I'm A.J.Preto, always eager to learn and happy to face new challenges.

I have a lot of experience finding creative solutions for demanding problems.
To do that, I continually expand my toolset.

About Me

1994 is the year I was born. It is also the year the Lion King, The Shawshank Redemption and Pulp Fiction were released. A pretty good year.


Growing up, I grew an interest in reading. About anything really, from Tintin to Dostoevsky, through Sagan and pretty much any book I could grab.


As I kept on reading, I also developed an interest in science. The drive to both of them was curiosity regarding the functioning of stuff, so it is not really that surprising they usually come holding hands, with philosophy lurking about.


When entering University, the interests seemed to only unfold broader and deeper. That can be quite challenging, but what is the point otherwise? Interacting with other people also showed it can be quite overwhelming, but, nevertheless, essential to actually accomplishing something nowadays.


Many things change, and when I edit this page in the future I bet I will erase many childish remarks, and unnecessary comments. However, the one constant that is yet to disappoint me is curiosity. I believe that will remain relevant, and the driving force for my actions.

Portfolio

Below, I list some of my most practical and marketable works, up until now mainly consisting of tools developed to address problems of a biological nature.

SynPred

SpotONE

POSEIDON

DrugTax

Opioid Receptors

RestAssured

MUG

Dopamine Receptors

Education

Academic Qualifications

Online Certificates

  • 2024: Differential Expression Analysis with limma in R, by DataCamp

  • 2024: RNA-Seq with Bioconductor in R, by DataCamp

  • 2024: Hypothesis Testing in Python, by DataCamp

  • 2023: Intermediate SQL, by DataCamp

  • 2023: Introduction to SQL, by DataCamp

  • 2023: Software Engineering Principles in Python, DataCamp

  • 2023: Azure: Create a Virtual Machine and Deploy a Web Server, by Coursera

  • 2023: Big data, by Xpand IT

  • 2023: HTML, by Team.it

  • 2023: Python, by Synopsis

  • 2023: SQL, by BNP Paribas

  • 2022: NCC Portugal AI for Science Bootcamp, OpenACC

  • 2022: Introduction to Git and GitHub, Coursera

  • 2022: Create Your First Web App with Python and Flask, Coursera

  • 2022: Python Data Science - Ranking in the top 10%, TestDome

  • 2022: Python - Ranking in the top 10%, TestDome

  • 2021: Post-university training in clinical neuropsychology, Cognos

  • 2020: Full Stack Web Development with Flask, Pirple

  • 2020: Machine Learning with Scikit-Learn, DataCamp

  • 2020: Python Data Science Toolbox (Part I), DataCamp

  • 2020: Intermediate Python, DataCamp

  • 2020: Introduction to Python, DataCamp

Publications

  • Multi-omics data integration identifies novel biomarkers and patient subgroups in inflammatory bowel disease
    António José Preto, Shaurya Chanana, Daniel Ence, Matthew D. Healy, Daniel Domingo-Fernandéz, Kiana A. West
    Journal of Crohn's and Colitis, 2025

  • Evaluating the generalizability of graph neural networks for predicting collision cross section
    Chloe Engler Hart, António José Preto, Shaurya Chanana, David Healey, Tobias Kind, Daniel Domingo-Fernandéz
    Journal of Cheminformatics, 2024

  • Natural Products Have Increased Rates of Clinical Trial Success throughout the Drug Development Process
    Daniel Domingo-Fernandéz, Yojana Gadiya, António José Preto, Christoph A. Krettler, Sarah Mubeen, August Allen, David Healey, Viswa Colluru
    Journal of Natural Products, 2024

  • Advancing Drug Safety in Drug Development: Bridging Computational Predictions for Enhanced Toxicity Prediction
    Ana M. B. Amorim, Luiz F. Piochi, Ana T. Gaspar, António J. Preto, Nícia Rosário-Ferreira, Irina S. Moreira
    Chemical Research in Toxicology, 2024

  • POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs: a new database and predictor
    António J. Preto, Ana B. Caniceiro, Francisco Duarte, Hugo Fernandes, Lino Ferreira, Joana Mourão, Irina S. Moreira
    Journal of Cheminformatics, 16 (18), 2024

