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Journal Articles
- 2024
[j23]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)- 2022
- [j22]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) - [j21]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) - 2020
- [j20]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): 1986-1988 (2020) - 2019
- [j19]Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes:
gMCS: fast computation of genetic minimal cut sets in large networks. Bioinform. 35(3): 535-537 (2019) - [j18]Luis Vitores Valcarcel, Verónica Torrano, Luis Tobalina, Arkaitz Carracedo, Francisco J. Planes:
rMTA: robust metabolic transformation analysis. Bioinform. 35(21): 4350-4355 (2019) - 2016
- [j17]Luis Tobalina, Jon Pey, Francisco J. Planes:
Direct calculation of minimal cut sets involving a specific reaction knock-out. Bioinform. 32(13): 2001-2007 (2016) - 2015
- [j16]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): 265-279 (2015) - [j15]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): 897-904 (2015) - [j14]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): 1771-1779 (2015) - 2014
- [j13]Jon Pey, Francisco J. Planes, John E. Beasley:
Refining carbon flux paths using atomic trace data. Bioinform. 30(7): 975-980 (2014) - [j12]Jon Pey, Francisco J. Planes:
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. Bioinform. 30(15): 2197-2203 (2014) - 2013
- [j11]Ander Muniategui, Jon Pey, Francisco J. Planes, Angel Rubio:
Joint analysis of miRNA and mRNA expression data. Briefings Bioinform. 14(3): 263-278 (2013) - [j10]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): 2009-2016 (2013) - [j9]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: 62 (2013) - [j8]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: 134 (2013) - 2011
- [j7]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): 534-540 (2011) - [j6]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): 140-146 (2011) - 2009
- [j5]Francisco J. Planes, John E. Beasley:
An optimization model for metabolic pathways. Bioinform. 25(20): 2723-2729 (2009) - [j4]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): 3158-3165 (2009) - [j3]Francisco J. Planes, John E. Beasley:
Path finding approaches and metabolic pathways. Discret. Appl. Math. 157(10): 2244-2256 (2009) - 2008
- [j2]Francisco J. Planes, John E. Beasley:
A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Briefings Bioinform. 9(5): 422-436 (2008) - 2007
- [j1]John E. Beasley, Francisco J. Planes:
Recovering metabolic pathways via optimization. Bioinform. 23(1): 92-98 (2007)
Coauthor Index
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