Publications
2025
- Bernardino, Beatriz de Campos
Boosting graph neural networks with knowledge for personalized medicine
Lisbon University - Canastra, Catarina , and Cátia Pesquita
A Systematic Evaluation of Knowledge Graph Embeddings for Gene-Disease Association Prediction
arXiv - Daghir-Wojtkowiak, Emilia et al.
Leveraging Knowledge for Explainable AI in Personalized Cancer Treatment: Challenges and Future Directions
Zenodo - Fiorelli, Manuel, Armando Stellato, Tiziano Lorenzetti
MAPLE: metadata-driven orchestration of ontology matching
International Journal of Metadata Semantics and Ontologies - Gordienko, Yuri, Nikita Gordienko, Vladyslav Taran, Anis Rojbi, Sergii Telenyk, Sergii Stirenko
Effect of natural and synthetic noise data augmentation on physical action classification by brain–computer interface and deep learning
frontiers (19) 2025 - Hoehndorf, Robert, Catia Pesquita, Fernando Zhapa-Camacho
Neuro-Symbolic AI in Life Sciences
IOS Press Ebooks - Kafitelis, Hector, Stamatiki Grammatikaki, Roubini Zakopoulou, Aristotelis Bamias, Michaelis V. Karamouzis, Konstantinos Stravodimos, and Maria Gazouli
Up-regulation of Cuproptosis-related lncRNAS in Patients Receiving Immunotherapy for Metastatic Clear Cell Renal Cell Carcinoma Indicates Progressive Disease
In vivo 2025 Jan-Feb;39(1):146-151 - Mateusz, Michal, Waleron, Ashwin Adrian Kallor, Aleksander Palkowski, Emilia Daghir-Wojtkowiak, Piyush Borole, Mikolaj Kocikowski, Karol Polom, Fabio Marino, Beatriz Monterde, Michele Mastromattei, Davide Venditti, Mark Stares, Ashita Singh, Theodore Hupp, Christophe Battail, Alexander Laird, Catia Pesquita, Luis Zapata, Stefan N. Symeonides, Ajitha Rajan, Fabio Massimo Zanzotto, Javier Antonio Alfaro
Expanding the definition of MHC Class I peptide binding promiscuity to support vaccine discovery across cancers with CARMEN
bioRxiv - Silva, Marta C, Susana Nunes, Laura Balbi, Ana Filipa Rodrigues, Catia Pesquita
KATY — Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity
Zenodo - Sousa, Rita T., Sara Silva, Catia Pesquita
Explaining protein–protein interactions with knowledge graph-based semantic similarity
ACM Digital Library - Zickuhr, Greice Michele, Hazem Abdullah, In Hwa Um, Alexander Laird, Peter Mullen, David J. Harrison, Alison L. Dickson
Clear Cell Renal Cell Carcinoma Patient-Derived Tumoroids characterisation by Spatial Mass Spectrometry, Histology and Multiplex Immunofluorescence
BioImage Archive - Yin, Liangwei, Pietro Traversa, Mohamed Elati, Yamir Moreno, Natalia Marek-Trzonkowska, Christophe Battail
Sample-specific network analysis identifies gene co-expression patterns of immunotherapy response in clear cell renal cell carcinoma
SCI 113061 - Zoziuk, Maksym,Vittorio Colizzi, Pavlo Krysenko, Maurizio Mattei, Roberta Bernardini, Fabio Massimo Zanzotto, ,Stefano Marini, Dmitri Koroliouk
Plant miRNAs for Improved Gene Regulation in a Wide Range of Human Cancers
Current issues in molecular biology
2024
- Balbi, Laura, Rita Sousa, Pedro Cotovio, Catia Pesquita
Injecting domain knowledge into graph neural networks for protein-protein interactions
Research Square - Bancet, Alexandre, Rita Frem, Florian Jeanneret, Angélique Mularoni, Pauline Bazelle, Caroline Roelants, Jean-Guy Delcros, Jean-François Guichou, Catherine Pillet, Isabelle Coste, Toufic Renno, Christophe Battail, Claude Cochet, Thierry Lomberget, Odile Filhol, Isabelle Krimm
Cancer selective cell death induction by a bivalent CK2 inhibitor targeting the ATP site and the allosteric αD pocket
iScience. 2024 Jan 12;27(2) - Canastra, Catarina Salema
Comparing link prediction and classification for Gene-Disease association discovery
Lisbon University - Christopher C. T. Sng, Ashwin Adrian Kallor, Benjamin S. Simpson, Georges Bedran, Javier Alfaro, Kevin Litchfield
Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy
Frontiers - Elshani, Mustafa, Hazem Abdullah, Ying Zhang, Alexander Laird, Peter Mullen, and David J. Harrison
Long-read Spatial Transcriptomic Profiling of Patient-derived ccRCC Tumoroids Reveals Heterogeneity in Isoform and Gene Expression
bioRxiv - Faria, Daniel, Patrícia Eugénio, Marta Contreiras Silva, Laura Balbi, Georges Bedran, Ashwin Adrian Kallor, Susana Nunes, Aleksander Palkowski, Michal Waleron, Javier A Alfaro, Catia Pesquita
The Immunopeptidomics Ontology (ImPO)
PubMed - Gordienko, Yuri, Maksym Shulha, Yuriy Kochura, Oleksandr Rokovyi, Vladyslav Taran, Oleg Alienin, Sergii Stirenko
Multimodal Metadata Augmentation for Federated Learning in Medical Applications
Springer Lecture Notes in Networks and Systems - Jeanneret, Florian, Pauline Bazelle, Sarah Schoch, Catherine Pillet, In Hwa Um, Assilah Bouzit, Bertrand Evrard, Evan Seffar, Frédéric Chalmel, Javier A. Alfaro, Catia Pesquita, Fabio Massimo Zanzotto, Mark Stares, Stefan N. Symeonides, Alexander Laird, Jean-Alexandre Long, Jean Luc Descotes, Delphine Pflieger, David J. Harrison, Odile Filhol, Håkan Axelson, Christophe Battail
Microenvironment of metastasis reveals key predictors of PD-1 blockade response in renal cell carcinoma
bioRxiv - Khmelnytskyi, Arsenii, Sergii Stirenko, and Yuri Gordienko
Hybrid Neural Networks for Medical Image Classification
Proceedings of 4th International Conference on Artificial Intelligence and Smart Energy - Macilenti, Giulio, Armando Stellato, Manuel Fiorelli
Prompting is not all you need Evaluating GPT-4 performance on a real-world ontology alignment use case
Procedia Computer Science - Paulino, Filipe José Bastos Benvindo
Explaining Predictions from Node Classification with Knowledge Graph Embeddings
Lisbon University - Pesquita, Catia et al.
Results of the Ontology Alignment Evaluation Initiative 2024
19th International Workshop on Ontology Matching - Sainero-Alcolado, Lourdes, Elisa Garde-Lapido, Marteinn Thor Snaebjörnsson, Sarah Schoch, Irene Stevens, María Victoria Ruiz-Pérez, Christine Dyrager, Vicent Pelechano, Håkan Axelson, Almut Schulze, Marie Arsenian-Henriksson
Targeting MYC induces lipid droplet accumulation by upregulation of HILPDA in clear cell renal cell carcinoma
Proc. Natl. Acad. Sci. - Scarpato, Noemi; Riondino, Silvia; Nourbakhsh, Aria; Roselli, Mario; Ferroni, Patrizia; Guadagni, Fiorella; Zanzotto, Fabio Massimo
Drug recommendation ranking for personalized medicine using outcomes of retrospective cancer patients
Expert Systems with Applications - Scarpato, Noemi, Aria Nourbakhsh, Patrizia Ferroni, Silvia Riondino, Mario Roselli, Francesca Fallucchi, Piero Barbanti, Fiorella Guadagni, Fabio Massimo Zanzotto
Evaluating Explainable Machine Learning Models for Clinicians
Cognitive Computation - Zickuhr, Greice M., In Hwa Um, Alexander Laird, David J. Harrison, and Alison L. Dickson
DESI-MSI-guided exploration of metabolic-phenotypic relationships reveals a correlation between PI 38:3 and proliferating cells in clear cell renal cell carcinoma via single-section co-registration of multimodal imaging
Analytical and Bioanalytical Chemistry - Zickuhr, Greice Michele, In Hwa Um, Alexander Laird, David J. Harrison, and Alison L. Dickson
Spatial Mass Spectrometry with Whole Slide Multiplex Immunofluorescence in Clear Cell Renal Cell Carcinoma
BioImage Archive
2023
- Anwana, Tima Otu, Katarzyna Barud, Michael Cepic, Emily Johnson, Max Königseder, and Marie-Catherine Wagner
Consent and Retrospective Data Collection
The Law and Ethics of Data Sharing in Health Sciences. Perspectives in Law, Business and Innovation. - Barud, Katarzyna et al.
