Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity

Microenvironment of metastasis reveals key predictors of PD-1 blockade response in renal cell carcinoma

Autori: Florian Jeanneret, 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
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.17.548676

Injecting domain knowledge into graph neural networks for protein-protein interactions

Autori: Laura Balbi, Rita Sousa, Pedro Cotovio, Catia Pesquita
Pubblicato in: 2024
Editore: Research Square Platform LLC
DOI: 10.21203/rs.3.rs-4228413/v1

Leveraging Knowledge for Explainable AI in Personalized Cancer Treatment: Challenges and Future Directions

Autori: Daghir-Wojtkowiak, Emilia; Alfaro, Javier; Mastromattei, Michele; Palkowski, Aleksander; Stares, Mark; Roca-Umbert, Ana; Krajnc, Andraž; Leoni, Riccardo; Boland, Anne; Nourbakhsh, Aria; Kallor, Ashwin Adrian; Ducki, Camille; Venditti, Davide; Montesano, Carla; Cipriani, Chiara; Faria, Daniel; PFLIEGER, Delphine; Zago, Elisa; Bardet, Etienne; Serrano, Filipa; Jeanneret, Florian; Alouges, Damien; L
Pubblicato in: Numero 1, 2025
Editore: Zenodo
DOI: 10.5281/zenodo.14643248

Spatial Mass Spectrometry with Whole Slide Multiplex Immunofluorescence in Clear Cell Renal Cell Carcinoma

Autori: Greice Michele Zickuhr, In Hwa Um, Alexander Laird, David J. Harrison, Alison L. Dickson
Pubblicato in: BioStudies Database, 2024
Editore: EMBL-EBI
DOI: 10.6019/s-biad1346

Expanding the definition of MHC Class I peptide binding promiscuity to support vaccine discovery across cancers with CARMEN

Autori: Michal Mateusz 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, null null, Ashita Singh, Theodore Hupp, Christophe Battail, Alexander Laird, Catia Pesquita, Luis Zapata, Stefan N. Symeonides, Ajitha Rajan, Fabio Massimo Zanzotto, Javier A
Pubblicato in: 2025
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.05.08.651510

Microenvironment of metastatic site reveals key predictors of PD-1 blockade response in renal cell carcinoma

Autori: Jeanneret, Florian; Bazelle, Pauline; Schoch, Sarah; Pillet, Catherine; Um, In Hwa; Bouzit, Assilah; Evrard, Bertrand; Seffar, Evan; Chalmel, Frédéric; Alfaro, Javier Antonio; Pesquita, Catia; Massimo Zanzotto, Fabio; Stares, Mark; Symeonides, Stefan; Laird, Alexander; Long, Jean Alexandre; Descotes, Jean Luc; Pflieger, Delphine; Harrison, David; Filhol, Odile; Axelson, Håkan; Battail, Christop
Pubblicato in: Numero 1, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8214477

Long-read Spatial Transcriptomic Profiling of Patient-derived ccRCC Tumoroids Reveals Heterogeneity in Isoform and Gene Expression

Autori: Mustafa Elshani, Hazem Abdullah, Ying Zhang, Alexander Laird, Peter Mullen, David J. Harrison
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.10.16.618643

A comprehensive library of canonical and non-canonical MHC class I antigens for cancer vaccine development

Autori: Georges Bedran, Tongjie Wang, Dominika Pankanin, et al.
Pubblicato in: bioRxiv, 2022
Editore: bioRxiv
DOI: 10.1101/2022.01.13.475872

Spatial Metabolomics co-registered with Multiplex Phenotyping for the Evaluation of Human Kidney Tissue

Autori: Greice M Zickuhr, In Hwa Um, Alexander Laird, David J Harrison, Alison L Dickson
Pubblicato in: bioRxiv 2023.11.10.566529, 2023
Editore: bioRxiv
DOI: 10.1101/2023.11.10.566529

Clear Cell Renal Cell Carcinoma Patient-Derived Tumoroids characterisation by Spatial Mass Spectrometry, Histology and Multiplex Immunofluorescence

Autori: Greice Michele Zickuhr, Hazem Abdullah, In Hwa Um, Alexander Laird, Peter Mullen, David J. Harrison, Alison L. Dickson
Pubblicato in: BioStudies Database, 2025
Editore: EMBL-EBI
DOI: 10.6019/s-biad1661

