Recovering metabolic pathways via optimization. - John E. Beasley; Francisco J. Planes (Bioinform., 2007)

A critical examination of stoichiometric and path-finding approaches to metabolic pathways. - Francisco J. Planes; John E. Beasley (Briefings Bioinform., 2008)

Computing the shortest elementary flux modes in genome-scale metabolic networks. - Luis F. de Figueiredo; Adam Podhorski; Angel Rubio; Christoph Kaleta; John E. Beasley; Stefan Schuster; Francisco J. Planes (Bioinform., 2009)

An optimization model for metabolic pathways. - Francisco J. Planes; John E. Beasley (Bioinform., 2009)

Path finding approaches and metabolic pathways. - Francisco J. Planes; John E. Beasley (Discret. Appl. Math., 2009)

Exploring metabolic pathways in genome-scale networks via generating flux modes. - Alberto Rezola; Luis F. de Figueiredo; Matthias Brock; Jon Pey; Adam Podhorski; Christoph Wittmann; Stefan Schuster; Alexander Bockmayr; Francisco J. Planes (Bioinform., 2011)

Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes. - Jon Pey; Constantinos Theodoropoulos; Alberto Rezola; Angel Rubio; Marta Cascante; Francisco J. Planes (Biosyst., 2011)

Joint analysis of miRNA and mRNA expression data. - Ander Muniategui; Jon Pey; Francisco J. Planes; Angel Rubio (Briefings Bioinform., 2013)

Selection of human tissue-specific elementary flux modes using gene expression data. - Alberto Rezola; Jon Pey; Luis F. de Figueiredo; Adam Podhorski; Stefan Schuster; Angel Rubio; Francisco J. Planes (Bioinform., 2013)

A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype. - Jon Pey; Luis Tobalina; Joaquín Prada J. de Cisneros; Francisco J. Planes (BMC Syst. Biol., 2013)

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. - Jon Pey; Kaspar Valgepea; Angel Rubio; John E. Beasley; Francisco J. Planes (BMC Syst. Biol., 2013)

Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. - Jon Pey; Francisco J. Planes (Bioinform., 2014)

Refining carbon flux paths using atomic trace data. - Jon Pey; Francisco J. Planes; John E. Beasley (Bioinform., 2014)

Advances in network-based metabolic pathway analysis and gene expression data integration. - Alberto Rezola; Jon Pey; Luis Tobalina; Ángel Rubio; John E. Beasley; Francisco J. Planes (Briefings Bioinform., 2015)

TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm. - Jon Pey; Juan A. Villar; Luis Tobalina; Alberto Rezola; José Manuel García Carrasco; John E. Beasley; Francisco J. Planes (Bioinform., 2015)

Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data. - Luis Tobalina; Rafael Bargiela; Jon Pey; Florian-Alexander Herbst; Iván Lores; David Rojo; Coral Barbas; Ana I. Peláez; Jesús Sánchez; Martin von Bergen; Jana Seifert; Manuel Ferrer; et al. (Bioinform., 2015)

Direct calculation of minimal cut sets involving a specific reaction knock-out. - Luis Tobalina; Jon Pey; Francisco J. Planes (Bioinform., 2016)

gMCS: fast computation of genetic minimal cut sets in large networks. - Iñigo Apaolaza; Luis Vitores Valcarcel; Francisco J. Planes (Bioinform., 2019)

rMTA: robust metabolic transformation analysis. - Luis Vitores Valcarcel; Verónica Torrano; Luis Tobalina; Arkaitz Carracedo; Francisco J. Planes (Bioinform., 2019)

On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. - Miguel Ponce de Leon; Iñigo Apaolaza; Alfonso Valencia; Francisco J. Planes (Bioinform., 2020)

A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism. - Iñigo Apaolaza; Edurne San José-Enériz; Luis Vitores Valcarcel; Xabier Agirre; Felipe Prósper; Francisco J. Planes (PLoS Comput. Biol., 2022)

BOSO: A novel feature selection algorithm for linear regression with high-dimensional data. - Luis Vitores Valcarcel; Edurne San José-Enériz; Xabier Cendoya; Ángel Rubio; Xabier Agirre; Felipe Prósper; Francisco J. Planes (PLoS Comput. Biol., 2022)

Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism. - Danel Olaverri-Mendizabal; Luis Vitores Valcarcel; Naroa Barrena; Carlos J. Rodríguez; Francisco J. Planes (Briefings Bioinform., 2024)