Digital health innovations - Good practice guide for obtaining consent for the use of personal health information for research and innovations
CEN Workshop Agreement 17933. - Bedran, Georges, Hans-Christof Gasser, Kenneth Weke, Tongjie Wang, Dominika Bedran, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Catia Pesquita, Håkan Axelson, Ajitha Rajan, David J. Harrison, Aleksander Palkowski, Maciej Pawlik, Maciej Parys,J. Robert O'Neill, Paul M. Brennan, Stefan N. Symeonides, David R. Goodlett, Kevin Litchfield, Robin Fahraeus, Ted R. Hupp, Sachin Kote, Javier A. Alfaro
The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
Cancer Immunology Research - Bedran, Georges et al.
Unraveling the glycosylated immunopeptidome with HLA-Glyco
Nat Commun 14, 3461 (2023). - Dovrolis, Nikolas, Hector Katifelis, Stamatiki Grammatikaki, Roubini Zakopoulou, Aristotelis Bamias, Michalis. V. Karamouzis, and Kyriakos Souliotis and Maria Gazouli
Inflammation and Immunity Gene Expression Patterns and Machine Learning Approaches in Association with Response to Immune-Checkpoint Inhibitors-Based Treatments in Clear Cell Renal Carcinoma
Cancers - Elshani, Mustafa, In Hwa Um, Steve Leung, Paul A. Reynolds, Alex Chapman, Mary Kudsy, and David J. Harrison
Transcription Factor NFE2L1 Decreases in Glomerulonephropathies after Podocyte Damage
Cells 2023, 12(17), 2165. - Florian, Jeanneret, Bazelle Pauline, Schoch Sarah, Pillet Catherine, Um In Hwa, Bouzit Assilah, Evrand Bertrand, Seffar Evan, Chalmel Frédéric, Alfaro Javier, Pesquita Catia, Zanzotto Fabio Massimo, Stares Mark, Symeonides Stefan, Laird Alexander, Long Jean-Alexandre, Descotes Jean-Luc, Pflieger Delphine, Harrison David, Filhol Odile, Axelson Håkan, Battail Christophe
Microenvironment of metastatic site reveals key predictors of PD-1 blockade response in renal cell carcinoma
Zenodo - Gordienko, Yuri, Maksym Shulha, Yuriy Kochura, Oleksandr Rokovyi, Oleg Alienin, Vladyslav Taran, and Sergii Stirenko
Ensemble Knowledge Distillation for Edge Intelligence in Medical Applications
Studies in Computational Intelligence, vol 1100 - Grammatikaki, Stamatiki et al.
The Role of HIF1-related Genes and Non-coding RNAs Expression in Clear Cell Renal Cell Carcinoma
In vivo (Athens, Greece) vol. 37,3 (2023): 1103-1110. - Grammatikaki, Stamatiki et al.
An Overview of Epigenetics in Clear Cell Renal Cell Carcinoma
In vivo (Athens, Greece) vol. 37,1 (2023): 1-10. - Kostiukevych, Kostiantyn et al.
Hierarchy of Hybrid Deep Neural Networks for Physical Action Classification by Brain-Computer Interface
Modern Machine Learning Technologies and Data Science Workshop MoMLeT&DS 2022 - Nunes, Susana, Rita T. Sousa, Catia Pesquita
Multi-domain knowledge graph embeddings for gene-disease association prediction
Journal of Biomedical Semantics - Onorati, Dario, et al.
