Results & Downloads

13 September, 2021

Paper published in Bioinformatics

Paper entitled: FUNKI: Interactive functional footprint-based analysis of omics data

7 September, 2021

Paper published in the Frontiers in Immunology

Paper entitled: “From Infection to Immunity: Understanding the Response to SARS-CoV2 Through In-Silico Modeling (SP)“

25 August, 2021

Paper published in Symmetry 2021

Paper entitled: “The Multiple Dimensions of Networks in Cancer: A Perspective”

24 August, 2021

Paper published in the Elsevier Journal

Paper entitled “Applications of single-cell and bulk RNA sequencing in onco-immunology”.

6 August, 2021

Paper published in the Special Issue Hepatoblastoma and Other Pediatric Liver Tumors

Paper entitled “Bridging molecular basis, prognosis, and treatment of pediatric liver tumors”.

6 August, 2021

Paper published in the Current Protocols in Bioinformatics.

Paper entitled “PIONEER: Pipeline for Generating High‐Quality Spectral Libraries for DIA‐MS Data”.

6 August, 2021

Paper published in the Journal for ImmunoTherapy of Cancer

Paper entitled “Identification and validation of viral antigens sharing sequence and structural homology with tumor-associated antigens (TAAs).”

4 August, 2021

Paper presented in the “Computer Vision for Microscopy Image Analysis (CVMI)” workshop

Paper entitled “Unsupervised Detection of Cancerous Regions in Histology Imagery using Image-to-Image Translation”

29 July, 2021

Paper published in Bioinformatics

Paper entitled: “Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)”

20 July, 2021

Paper published in Physics of Life Reviews: pp. 132-134

Paper entiteld: „Adaptation through the lense of single-cell multi-omics data Comment on “Dynamic and thermodynamic models of adaptation” by A.N. Gorban et al.”

16 July, 2021

Paper published in the BIORXIV.

Paper entitled “Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive neoplasms in children and young adults”.

12 July, 2021

Paper published in Bioinformatics

Paper entitled: “On the feasibility of deep learning applications using raw mass spectrometry data”

12 July, 2021

Paper published in Bioinformatics

Paper entitled: “TITAN: T-cell receptor specificity prediction with bimodal attention networks“

24 June, 2021

Paper published in Bioinformatics

Paper entitled: “SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems”

23 June, 2021

Paper published in the Proceedings of International Conference on Machine Learning (ICML) 2021

A new network inference algorithm from TUDA with iPC acknowledge was published in the ICML 2021. Paper entitled “Active Learning of Continuous-Time Bayesian Networks Through Interventions”.

26 May, 2021

Estimage: a webserver hub for the computation of methylation age (SP)

Article published in the Nucleic Acids Research Journal.

30 April, 2021

Artificial Intelligence in Cancer Research: learning at different levels of data granularity

Article published in the Molecular Oncology Journal, Volume 15, Issue 4 Pages 817-829.

29 April, 2021

Article published in the Cancer Cell Journal, Volume 39, Issue 6, P 810-826

Article entitled “STAG2 mutations alter CTCF-anchored loop extrusion, reduce cis-regulatory interactions and EWSR1-FLI1 activity in Ewing sarcoma”.

26 March, 2021

The multilayer community structure of medulloblastoma

Article published in the iScience Journal, Volume 24, ISSUE 4 by partner Barcelona Supercomputing Center (BSC).

25 March, 2021

Paper published in Machine Learning: Science and Technology

Paper entitled: “Data-driven molecular design for discovery and synthesis of novel ligands: a case study on SARS-CoV-2”

12 March, 2021

Publication in the Journal of Medical Internet Research (JMIR).

Article entitled “Artificial Intelligence–Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development”.

Published in the JMIR, Volume 23 Issue 3 by partner Barcelona Supercomputing Center (BSC).

22 February, 2021

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Article published in the Science Advances Journal, Vol. 7, no. 6.

27 January, 2021

Paper published in the International Joint Conference on Neural Networks-2021 (IJCNN2021)

Paper entitled: “Clinical trajectories estimated from bulk tumoral molecular proles using elastic principal trees”

10 December, 2020

Benchmarking of cell type deconvolution pipelines for transcriptomics data

Article published in “Nature Communications” (2020, 11:5650) by partner UGENT

22 November, 2020

FPGA Accelerated Analysis of Boolean Gene Regulatory Networks

Article published in the IEEE/ACM Transactions on Computational Biology and Bioinformatics ( Volume: 17, Issue: 6)

22 November, 2020

COSIFER: a Python package for the consensus inference of molecular interaction networks

Article published in the Bioinformatics Journal.

