Results & Downloads
Benchmarking of cell type deconvolution pipelines for transcriptomics data
Article published in “Nature Communications” (2020, 11:5650) by partner UGENT
Journal article in MICCAI 2020
XLAB contributed to 23rd International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2020) with an article about anomaly detection in visual data.
D2.2 “Initial infrastructure framework”
An initial demonstrator of the iPC infrastructure is reviewed. The platform’s architecture is based on modules, which allow parallel developments and integration of different open source-based software components. This allows us to leverage other efforts and contribute towards its sustainability and maintainability. The release of a minimum viable platform is allowing us to capture early feedback from researchers at iPC.
Inferring clonal composition from multiple tumor biopsies
Knowledge about the clonal evolution of a tumor can help to interpret the function of its genetic alterations by identifying initiating events and events that contribute to the selective advantage of proliferative, metastatic, and drug-resistant subclones.
ICML 2020 paper
TUDA submitted a manuscript about continous-time Bayesian networks to the 37th International Conference on Machine Learning.
D1.1 “Collection of public molecular and clinical data”
The development of iPC predictive models for paediatric cancer genesis, progression, and response to therapies, as well as patient response to therapy, requires a vast quantity of molecular and clinical training data. In this deliverable, we have assembled a collection of these data to enable model construction and testing.
Publication in Nucleic Acids Research
IBM published a new paper about their web service “PaccMann”.
Publication in Cancers 2020
“Comprehensive Map of the Regulated Cell Death Signaling Network” in Issue 990 of the “Cancers” Journal by CURIE.
AAAI 2020 paper
TUDA contributed to the 34th Conference on Artificial Intelligence with the paper “A Variational Perturbative Approach to Planning in Graph-Based Markov Decision Processes”.
Ewing sarcoma book
CURIE contributed to the Springer book “Ewing Sarcoma – Methods and Protocols, Springer”.
Publication in Journal of Hepatology
IGTP contributed with a paper entitled “Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications”.
ROSUS 2020 paper
XLAB published a paper about “Visual Anomaly Detection in Domains with Limited Amount of Labeled Data”.
Publication in Entropy
CURIE published a paper on “Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph”
CURIE elaborates on a better understanding of the intratumoral heterogeneity of Ewing sarcoma.
Publication in Molecular Pharmaceutics
IBM and UKL-HD published a paper on “Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders”
Publication in Blood Advances
BCM’s paper on “Atovaquone is active against AML by upregulating the integrated stress pathway and suppressing oxidative phosphorylation”
NeurIPS 2019 paper
TUDA’s paper “Scalable Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data” was accepted
NeurIPS 2019 paper
IBM’s paper “PaccMannRL: Designing anticancer drugs from transcriptomic data via reinforcement learning” was accepted
Publication in Bioinformatics Journal
CURIE published a paper on “cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats”
Publication in Cell Reports
Publication by CURIE on “Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution”
Publication in International Journal of Molecular Sciences
CURIE published a paper on “Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets”
The RNA Atlas
UGent and collaborators present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines.
Using attention-based neural networks to enable explainable drug sensitivity prediction
Published by Manica Matteo; Oskooei Ali; Born Jannis; Subramanian Vigneshwari; Saez-Rodriguez Julio; Rodriguez Martinez Maria
Inferring context specific PPI networks
Publishes by Manica Matteo; Mathis Roland; Cadow Joris; Rodriguez Martinez Maria
Interpretability for computational biology
Published by Nguyen An-phi; Rodriguez-Martinez
PIMKL: Pathway Induced Multiple Kernel Learning
Published by Manica Matteo; Cadow Joris; Mathis Roland; Rodriguez Martinez Maria
Interpretable classification of molecular measurements
Publication by Cadow Joris
Interpretability for computational biology
Publication by Nguyen An-phi; Rodriguez-Martinez Maria
Using attention-based neural networks
Publication on enabling explainable drug sensitivity prediction on multimodal data by Manica Matteo; Oskooei Ali; Born Jannis; Subramanian Vigneshwari; Saez-Rodriguez Julio; Rodriguez Martinez Maria
Computer Modeling of Clonal Dominance
Publication on Memory-Anti-Naïve and Its Curbing by Attrition by Castiglione, Filippo; Ghersi, Dario; Celada, Franco.
From causal pathways to drug-response targets
Presentation from Rosa Hernansaiz Ballesteros on multi-omic analysis to contextualise large signalling networks on 6th June 2019 at EMBL-EBI, Hixton, UK.
Find out more about identifying effective personalized medicine for paediatric cancer in the explanatory video.
The official leaflet of the iPC H2020 project containing Partners, Project Information, Mission, Vision and Goals of the project.
Assessing reproducibility of matrix factorization methods in independent transcriptomes
Publication by Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev
D10.1 “Internal and external IT communication infrastructure and project website”
This deliverable constitutes the launch of the internal and external iPC communication infrastructure including the establishment of mailing lists, new IT infrastructure and the iPC website.
D11.1 “Project Quality Plan”
A handbook of the project management process, review process, quality checks, meeting organisation, which is communicated to all partners.
New European Project Squares off against Paediatric Cancer
The Austrian-managed iPC project is now underway and bringing hope to the children with cancer
The official announcement letter contains all relevant information about the iPC H2020 project.