Scientific Publications

10 September, 2022

Paper Published in Proteomics

Paper entitled: “Opportunities for pharmacoproteomics in biomarker discovery”

30 August, 2022

Paper Published in Cancers

Paper entitled: “Targeting the Unwindosome by Mebendazole Is a Vulnerability of Chemoresistant Hepatoblastoma”

14 July, 2022

Paper published in Cancer Cell

Paper entitled: “Pan-cancer proteomic map of 949 human cell lines”

28 June, 2022

Paper published in Nature Communication

Paper entitled: “MYCN-driven fatty acid uptake is a metabolic vulnerability in neuroblastoma”

27 June, 2022

Paper published in Bioinformatics

Paper entitled: “DECODE: a computational pipeline to discover T cell receptor binding rules”

21 June, 2022

Paper published in Cell Reports

Paper entitled: “MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines”

30 May, 2022

Consensus multi-omics subtypes of paediatric cancers

We report on the implementation of a method for multilayer community trajectory analysis and its applications, including a published study on medulloblastoma, a study on congenital myasthenic syndromes, and a study on the functional characterization of commonalities among a selection of paediatric tumours.

13 May, 2022

Paper published in Journal of Hepatology

Paper entitled: “Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive hepatocellular neoplasms in children and adolescents”

11 May, 2022

Paper published in Molecular Cell

Paper entitled: “Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions”

6 April, 2022

Paper published in Bioinformatics

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

5 April, 2022

Paper published in Cancer Science

Paper entitled: “Mutational spectrum of ATRX aberrations in neuroblastoma and associated patient and tumor characteristics”

31 March, 2022

Paper published in Nature Communication

Paper entitled: “A single-cell analysis of breast cancer cell lines to study tumour 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“

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”

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”

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”

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)”

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”

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.

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

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