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
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2024

  1. results
    The multimodality cell segmentation challenge: toward universal solutions
    Jun Ma, Ronald Xie, Shamini Ayyadhury, and 8 more authors
    Nature Methods
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  2. results
    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
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  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
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  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
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  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)
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  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)
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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
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  2. results
    preprint
    Development and Prospective Validation of a Fully Automatic Bi-Parametric MRI Radiomics Signature to Predict Prostate Cancer Disease Aggressiveness: A Multi-Centric Study Using Over 4000 Patients
    Ana Carolina Rodrigues, José Almeida, Nuno Rodrigues, and 8 more authors
  3. 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
  4. 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
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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
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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
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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
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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
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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
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  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
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  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
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  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
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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
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  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
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  3. chapter
    Computational studies of G protein-coupled receptor complexes: Structure and dynamics
    Ozge Sensoy, José Guilherme Almeida, Javeria Shabbir, and 2 more authors
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  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
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  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