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individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology


Initial infrastructure framework

An initial demonstrator of the platform infrastructure will be delivered, for further development and optimisation throughout the project.

Collection of molecular-interaction data from high-throughput assays, perturbation and essentiality assays, molecular data and clinical annotations from ongoing and past clinical trials

A comprehensive collection and analyses of curated data and molecular assays sourced from large-scale experiments and databases.

Project quality plan

A handbook of the project management process, review process, quality checks, meeting organisation, which is communicated to all partners.

Internal and external IT communication infrastructure and project website

This deliverable constitutes the launch of the internal iPC communication infrastructure including the establishment of mailing lists, a subversion repository server and the iPC website.

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Inferring clonal composition from multiple tumor biopsies

Author(s): Matteo Manica, Hyunjae Ryan Kim, Roland Mathis, Philippe Chouvarine, Dorothea Rutishauser, Laura De Vargas Roditi, Bence Szalai, Ulrich Wagner, Kathrin Oehl, Karim Saba, Arati Pati, Julio Saez-Rodriguez, Angshumoy Roy, Donald W. Parsons, Peter J. Wild, María Rodríguez Martínez, Pavel Sumazin
Published in: npj Systems Biology and Applications, Issue 6/1, 2020, ISSN 2056-7189
DOI: 10.1038/s41540-020-00147-5

Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications

Author(s): Juan Carrillo-Reixach, Laura Torrens, Marina Simon-Coma, Laura Royo, Montserrat Domingo-Sàbat, Jordi Abril-Fornaguera, Nicholas Akers, Margarita Sala, Sonia Ragull, Magdalena Arnal, Núria Villalmanzo, Stefano Cairo, Alberto Villanueva, Roland Kappler, Marta Garrido, Laura Guerra, Constantino Sábado, Gabriela Guillén, Mar Mallo, David Piñeyro, María Vázquez-Vitali, Olga Kuchuk, María Elena
Published in: Journal of Hepatology, Issue 73/2, 2020, Page(s) 328-341, ISSN 0168-8278
DOI: 10.1016/j.jhep.2020.03.025

PaccMann: a web service for interpretable anticancer compound sensitivity prediction

Author(s): Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
Published in: Nucleic Acids Research, Issue 48/W1, 2020, Page(s) W502-W508, ISSN 0305-1048
DOI: 10.1093/nar/gkaa327

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

Author(s): Jean-Marie Ravel, L. Cristobal Monraz Gomez, Nicolas Sompairac, Laurence Calzone, Boris Zhivotovsky, Guido Kroemer, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
Published in: Cancers, Issue 12/4, 2020, Page(s) 990, ISSN 2072-6694
DOI: 10.3390/cancers12040990

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Author(s): Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev
Published in: Bioinformatics, Issue 35/21, 2019, Page(s) 4307-4313, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz225

Atovaquone is active against AML by upregulating the integrated stress pathway and suppressing oxidative phosphorylation

Author(s): Alexandra M. Stevens, Michael Xiang, Lisa N. Heppler, Isidora Tošić, Kevin Jiang, Jaime O. Munoz, Amos S. Gaikwad, Terzah M. Horton, Xin Long, Padmini Narayanan, Elizabeth L. Seashore, Maci C. Terrell, Raushan Rashid, Michael J. Krueger, Alicia E. Mangubat-Medina, Zachary T. Ball, Pavel Sumazin, Sarah R. Walker, Yoshimasa Hamada, Seiichi Oyadomari, Michele S. Redell, David A. Frank
Published in: Blood Advances, Issue 3/24, 2019, Page(s) 4215-4227, ISSN 2473-9529
DOI: 10.1182/bloodadvances.2019000499

Computer Modeling of Clonal Dominance: Memory-Anti-Naïve and Its Curbing by Attrition

Author(s): Filippo Castiglione, Dario Ghersi, Franco Celada
Published in: Frontiers in Immunology, Issue 10, 2019, ISSN 1664-3224
DOI: 10.3389/fimmu.2019.01513

Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders

Author(s): Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Sáez-Rodríguez, María Rodríguez Martínez
Published in: Molecular Pharmaceutics, Issue 16/12, 2019, Page(s) 4797-4806, ISSN 1543-8384
DOI: 10.1021/acs.molpharmaceut.9b00520

