2018

PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks
Ali Oskooei, Jannis Born, Matteo Manica, Vigneshwari Submramanian, Julio Saez-Rodriguez, Maria Rodriguez-Martinez
Workshop Machine Learning for Molecules and Materials at NeurIPS 2018

PIMKL: Pathway Induced Multiple Kernel Learning
Matteo Manica, Joris Cadow, Roland Mathis and María Martínez Rodríguez
Journal: Nature - npj Systems Biology and Applications

Patient-specific prostate logical models allow clinical stratification of patients and personalized drug treatment
Arnau Montagud, Jonas Béal, Pauline Traynard, Luis Tobalina, Julio Sáez-Rodríguez, Emmanuel Barillot and Laurence Calzone
Conference: 17th European Conference on Computational Biology - ECCB 2018

Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
Tiannan Guo, Augustin Luna, Ching Chiek Koh, Vinodh Rajapakse, Zhicheng Wu, Michael Patrick Menden, Yongran Cheng, Laurence Calzone, Loredana Martignetti, Alessandro Ori, Murat Iskar, Ludovic Gillet, Qing Zhong, Sudhir Varma, Uwe Schmitt, Peng Qiu, Yaoting Sun, Yi zhu, Peter Wild, Garnett Mathew, Peer Bork, Martin Beck, Julio Saez-Rodriguez, William Reinhold, Chris Sander, Yves Pommier, Ruedi Aebersold
BioRXiv (pre-print)

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients
Jonas Béal, Arnau Montagud, Pauline Traynard, Emmanuel Barillot, Laurence Calzone
Journal: special issue of Frontiers in Physiology on “Logical Modeling of Cellular Processes: From Software Development to Network Dynamics”

Instantiation of Patient-Specific Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients
Arnau Montagud, Jonas Béal, Pauline Traynard, Emmanuel Barillot, Laurence Calzone
Conference: 3rd European Conference on Translational Bioinformatics: Biomedical Big Data Supporting Precision Medicine (ECTB 2018)

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer
H. Alexander Ebhardt, Alex Root, Yansheng Liua, Nicholas Paul Gauthier, Chris Sander, Ruedi Aebersold

Cluster Variatonal Approximations for Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data
Dominik Linzer, Heinz Koeppl, December 2018
NeurIP 2018 (NIPS 2018)

Collapsed Variational Inference for Nonparametric Bayesian Group Factor Analysis
Sikun Yang, Heinz Koeppl, November 2018
2018 IEEE International Conference on Data Mining (ICDM 2018)

Batch effects in large-scale proteomic studies: diagnostics and correction
Jelena Cuklina, Chloe Lee, Evan G Williams,Tatjana Sajic, Ben Collins, Maria Rodriguez-Martinez, Patrick Pedrioli, Ruedi Aebersold
HUPO 2018, October 2018.

Network reconstruction from time-course perturbation data using multivariate gaussian processes
Sara Al-Sayed and Heinz Koeppl, September 2018
EEE MLSP ’18: Machine Learning for Signal Processing

Logical versus kinetic modeling of biological networks: applications in cancer research
Laurence Calzone, Emmanuel Barillot and Andrei Zinovyev
COSB - Current Opinion in Chemical Engineering (Review), September, 2018.

How to find the right drug for each patient? Advances and challenges in pharmacogenomics
Angeliki Kalamara, Luis Tobalina and Julio Saez-Rodriguez COSB – Current Opinion in Systems Biology, August, 2018.

PhysiBoSS: a multi-scale agent based modelling framework integrating physical dimension and cell signalling
Gaelle Letort, Arnau Montagud, Gautier Stoll, Randy Heiland, Emmanuel Barillot, Paul Macklin, Andrei Zinovyev and Laurence Calzone
Bioinformatics journal, August, 2018.

LIN28 selectively modulates a subclass of let-7 microRNAs
Ustianenko et al., Molecular Cell 71, pp 271-283, July 2018

Dependent Relational Gamma Process Models for Longitudinal Networks
Sikun Yang, Heinz Koeppl ICML 2018 – International Conference on Machine Learning, July, 2018.

Pan-cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context
Chiu et al., Cell Reports 23, pp 297 – 312, June 2018

Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers
Guo et al, Life Science Alliance 1, no2 (May 29, 2018):e201800042

Pan-cancer analysis of lncRNA regulation supports their targeting of cancer genes in each tumor context
Hua-Sheng Chiu, Sonal Somvanshi, Ektaben Patel, Ting-Wen Chen, Vivek P. Singh, Barry Zorman, Sagar L. Patil, Yinghong Pan, Sujash S. Chatterjee, The Cancer Genome Atlas Research Network (TCGA), Anil K. Sood, Preethi H. Gunaratne, Pavel Sumazin
Cell Reports, April, 2018.

A Poisson Gamma Probabilistic Model for Latent Node-group Memberships in Dynamic Networks
Sikun Yang, Heinz Koeppl
Thirty-Second AAAI Conference on Artificial Intelligence (AAAI2018), February, 2018.


2017

Community assessment of cancer drug combination screens identifies strategies for synergy prediction
Michael P Menden, Dennis Wang, Yuanfang Guan, Michael Mason, Bence Szalai, Krishna C Bulusu, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, DREAM Consortium, In Sock Jang, Zara Ghazoui, Mehmet Eren Ahsen, Robert Vogel, Elias Chaibub Neto, Thea Norman, Eric KY Tang, Mathew J Garnett, Giovanni Di Veroli, Steve Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R. Dry, Julio Saez-Rodriguez
DREAM challenges, October, 2017.

Application of network diffusion approaches to drug screenings: A perspective on multi-layered networks derived from cell lines and drugs (Poster)
Vigneshwari Subramanian, Bence Szalai, Luis Tobalina, Julio Saez-Rodriguez
17th Workshop on Network Tools and Applications for Biology: Methods, tools and platforms for Personalized Medicine in the Big Data Era (NETTAB) , October, 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.