  • DELFOS—Drug Efficacy Leveraging Forked and Specialized Networks—Benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity
    Luiz Felipe Piochi, António J. Preto, Irina S. Moreira
    Bioinformatics, btad645, 2023

  • MUG: A mutation overview of GPCR subfamily A17 receptors
    Ana B. Caniceiro, Beatriz Bueschbell, Carlos A. V. Barreto, António J. Preto, Irina S. Moreira
    Computational and Structural Biotechnology Journal, vol. 21, 586-600, 2023

  • DrugTax: package for drug taxonomy identification and explainable feature extraction
    Preto, A.J., Correia, P.C., Moreira, I.S.
    Journal of Cheminformatics, vol. 14, 73, 2022

  • Arrestin and G Protein Interactions with GPCRs: A Structural Perspective
    Carlos A. V. Barreto, Salete J. Baptista, Beatriz Bueschbell, Pedro R. Magalhães, António J. Preto, Agostinho Lemos, Nícia Rosário-Ferreira, Anke S.Schiedel, Miguel Machuqueiro, Rita Melo, Irina S. Moreira
    GPCRs as Therapeutic Targets, Chapter 5, 2022

  • SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning
    António J. Preto, Pedro Matos-Filipe, Joana Mourão, Irina S Moreira
    GigaScience, vol. 11, giac087, 2022

  • From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes?
    L. F. Piochi, A. T. Gaspar, N. Rosário-Ferreira A. J. Preto, I. S. Moreira
    Advances in Protein Chemistry and Structural Biology, vol. 131, 45-83, 2022

  • Targeting GPCRs Via Multi-Platforms Arrays and AI
    A. J. Preto, C. Marques-Pereira, Salete J. Baptista, B. Bueschbell, Carlos A. V. Barreto, A. T. Gaspar, I. Pinheiro, N. Pereira, M. Pires, D. Ramalhão, D. Silvério, N. Rosário-Ferreira, R. Melo, J. Mourão, I. S. Moreira
    Comprehensive Pharmacology, Chapter 2 (08), 135-162, 2022

  • MENSAdb: a thorough structural analysis of membrane protein dimers
    Pedro Matos-Filipe*, António J. Preto*, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira, * joint first authors
    Database, vol. 2021, baab013, 2021

  • Decoding Partner Specificity of Opioid Receptor Family
    Carlos A. V. Barreto, Salete J Baptista, António J. Preto, Daniel Silvério, Rita Melo, Irina S. Moreira
    fronties in Molecular Biosciences, vol. 8, 715215, 2021

  • SPOTONE: Hot Spots on Protein Complexes with Extremely Randomized Trees via Sequence-Only Features
    A. J. Preto, Irina S. Moreira
    International Journal of Molecular Sciences, vol. 21(19), 7281, 2020

  • Predicting Hot Spots Using a Deep Neural Network Approach
    A. J. Preto, Pedro Matos-Filipe, José G. de Almeida, Joana Mourão, Irina S. Moreira
    Artificial Neural Networks, Methods in Molecular Biology book series, vol. 2190, 267-288, 2020

  • Understanding the Binding Specificity of G-Protein Coupled Receptors toward G-Proteins and Arrestins: Application to the Dopamine Receptor Family
    A. J. Preto, Carlos A. V. Barreto, Salete J. Baptista, José Guilherme de Almeida, Agostinho Lemos, André Melo, M. Natália D. S. Cordeiro, Zeynep Kurkcuoglu, Rita Melo, Irina S. Moreira
    Journal of Chemical Information and Modelling, vol. 60(8), 3969-3984, 2020

  • The Central Role of Non-Structural Protein 1 (NS1) in Influenza Biology and Infection
    Nícia Rosário-Ferreira, A. J. Preto, Rita Melo, Irina S. Moreira and Rui M. M. Brito
    International Journal of Molecular Sciences, vol. 21(4), 1511, 2020


  • An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population
    Melo, R.; Lemos, Agostinho; Preto, António J.; Bueschbell, Beatriz; Matos-Filipe, Pedro; Barreto, Carlos; Almeida, José G.; Silva, Rúben D. M.; Correia, João D. G.; Moreira, Irina S
    Current Medicinal Chemistry, vol. 27(5), 760-794, 2020

