Francisco Planes
Francisco Planes
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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ...
Nature protocols 14 (3), 639-702, 2019
Computing the shortest elementary flux modes in genome-scale metabolic networks
LF De Figueiredo, A Podhorski, A Rubio, C Kaleta, JE Beasley, ...
Bioinformatics 25 (23), 3158-3165, 2009
Joint analysis of miRNA and mRNA expression data
A Muniategui, J Pey, FJ Planes, A Rubio
Briefings in bioinformatics 14 (3), 263-278, 2013
CANCERTOOL: a visualization and representation interface to exploit cancer datasets
AR Cortazar, V Torrano, N Martín-Martín, A Caro-Maldonado, L Camacho, ...
Cancer research 78 (21), 6320-6328, 2018
A critical examination of stoichiometric and path-finding approaches to metabolic pathways
FJ Planes, JE Beasley
Briefings in bioinformatics 9 (5), 422-436, 2008
Exploring metabolic pathways in genome-scale networks via generating flux modes
A Rezola, LF de Figueiredo, M Brock, J Pey, A Podhorski, C Wittmann, ...
Bioinformatics 27 (4), 534-540, 2011
Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
J Seifert, FA Herbst, P Halkjær Nielsen, FJ Planes, N Jehmlich, M Ferrer, ...
Proteomics 13 (18-19), 2786-2804, 2013
Path finding methods accounting for stoichiometry in metabolic networks
J Pey, J Prada, JE Beasley, FJ Planes
Genome biology 12, 1-14, 2011
Recovering metabolic pathways via optimization
JE Beasley, FJ Planes
Bioinformatics 23 (1), 92-98, 2007
An in-silico approach to predict and exploit synthetic lethality in cancer metabolism
I Apaolaza, E San José-Eneriz, L Tobalina, E Miranda, L Garate, X Agirre, ...
Nature communications 8 (1), 459, 2017
Advances in network-based metabolic pathway analysis and gene expression data integration
A Rezola, J Pey, L Tobalina, Á Rubio, JE Beasley, FJ Planes
Briefings in bioinformatics 16 (2), 265-279, 2015
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks
J Pey, FJ Planes
Bioinformatics 30 (15), 2197-2203, 2014
Path finding approaches and metabolic pathways
FJ Planes, JE Beasley
Discrete Applied Mathematics 157 (10), 2244-2256, 2009
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
L Tobalina, R Bargiela, J Pey, FA Herbst, I Lores, D Rojo, C Barbas, ...
Bioinformatics 31 (11), 1771-1779, 2015
Characterization of complete lncRNAs transcriptome reveals the functional and clinical impact of lncRNAs in multiple myeloma
A Carrasco-Leon, T Ezponda, C Meydan, LV Valcárcel, R Ordonez, ...
Leukemia 35 (5), 1438-1450, 2021
Selection of human tissue-specific elementary flux modes using gene expression data
A Rezola, J Pey, LF de Figueiredo, A Podhorski, S Schuster, A Rubio, ...
Bioinformatics 29 (16), 2009-2016, 2013
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm
J Pey, JA Villar, L Tobalina, A Rezola, JM García, JE Beasley, FJ Planes
Bioinformatics 31 (6), 897-904, 2015
Refining carbon flux paths using atomic trace data
J Pey, FJ Planes, JE Beasley
Bioinformatics 30 (7), 975-980, 2014
gMCS: fast computation of genetic minimal cut sets in large networks
I Apaolaza, LV Valcarcel, FJ Planes
Bioinformatics 35 (3), 535-537, 2019
An extended reconstruction of human gut microbiota metabolism of dietary compounds
T Blasco, S Pérez-Burillo, F Balzerani, D Hinojosa-Nogueira, ...
Nature communications 12 (1), 4728, 2021
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