, 2016.
  6. Matteo Manica, Roland Mathis, María Rodríguez-Martínez,
    “CoDON: a learning framework for linking genomics and transcriptomics data to protein expression,”
    European Conference on Computational Biology, The Hague, Netherlands, September 3-7, 2016.
  7. Sunil Kumar, Serena Di Palma, Bernd Bodenmiller, María Rodríguez Martínez, Heinz Koeppl,
    “Temporal Pattern Identification using Fused L1-Regularization,”
    All SystemsX.ch Day, Bern, Switzerland, September 1, 2016.
  8. Marianna Rapsomaniki, Xiaokang Lun, Bernd Bodenmiller and María Rodríguez Martínez,
    “Reconstructing trajectories of cell cycle evolution using single-cell mass cytometry data,”
    Intelligent Systems for Molecular Biology (ISMB), Orlando, Florida, USA, July 8-12, 2016 (F1000 Research best poster award).
  9. Jelena Čuklina, Yibo Wu, Evan G. Williams, María Rodríguez Martínez, Ruedi Aebersold
    “Integration of multi-omics data for prediction of metabolic traits,”
    (poster), LATSIS Symposium on Personalized Medicine, Zurich, Switzerland, June 27-29, 2016.
  10. Malamati Koletou, Maria Gabrani, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rudolf Aebersold, Peter Wild, María Rodríguez Martínez,
    “A Computational framework for systems pathology of prostate cancer,”
    Systems Biology of Human Diseases, Boston, MA, USA, June 14-16, 2016.
  11. Malamati Koletou, Maria Gabrani, Tiannan Guo, Qing Zhong, Ulrich Wagner, Rudolf Aebersold, Peter Wild, María Rodríguez Martínez,
    “A Computational framework for systems pathology of prostate cancer,”
    Systems Biology of Human Diseases, Boston, MA, USA, June 14-16, 2016.
  12. Sunil Kumar, Xiaokang Lun, Bernd Bodenmiller, María Rodríguez Martínez, Heinz Koeppl,
    “Probabilistic pathway reconstruction from dynamic single-cell signaling data,”
    Systems Biology of Human Diseases, Boston, MA, USA, June 14-16, 2016.
  13. Marianna Rapsomaniki, Xiaokang Lun, Bernd Bodenmiller and María Rodríguez Martínez,
    “Cell-to-cell heterogeneity unraveled by computational analysis of single-cell mass cytometry data: cell cycle patterns and trajectories,”
    6th Conference on Systems Biology of Mammalian Cells (SBMC), Munich, Germany, April 6-8, 2016.