Publications in collaboration with researchers from Universidade Do Porto (18)

2021

  1. Computational Resources and Strategies to Construct Single-Molecule Models of FISH

    Methods in Molecular Biology (Humana Press Inc.), pp. 317-330

  2. Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae

    Briefings in bioinformatics, Vol. 22, Núm. 1, pp. 219-231

2020

  1. Application of Agent-Based Modelling to Simulate Ribosome Translation

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2019

  1. Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli

    Computers in Biology and Medicine, Vol. 107, pp. 218-226

  2. DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research

    Computers in Biology and Medicine, Vol. 107, pp. 197-205

2018

  1. Agent-based model of diffusion of N-acyl homoserine lactones in a multicellular environment of Pseudomonas aeruginosa and Candida albicans

    Biofouling, Vol. 34, Núm. 3, pp. 335-345

2017

  1. Critical review on biofilm methods

    Critical Reviews in Microbiology, Vol. 43, Núm. 3, pp. 313-351

  2. Polymicrobial ventilator-associated pneumonia: Fighting in vitro Candida albicans-pseudomonas aeruginosa biofilms with antifungal-antibacterial combination therapy

    PLoS ONE, Vol. 12, Núm. 1

2016

  1. Computational resources and strategies to construct single-molecule metabolic models of microbial cells

    Briefings in Bioinformatics, Vol. 17, Núm. 5, pp. 863-876

  2. FISHji: New ImageJ macros for the quantification of fluorescence in epifluorescence images

    Biochemical Engineering Journal, Vol. 112, pp. 61-69

  3. Single Molecule Simulation of Diffusion and Enzyme Kinetics

    Journal of Physical Chemistry B, Vol. 120, Núm. 16, pp. 3809-3820

2015

  1. Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework

    BioMed Research International, Vol. 2015

  2. Enabling systematic, harmonised and large-scale biofilms data computation: The biofilms experiment workbench

    Computer Methods and Programs in Biomedicine, Vol. 118, Núm. 3, pp. 309-321

2014

  1. BEW: Bioinformatics Workbench for Analysis of Biofilms Experimental Data

    Advances in Intelligent Systems and Computing

  2. Designing an ontology tool for the unification of biofilms data

    Advances in Intelligent Systems and Computing

  3. Minimum information about a biofilm experiment (MIABiE): Standards for reporting experiments and data on sessile microbial communities living at interfaces

    Pathogens and Disease

2012

  1. A systematic approach to the interrogation and sharing of standardised biofilm signatures

    Advances in Intelligent and Soft Computing

  2. Biofomics: A web platform for the systematic and standardized collection of high-throughput biofilm data

    PLoS ONE, Vol. 7, Núm. 6