Scientific Publications
Publication in the Journal “Nature Communications”
Article entitled: “Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes”
Publication in the Journal „Cancer Cell“
Article entitled: “Integrative analysis of neuroblastoma by single-cell RNA sequencing indentifies the NECTIN2-TIGIT axis as a target for immunotherapy”
Publication in the Journal „Hepatology Communications”
Article entitled: “Targeting G9a/DNMT1 methyltransferase activity impedes IGF2-mediated survival in hepatoblastoma”
Publication in the Journal “2023 Life Science Alliance LLC”
Article entitled: “Proteomic-based stratification of intermediate-risk prostate cancer patients”
Publication in the Journal “Analytical Chemistry”
Article entitled: “Heat ‘n Beat: A universal high-throughput end-to-end proteomics sample processing platform in under an hour”
Publication in the Journal “Hepatology“
Article entitled “Computational drug prediction in hepatoblastoma by integrating pan-cancer transcriptomics with pharmacological response”
Publication in the Journal „European Journal of Cancer”
Article entitled: “Adoptive cell therapy in pediatric extracranial solid tumors: current approaches and future challenges”
Paper published in PLOS ONE
Paper entitled: “Two opposing gene expression patterns within ATRX aberrant neutoblastoma”
Paper published in Digital Discovery
Paper entitled: “Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes”
Paper published in Journal of Hepatology
Paper entitled: “Identification and experimental validation of druggable epigenetic targets in hepatoblastoma”
Paper Published in Digital Discovery
Paper entitled: “Chemical representation learning for toxicity prediction”
Paper published in Frontiers in Oncology
Paper entitled: “Quantitative proteomic studies addressing unmet clinical needs in sarcoma”
Paper published in Molecular Cancer Therapeutics
Paper entitled: “Identification of IGF2 as Genomic Driver and Actionable Therapeutic Target in Hepatoblastoma”
Paper published in Briefings in Bioinformatics
Paper entitled: “FLAN: feature-wise latent additive neural models for biological applications”
Paper published in IEEE
Paper entitled: “Why the winner is the best”
Publication in the Journal “NAR Genomics and Bioinformatics”
Article entitled: „ Single-cell gene set enrichment analysis and transfer learning for functional annotation of scRNA-seq data”
Paper published in the 26th International Conference on Artificial Intelligence and Statistics (AISTATS)
Paper entitled “Isotropic Gaussian Processes on Finite Spaces of Graphs”
Paper Published in Bioinformatics Advances
Paper entitled: “MonoNet: enhancing interpretability in neural networks via monotonic features”
Paper published in the 39th Conference on Uncertainty in Artificial Intelligence (UAI 2023)
Paper entitled “Aligned Diffusion Schroedinger Bridges”
Paper Published in Cell Reports
Paper entitled: “Systematic multi-omics cell line profiling uncovers principles of Ewing sarcoma fusion oncogene-mediated gene regulation”
Publication in the Journal “Medical Image Analysis (Elsevier)”
Article entitled: „SegPC-2021: A challenge & dataset on segmentation of Multiple Myeloma plasma cells from microscopic images”
Publication in the Journal “Bioinformatics”
Article entitled: “Computational modelling in health and disease: highlights of the 6th annual SysMod meeting”
Paper Published in Proteomics
Paper entitled: “Opportunities for pharmacoproteomics in biomarker discovery”
Paper Published in Cancers
Paper entitled: “Targeting the Unwindosome by Mebendazole Is a Vulnerability of Chemoresistant Hepatoblastoma”
Paper published in Proteomics
Paper entitled: “Clinical applications of mass spectrometry-based proteomics in cancer: Where are we?”
Paper published
Paper entitled: “Computational challenges of cell cycle analysis using single cell transcriptomics”
Conference Paper “ECML PKDD International Workshop on eXplainable Knowledge Discovery in Data Mining”
Paper entitled: “Is Attention Interpretation? A Quantitative Assessment On Sets”
Paper published in Cancer Cell
Paper entitled: “Pan-cancer proteomic map of 949 human cell lines”
Publication in the Journal “Nature Communications”
Article entitled: “The HHIP-AS1 lncRNA promotes tumorigenicity through stabilization of dynein complex 1 in human SHH-driven tumors”
Paper published in Nature Communication
Paper entitled: “MYCN-driven fatty acid uptake is a metabolic vulnerability in neuroblastoma”
Paper published in Bioinformatics
Paper entitled: “DECODE: a computational pipeline to discover T cell receptor binding rules”
Paper published in Cell Reports
Paper entitled: “MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines”
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.
