publications

2025

1. results

   first author

   Impact of Scanner Manufacturer, Endorectal Coil Use, and Clinical Variables on Deep Learning-assisted Prostate Cancer Classification Using Multiparametric MRI

   José Guilherme de Almeida, Nuno M. Rodrigues, Ana Sofia Castro Verde, and 11 more authors

   Radiology: Artificial Intelligence

   Link to paper
2. results

   first author

   Automatic sequence identification in multicentric prostate multiparametric MRI datasets for clinical machine-learning

   José Guilherme Almeida, Ana Sofia Castro Verde, Carlos Bilreiro, and 8 more authors

   Insights into Imaging

   Link to paper
3. results

   first author

   Auto-METRICS: LLM-assisted scientific quality control for radiomics research

   José Guilherme Almeida, and Nickolas Papanikolaou

   European Journal of Radiology
4. results

   first author

   Effective reduction of unnecessary biopsies through a deep-learning-assisted aggressive prostate cancer detector

   Nuno M Rodrigues, José Guilherme Almeida, Ana Sofia Castro Verde, and 8 more authors

   Scientific Reports

   Link to paper
5. review

   first author

   Medical machine learning operations: a framework to facilitate clinical AI development and deployment in radiology

   José Guilherme Almeida, Christina Messiou, Sam J Withey, and 3 more authors

   European Radiology

   Link to paper
6. results

   preprint

   Rad-Path Correlation of Deep Learning Models for Prostate Cancer Detection on MRI

   ASC Verde, JG Almeida, F Mendes, and 8 more authors

   medRxiv
7. review

   AI Models in Cancer Diagnosis and Prognosis

   Dimitris Filos, Stavros Sykiotis, Ioannis Tzortzis, and 8 more authors
8. review

   first author

   Foundation models for radiology—the position of the AI for Health Imaging (AI4HI) network

   José Guilherme Almeida, Leonor Cerdá Alberich, Gianna Tsakou, and 5 more authors

   Insights into Imaging
9. results

   proceeding

   Uplift Modeling for Treatment Effect Estimation in the Prostate Cancer Treatment Landscape

   Ana Rodrigues, Nuno Rodrigues, José Guilherme Almeida, and 8 more authors

   In Iberian Conference on Pattern Recognition and Image Analysis
10. results

    first author

    Improving Clinically Significant Prostate Cancer Detection with a Multimodal Machine Learning Approach: A Large-Scale Multicenter Study

    Ana Carolina Rodrigues, José Guilherme Almeida, Nuno Rodrigues, and 8 more authors

    Radiology: Imaging Cancer
11. results

    Telomere attrition becomes an instrument for clonal selection in aging hematopoiesis and leukemogenesis

    Matthew A McLoughlin, Sruthi Cheloor Kovilakam, William G Dunn, and 8 more authors

    Nature Genetics
12. results

    first author

    Self-supervised learning leads to improved performance in biparametric prostate MRI classification

    José Guilherme Almeida, Ana Sofia Castro Verde, Ana Mascarenhas Gaivão, and 8 more authors

    Computers in Biology and Medicine
13. results

    first author

    preprint

    Classpose: foundation model-driven whole slide image-scale cell phenotyping in H&E

    Soham Mandal, José Guilherme Almeida, Nickolas Papanikolaou, and 1 more author

    bioRxiv

2024

1. results

   The multimodality cell segmentation challenge: toward universal solutions

   Jun Ma, Ronald Xie, Shamini Ayyadhury, and 8 more authors

   Nature Methods

   Link to paper
2. results

   first author

   Analysis of domain shift in whole prostate gland, zonal and lesions segmentation and detection, using multicentric retrospective data

   Nuno Miguel Rodrigues, José Guilherme Almeida, Ana Sofia Castro Verde, and 8 more authors

   Computers in Biology and Medicine

   Link to paper
3. results

   first author

   preprint

   Self-Supervised Learning for Volumetric Imaging: A Prostate Cancer Biparametric Magnetic Resonance Imaging Case Study

   José Almeida, Ana Sofia Castro Verde, Ana Gaivão, and 8 more authors

   Available at SSRN 4864797

   Link to paper
4. results

   Deep Learning Features Can Improve Radiomics-Based Prostate Cancer Aggressiveness Prediction

   Nuno M Rodrigues, José Guilherme Almeida, Ana Rodrigues, and 6 more authors

   JCO Clinical Cancer Informatics

   Link to paper
5. results

   proceeding

   Radiomics-Based Reliable Predictions of Side Effects After Radiotherapy for Prostate Cancer

   Giulio Del Corso, Eva Pachetti, Rossana Buongiorno, and 8 more authors

   In 2024 IEEE International Symposium on Biomedical Imaging (ISBI)

