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

Autores: 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
Publicado en: 2024
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.07.17.548676

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

Autores: Laura Balbi, Rita Sousa, Pedro Cotovio, Catia Pesquita
Publicado en: 2024
Editor: 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

Autores: 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
Publicado en: Edición 1, 2025
Editor: Zenodo
DOI: 10.5281/zenodo.14643248

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

Autores: Greice Michele Zickuhr, In Hwa Um, Alexander Laird, David J. Harrison, Alison L. Dickson
Publicado en: BioStudies Database, 2024
Editor: 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

Autores: 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
Publicado en: 2025
Editor: 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

Autores: 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
Publicado en: Edición 1, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8214477

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

Autores: Mustafa Elshani, Hazem Abdullah, Ying Zhang, Alexander Laird, Peter Mullen, David J. Harrison
Publicado en: 2024
Editor: 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

Autores: Georges Bedran, Tongjie Wang, Dominika Pankanin, et al.
Publicado en: bioRxiv, 2022
Editor: bioRxiv
DOI: 10.1101/2022.01.13.475872

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

Autores: Greice M Zickuhr, In Hwa Um, Alexander Laird, David J Harrison, Alison L Dickson
Publicado en: bioRxiv 2023.11.10.566529, 2023
Editor: 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

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

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

Autores: Catarina Canastra, Cátia Pesquita
Publicado en: 2025
Editor: Cornell University
DOI: 10.48550/arxiv.2504.08445

Neuro-Symbolic AI in Life Sciences

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

Deep Learning with Metadata Augmentation for Classification of Diabetic Retinopathy Level

Autores: Shulha, M., Gordienko, Y., Stirenko, S.
Publicado en: Proceedings of Third International Conference on Sustainable Expert Systems . Lecture Notes in Networks and Systems, 2023, Página(s) 613–630, ISBN 978-981-19-7873-9
Editor: Springer

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

Autores: Tomko, M., Pavliuchenko, M., Pavliuchenko, I., Gordienko, Y., Stirenko, S.
Publicado en: Inventive Computation and Information Technologies. Lecture Notes in Networks and Systems, Edición vol 563, 2023, Página(s) 885–902, ISBN 978-981-19-7401-4
Editor: Springer

Consent and Retrospective Data Collection

Autores: Anwana, T.O., Barud, K., Cepic, M., Johnson, E., Königseder, M., Wagner, MC
Publicado en: The Law and Ethics of Data Sharing in Health Sciences, 2023, Página(s) 99–125, ISBN 978-981-99-6539-7
Editor: Springer
DOI: 10.1007/978-981-99-6540-3_7

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

Autores: Statkevych, R., Gordienko, Y., Stirenko, S.
Publicado en: Advances in Computer Science for Engineering and Education. ICCSEEA 2022. Lecture Notes on Data Engineering and Communications Technologies, Edición vol 134, 2022, Página(s) 488–498, ISBN 978-3-031-04811-1
Editor: 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

Autores: Statkevych, R., Gordienko, Y., Stirenko, S.
Publicado en: Artificial Intelligence and Soft Computing. ICAISC 2023. Lecture Notes in Computer Science, Edición vol 14125, 2023, Página(s) 251–262, ISBN 978-3-031-42504-2
Editor: Springer
DOI: 10.1007/978-3-031-42505-9_22

Implementation of Personalized Medicine by Artificial Intelligence Platform

Autores: Yakimenko, Y., Stirenko, S., Koroliouk, D., Gordienko, Y., Zanzotto, F.M.
Publicado en: Soft Computing for Security Applications. Advances in Intelligent Systems and Computing, Edición vol 1428, 2022, Página(s) 597–611, ISBN 978-981-19-3589-3
Editor: Springer
DOI: 10.1007/978-981-19-3590-9_46

Ensemble Knowledge Distillation for Edge Intelligence in Medical Applications

Autores: Gordienko, Y. et al.
Publicado en: Advancements in Knowledge Distillation: Towards New Horizons of Intelligent Systems. Studies in Computational Intelligence, Edición vol 1100, 2023, Página(s) 135–168, ISBN 978-3-031-32094-1
Editor: Springer
DOI: 10.1007/978-3-031-32095-8_5

Impact of Multimodal Model Complexity on Classification of Diabetic Retinopathy Level

Autores: Shulha, M., Gordienko, Y., Stirenko, S.
Publicado en: Computational Intelligence, Data Analytics and Applications. ICCIDA 2022. Lecture Notes in Networks and Systems, Edición vol 643, 2023, Página(s) 168–180, ISBN 978-3-031-27098-7
Editor: Springer