Paper published in Journal of Hepatology
Paper entitled: “Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive hepatocellular neoplasms in children and adolescents”
Paper published in Molecular Cell
Paper entitled: “Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions”
Paper published in Bioinformatics
Paper entitled: “BIODICA: a computational environment for Independent Component Analysis of omics data”
Paper published in Cancer Science
Paper entitled: “Mutational spectrum of ATRX aberrations in neuroblastoma and associated patient and tumor characteristics”
Paper published in Nature Communication
Paper entitled: “A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response”
Paper published in frontiers in Molecular Bioscience
Paper entitled: „Modeling Progression of Single Cell Populations Through the Cell Cycle as a Sequence of Switches“
Paper published in iScience
Paper entitled: “Machine learning for multi-omics data integration in cancer“
Paper published in BMC Bioinformatics
Paper entitled: “Emulating complex simulations by machine learning methods (SP)”
Paper will be presented at SPIE Medical Imaging
Paper entitled: “Segmentation of Multiple Myeloma Plasma Cells in Microscopy Images with Noisy Labels” (Presentation)
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”
Paper published in BMC Bioinformatics
Paper entitled “DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification”
Paper published in Bioinformatics
Paper entitled: “FUNKI: Interactive functional footprint-based analysis of omics data”
Paper published in the Frontiers in Immunology
Paper entitled: “From Infection to Immunity: Understanding the Response to SARS-CoV2 Through In-Silico Modeling (SP)“
Paper published in PNAS
Paper entitled: “Defects in 8-oko-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma”
Paper published in Symmetry 2021
Paper entitled: “The Multiple Dimensions of Networks in Cancer: A Perspective”
Paper published in the Elsevier Journal
Paper entitled “Applications of single-cell and bulk RNA sequencing in onco-immunology”.
Paper published in Advanced Science
Paper entitled: “CHAF1A Blocks Neuronal Differentiation and Promotes Neuroblastoma Oncogenesis via Metabolic Reprogramming”
Paper published in the Special Issue Hepatoblastoma and Other Pediatric Liver Tumors
Paper entitled “Bridging molecular basis, prognosis, and treatment of pediatric liver tumors”.
Paper published in the Current Protocols in Bioinformatics.
Paper entitled “PIONEER: Pipeline for Generating High‐Quality Spectral Libraries for DIA‐MS Data”.
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).”
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”
Paper published in Bioinformatics
Paper entitled: “Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)”
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.”
Paper published in the BIORXIV
Paper entitled “Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive neoplasms in children and young adults”.
Paper published in Bioinformatics
Paper entitled: “On the feasibility of deep learning applications using raw mass spectrometry data”
Paper published in Bioinformatics
Paper entitled: “TITAN: T-cell receptor specificity prediction with bimodal attention networks“
Paper published in NATURE COMMUNICATIONS
Paper entitled: “Restoration of the molecular clock is tumor suppressive in neuroblastoma”
Paper published in Bioinformatics
Paper entitled: “SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems”
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”.
Publication in the Journal “Briefings in Bioinformatics”
Article entitled “It’s FLAN time! Summing feature-wise latent representations for interpretability”
Paper published in Nature Biotechnology
Paper entitled: “The RNA Atlas expands the catalog of human non-coding RNAs”
“Estimage: a webserver hub for the computation of methylation age (SP)”
Article published in the Nucleic Acids Research Journal.
“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.
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”.
“The multilayer community structure of medulloblastoma”
Article published in the iScience Journal, Volume 24, ISSUE 4 by partner Barcelona Supercomputing Center (BSC).
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”
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).
“Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell”
Article published in the Science Advances Journal, Vol. 7, no. 6.
Paper published in Scientifc Reports
Paper entitled: “MDM4 inhibition: a novel therapeutic strategy to reactivate p53 in hepatoblastoma”
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”
“Benchmarking of cell type deconvolution pipelines for transcriptomics data”
Article published in “Nature Communications” (2020, 11:5650) by partner UGENT
“FPGA Accelerated Analysis of Boolean Gene Regulatory Networks”
Article published in the IEEE/ACM Transactions on Computational Biology and Bioinformatics ( Volume: 17, Issue: 6)
“COSIFER: a Python package for the consensus inference of molecular interaction networks”
Article published in the Bioinformatics Journal.
Paper published in Briefings in Bioinformatics
Paper entitled: “Deep learning in systems medicine”
“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.
Paper published in Frontiers in Cell and Developmental Biology.
Paper entitled: “Designing a Network Proximity-Based Drug Repurposing Strategy for COVID-19”
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.
“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.
Paper presented at International Conference of Machine Learning 2020 (ICML 2020)
Paper entitled: “Continuous-Time Bayesian Networks with Clocks (Conference Proceedings/Presentation)”
Paper published in BMC Bioinformatics
Paper entitled: “Methylation data imputation performances under different representations and missingness patterns”
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”
Publication in Molecular Pharmaceutics
IBM and UKL-HD published a paper on “Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders”
Paper published in Scientific Reports (Sci Rep)
Paper entitled: “Stabilized Reconstruction of Signaling Networks from Single-Cell Cue-Response Data”
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”
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”
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”
Published 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.
“Assessing reproducibility of matrix factorization methods in independent transcriptomes”
Publication by Laura Cantini, Ulykbek Kairov, Aurélien de Reyniès, Emmanuel Barillot, François Radvanyi, Andrei Zinovyev