A Systematic Evaluation of Knowledge Graph Embeddings for Gene-Disease Association Prediction

Autori: Catarina Canastra, Cátia Pesquita
Pubblicato in: 2025
Editore: Cornell University
DOI: 10.48550/arxiv.2504.08445

Neuro-Symbolic AI in Life Sciences

Autori: Robert Hoehndorf, Catia Pesquita, Fernando Zhapa-Camacho
Pubblicato in: Frontiers in Artificial Intelligence and Applications, Handbook on Neurosymbolic AI and Knowledge Graphs, 2025
Editore: IOS Press
DOI: 10.3233/faia250239

Deep Learning with Metadata Augmentation for Classification of Diabetic Retinopathy Level

Autori: Shulha, M., Gordienko, Y., Stirenko, S.
Pubblicato in: Proceedings of Third International Conference on Sustainable Expert Systems . Lecture Notes in Networks and Systems, 2023, Pagina/e 613–630, ISBN 978-981-19-7873-9
Editore: Springer

Multi-label Classification of Cervix Types with Image Size Optimization for Cervical Cancer Prescreening by Deep Learning

Autori: Tomko, M., Pavliuchenko, M., Pavliuchenko, I., Gordienko, Y., Stirenko, S.
Pubblicato in: Inventive Computation and Information Technologies. Lecture Notes in Networks and Systems, Numero vol 563, 2023, Pagina/e 885–902, ISBN 978-981-19-7401-4
Editore: Springer

Consent and Retrospective Data Collection

Autori: Anwana, T.O., Barud, K., Cepic, M., Johnson, E., Königseder, M., Wagner, MC
Pubblicato in: The Law and Ethics of Data Sharing in Health Sciences, 2023, Pagina/e 99–125, ISBN 978-981-99-6539-7
Editore: Springer
DOI: 10.1007/978-981-99-6540-3_7

Improving U-Net Kidney Glomerulus Segmentation with Fine-Tuning, Dataset Randomization and Augmentations

Autori: Statkevych, R., Gordienko, Y., Stirenko, S.
Pubblicato in: Advances in Computer Science for Engineering and Education. ICCSEEA 2022. Lecture Notes on Data Engineering and Communications Technologies, Numero vol 134, 2022, Pagina/e 488–498, ISBN 978-3-031-04811-1
Editore: Springer
DOI: 10.1007/978-3-031-04812-8_42

Expansion Rate Parametrization and K-Fold Based Inference with U-Net Neural Networks for Multiclass Medical Image Segmentation

Autori: Statkevych, R., Gordienko, Y., Stirenko, S.
Pubblicato in: Artificial Intelligence and Soft Computing. ICAISC 2023. Lecture Notes in Computer Science, Numero vol 14125, 2023, Pagina/e 251–262, ISBN 978-3-031-42504-2
Editore: Springer
DOI: 10.1007/978-3-031-42505-9_22

Implementation of Personalized Medicine by Artificial Intelligence Platform

Autori: Yakimenko, Y., Stirenko, S., Koroliouk, D., Gordienko, Y., Zanzotto, F.M.
Pubblicato in: Soft Computing for Security Applications. Advances in Intelligent Systems and Computing, Numero vol 1428, 2022, Pagina/e 597–611, ISBN 978-981-19-3589-3
Editore: Springer
DOI: 10.1007/978-981-19-3590-9_46

Ensemble Knowledge Distillation for Edge Intelligence in Medical Applications

Autori: Gordienko, Y. et al.
Pubblicato in: Advancements in Knowledge Distillation: Towards New Horizons of Intelligent Systems. Studies in Computational Intelligence, Numero vol 1100, 2023, Pagina/e 135–168, ISBN 978-3-031-32094-1
Editore: Springer
DOI: 10.1007/978-3-031-32095-8_5

Impact of Multimodal Model Complexity on Classification of Diabetic Retinopathy Level

Autori: Shulha, M., Gordienko, Y., Stirenko, S.
Pubblicato in: Computational Intelligence, Data Analytics and Applications. ICCIDA 2022. Lecture Notes in Networks and Systems, Numero vol 643, 2023, Pagina/e 168–180, ISBN 978-3-031-27098-7
Editore: Springer