Hybrid Neural Networks for Medical Image Classification

Autores: Arsenii Khmelnytskyi, Sergii Stirenko, Yuri Gordienko
Publicado en: Information Systems Engineering and Management, Proceedings of 4th International Conference on Artificial Intelligence and Smart Energy, 2024, Página(s) 462-474
Editor: Springer Nature Switzerland
DOI: 10.1007/978-3-031-61471-2_35

Multimodal Metadata Augmentation for Federated Learning in Medical Applications

Autores: Yuri Gordienko, Maksym Shulha, Yuriy Kochura, Oleksandr Rokovyi, Vladyslav Taran, Oleg Alienin, Sergii Stirenko
Publicado en: Lecture Notes in Networks and Systems, Proceedings of Ninth International Congress on Information and Communication Technology, 2024, Página(s) 537-547
Editor: Springer Nature Singapore
DOI: 10.1007/978-981-97-3299-9_43

VOWLMap: graph-based ontology alignment visualization and editing

Autores: Ana Guerreiro, Catia Pesquita, and Daniel Faria
Publicado en: International Semantic Web Conference (ISWC) 2021: Posters, Demos, and Industry Tracks., Edición Vol-2980, 2021
Editor: CEUR Workshop Proceedings

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

Autores: Kostiantyn Kostiukevych, Yuri Gordienko, Nikita Gordienko, Oleksandr Rokovyi, and Sergii Stirenko
Publicado en: MoMLeT+DS 2022: 4th International Workshop on Modern Machine Learning Technologies and Data Science, 2023
Editor: CEUR Workshop Proceedings

Results of the Ontology Alignment Evaluation Initiative 2021

Autores: 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
Publicado en: 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, Edición 1, 2021
Editor: CEUR Workshop Proceedings

Results of the Ontology Alignment Evaluation Initiative 2024

Autores: 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
Publicado en: ISSN: 1613-0073, Edición 1, 2024
Editor: 19th International Workshop on Ontology Matching
DOI: 10.5445/ir/1000179469

HoechstGAN: Virtual Lymphocyte Staining Using Generative Adversarial Networks

Autores: Georg Wölflein, In Hwa Um, David J Harrison, Ognjen Arandjelović
Publicado en: 2023
Editor: arxiv
DOI: 10.48550/arxiv.2210.06909

Extending agreementmakerlight to perform holistic ontology matching

Autores: Marta Contreiras Silva, Daniel Faria, and Catia Pesquit
Publicado en: 2022
Editor: 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

Autores: Barud, Katarzyna et al.
Publicado en: CEN Workshop Agreement 17933, 2023
Editor: CEN

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

Autores: Silva, Marta C.; Nunes, Susana; Balbi, Laura; Rodrigues, Ana Filipa; Pesquita, Catia
Publicado en: Edición 1, 2025
Editor: ESWC Project Networking
DOI: 10.5281/zenodo.15609794

Pattern-Guided Association Rule Mining for Complex Ontology Alignment

Autores: Beatriz Lima, Daniel Faria, and Catia Pesquita
Publicado en: International Semantic Web Conference (ISWC) 2021: Posters, Demos, and Industry Tracks, Edición Vol-2980, 2021
Editor: CEUR Workshop Proceedings

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

Autores: Gordienko, Nikita, Oleksandr Rokovyi, Yuri Gordienko, and Sergii Stirenko
Publicado en: 2022
Editor: Springer

Results of the ontology alignment evaluation initiative 2023

Autores: 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
Publicado en: 18th International Workshop on Ontology Matching (OM 2023), Edición 1, 2023
Editor: INRIA.HAL.SCIENCE Web Portal

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

Autores: Vladyslav Shlianin, Yuri Gordienko, and Sergii Stirenko1
Publicado en: 2023
Editor: CEUR Workshop Proceedings

Matching Multiple Ontologies to Build aKnowledge Graph for Personalized Medicine

Autores: Marta Contreiras Silva , Daniel Faria, and Catia Pesquit
Publicado en: 2023
Editor: 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

Autores: Nikita Gordienko, Oleksandr Rokovyi, Yuri Gordienko & Sergii Stirenko
Publicado en: HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments, Edición 1, 2022
Editor: 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

Autores: Nikita Gordienko, Oleksandr Rokovyi, Yuri Gordienko & Sergii Stirenko
Publicado en: HCI International 2022 - Late Breaking Papers. Multimodality in Advanced Interaction Environments, 2022, Página(s) 453–468, ISBN 978-3-031-17617-3
Editor: Springer
DOI: 10.1007/978-3-031-17618-0_32

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

Autores: Kostiantyn Kostiukevych, Yuri Gordienko, Nikita Gordienko, Oleksandr Rokovyi, and Sergii Stirenko
Publicado en: 2022
Editor: CEUR Workshop Proceedings

