| 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 | 286 | 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 | 200 | 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 | 114 | 2013 |
| A critical examination of stoichiometric and path-finding approaches to metabolic pathways FJ Planes, JE Beasley Briefings in bioinformatics 9 (5), 422-436, 2008 | 70 | 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 | 63 | 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 | 57 | 2013 |
| Path finding methods accounting for stoichiometry in metabolic networks J Pey, J Prada, JE Beasley, FJ Planes Genome biology 12 (5), 1-14, 2011 | 50 | 2011 |
| Recovering metabolic pathways via optimization JE Beasley, FJ Planes Bioinformatics 23 (1), 92-98, 2007 | 49 | 2007 |
| 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 | 35 | 2014 |
| 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 | 33 | 2015 |
| Path finding approaches and metabolic pathways FJ Planes, JE Beasley Discrete Applied Mathematics 157 (10), 2244-2256, 2009 | 31 | 2009 |
| 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 | 30 | 2018 |
| 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), 1-9, 2017 | 29 | 2017 |
| 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 | 29 | 2013 |
| 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 | 28 | 2015 |
| Refining carbon flux paths using atomic trace data J Pey, FJ Planes, JE Beasley Bioinformatics 30 (7), 975-980, 2014 | 23 | 2014 |
| 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 | 19 | 2015 |
| Integrating tracer-based metabolomics data and metabolic fluxes in a linear fashion via elementary carbon modes J Pey, A Rubio, C Theodoropoulos, M Cascante, FJ Planes Metabolic engineering 14 (4), 344-353, 2012 | 14 | 2012 |
| Direct calculation of minimal cut sets involving a specific reaction knock-out L Tobalina, J Pey, FJ Planes Bioinformatics 32 (13), 2001-2007, 2016 | 13 | 2016 |
| A network-based approach for predicting key enzymes explaining metabolite abundance alterations in a disease phenotype J Pey, L Tobalina, JPJ De Cisneros, FJ Planes BMC systems biology 7 (1), 1-12, 2013 | 13 | 2013 |