  • Prediction and targeting of GPCR oligomer interfaces
    Carlos A. V. Barreto, Salete J. Baptista, António José Preto, Pedro Matos-Filipe, Joana Mourão, Rita Melo, Irina Moreira
    Progress in Molecular Biology and Translational Science, vol. 169, 105-149, 2020

  • A complete assessment of dopamine receptor-ligand interactions through computational methods
    Beatriz Bueschbell, Carlos A. V. Barreto, António J. Preto, Anke C. Schiedel, Irina S. Moreira
    Molecules, vol. 24(7), 1196, 2019

  • Structural Characterization of Membrane Protein Dimers
    António J. Preto, Pedro Matos-Filipe, Panagiotis I. Koukos, Pedro Renault, Sérgio F. Sousa, Irina S. Moreira
    Protein Supersecondary Structures, part of the Methods in Moleculer Biology book series, vol. 1958, 403-436, 2019

  • In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson's Disease
    Lemos, Agostinho; Melo, Rita; Preto, António J.; Almeida, José Guilherme; Moreira, Irina Sousa; Dias Soeiro Cordeiro, Maria Natália
    Current Neuropharmacology, vol. 16(6), 786-848, 2018

  • Computational Approaches in Antibody-drug Conjugate Optimization for Targeted Cancer Therapy
    Melo, Rita; Lemos, Agostinho; Preto, António J.; Almeida, José G.; Correia, João D. G.; Sensoy Ozge; Moreira, Irina S.
    Current Topics in Medicinal Chemistry, vol. 18(13), 1091-1109, 2018

  • Computational Tools for the Structural Characterization of Proteins and Their Complexes from Sequence-Evolutionary Data
    Preto, António J.; Almeida, José G.; Schaarschmidt, Joerg; Xue, Li C.; Moreira Irina S.; Bonvin, Alexandre M. J. J; Meyers, Robert A.
    Encyclopedia of Analytical Chemistry, 1-19, 2018

  • Alpha-helical and beta-sheet membrane- membrane protein dimers: centralizing information
    Pedro Matos-Filipe, António José Preto, Panos Koukos, Alexandre Bonvin, Irina Moreira
    MOL2NET'17, Conference on Molecular, Biomedical and Computational Sciences and Engineering, 3, 2017

  • Creating a valid in silico Dopamine D2-receptor model for small molecular docking studies
    Beatriz Bueschbell, António J. Preto, Carlos A. V. Barreto, Anke C. Schiedel, Irina S. Moreira
    MOL2NET, International Conference Series on Multidisciplinary Sciences, 3, 2017

  • Membrane proteins structures: A review on computational modeling tools
    José G. Almeida *, António J. Preto*, Panagiotis I. Koukos, Alexandre M. J. J. Bonvin, Irina S. Moreira, * joint first authors
    Biochimica et Biophysica Acta (BBA) - Biomembranes, 1859(10), 2021-2039, 2017

  • A bioinformatics approach for the understanding of membrane protein complexes
    António José Preto Martins Gomes
    Master's Degree Thesis, Master's Degree in Biochemistry, University of Coimbra, advisors: Professor Ana Luísa Carvalho and Professor Irina S. Moreira 2017

  • SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots
    Irina S. Moreira, Panagiotis I. Koukos, Rita Melo, José G. Almeida, António J. Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H. Gumus, Joaquim Costa, Alexandre M. J. J. Bonvin
    Scientific Reports, vol. 7, 8007, 2017

  • Coevolution importance on binding Hot-Spot prediction methods
    José G. Almeida, António J. Preto, Rita Melo, Zeynep H. Gumus, Joaquim Costa, Alexandre M. J. J. Bonvin, Irina S. Moreira
    MOL2NET 2016, International Conference on Multidisciplinary Sciences, 2, 2016

Roles

  • 2012
  • 2013
  • 2014
  • 2015
  • 2016
  • 2017
  • 2018
  • 2019
  • 2020
  • 2021
  • 2022
  • 2023
  • 2024
  • Present

Events

To access the events I attended as both participant and lecturer, as well as the ones I organized, please click the widgets below.

Organised

Lectured/Mentored

Participated

Contact

If you wish to contact me please do it through martinsgomes.jose@gmail.com or any of the social networks displayed at the bottom of the navigation menu.