Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. - Miguel Rocha 001; José P. Pinto; Isabel Rocha; Eugénio C. Ferreira (CIBCB, 2007)

Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. - Miguel Rocha 001; Rui Mendes 001; Paulo Maia; José P. Pinto; Isabel Rocha; Eugénio C. Ferreira (EPIA Workshops, 2007)

Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. - Miguel Rocha 001; José P. Pinto; Isabel Rocha; Eugénio C. Ferreira (EvoBIO, 2007)

Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis. - José P. Pinto; Oscar Dias; Anália Lourenço; Sónia Carneiro; Eugénio C. Ferreira; Isabel Rocha; Miguel Rocha 001 (IWPACBB, 2008)

Natural computation meta-heuristics for the in silico optimization of microbial strains. - Miguel Rocha 001; Paulo Maia; Rui Mendes 001; José P. Pinto; Eugénio C. Ferreira; Jens Nielsen; Kiran Raosaheb Patil; Isabel Rocha (BMC Bioinform., 2008)

A software tool for network topology analysis under a metabolic engineering perspective. - José P. Pinto; Isabel Rocha; Miguel Rocha 001 (BCB, 2010)

OptFlux: an open-source software platform for in silico metabolic engineering. - Isabel Rocha; Paulo Maia; Pedro Evangelista; Paulo Vilaça; Simão Soares; José P. Pinto; Jens Nielsen; Kiran Raosaheb Patil; Eugénio C. Ferreira; Miguel Rocha 001 (BMC Syst. Biol., 2010)

Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. - Anália Lourenço; Sónia Carneiro; José P. Pinto; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (PACBB, 2011)

Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. - José Pedro Pinto; Isabel Rocha; Miguel Rocha 001 (PRIB, 2011)

A Study of the Short and Long-term Regulation of E. coli Metabolic Pathways. - Anália Lourenço; Sónia Carneiro; José P. Pinto; Miguel Rocha 001; Eugénio C. Ferreira; Isabel Rocha (J. Integr. Bioinform., 2011)

Computational tools for large-scale biological network analysis - José Pedro Pinto (2012)

TAG4VD: a game for collaborative video annotation. - José Pedro Pinto; Paula Viana (ImmersiveMe@ACM Multimedia, 2013)

UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks. - Ravi Kiran Reddy Kalathur; José Pedro Pinto; Miguel A. Hernández-Prieto; Rui S. R. Machado; Dulce Almeida; Gautam Chaurasia; Matthias E. Futschik (Nucleic Acids Res., 2014)

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. - José P. Pinto; Ravi Kiran Reddy Kalathur; Rui S. R. Machado; Joana M. Xavier; José Bragança; Matthias E. Futschik (Nucleic Acids Res., 2014)

Using the crowd to boost video annotation processes: a game based approach. - José Pedro Pinto; Paula Viana (CVMP, 2015)

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. - José P. Pinto; Ravi Kiran Reddy Kalathur; Daniel V. Oliveira 001; Tânia Barata; Rui S. R. Machado; Susana Machado; Ivette Pacheco-Leyva; Isabel Duarte; Matthias E. Futschik (Nucleic Acids Res., 2015)

A Hands-on Approach on Botnets for Behavior Exploration. - João Pedro Dias; José Pedro Pinto; José Magalhães Cruz (IoTBDS, 2017)

A collaborative approach for semantic time-based video annotation using gamification. - Paula Viana; José Pedro Pinto (Hum. centric Comput. Inf. Sci., 2017)

GymApp: A Real Time Physical Activity Trainner on Wearable Devices. - Paula Viana; Tiago Ferreira 004; Lourenco Castro; Márcio Soares; José Pedro Pinto; Maria Teresa Andrade; Pedro Carvalho (HSI, 2018)

Growing Smart Cities on an Open-Data-Centric Cyber-Physical Platform. - José Pedro Pinto; João Pedro Dias; Rosaldo J. F. Rossetti (ISC2, 2018)

YouTube Timed Metadata Enrichment Using a Collaborative Approach. - José Pedro Pinto; Paula Viana (MISSI, 2018)

StemMapper: a curated gene expression database for stem cell lineage analysis. - José P. Pinto; Rui S. R. Machado; Ramiro Magno; Daniel V. Oliveira 001; Susana Machado; Raquel P. Andrade; José Bragança; Isabel Duarte; Matthias E. Futschik (Nucleic Acids Res., 2018)

Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures. - Tiehang Duan; José P. Pinto; Xiaohui Xie (Bioinform., 2019)

Improving Youtube video retrieval by integrating crowdsourced timed metadata. - José Pedro Pinto; Paula Viana (J. Intell. Fuzzy Syst., 2019)

Semantic Storytelling Automation: A Context-Aware and Metadata-Driven Approach. - Paula Viana; Pedro Carvalho; Maria Teresa Andrade; Pieter P. Jonker; Vasileios Papanikolaou; Inês N. Teixeira; Luís Vilaça; José P. Pinto; Tiago Soares da Costa (ACM Multimedia, 2020)

Deep learning and multivariate time series for cheat detection in video games. - José Pedro Pinto; André Pimenta; Paulo Novais (Mach. Learn., 2021)

Improving word embeddings in Portuguese: increasing accuracy while reducing the size of the corpus. - José Pedro Pinto; Paula Viana; Inês N. Teixeira; Maria T. Andrade 001 (PeerJ Comput. Sci., 2022)