Results & Downloads

6 April, 2022

Paper published in Bioinformatics

Paper entitled: BIODICA: a computational environment for Independent Component Analysis of omics data

31 March, 2022

Paper published in Nature Communication

Paper entitled: A single-cell atlas of breast cancer cell lines to study tumour 2 heterogeneity and drug response

1 February, 2022

Paper published in frontiers in Molecular Bioscience

Paper entitled: „Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches“

22 January, 2022

Paper published in iScience

Paper entitled: “Machine learning for multi-omics data integration in cancer“

30 November, 2021

D3.3 Integration of INtERAcT, MelanomaMine and LimTox and application to biomedical publications on paediatric cancers

This deliverable reports on the integration of INtERAcT and the implemented text mining workflow. The workflow was developed to adapt LimTox and MelanomaMine to pediatric tumor abstracts from PubMed and relies on INtERAcT in its downstream component of inferring molecular associations between entities extracted from unstructured text.

30 November, 2021

D1.3 Synthetic data for testing and training patient, cancer, and drug models

Synthetic data generation is emerging as an important solution for precision medicine. Therefore, an explainable Variational AutoEncoder (VAE) model is developed for synthetic transcriptomics data generation in medulloblastoma. The model can be used to complement and interpolate available data with synthetic instances. It is also transparent as it is able to match the learned latent variables with unique gene expression patterns. The model can also be adapted to other pediatric cancers and the resulting synthetic datasets used to test and train patient, cancer, and drug models in other work packages of the iPC project.

12 November, 2021

Paper published in BMC Bioinformatics

Paper entitled: “Emulating complex simulations by machine learning methods (SP)”

8 November, 2021

Paper will be presented at SPIE Medical Imaging

Paper entitled: “Segmentation of Multiple Myeloma Plasma Cells in Microscopy Images with Noisy Labels” (Presentation)

28 October, 2021

Paper published in bioRxiv

Paper entitled: “Loss of p16INK4a in neuroblastoma cells induces shift to an immature state with mesenchymal characteristics and increases sensitivity to EGFR inhibitors”

2 October, 2021

Paper published in BMC Bioinformatics

Paper entitled “DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification”

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”.

8 August, 2021

Paper published in Advanced Science

Paper entitled: “CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming”

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“

28 June, 2021

Paper published in NATURE COMMUNICATIONS

Paper entitled: “Restoration of the molecular clock is tumor suppressive in neuroblastoma”

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”.

17 June, 2021

Paper published in Nature Biotechnology

Paper entitled: “The RNA Atlas expands the catalog of human non-coding RNAs”

7 June, 2021

D4.2 An interactive online atlas of interconnected network maps based on the NaviCell platform

With the development of the NaviCell 3.0 web server, there is a complete and automated web-based infrastructure for hosting molecular maps, patient similarity network maps, and multi-omics datasets for the project. The NaviCell platform supports molecular map navigation and exploration using the Google maps™ engine. The logic of navigation is taken from Google maps. This NaviCell 3.0 web-server is freely available and several step-by-step tutorials are accessible.

2 June, 2021

D7.1 Application of software enabling computational deconvolution of bulk RNA-sequencing data to immune cell profiles of patient samples

Computational deconvolution of bulk RNA-sequencing data to infer cell type composition of a sample is challenging. Benchmarking of various computational deconvolution tools revealed various data processing parameters that impact deconvolution accuracy and revealed the importance of a complete reference matrix. As a complete reference matrix is often not available, an algorithm was designed that can handle missing cell types. This algorithm can be applied to establish the immune cell repertoire of primary tumor biopsies without prior knowledge of the full spectrum of cell types in the biopsy.

2 June, 2021

D3.1 Identification of important regulatory elements using multi-level matrix factorization approaches

D3.1 describes the techniques for dimensionality reduction used in iPC and their application to a selection of cohorts (at different omics levels) as well as a meta-analysis of the four solid tumor types of interest. The goal of the deliverable is to provide a list of pathways and biological functions having a key role in multiple paediatric cancers.

31 May, 2021

D3.2 Adaptation of MelanomaMine and LiMTox to the analysis of paediatric cancers and application to biomedical publications on paediatric cancers

The paper reports on the implementation of the iPC text mining workflow and three use cases for extracting biomedical information from large volumes. The workflow builds on the general framework of two text mining tools, LimTox and MelanomaMine. These tools will be used in the framework of the iPC project but also beyond, having a clear impact in the research community.

28 May, 2021

D8.1 Data-driven model for molecular targets and drug repositioning

This deliverable provides a detailed overview of the proposed computational tool for predicting patient-specific drugs with potential therapeutic benefit for paediatric cancer treatment and provides, for example, evidence for the goodness of the model in predicting such patient-specific drugs.

28 May, 2021

D2.3 Recommended metadata standards and portal prototype

The iPC project aims to ensure interoperability of data between different resources, so the platform must enforce principles and well-defined standards for data accessibility, usability, and registration. This deliverable provides an overview of the different approaches to representing metadata within the iPC Platform, and the efforts to integrate and leverage them within the iPC Catalog and the overall iPC Central Computational and Data Platform to enable meaningful management of research data.

28 May, 2021

D1.2 Collection of high-quality clinical and molecular paediatric cancer datasets as well as other tumour types

In this deliverable, demographic, clinical, and molecular profiles were collected for several pediatric and adult tumors. In addition, the focus here is on collections of single cell profiles of high risk cancers. The datasets will be used to evaluate the effects of treatments and perturbations on cancer cells, build models, and provide information on deciphering regulatory interactions. These data will allow characterization of cancer cell types that predict treatment outcome, as well as cell types that are resistant to therapies.

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.

3 February, 2021

Paper published in Scientifc Reports

Paper entitled: “MDM4 inhibition: a novel therapeutic strategy to reactivate p53 in hepatoblastoma”

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”

15 January, 2021

D4.1 Building of cancer type-specific multi-layered molecular and patient similarity networks

iPC uses network inference techniques and applies a selection of pediatric patient cohorts at different omic levels. Networks will be generated, for example, for the generation of molocular patient networks to be used in downstream project activities involving the use of networks.

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.

16 November, 2020

Paper published in Briefings in Bioinformatics

Paper entitled: “Deep learning in systems medicine”

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. 

6 October, 2020

Paper published in Frontiers in Cell and Developmental Biology.

Paper entitled: “Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19”

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

Paper presented at International Conference of Machine Learning 2020 (ICML 2020)

Paper entitled: “Continuous-Time Bayesian Networks with Clocks (Conference Proceedings/Presentation)”

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”

Published 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

Video

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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