Hybrid Neural Networks for Medical Image Classification

Autori: Arsenii Khmelnytskyi, Sergii Stirenko, Yuri Gordienko
Pubblicato in: Information Systems Engineering and Management, Proceedings of 4th International Conference on Artificial Intelligence and Smart Energy, 2024, Pagina/e 462-474
Editore: Springer Nature Switzerland
DOI: 10.1007/978-3-031-61471-2_35

Multimodal Metadata Augmentation for Federated Learning in Medical Applications

Autori: Yuri Gordienko, Maksym Shulha, Yuriy Kochura, Oleksandr Rokovyi, Vladyslav Taran, Oleg Alienin, Sergii Stirenko
Pubblicato in: Lecture Notes in Networks and Systems, Proceedings of Ninth International Congress on Information and Communication Technology, 2024, Pagina/e 537-547
Editore: Springer Nature Singapore
DOI: 10.1007/978-981-97-3299-9_43

VOWLMap: graph-based ontology alignment visualization and editing

Autori: Ana Guerreiro, Catia Pesquita, and Daniel Faria
Pubblicato in: International Semantic Web Conference (ISWC) 2021: Posters, Demos, and Industry Tracks., Numero Vol-2980, 2021
Editore: CEUR Workshop Proceedings

Hierarchy of Hybrid Deep Neural Networks for Physical Action Classification by Brain-Computer Interface

Autori: Kostiantyn Kostiukevych, Yuri Gordienko, Nikita Gordienko, Oleksandr Rokovyi, and Sergii Stirenko
Pubblicato in: MoMLeT+DS 2022: 4th International Workshop on Modern Machine Learning Technologies and Data Science, 2023
Editore: CEUR Workshop Proceedings

Results of the Ontology Alignment Evaluation Initiative 2021

Autori: Abd Nikooie Pour, Mina; Algergawy, Alsayed; Amardeilh, Florence; Amini, Reihaneh; Fallatah, Omaima; Faria, Daniel; Fundulaki, Irini; Harrow, Ian; Hertling, Sven; Hitzler, Pascal; Huschka, Martin; Ibanescu, Liliana; Jiménez-Ruiz, Ernesto; Karam, Naouel; Laadhar, Amir; Lambrix, Patrick; Li, Huanyu; Li, Ying; Michel, Franck; Nasr, Engy; Paulheim, Heiko; Pesquita, Catia; Portisch, Jan; Roussey, Cathe
Pubblicato in: Pour, M A N, Algergawy, A, Amardeilh, F, Amini, R, Fallatah, O, Faria, D, Fundulaki, I, Harrow, I, Hertling, S, Hitzler, P, Huschka, M, Ibanescu, L, Jiḿenez-Ruiz, E, Karam, N, Laadhar, A, Lambrix, P, Li, H, Li, Y, Michel, F, Nasr, E, Paulheim, H, Pesquita, C, Portisch, J, Roussey, C, Saveta, T, Shvaiko, P, Splendiani, A, Trojahn, Ć, Vatǎšcinova, J, Yaman, B, Zamaza, O & Zhou, L 2021, 'Results, Numero 1, 2021
Editore: CEUR Workshop Proceedings

Results of the Ontology Alignment Evaluation Initiative 2024

Autori: Pour, Mina Abd Nikooie; Algergawy, Alsayed; Blomqvist, Eva; Buche, Patrice; Chen, Jiaoyan; Cotovio, Pedro Giesteira; Coulet, Adrien; Cufi, Julien; Dong, Hang; Faria, Daniel; Ferraz, Lucas; Hertling, Sven; He, Yuan; Horrocks, Ian; Ibanescu, Liliana; Jain, Dr Sarika; Jiménez-Ruiz, Ernesto; Karam, Naouel; Kraus, Felix; Lambrix, Patrick; Li, Huanyu; Li, Ying; Monnin, Pierre; Paulheim, Heiko; Pesquita
Pubblicato in: ISSN: 1613-0073, Numero 1, 2024
Editore: 19th International Workshop on Ontology Matching
DOI: 10.5445/ir/1000179469

HoechstGAN: Virtual Lymphocyte Staining Using Generative Adversarial Networks

Autori: Georg Wölflein, In Hwa Um, David J Harrison, Ognjen Arandjelović
Pubblicato in: 2023
Editore: arxiv
DOI: 10.48550/arxiv.2210.06909