The Dark Side of the Language: Syntax-Based Neural Networks Rivaling Transformers in Definitely Unseen Sentences
2023 IEEE/WIC International Conference on Web Intelligence and Intelligent Agent Technology - Pesquita, Catia et al.
Results of the Ontology Alignment Evaluation Initiative 2023
18th International Workshop on Ontology Matching - Séraudie, Irinka, Catherine Pillet, Beatrice Cesana, Pauline Bazelle, Florian Jeanneret, Bertrand Evrard, Frédéric Chalmel, Assilah Bouzit, Christophe Battail, Jean-Alexandre Long, Jean Luc Descotes, Claude Cochet, and Odile Filhol
A new scaffold-free tumoroid model provides a robust preclinical tool to investigate invasion and drug response in Renal Cell Carcinoma
Cell Death & Disease (14) 622 - Shlianin, Vladyslav, Yuri Gordienko and Sergii Stirenko
Link Prediction Method in Graph Objects by Auto Encoding in Graph Neural Networks
Modern Machine Learning Technologies and Data Science Workshop MoMLeT&DS 2022. Leiden, The Netherlands, November 25-26, 2022. - Shulha, Maksym, Yuri Gordienko, and Sergii Stirenko
Deep Learning with Metadata Augmentation for Classification of Diabetic Retinopathy Level
Proceedings of Third International Conference on Sustainable Expert Systems . Lecture Notes in Networks and Systems, vol 587. Springer, Singapore. - Shulha, Maksym, Yuri Gordienko, and Sergii Stirenko
Impact of Multimodal Model Complexity on Classification of Diabetic Retinopathy Level
Computational Intelligence, Data Analytics and Applications. ICCIDA 2022. Lecture Notes in Networks and Systems, vol 643. Springer, Cham. - Silva, Marta Contreiras, Daniel Faria, and Catia Pesquita
Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine
ESWC 2022, May 29 - June 2, Hersonisoss, Greece. - Statkevych, Roman , Yuri Gordienko, and Sergii Stirenko
Expansion Rate Parametrization and K-Fold Based Inference with U-Net Neural Networks for Multiclass Medical Image Segmentation
Lecture Notes in Computer Science, vol 14125 - Tomko, Maryna et al.
Multi-label Classification of Cervix Types with Image Size Optimization for Cervical Cancer Prescreening by Deep Learning
Inventive Computation and Information Technologies. Lecture Notes in Networks and Systems, vol 563. Springer, Singapore. - Traversa Pietro, Guilherme Ferraz de Arruda, Alexei Vazquez, and Yamir Moreno
Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs
Entropy 2023, 25(11), 1537. - Wölfein, Georg, In Hwa Um, David Harrison, and Ognjen Arandjelovic
HoechstGAN: Virtual Lymphocyte Staining Using Generative Adversarial Networks
IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) 2023, https://wacv2023.thecvf.com/. - Wölflein, Georg, In Hwa Um, David J. Harrison, and Ognjen Arandjelović
Whole-Slide Images and Patches of Clear Cell Renal Cell Carcinoma Tissue Sections Counterstained with Hoechst 33342, CD3, and CD8 Using Multiple Immunofluorescence
Data. 2023; 8(2):40. - Zickuhr, Greice M., In Hwa Um, Alexander Laird, David J Harrison, and Alison L Dickson
Spatial Metabolomics co-registered with Multiplex Phenotyping for the Evaluation of Human Kidney Tissue
BioRxiv
2022
- Bedran, Georges, Tongjie Wang, Dominika Pankanin, et al.
A comprehensive library of canonical and non-canonical MHC class I antigens for cancer vaccine development
Biorxiv. - Contreiras Silva, Marta, Patrícia Eugénio, Daniel Faria, and Catia Pesquita
Ontologies and Knowledge Graphs in Oncology Research
Cancers 14 (8), 1906. - Contreiras Silva, Marta, Daniel Faria and Catia Pesquita
Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine
ESWC 2022, May 29 - June 2, Hersonisson (GR). - Contreiras Silva, Marta, Daniel Faria and Catia Pesquita
Extending AgreementMakerLight to Perform Holistic Ontology Matching
ESWC 2022, May 29 - June 2, Hersonisson (GR). - De Filippis, Raffaele et al.
