Francisco J. Planes

26 papers Journal 26
YearRankTypeTitle / Venue / Authors
2024 J jnl
BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.
Bioinform.
Telmo Blasco, Francesco Balzerani, Luis Vitores Valcarcel, Pedro Larrañaga, Concha Bielza, María Pilar Francino, José Ángel Rufián-Henares, Francisco J. Planes, Sergio Pérez-Burillo
2024 J jnl
Review and meta-analysis of the genetic Minimal Cut Set approach for gene essentiality prediction in cancer metabolism.
Briefings Bioinform.
Danel Olaverri-Mendizabal, Luis Vitores Valcarcel, Naroa Barrena, Carlos J. Rodríguez, Francisco J. Planes
2024 J jnl
gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python.
Bioinform.
Carlos J. Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, Luis Vitores Valcarcel, Francisco J. Planes
2024 J jnl
q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.
Bioinform.
Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo, María Pilar Francino, José Ángel Rufián-Henares, Luis Vitores Valcarcel, Francisco J. Planes
2022 J jnl
A network-based approach to integrate nutrient microenvironment in the prediction of synthetic lethality in cancer metabolism.
PLoS Comput. Biol.
Iñigo Apaolaza, Edurne San José-Enériz, Luis Vitores Valcarcel, Xabier Agirre, Felipe Prósper, Francisco J. Planes
2022 J jnl
BOSO: A novel feature selection algorithm for linear regression with high-dimensional data.
PLoS Comput. Biol.
Luis Vitores Valcarcel, Edurne San José-Enériz, Xabier Cendoya, Ángel Rubio, Xabier Agirre, Felipe Prósper, Francisco J. Planes
2020 J jnl
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models.
Bioinform.
Miguel Ponce de Leon, Iñigo Apaolaza, Alfonso Valencia, Francisco J. Planes
2019 J jnl
gMCS: fast computation of genetic minimal cut sets in large networks.
Bioinform.
Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes
2019 J jnl
rMTA: robust metabolic transformation analysis.
Bioinform.
Luis Vitores Valcarcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J. Planes
2016 J jnl
Direct calculation of minimal cut sets involving a specific reaction knock-out.
Bioinform.
Luis Tobalina, Jon Pey, Francisco J. Planes
2015 J jnl
Advances in network-based metabolic pathway analysis and gene expression data integration.
Briefings Bioinform.
Alberto Rezola, Jon Pey, Luis Tobalina, Ángel Rubio, John E. Beasley, Francisco J. Planes
2015 J jnl
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data.
Bioinform.
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
2015 J jnl
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm.
Bioinform.
Jon Pey, Juan A. Villar, Luis Tobalina, Alberto Rezola, José Manuel García Carrasco, John E. Beasley, Francisco J. Planes
2014 J jnl
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks.
Bioinform.
Jon Pey, Francisco J. Planes
2014 J jnl
Refining carbon flux paths using atomic trace data.
Bioinform.
Jon Pey, Francisco J. Planes, John E. Beasley
2013 J jnl
A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype.
BMC Syst. Biol.
Jon Pey, Luis Tobalina, Joaquín Prada J. de Cisneros, Francisco J. Planes
2013 J jnl
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways.
BMC Syst. Biol.
Jon Pey, Kaspar Valgepea, Angel Rubio, John E. Beasley, Francisco J. Planes
2013 J jnl
Joint analysis of miRNA and mRNA expression data.
Briefings Bioinform.
Ander Muniategui, Jon Pey, Francisco J. Planes, Angel Rubio
2013 J jnl
Selection of human tissue-specific elementary flux modes using gene expression data.
Bioinform.
Alberto Rezola, Jon Pey, Luis F. de Figueiredo, Adam Podhorski, Stefan Schuster, Angel Rubio, Francisco J. Planes
2011 J jnl
Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes.
Biosyst.
Jon Pey, Constantinos Theodoropoulos, Alberto Rezola, Angel Rubio, Marta Cascante, Francisco J. Planes
2011 J jnl
Exploring metabolic pathways in genome-scale networks via generating flux modes.
Bioinform.
Alberto Rezola, Luis F. de Figueiredo, Matthias Brock, Jon Pey, Adam Podhorski, Christoph Wittmann, Stefan Schuster, Alexander Bockmayr, Francisco J. Planes
2009 J jnl
An optimization model for metabolic pathways.
Bioinform.
Francisco J. Planes, John E. Beasley
2009 J jnl
Computing the shortest elementary flux modes in genome-scale metabolic networks.
Bioinform.
Luis F. de Figueiredo, Adam Podhorski, Angel Rubio, Christoph Kaleta, John E. Beasley, Stefan Schuster, Francisco J. Planes
2009 J jnl
Path finding approaches and metabolic pathways.
Discret. Appl. Math.
Francisco J. Planes, John E. Beasley
2008 J jnl
A critical examination of stoichiometric and path-finding approaches to metabolic pathways.
Briefings Bioinform.
Francisco J. Planes, John E. Beasley
2007 J jnl
Recovering metabolic pathways via optimization.
Bioinform.
John E. Beasley, Francisco J. Planes