Extending agreementmakerlight to perform holistic ontology matching

Autori: Marta Contreiras Silva, Daniel Faria, and Catia Pesquit
Pubblicato in: 2022
Editore: LASIGE, Faculdade de Ciˆencias da Universidade de Lisboa, Portugal

Digital health innovations - Good practice guide for obtaining consent for the use of personal health information for research and innovations

Autori: Barud, Katarzyna et al.
Pubblicato in: CEN Workshop Agreement 17933, 2023
Editore: CEN

KATY — Knowledge At the Tip of Your fingers: Clinical Knowledge for Humanity

Autori: Silva, Marta C.; Nunes, Susana; Balbi, Laura; Rodrigues, Ana Filipa; Pesquita, Catia
Pubblicato in: Numero 1, 2025
Editore: ESWC Project Networking
DOI: 10.5281/zenodo.15609794

Pattern-Guided Association Rule Mining for Complex Ontology Alignment

Autori: Beatriz Lima, Daniel Faria, and Catia Pesquita
Pubblicato in: International Semantic Web Conference (ISWC) 2021: Posters, Demos, and Industry Tracks, Numero Vol-2980, 2021
Editore: CEUR Workshop Proceedings

Hybrid Convolutional, Recurrent and Attention-Based Architectures of Deep Neural Networks for Classification of Human-Computer Interaction by Electroencephalography

Autori: Gordienko, Nikita, Oleksandr Rokovyi, Yuri Gordienko, and Sergii Stirenko
Pubblicato in: 2022
Editore: Springer

Results of the ontology alignment evaluation initiative 2023

Autori: Pour, Mina Abd Nikooie; Algergawy, Alsayed; Buche, Patrice; Castro, Leyla Jael; Chen, Jiaoyan; Coulet, Adrien; Cufi, Julien; Dong, Hang; Fallatah, Omaima; Faria, Daniel; Fundulaki, Irini; Hertling, Sven; He, Yuan; Horrocks, Ian; Huschka, Martin; Ibanescu, Liliana; Jain, Dr Sarika; Jiménez-Ruiz, Ernesto; Karam, Naouel; Lambrix, Patrick; Li, Huanyu; Li, Ying; Monnin, Pierre; Nasr, Engy; Paulheim, H
Pubblicato in: 18th International Workshop on Ontology Matching (OM 2023), Numero 1, 2023
Editore: INRIA.HAL.SCIENCE Web Portal

Link Prediction Method in Graph Objects by Auto Encoding in Graph Neural Networks

Autori: Vladyslav Shlianin, Yuri Gordienko, and Sergii Stirenko1
Pubblicato in: 2023
Editore: CEUR Workshop Proceedings

Matching Multiple Ontologies to Build aKnowledge Graph for Personalized Medicine

Autori: Marta Contreiras Silva , Daniel Faria, and Catia Pesquit
Pubblicato in: 2023
Editore: LASIGE, Faculdade de Ciˆencias da Universidade de Lisboa, Portugal

Home HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments Conference paperHybrid Convolutional, Recurrent and Attention-Based Architectures of Deep Neural Networks for Classification of Human-Computer Interaction by Electroencephalography

Autori: Nikita Gordienko, Oleksandr Rokovyi, Yuri Gordienko & Sergii Stirenko
Pubblicato in: HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments, Numero 1, 2022
Editore: Springer Nature Link

Home HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments Conference paperHybrid Convolutional, Recurrent and Attention-Based Architectures of Deep Neural Networks for Classification of Human-Computer Interaction by Electroencephalography

Autori: Nikita Gordienko, Oleksandr Rokovyi, Yuri Gordienko & Sergii Stirenko
Pubblicato in: HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments, 2022, Pagina/e 453–468, ISBN 978-3-031-17617-3
Editore: Springer
DOI: 10.1007/978-3-031-17618-0_32

Hierarchy of Hybrid Deep Neural Networks for Physical Action Classification by Brain-Computer Interface

Autori: Kostiantyn Kostiukevych, Yuri Gordienko, Nikita Gordienko, Oleksandr Rokovyi, and Sergii Stirenko
Pubblicato in: 2022
Editore: CEUR Workshop Proceedings