Use of High-Plex Data Reveals Novel Insights into the Tumour Microenvironment of Clear Cell Renal Cell Carcinoma
Cancers 14 (21), 5387. - Gordienko, Nikita, Oleksandr Rokovyi, Yuri Gordienko, Sergii Stirenko
Hybrid Convolutional, Recurrent and Attention-Based Architectures of Deep Neural Networks for Classification of Human-Computer Interaction by Electroencephalography
Gordienko, N., Rokovyi, O., Gordienko, Y., Stirenko, S. (2022). Hybrid Convolutional, Recurrent and Attention-Based Architectures of Deep Neural Networks for Classification of Human-Computer Interaction by Electroencephalography. In: Kurosu, M., et al. HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments. HCII 2022. Lecture Notes in Computer Science, vol 13519, pp 453-468. Springer: Cham. - Kostiukevych, Kostiantyn, Yuri Gordienko, Nikita Gordienko, Oleksandr Rokovyi, and Sergii Stirenko
Hierarchy of Hybrid Deep Neural Networks for Physical Action Classification by Brain-Computer Interface
Modern Machine Learning Technologies and Data Science Workshop MoMLeT&DS 2022. Leiden, The Netherlands, November 25-26, 2022. - Oholtsov, Illia, Yuri Gordienko, and Sergii Stirenko
Effect of Small Dataset Quality on Deep Neural Network Performance for Lyme Disease Classification
In: Ranganathan, G., Fernando, X., Piramuthu, S. (eds) Soft Computing for Security Applications. Advances in Intelligent Systems and Computing, vol 1428, pp 561-573. Springer, Singapore. - Shlianin, Vladyslav, Yuri Gordienko, and Sergii Stirenko
Link Prediction Method in Graph Objects by Auto Encoding in Graph Neural Networks
Modern Machine Learning Technologies and Data Science Workshop MoMLeT&DS 2022. Leiden, The Netherlands, November 25-26, 2022. - Statkevych, Roman, Yuri Gordienko, Sergii Stirenko
Improving U-Net Kidney Glomerulus Segmentation with Fine-Tuning, Dataset Randomization and Augmentations
In: Hu, Z., Dychka, I., Petoukhov, S., He, M. (eds) Advances in Computer Science for Engineering and Education. ICCSEEA 2022. Lecture Notes on Data Engineering and Communications Technologies, vol 134. pp. 488-498. Springer, Cham. - Yakimenko, Yurii, Sergii Stirenko, Dimitri Koroliouk, Yuri Gordienko, and Fabio Massimo Zanzotto
Implementation of Personalized Medicine by Artificial Intelligence Platform
In: Ranganathan, G., Fernando, X., Piramuthu, S. (eds) Soft Computing for Security Applications. Advances in Intelligent Systems and Computing, vol 1428, pp 597-611. Springer, Singapore.
2021
- Doms, Volodymyr, Yuri Gordienko, Yuriy Kochura, Oleksandr Rokovyi, Oleg Alienin, Sergii Stirenko
Deep Learning for Melanoma Detection with Testing Time Data Augmentation
In: Lecture Notes on Data Engineering and Communications Technologies Advances in Artificial Systems for Logistics Engineering, pp 131-140. Cham: Springer International Publishing. - Guerreiro, Ana, Catia Pesquita, and Daniel Faria
VOWLMap: Graph-based Ontology Alignment Visualization and Editing
CEUR Workshop Proceedings 2980. - Lima, Beatriz, Daniel Faria, and Catia Pesquita
Pattern-Guided Association Rule Mining for Complex Ontology Alignment
CEUR Workshop Proceedings 2980. - Pesquita, Catia et al.
Results of the Ontology Alignment Evaluation Initiative 2021
CEUR Workshop Proceedings 3061.