   Link to paper
6. results

   proceeding

   StitchPro for Computational Pathology Stitching in Patients with Prostate Cancer

   Ana Sofia Castro Verde, José Guilherme Almeida, Jorge Fonseca, and 3 more authors

   In 2024 IEEE International Symposium on Biomedical Imaging (ISBI)

   Link to paper

2023

1. results

   first author

   Computational analysis of peripheral blood smears detects disease-associated cytomorphologies

   José Guilherme de Almeida, Emma Gudgin, Martin Besser, and 5 more authors

   Nature Communications

   Link to paper Tweetorial
2. results

   preprint

   Testing the Segment Anything Model on radiology data

   José Guilherme Almeida, Nuno M Rodrigues, Sara Silva, and 1 more author

   arXiv preprint arXiv:2312.12880

   Link to paper
3. results

   proceeding

   Performance Analysis of Self-Supervised Strategies for Standard Genetic Programming

   Nuno Rodrigues, José Almeida, and Sara Silva

   In Proceedings of the Companion Conference on Genetic and Evolutionary Computation

   Link to paper

2022

1. results

   first author

   The longitudinal dynamics and natural history of clonal haematopoiesis

   Margarete A Fabre, José Guilherme de Almeida, Edoardo Fiorillo, and 8 more authors

   Nature

   Link to paper Tweetorial

2021

1. method

   Predicting Hot Spots Using a Deep Neural Network Approach

   António J Preto, Pedro Matos-Filipe, José Guilherme de Almeida, and 2 more authors

   Link to paper

2020

1. results

   Understanding the binding specificity of G-Protein coupled receptors toward G-proteins and arrestins: Application to the dopamine receptor family

   António J Preto, Carlos AV Barreto, Salete J Baptista, and 7 more authors

   Journal of Chemical Information and Modeling

   Link to paper

2019

1. results

   Dynamical rearrangement of human epidermal growth factor receptor 2 upon antibody binding: effects on the dimerization

   Pedro R Magalhães, Miguel Machuqueiro, José Guilherme de Almeida, and 7 more authors

   Biomolecules

   Link to paper

2018

1. review

   In silico studies targeting G-protein coupled receptors for drug research against Parkinson’s disease

   Agostinho Lemos, Rita Melo, Antonio J Preto, and 3 more authors

   Current neuropharmacology

   Link to paper
2. review

   first author

   Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence-Evolutionary Data

   Antonio J Preto, José Guilherme Almeida, Joerg Schaarschmidt, and 3 more authors

   Encyclopedia of Analytical Chemistry: Applications, Theory and Instrumentation

   Link to paper
3. review

   Computational approaches in antibody-drug conjugate optimization for targeted cancer therapy

   Rita Melo, Agostinho Lemos, Antonio J Preto, and 4 more authors

   Current topics in medicinal chemistry

   Link to paper
4. review

   An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population

   Rita Melo, Agostinho Lemos, António J Preto, and 7 more authors

   Current medicinal chemistry

   Link to paper

2017

1. results

   SpotOn: high accuracy identification of protein-protein interface hot-spots

   Irina S Moreira, Panagiotis I Koukos, Rita Melo, and 7 more authors

   Scientific reports

   Link to paper
2. review

   first author

   Membrane proteins structures: A review on computational modeling tools

   José Guilherme de Almeida, Antonio J Preto, Panagiotis I Koukos, and 2 more authors

   Biochimica et Biophysica Acta (BBA)-Biomembranes

   Link to paper
3. chapter

   Computational studies of G protein-coupled receptor complexes: Structure and dynamics

   Ozge Sensoy, José Guilherme Almeida, Javeria Shabbir, and 2 more authors

   Link to paper
4. results

   Effect of tolbutamide on tetraethylammonium-induced postsynaptic zinc signals at hippocampal mossy fiber-CA3 synapses

   Fatima C Bastos, Vanessa N Corceiro, Sandra A Lopes, and 7 more authors

   Canadian Journal of Physiology and Pharmacology

   Link to paper
5. results

   proceeding

   Structural mechanism of HER2-antibodies complexes by molecular dynamics studies

   Rita Melo, José Guilherme Almeida, Sandra Cabo Verde, and 3 more authors

   In Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition
6. results

   proceeding

   first author

   Using big-data to understand the protein interface landscape

   José Guilherme Almeida, Alexandre Bonvin, and Irina Moreira

   In Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition
7. results

   proceeding

   first author

   Coevolution importance on binding Hot-Spot prediction methods

   José Guilherme Almeida, António J Preto, Rita Melo, and 4 more authors

   In MOL2NET 2016, International Conference on Multidisciplinary Sciences, 2nd edition