Effect of Small Dataset Quality on Deep Neural Network Performance for Lyme Disease Classification

Autori: Oholtsov, I., Gordienko, Y., Stirenko, S
Pubblicato in: Soft Computing for Security Applications. Advances in Intelligent Systems and Computing, Numero vol 1428, 2022, Pagina/e 561–573, ISBN 978-981-19-3589-3
Editore: Springer

The Dark Side of the Language: Syntax-Based Neural Networks Rivaling Transformers in Definitely Unseen Sentences

Autori: Dario Onorati, Leonardo Ranaldi, Aria Nourbakhsh, Arianna Patrizi, Elena Sofia Ruzzetti, Michele Mastromattei, Francesca Fallucchi, Fabio Massimo Zanzotto
Pubblicato in: 2023 IEEE International Conference on Web Intelligence and Intelligent Agent Technology (WI-IAT), 2024, Pagina/e 111-118
Editore: IEEE
DOI: 10.1109/wi-iat59888.2023.00021

Link Prediction Method in Graph Objects by Auto Encoding in Graph Neural Networks

Autori: Vladyslav Shlianin, Yuri Gordienko, and Sergii Stirenko
Pubblicato in: 2022
Editore: ISSN 1613-0073 CEUR Workshop Proceedings

Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine

Autori: Marta Contreiras Silva, Daniel Faria, and Catia Pesquit
Pubblicato in: 2022
Editore: LASIGE, Faculdade de Ciencias da Universidade de Lisboa, Portugal

Targeting MYC induces lipid droplet accumulation by upregulation of HILPDA in clear cell renal cell carcinoma

Autori: Lourdes Sainero-Alcolado, 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 121, 2024, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2310479121

Drug recommendation ranking for personalized medicine using outcomes of retrospective cancer patients

Autori: Noemi Scarpato, Silvia Riondino, Aria Nourbakhsh, Mario Roselli, Patrizia Ferroni, Fiorella Guadagni, Fabio Massimo Zanzotto
Pubblicato in: Expert Systems with Applications, Numero 256, 2024, Pagina/e 124859, ISSN 0957-4174
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.eswa.2024.124859

Whole-Slide Images and Patches of Clear Cell Renal Cell Carcinoma Tissue Sections Counterstained with Hoechst 33342, CD3, and CD8 Using Multiple Immunofluorescence

Autori: Wölflein, G.; Um, I.H.; Harrison, D.J.; Arandjelović, O.
Pubblicato in: Data, Numero 8, 40, 2023, ISSN 2306-5729
Editore: MDPI
DOI: 10.3390/data8020040

Up-regulation of Cuproptosis-related lncRNAS in Patients Receiving Immunotherapy for Metastatic Clear Cell Renal Cell Carcinoma Indicates Progressive Disease

Autori: HECTOR KATIFELIS, STAMATIKI GRAMMATIKAKI, ROUBINI ZAKOPOULOU, ARISTOTELIS BAMIAS, MICHALIS V. KARAMOUZIS, KONSTANTINOS STRAVODIMOS, MARIA GAZOULI
Pubblicato in: In Vivo, Numero 39, 2025, Pagina/e 146-151, ISSN 0258-851X
Editore: International Institute of Anticancer Research
DOI: 10.21873/invivo.13812

Effect of natural and synthetic noise data augmentation on physical action classification by brain–computer interface and deep learning

Autori: Yuri Gordienko, Nikita Gordienko, Vladyslav Taran, Anis Rojbi, Sergii Telenyk, Sergii Stirenko
Pubblicato in: Frontiers in Neuroinformatics, Numero 19, 2025, ISSN 1662-5196
Editore: Frontiers Research Foundation
DOI: 10.3389/fninf.2025.1521805

Multi-domain knowledge graph embeddings for gene-disease association prediction

Autori: Susana Nunes, Rita T. Sousa, Catia Pesquita
Pubblicato in: Journal of Biomedical Semantics, Numero 14, 2023, ISSN 2041-1480
Editore: Springer Science and Business Media LLC
DOI: 10.1186/s13326-023-00291-x

Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy

Autori: Christopher C. T. Sng, Ashwin Adrian Kallor, Benjamin S. Simpson, Georges Bedran, Javier Alfaro, Kevin Litchfield
Pubblicato in: Frontiers in Immunology, Numero 15, 2024, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/fimmu.2024.1347542

