2017

Logic modeling in quantitative systems pharmacology (Journal Paper)
Pauline Traynard, Luis Tobalina, Federica Eduati, Laurence Calzone, Julio Saez-Rodriguez
CPT: Pharmacometrics and Systems Pharmacology, Volume 6, Issue 8, August 2017.

MaBoSS 2.0: an environment for stochastic Boolean modeling (Journal Paper)
Gautier Stoll, Barthelemy Caron, Eric Viara, Aurelian Dugourd, Andrei Zinovyev, Aurelien Naldi, Guido Kroemer, Emmanue Barillot, Laurence Calzone
Bioinformatics, Volume 33, Issue 14, July 2017.

Selection of stable biomarker signature for prediction of metabolic phenotypes (Poster)
Jelena Čuklina, Yibo Wu, Evan G. Williams, María Rodríguez Martínez, Ruedi Aebersold
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

DeepGRN: Deciphering gene deregulation in cancer development using deep learning (Poster)
Roland Mathis, Matteo Manica, Maria Rodriguez Martinez
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

Inferring network statistics from high-dimensional undersampled time-course data (Poster)
Dominik Linzner, Heinz Koeppl
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

Fast biological network reconstruction from high-dimensional time-course perturbation data using sparse multivariate Gaussian processes (Poster)
Sara Al-Sayed, Heinz Koeppl
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

Logic modeling in quantitative systems pharmacology (Poster)
Pauline Traynard, Luis Tobalina, Federica Eduati, Laurence Calzone, Julio Saez-Rodriguez
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

Incorporating patient-specific molecular data into a logic model of prostate cancer (Poster)
Pauline Traynard, Jonas Beal, Luis Tobalina, Emmanuel Barillot, Julio Saez-Rodriguez, Laurence Calzone
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

Inferring clonal composition from multiple tumor biopsies (Technical Note)
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, Pavel Sumazin
25th Conference on Intelligent Systems for Molecular Biology / 16th European Conference on Computational Biology (ISMB/ECCB), July 2017.

2016

Integration of Multi-omics Data for Prediction of Metabolic Traits (Poster)
Jelena Čuklina, Yibo Wu, Evan. G. Williams, Maria Rodríguez-Martínez; Ruedi Aebersold
LATSIS Symposium on Personalized Medicine (LATSIS), 2016.

Pypath and Omnipath: integrate, analyze and extract signaling networks from literature curated resources (Poster)
Dénes Türei, Luis Tobalina, David Henriques, Pauline Traynard, Laurence Calzone, Tamás Korcsmáros, Julio Saez-Rodriguez
17th International Conference on Systems Biology (ICSB), 2016.

Building a Boolean model of signaling pathways altered in prostate cancer (Poster)
Pauline Traynard, Luis Tobalina, David Henriques, Emmanuel Barillot, Julio Saez-Rodriguez, Laurence Calzone
17th International Conference on Systems Biology (ICSB), 2016.

Stratification of prostate cancer patients based on molecular interaction profiles (Poster)
Roland Mathis, Matteo Manica, María Rodríguez Martínez
All SystemsX.ch Day, 2016.

CoDON: a learning framework for linking genomics and transcriptomics data to protein expression (Poster)
Matteo Manica, Roland Mathis, María Rodríguez Martínez
All SystemsX.ch Day, 2016.

Proteome heterogeneity in benign and malignant prostate tissue (Poster)
Tiannan Guo, Li Li, Qing Zhong, Niels J. Rupp, Konstantina Charmpi, Christine E. Wong, Ulrich Wagner, Jan H. Rueschoff, Wolfram Jochum, Christian Fankhauser, Karim Saba, Cedric Poyet, Peter J. Wild, Ruedi Aebersold, Andreas Beyer
All SystemsX.ch Day, 2016.

An integrative Systems Biology approach to advance in the understanding and treatment of prostate cancer (Poster)
Luis Tobalina, David Henriques, Julio Saez-Rodriguez
Bioinformatics for Young inTernational researchers (byteMAL), 2016.