Francisco J. Planes

According to our database, Francisco J. Planes authored at least 27 papers between 2007 and 2026.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2026

gMISpy: integration of complex regulatory networks and genome scale metabolic models.

Carlos J. Rodriguez-Flores, Naroa Barrena, Loïc Paulevé, Francisco J. Planes

Bioinform., 2026

2024

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., May, 2024

gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python.

Carlos J. Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, Luis Vitores Valcarcel, Francisco J. Planes

Bioinform., 2024

BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.

Telmo Blasco, Francesco Balzerani, Luis Vitores Valcarcel, Pedro Larrañaga, Concha Bielza, María Pilar Francino, José Ángel Rufián-Henares, Francisco J. Planes, Sergio Pérez-Burillo

Bioinform., 2024

q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.

Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo, María Pilar Francino, José Ángel Rufián-Henares, Luis Vitores Valcarcel, Francisco J. Planes

Bioinform., 2024

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

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

2020

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

2019

rMTA: robust metabolic transformation analysis.

Luis Vitores Valcarcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J. Planes

Bioinform., 2019

gMCS: fast computation of genetic minimal cut sets in large networks.

Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes

Bioinform., 2019

2016

Direct calculation of minimal cut sets involving a specific reaction knock-out.

Luis Tobalina, Jon Pey, Francisco J. Planes

Bioinform., 2016

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, Francisco J. Planes

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

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

2014

Refining carbon flux paths using atomic trace data.

Jon Pey, Francisco J. Planes, John E. Beasley

Bioinform., 2014

Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks.

Jon Pey, Francisco J. Planes

Bioinform., 2014

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

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

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

Joint analysis of miRNA and mRNA expression data.

Ander Muniategui, Jon Pey, Francisco J. Planes, Angel Rubio

Briefings Bioinform., 2013

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

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

2009

Path finding approaches and metabolic pathways.

Francisco J. Planes, John E. Beasley

Discret. Appl. Math., 2009

An optimization model for metabolic pathways.

Francisco J. Planes, John E. Beasley

Bioinform., 2009

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

2008

A critical examination of stoichiometric and path-finding approaches to metabolic pathways.

Francisco J. Planes, John E. Beasley

Briefings Bioinform., 2008

2007

Recovering metabolic pathways via optimization.

John E. Beasley, Francisco J. Planes

Bioinform., 2007