Explaining protein–protein interactions with knowledge graph-based semantic similarity

Autori: Rita T. Sousa, Sara Silva, Catia Pesquita
Pubblicato in: Computers in Biology and Medicine, Numero 170, 2024, Pagina/e 108076, ISSN 0010-4825
Editore: Pergamon Press Ltd.
DOI: 10.1016/j.compbiomed.2024.108076

A new scaffold-free tumoroid model provides a robust preclinical tool to investigate invasion and drug response in Renal Cell Carcinoma

Autori: Irinka Séraudie, Catherine Pillet, Beatrice Cesana, Pauline Bazelle, Florian Jeanneret, Bertrand Evrard, Frédéric Chalmel, Assilah Bouzit, Christophe Battail, Jean-Alexandre Long, Jean Luc Descotes, Claude Cochet, Odile Filhol
Pubblicato in: Cell Death & Disease, Numero 14, 2023, ISSN 2041-4889
Editore: Nature Publishing Group
DOI: 10.1038/s41419-023-06133-z

MAPLE: metadata-driven orchestration of ontology matching

Autori: Manuel Fiorelli, Armando Stellato, Tiziano Lorenzetti
Pubblicato in: International Journal of Metadata, Semantics and Ontologies, Numero 17, 2025, Pagina/e 18-39, ISSN 1744-2621
Editore: Inderscience Enterprises
DOI: 10.1504/ijmso.2024.145508

Plant miRNAs for Improved Gene Regulation in a Wide Range of Human Cancers

Autori: Maksym Zoziuk, Vittorio Colizzi, Pavlo Krysenko, Maurizio Mattei, Roberta Bernardini, Fabio Massimo Zanzotto, Stefano Marini, Dmitri Koroliouk
Pubblicato in: Current Numeros in Molecular Biology, Numero 47, 2025, Pagina/e 42, ISSN 1467-3045
Editore: MDPI AG
DOI: 10.3390/cimb47010042

Transcription Factor NFE2L1 Decreases in Glomerulonephropathies after Podocyte Damage

Autori: Elshani, M.; Um, I.H.; Leung, S.; Reynolds, P.A.; Chapman, A.; Kudsy, M.; Harrison, D.J.
Pubblicato in: Cells, Numero 12(17), 2165, 2023, ISSN 2073-4409
Editore: MDPI
DOI: 10.3390/cells12172165

Sample-specific network analysis identifies gene co-expression patterns of immunotherapy response in clear cell renal cell carcinoma

Autori: Liangwei Yin, Pietro Traversa, Mohamed Elati, Yamir Moreno, Natalia Marek-Trzonkowska, Christophe Battail
Pubblicato in: iScience, Numero 28, 2025, Pagina/e 113061, ISSN 2589-0042
Editore: Elsevier BV
DOI: 10.1016/j.isci.2025.113061

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

Autori: Greice M. Zickuhr, In Hwa Um, Alexander Laird, David J. Harrison, Alison L. Dickson
Pubblicato in: Analytical and Bioanalytical Chemistry, Numero 416, 2024, Pagina/e 4015-4028, ISSN 1618-2642
Editore: Springer Verlag
DOI: 10.1007/s00216-024-05339-0

Unraveling the glycosylated immunopeptidome with HLA-Glyco

Autori: Bedran, G., Polasky, D.A., Hsiao, Y. et al.
Pubblicato in: Nature Communications, Numero 14, 3461, 2023, ISSN 2041-1723
Editore: Nature Publishing Group

Cancer selective cell death induction by a bivalent CK2 inhibitor targeting the ATP site and the allosteric αD pocket

Autori: Alexandre Bancet, 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
Pubblicato in: iScience, Numero 27, 2025, Pagina/e 108903, ISSN 2589-0042
Editore: Elsevier BV
DOI: 10.1016/j.isci.2024.108903

Evaluating Explainable Machine Learning Models for Clinicians

Autori: Noemi Scarpato, Aria Nourbakhsh, Patrizia Ferroni, Silvia Riondino, Mario Roselli, Francesca Fallucchi, Piero Barbanti, Fiorella Guadagni, Fabio Massimo Zanzotto
Pubblicato in: Cognitive Computation, Numero 16, 2024, Pagina/e 1436-1446, ISSN 1866-9956
Editore: Springer Verlag
DOI: 10.1007/s12559-024-10297-x