14 October, 2020

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.

8 October, 2020

Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19

The ongoing COVID-19 pandemic still requires fast and effective efforts from all fronts, including epidemiology, clinical practice, molecular medicine, and pharmacology. 

1 October, 2020

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.

3 September, 2020

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. 

2 July, 2020

ICML 2020 paper

TUDA submitted a manuscript about continous-time Bayesian networks to the 37th International Conference on Machine Learning.

1 July, 2020

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.

29 June, 2020

Paper published in BMC Bioinformatics

Paper entitled: “Methylation data imputation performances under different representations and missingness patterns”

13 May, 2020

Publication in Nucleic Acids Research

IBM published a new paper about their web service “PaccMann”.

17 April, 2020

Publication in Cancers 2020

“Comprehensive Map of the Regulated Cell Death Signaling Network” in Issue 990 of the “Cancers” Journal by CURIE.

3 April, 2020

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”.

1 April, 2020

Ewing sarcoma book

CURIE contributed to the Springer book “Ewing Sarcoma – Methods and Protocols, Springer”.

30 March, 2020

Publication in Journal of Hepatology

IGTP contributed with a paper entitled “Epigenetic footprint enables molecular risk stratification of hepatoblastoma with clinical implications”.

19 March, 2020

ROSUS 2020 paper

XLAB published a paper about “Visual Anomaly Detection in Domains with Limited Amount of Labeled Data”.

6 March, 2020

Publication in Entropy

CURIE published a paper on “Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph”

3 March, 2020

Press Release

CURIE elaborates on a better understanding of the intratumoral heterogeneity of Ewing sarcoma.

30 January, 2020

Publication in Molecular Pharmaceutics

IBM and UKL-HD published a paper on “Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders”

27 January, 2020

Paper published in Scientific Reports (Sci Rep)

Paper entitled: “Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data”

24 January, 2020

Publication in Blood Advances

BCM’s paper on “Atovaquone is active against AML by upregulating the integrated stress pathway and suppressing oxidative phosphorylation”

21 January, 2020

NeurIPS 2019 paper

TUDA’s paper “Scalable Structure Learning of Continuous-Time Bayesian Networks from Incomplete Data” was accepted

16 January, 2020

NeurIPS 2019 paper

IBM’s paper “PaccMannRL: Designing anticancer drugs from transcriptomic data via reinforcement learning” was accepted

15 January, 2020

Publication in Bioinformatics Journal

CURIE published a paper on “cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats”

18 November, 2019

Paper published in Explainable AI in Healthcare and Medicine

Paper entitled: “DeStress: Deep Learning for Unsupervised Identification of Mental Stress in Firefighters from Heart-rate Variability (HRV) Data”

25 October, 2019

Publication in Cell Reports

Publication by CURIE on “Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution”

25 October, 2019

Publication in International Journal of Molecular Sciences

CURIE published a paper on “Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets”

17 October, 2019

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.

16 September, 2019

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

16 September, 2019

Inferring context specific PPI networks

Publishes by Manica Matteo; Mathis Roland; Cadow Joris; Rodriguez Martinez Maria

16 September, 2019

Interpretability for computational biology

Published by Nguyen An-phi; Rodriguez-Martinez

16 September, 2019

PIMKL: Pathway Induced Multiple Kernel Learning

Published by Manica Matteo; Cadow Joris; Mathis Roland; Rodriguez Martinez Maria

16 September, 2019

Interpretable classification of molecular measurements

Publication by Cadow Joris

28 August, 2019

Interpretability for computational biology

Publication by Nguyen An-phi; Rodriguez-Martinez Maria

28 August, 2019

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

29 July, 2019

Computer Modeling of Clonal Dominance

Publication on Memory-Anti-Naïve and Its Curbing by Attrition by Castiglione, Filippo; Ghersi, Dario; Celada, Franco.

29 July, 2019

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.

19 July, 2019


Find out more about identifying effective personalized medicine for paediatric cancer in the explanatory video. 

15 April, 2019

iPC Leaflet

The official leaflet of the iPC H2020 project containing Partners, Project Information, Mission, Vision and Goals of the project.

2 April, 2019

Assessing reproducibility of matrix factorization methods in independent transcriptomes

Publication by Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev

1 April, 2019

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.

26 March, 2019

D11.1 “Project Quality Plan”

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

7 March, 2019

Press Release

New European Project Squares off against Paediatric Cancer

The Austrian-managed iPC project is now underway and bringing hope to the children with cancer

1 January, 2019

Announcement Letter

The official announcement letter contains all relevant information about the iPC H2020 project.

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