Evaluating Pathway Enumeration Algorithms in Metabolic Engineering Case Studies. - Filipe Liu; Paulo Vilaça; Isabel Rocha; Miguel Rocha 001 (PACBB, 2014)

Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. - Filipe Liu; Paulo Vilaça; Isabel Rocha; Miguel Rocha 001 (Comput. Methods Programs Biomed., 2015)

Evaluation and development of algorithms and computational tools for metabolic pathway optimization - Filipe Liu (2018)

A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions. - Vítor Vieira; Jorge Ferreira; Rúben Rodrigues; Filipe Liu; Miguel Rocha 001 (J. Integr. Bioinform., 2019)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum). - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

TranSyT, an innovative framework for identifying transport systems. - Emanuel Cunha; Davide Lagoa; José P. Faria; Filipe Liu; Christopher S. Henry; Oscar Dias (Bioinform., 2023)