Ontologies and Knowledge Graphs in Oncology Research

Autori: Silva, Marta Contreiras, Patrícia Eugénio, Daniel Faria, and Catia Pesquita
Pubblicato in: Cancers 2022, Numero 14(8), 1906, 2022, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14081906

An Overview of Epigenetics in Clear Cell Renal Cell Carcinoma

Autori: STAMATIKI GRAMMATIKAKI, HECTOR KATIFELIS, AMMAD AHMAD FAROOQI, KONSTANTINOS STRAVODIMOS, MICHALIS V. KARAMOUZIS, KYRIAKOS SOULIOTIS, DIMITRIOS VARVARAS and MARIA GAZOULI
Pubblicato in: In Vivo, Numero 37 (1) 1-10, 2023, ISSN 0258-851X
Editore: International Institute of Anticancer Research
DOI: 10.21873/invivo.13049

The Role of HIF1-related Genes and Non-coding RNAs Expression in Clear Cell Renal Cell Carcinoma

Autori: STAMATIKI GRAMMATIKAKI, HECTOR KATIFELIS, KONSTANTINOS STRAVODIMOS, EMMANOUIL BAKOLAS, NIKOLAOS KAVANTZAS, DIMITRA GRIGORIADOU, MARIA GAZOULI
Pubblicato in: In Vivo, Numero 37 (3) 1103-1110, 2023, ISSN 0258-851X
Editore: International Institute of Anticancer Research
DOI: 10.21873/invivo.13185

Prompting is not all you need Evaluating GPT-4 performance on a real-world ontology alignment use case

Autori: Giulio Macilenti, Armando Stellato, Manuel Fiorelli
Pubblicato in: Procedia Computer Science, Numero 246, 2025, Pagina/e 1289-1298, ISSN 1877-0509
Editore: Elsevier BV
DOI: 10.1016/j.procs.2024.09.557

The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides

Autori: Georges Bedran, 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, Jav
Pubblicato in: Cancer Immunology Research, Numero 11, 2023, Pagina/e 747-762, ISSN 2326-6066
Editore: American Association for Cancer Research Inc.
DOI: 10.1158/2326-6066.cir-22-0621

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

Autori: Dovrolis, N.; Katifelis, H.; Grammatikaki, S.; Zakopoulou, R.; Bamias, A.; Karamouzis, M.V.; Souliotis, K.; Gazouli, M.
Pubblicato in: Cancers, Numero 15(23), 5637, 2023, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers15235637

Use of High-Plex Data Reveals Novel Insights into the Tumour Microenvironment of Clear Cell Renal Cell Carcinoma

Autori: De Filippis R, Wölflein G, Um IH, Caie PD, Warren S, White A, Suen E, To E, Arandjelović O, Harrison DJ
Pubblicato in: Cancers, Numero Cancers 14, no. 21: 5387, 2022, ISSN 2072-6694
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14215387

The Immunopeptidomics Ontology (ImPO)

Autori: Daniel Faria, Patrícia Eugénio, Marta Contreiras Silva, Laura Balbi, Georges Bedran, Ashwin Adrian Kallor, Susana Nunes, Aleksander Palkowski, Michal Waleron, Javier A Alfaro, Catia Pesquita
Pubblicato in: Database, Numero 2024, 2024, ISSN 1758-0463
Editore: Oxford University Press
DOI: 10.1093/database/baae014

Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs

Autori: Traversa, P.; Ferraz de Arruda, G.; Vazquez, A.; Moreno, Y.
Pubblicato in: Entropy, Numero 25, 1537, 2023, ISSN 1099-4300
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e25111537

Comparing link prediction and classification for Gene-Disease association discovery

Autori: Canastra, Catarina Salema
Pubblicato in: Numero 3, 2024
Editore: Universidade de Lisboa

Explaining Predictions from Node Classification with Knowledge Graph Embeddings

Autori: Paulino, Filipe José Bastos Benvindo
Pubblicato in: Numero 1, 2024
Editore: Universidade de lisboa

Boosting graph neural networks with knowledge for personalized medicine

Autori: Bernardino, Beatriz de Campos
Pubblicato in: Numero 1, 2025
Editore: Universidade de Lisboa

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