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

Autores: Oholtsov, I., Gordienko, Y., Stirenko, S
Publicado en: Soft Computing for Security Applications. Advances in Intelligent Systems and Computing, Edición vol 1428, 2022, Página(s) 561–573, ISBN 978-981-19-3589-3
Editor: Springer

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

Autores: Dario Onorati, Leonardo Ranaldi, Aria Nourbakhsh, Arianna Patrizi, Elena Sofia Ruzzetti, Michele Mastromattei, Francesca Fallucchi, Fabio Massimo Zanzotto
Publicado en: 2023 IEEE International Conference on Web Intelligence and Intelligent Agent Technology (WI-IAT), 2024, Página(s) 111-118
Editor: IEEE
DOI: 10.1109/wi-iat59888.2023.00021

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

Autores: Vladyslav Shlianin, Yuri Gordienko, and Sergii Stirenko
Publicado en: 2022
Editor: ISSN 1613-0073 CEUR Workshop Proceedings

Matching Multiple Ontologies to Build a Knowledge Graph for Personalized Medicine

Autores: Marta Contreiras Silva, Daniel Faria, and Catia Pesquit
Publicado en: 2022
Editor: 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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 121, 2024, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2310479121

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

Autores: Noemi Scarpato, Silvia Riondino, Aria Nourbakhsh, Mario Roselli, Patrizia Ferroni, Fiorella Guadagni, Fabio Massimo Zanzotto
Publicado en: Expert Systems with Applications, Edición 256, 2024, Página(s) 124859, ISSN 0957-4174
Editor: 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

Autores: Wölflein, G.; Um, I.H.; Harrison, D.J.; Arandjelović, O.
Publicado en: Data, Edición 8, 40, 2023, ISSN 2306-5729
Editor: 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

Autores: HECTOR KATIFELIS, STAMATIKI GRAMMATIKAKI, ROUBINI ZAKOPOULOU, ARISTOTELIS BAMIAS, MICHALIS V. KARAMOUZIS, KONSTANTINOS STRAVODIMOS, MARIA GAZOULI
Publicado en: In Vivo, Edición 39, 2025, Página(s) 146-151, ISSN 0258-851X
Editor: 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

Autores: Yuri Gordienko, Nikita Gordienko, Vladyslav Taran, Anis Rojbi, Sergii Telenyk, Sergii Stirenko
Publicado en: Frontiers in Neuroinformatics, Edición 19, 2025, ISSN 1662-5196
Editor: Frontiers Research Foundation
DOI: 10.3389/fninf.2025.1521805

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

Autores: Susana Nunes, Rita T. Sousa, Catia Pesquita
Publicado en: Journal of Biomedical Semantics, Edición 14, 2023, ISSN 2041-1480
Editor: 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

Autores: Christopher C. T. Sng, Ashwin Adrian Kallor, Benjamin S. Simpson, Georges Bedran, Javier Alfaro, Kevin Litchfield
Publicado en: Frontiers in Immunology, Edición 15, 2024, ISSN 1664-3224
Editor: Frontiers Media SA
DOI: 10.3389/fimmu.2024.1347542

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

Autores: Rita T. Sousa, Sara Silva, Catia Pesquita
Publicado en: Computers in Biology and Medicine, Edición 170, 2024, Página(s) 108076, ISSN 0010-4825
Editor: 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

Autores: 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
Publicado en: Cell Death & Disease, Edición 14, 2023, ISSN 2041-4889
Editor: Nature Publishing Group
DOI: 10.1038/s41419-023-06133-z

MAPLE: metadata-driven orchestration of ontology matching

Autores: Manuel Fiorelli, Armando Stellato, Tiziano Lorenzetti
Publicado en: International Journal of Metadata, Semantics and Ontologies, Edición 17, 2025, Página(s) 18-39, ISSN 1744-2621
Editor: Inderscience Enterprises
DOI: 10.1504/ijmso.2024.145508

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

Autores: Maksym Zoziuk, Vittorio Colizzi, Pavlo Krysenko, Maurizio Mattei, Roberta Bernardini, Fabio Massimo Zanzotto, Stefano Marini, Dmitri Koroliouk
Publicado en: Current Edicións in Molecular Biology, Edición 47, 2025, Página(s) 42, ISSN 1467-3045
Editor: MDPI AG
DOI: 10.3390/cimb47010042

Transcription Factor NFE2L1 Decreases in Glomerulonephropathies after Podocyte Damage

Autores: Elshani, M.; Um, I.H.; Leung, S.; Reynolds, P.A.; Chapman, A.; Kudsy, M.; Harrison, D.J.
Publicado en: Cells, Edición 12(17), 2165, 2023, ISSN 2073-4409
Editor: MDPI
DOI: 10.3390/cells12172165