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

Author(s): Nicolas Sompairac, Petr V. Nazarov, Urszula Czerwinska, Laura Cantini, Anne Biton, Askhat Molkenov, Zhaxybay Zhumadilov, Emmanuel Barillot, Francois Radvanyi, Alexander Gorban, Ulykbek Kairov, Andrei Zinovyev
Published in: International Journal of Molecular Sciences, Issue 20/18, 2019, Page(s) 4414, ISSN 1422-0067
DOI: 10.3390/ijms20184414

Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

Author(s): Marie-Ming Aynaud, Olivier Mirabeau, Nadege Gruel, Sandrine Grossetête, Valentina Boeva, Simon Durand, Didier Surdez, Olivier Saulnier, Sakina Zaïdi, Svetlana Gribkova, Aziz Fouché, Ulykbek Kairov, Virginie Raynal, Franck Tirode, Thomas G.P. Grünewald, Mylene Bohec, Sylvain Baulande, Isabelle Janoueix-Lerosey, Jean-Philippe Vert, Emmanuel Barillot, Olivier Delattre, Andrei Zinovyev
Published in: Cell Reports, Issue 30/6, 2020, Page(s) 1767-1779.e6, ISSN 2211-1247
DOI: 10.1016/j.celrep.2020.01.049

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats

Author(s): Irina Balaur, Ludovic Roy, Alexander Mazein, S Gökberk Karaca, Ugur Dogrusoz, Emmanuel Barillot, Andrei Zinovyev
Published in: Bioinformatics, Issue 36/8, 2020, Page(s) 2620-2622, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btz969

Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph

Author(s): Luca Albergante, Evgeny Mirkes, Jonathan Bac, Huidong Chen, Alexis Martin, Louis Faure, Emmanuel Barillot, Luca Pinello, Alexander Gorban, Andrei Zinovyev
Published in: Entropy, Issue 22/3, 2020, Page(s) 296, ISSN 1099-4300
DOI: 10.3390/e22030296

Trajectories, bifurcations and pseudotime in large clinical datasets

Author(s): Sergey E. Golovenkin, Jonathan Bac, Alexander Chervov, Evgeny M. Mirkes, Yuliya V. Orlova, Emmanuel Barillot, Alexander N. Gorban and Andrei Zinovyev
Published in: 2020
DOI: 10.5281/zenodo.4018714

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Author(s): Lorenzi, Lucia; Chiu, Hua-Sheng; Cobos, Francisco Avila; Gross, Stephen; Volders, Pieter-Jan; Cannoodt, Robrecht; Nuytens, Justine; Vanderheyden, Katrien; Anckaert, Jasper; Lefever, Steve; Goovaerts, Tine; Birkballe Hansen, Thomas; Kuersten, Scott; Nijs, Nele; Taghon, Tom; Vermaelen, Karim; Bracke, Ken R.; Saeys, Yvan; De Meyer, Tim; Deshpande, Nandan; Anande, Govardhan; Chen, Ting-Wen; Wilkins, M
Published in: Issue 7, 2019
DOI: 10.1101/807529

Image Synthesis as a Pretext for Unsupervised Histopathological Diagnosis

Author(s): Stepec, D.; Skocaj, D.
Published in: Issue 1, 2020
DOI: 10.5281/zenodo.4288328

Scalable Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data

Author(s): Dominik Linzner Michael Schmidt Heinz Koeppl
Published in: 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), 2019

A Variational Perturbative Approach to Planning in Graph-based Markov Decision Processes

Author(s): Dominik Linzner Heinz Koeppl
Published in: Association for the Advancement of Artificial Intelligence, 2019

Continuous-Time Bayesian Networks with Clocks

Author(s): Engelmann, Nikolai; Linzner, Dominik; Koeppl, Heinz
Published in: Issue 10, 2020
DOI: 10.5281/zenodo.3957199

PaccMannRL: Designing anticancer drugs from transcriptomic data via reinforcement learning

Author(s): Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez Martínez
Published in: 2019
DOI: 10.5281/zenodo.3610233

ROSUS 2020 - Računalniška obdelava slik in njena uporaba v Sloveniji 2020: Zbornik 15. strokovne konference

Author(s): Dejan Štepec, Danijel Skočaj
Published in: 2020
DOI: 10.18690/978-961-286-337-1

Systems biology analysis for Ewing sarcoma

Author(s): Petrizzelli, Marianyela; Merlevede, Jane; Zinovyev, Andrei
Published in: Issue 2, 2020
DOI: 10.5281/zenodo.3952244