Francisco J. Planes

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 7

Top Topics

Metabolic Networks

Gene Expression

Linear Regression

Saccharomyces Cerevisiae

Top Venues

Briefings Bioinform.

PLoS Comput. Biol.

Publications

Danel Olaverri-Mendizabal, Luis Vitores Valcarcel, Naroa Barrena, Carlos J. Rodríguez, Francisco J. Planes
Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism. Briefings Bioinform. 25 (3) (2024)
Iñigo Apaolaza, Edurne San José-Enériz, Luis Vitores Valcarcel, Xabier Agirre, Felipe Prósper, Francisco J. Planes
A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism. PLoS Comput. Biol. 18 (3) (2022)
Luis Vitores Valcarcel, Edurne San José-Enériz, Xabier Cendoya, Ángel Rubio, Xabier Agirre, Felipe Prósper, Francisco J. Planes
BOSO: A novel feature selection algorithm for linear regression with high-dimensional data. PLoS Comput. Biol. 18 (5) (2022)
Miguel Ponce de Leon, Iñigo Apaolaza, Alfonso Valencia, Francisco J. Planes
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models. Bioinform. 36 (6) (2020)
Luis Vitores Valcarcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J. Planes
rMTA: robust metabolic transformation analysis. Bioinform. 35 (21) (2019)
Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes
gMCS: fast computation of genetic minimal cut sets in large networks. Bioinform. 35 (3) (2019)
Luis Tobalina, Jon Pey, Francisco J. Planes
Direct calculation of minimal cut sets involving a specific reaction knock-out. Bioinform. 32 (13) (2016)
Jon Pey, Juan A. Villar, Luis Tobalina, Alberto Rezola, José Manuel García Carrasco, John E. Beasley, Francisco J. Planes
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm. Bioinform. 31 (6) (2015)
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, Francisco J. Planes
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data. Bioinform. 31 (11) (2015)
Alberto Rezola, Jon Pey, Luis Tobalina, Ángel Rubio, John E. Beasley, Francisco J. Planes
Advances in network-based metabolic pathway analysis and gene expression data integration. Briefings Bioinform. 16 (2) (2015)
Jon Pey, Francisco J. Planes
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. Bioinform. 30 (15) (2014)
Jon Pey, Francisco J. Planes, John E. Beasley
Refining carbon flux paths using atomic trace data. Bioinform. 30 (7) (2014)
Alberto Rezola, Jon Pey, Luis F. de Figueiredo, Adam Podhorski, Stefan Schuster, Angel Rubio, Francisco J. Planes
Selection of human tissue-specific elementary flux modes using gene expression data. Bioinform. 29 (16) (2013)
Jon Pey, Kaspar Valgepea, Angel Rubio, John E. Beasley, Francisco J. Planes
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. BMC Syst. Biol. 7 (2013)
Ander Muniategui, Jon Pey, Francisco J. Planes, Angel Rubio
Joint analysis of miRNA and mRNA expression data. Briefings Bioinform. 14 (3) (2013)
Jon Pey, Luis Tobalina, Joaquín Prada J. de Cisneros, Francisco J. Planes
A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype. BMC Syst. Biol. 7 (2013)
Jon Pey, Constantinos Theodoropoulos, Alberto Rezola, Angel Rubio, Marta Cascante, Francisco J. Planes
Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes. Biosyst. 105 (2) (2011)
Alberto Rezola, Luis F. de Figueiredo, Matthias Brock, Jon Pey, Adam Podhorski, Christoph Wittmann, Stefan Schuster, Alexander Bockmayr, Francisco J. Planes
Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinform. 27 (4) (2011)
Luis F. de Figueiredo, Adam Podhorski, Angel Rubio, Christoph Kaleta, John E. Beasley, Stefan Schuster, Francisco J. Planes
Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinform. 25 (23) (2009)
Francisco J. Planes, John E. Beasley
An optimization model for metabolic pathways. Bioinform. 25 (20) (2009)
Francisco J. Planes, John E. Beasley
Path finding approaches and metabolic pathways. Discret. Appl. Math. 157 (10) (2009)
Francisco J. Planes, John E. Beasley
A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Briefings Bioinform. 9 (5) (2008)
John E. Beasley, Francisco J. Planes
Recovering metabolic pathways via optimization. Bioinform. 23 (1) (2007)