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

Autores: Liangwei Yin, Pietro Traversa, Mohamed Elati, Yamir Moreno, Natalia Marek-Trzonkowska, Christophe Battail
Publicado en: iScience, Edición 28, 2025, Página(s) 113061, ISSN 2589-0042
Editor: 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

Autores: Greice M. Zickuhr, In Hwa Um, Alexander Laird, David J. Harrison, Alison L. Dickson
Publicado en: Analytical and Bioanalytical Chemistry, Edición 416, 2024, Página(s) 4015-4028, ISSN 1618-2642
Editor: Springer Verlag
DOI: 10.1007/s00216-024-05339-0

Unraveling the glycosylated immunopeptidome with HLA-Glyco

Autores: Bedran, G., Polasky, D.A., Hsiao, Y. et al.
Publicado en: Nature Communications, Edición 14, 3461, 2023, ISSN 2041-1723
Editor: Nature Publishing Group

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

Autores: 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
Publicado en: iScience, Edición 27, 2025, Página(s) 108903, ISSN 2589-0042
Editor: Elsevier BV
DOI: 10.1016/j.isci.2024.108903

Evaluating Explainable Machine Learning Models for Clinicians

Autores: Noemi Scarpato, Aria Nourbakhsh, Patrizia Ferroni, Silvia Riondino, Mario Roselli, Francesca Fallucchi, Piero Barbanti, Fiorella Guadagni, Fabio Massimo Zanzotto
Publicado en: Cognitive Computation, Edición 16, 2024, Página(s) 1436-1446, ISSN 1866-9956
Editor: Springer Verlag
DOI: 10.1007/s12559-024-10297-x

Ontologies and Knowledge Graphs in Oncology Research

Autores: Silva, Marta Contreiras, Patrícia Eugénio, Daniel Faria, and Catia Pesquita
Publicado en: Cancers 2022, Edición 14(8), 1906, 2022, ISSN 2072-6694
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/cancers14081906

An Overview of Epigenetics in Clear Cell Renal Cell Carcinoma

Autores: STAMATIKI GRAMMATIKAKI, HECTOR KATIFELIS, AMMAD AHMAD FAROOQI, KONSTANTINOS STRAVODIMOS, MICHALIS V. KARAMOUZIS, KYRIAKOS SOULIOTIS, DIMITRIOS VARVARAS and MARIA GAZOULI
Publicado en: In Vivo, Edición 37 (1) 1-10, 2023, ISSN 0258-851X
Editor: 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

Autores: STAMATIKI GRAMMATIKAKI, HECTOR KATIFELIS, KONSTANTINOS STRAVODIMOS, EMMANOUIL BAKOLAS, NIKOLAOS KAVANTZAS, DIMITRA GRIGORIADOU, MARIA GAZOULI
Publicado en: In Vivo, Edición 37 (3) 1103-1110, 2023, ISSN 0258-851X
Editor: 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

Autores: Giulio Macilenti, Armando Stellato, Manuel Fiorelli
Publicado en: Procedia Computer Science, Edición 246, 2025, Página(s) 1289-1298, ISSN 1877-0509
Editor: 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

Autores: 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
Publicado en: Cancer Immunology Research, Edición 11, 2023, Página(s) 747-762, ISSN 2326-6066
Editor: 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

Autores: Dovrolis, N.; Katifelis, H.; Grammatikaki, S.; Zakopoulou, R.; Bamias, A.; Karamouzis, M.V.; Souliotis, K.; Gazouli, M.
Publicado en: Cancers, Edición 15(23), 5637, 2023, ISSN 2072-6694
Editor: 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

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

The Immunopeptidomics Ontology (ImPO)

Autores: 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
Publicado en: Database, Edición 2024, 2024, ISSN 1758-0463
Editor: Oxford University Press
DOI: 10.1093/database/baae014

Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs

Autores: Traversa, P.; Ferraz de Arruda, G.; Vazquez, A.; Moreno, Y.
Publicado en: Entropy, Edición 25, 1537, 2023, ISSN 1099-4300
Editor: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e25111537

Comparing link prediction and classification for Gene-Disease association discovery

Autores: Canastra, Catarina Salema
Publicado en: Edición 3, 2024
Editor: Universidade de Lisboa

Explaining Predictions from Node Classification with Knowledge Graph Embeddings

Autores: Paulino, Filipe José Bastos Benvindo
Publicado en: Edición 1, 2024
Editor: Universidade de lisboa

Boosting graph neural networks with knowledge for personalized medicine

Autores: Bernardino, Beatriz de Campos
Publicado en: Edición 1, 2025
Editor: Universidade de Lisboa

Resultado final

Publicaciones

Compartir esta página Compartir esta página en las redes sociales

Descargar Descargar el contenido de la página