Control analysis in the identification of key enzymes driving metabolic adaptations: Towards drug target discovery. - Atauri, Pedro de; Foguet, Carles; Cascante, Marta (Biosyst., 2023)

Integrating systemic and molecular levels to infer key drivers sustaining metabolic adaptations. - Atauri, Pedro de; Tarrado-Castellarnau, Míriam; Tarragó-Celada, Josep; Foguet, Carles; Karakitsou, Effrosyni; Centelles, Josep J.; Cascante, Marta (PLoS Comput. Biol., 2021)

Interoperable and scalable data analysis with microservices: applications in metabolomics. - Khoonsari, Payam Emami; Moreno, Pablo A.; Bergmann, Sven; Burman, Joachim; Capuccini, Marco; Carone, Matteo; Cascante, Marta; Atauri, Pedro de; Foguet, Carles; González-Beltrán, Alejandra N.; Hankemeier, Thomas; Haug, Kenneth; et al. (Bioinform., 2019)

p13CMFA: Parsimonious 13C metabolic flux analysis. - Foguet, Carles; Jayaraman, Anusha; Marin, Silvia; Selivanov, Vitaly A.; Moreno, Pablo A.; Messeguer, Ramon; Atauri, Pedro de; Cascante, Marta (PLoS Comput. Biol., 2019)

Model-driven discovery of long-chain fatty acid metabolic reprogramming in heterogeneous prostate cancer cells. - Mas, Igor Marín de; Aguilar, Esther; Zodda, Erika; Balcells, Cristina; Marin, Silvia; Dallmann, Guido; Thomson, Timothy M.; Papp, Balázs; Cascante, Marta (PLoS Comput. Biol., 2018)

Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach. - Mas, Igor Marín de; Fanchon, Eric; Papp, Balázs; Kalko, Susana G.; Roca, Josep; Cascante, Marta (Bioinform., 2017)

MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. - Selivanov, Vitaly A.; Benito, Adrián; Miranda, Anibal; Aguilar, Esther; Polat, Ibrahim Halil; Centelles, Josep J.; Jayaraman, Anusha; Lee, Paul W.-N.; Marin, Silvia; Cascante, Marta (BMC Bioinform., 2017)

The future of metabolomics in ELIXIR. - Rijswijk, Merlijn N. van; Beirnaert, Charlie; Caron, Christophe; Cascante, Marta; Angel, Victoria Dominguez Del; Dunn, Warwick B.; Ebbels, Timothy M. D.; Giacomoni, Franck; González-Beltrán, Alejandra N.; Hankemeier, Thomas; Haug, Kenneth; Izquierdo-García, Jose L.; et al. (F1000Research, 2017)

ChainRank, a chain prioritisation method for contextualisation of biological networks. - Tényi, Ákos; Atauri, Pedro de; Gomez-Cabrero, David; Cano, Isaac; Clarke, Kim; Falciani, Francesco; Cascante, Marta; Roca, Josep; Maier, Dieter (BMC Bioinform., 2016)

HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data. - Foguet, Carles; Marin, Silvia; Selivanov, Vitaly A.; Fanchon, Eric; Lee, Wai-Nang Paul; Guinovart, Joan J.; Atauri, Pedro de; Cascante, Marta (PLoS Comput. Biol., 2016)

Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes. - Binns, Michael; Atauri, Pedro de; Vlysidis, Anestis; Cascante, Marta; Theodoropoulos, Constantinos (BMC Bioinform., 2015)

13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes. - Guzmán, Shirley; Marin, Silvia; Miranda, Anibal; Selivanov, Vitaly A.; Centelles, Josep J.; Harmancey, Romain; Smih, Fatima; Turkieh, Annie; Durocher, Yves; Zorzano, Antonio; Rouet, Philippe; Cascante, Marta (BMC Syst. Biol., 2014)

Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis. - Selivanov, Vitaly A.; Cascante, Marta; Friedman, Mark; Schumaker, Mark F.; Trucco, Massimo; Votyakova, Tatyana V. (PLoS Comput. Biol., 2012)

Do elementary flux modes combine linearly at the "atomic" level? Integrating tracer-based metabolomics data and elementary flux modes. - Pey, Jon; Theodoropoulos, Constantinos; Rezola, Alberto; Rubio, Angel; Cascante, Marta; Planes, Francisco J. (Biosyst., 2011)

Knowledge management for systems biology a general and visually driven framework applied to translational medicine. - Maier, Dieter; Kalus, Wenzel; Wolff, Martin; Kalko, Susana G.; Roca, Josep; Mas, Igor Marín de; Turan, Nil; Cascante, Marta; Falciani, Francesco; Hernandez, Miguel; Villà-Freixa, Jordi; Losko, Sascha (BMC Syst. Biol., 2011)

Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions. - Mas, Igor Marín de; Selivanov, Vitaly A.; Marin, Silvia; Roca, Josep; Oresic, Matej; Agius, Loranne; Cascante, Marta (BMC Syst. Biol., 2011)

Reactive Oxygen Species Production by Forward and Reverse Electron Fluxes in the Mitochondrial Respiratory Chain. - Selivanov, Vitaly A.; Votyakova, Tatyana V.; Pivtoraiko, Violetta N.; Zeak, Jennifer; Sukhomlin, Tatiana; Trucco, Massimo; Roca, Josep; Cascante, Marta (PLoS Comput. Biol., 2011)

A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease. - Turan, Nil; Kalko, Susana G.; Stincone, Anna; Clarke, Kim; Sabah, Ayesha; Howlett, Katherine; Curnow, S. John; Rodriguez, Diego A.; Cascante, Marta; O'Neill, Laura; Egginton, Stuart; Roca, Josep; et al. (PLoS Comput. Biol., 2011)

Edelfosine-induced metabolic changes in cancer cells that precede the overproduction of reactive oxygen species and apoptosis. - Selivanov, Vitaly A.; Vizán, Pedro; Mollinedo, Faustino; Fan, Teresa W.-M.; Lee, Paul W.-N.; Cascante, Marta (BMC Syst. Biol., 2010)

Bistability of Mitochondrial Respiration Underlies Paradoxical Reactive Oxygen Species Generation Induced by Anoxia. - Selivanov, Vitaly A.; Votyakova, Tatyana V.; Zeak, Jennifer; Trucco, Massimo; Roca, Josep; Cascante, Marta (PLoS Comput. Biol., 2009)

Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy. - Vera, Julio; Curto, Raul; Cascante, Marta; Torres, Néstor V. (Bioinform., 2007)

Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis. - Selivanov, Vitaly A.; Marin, Silvia; Lee, Paul W.-N.; Cascante, Marta (Bioinform., 2006)

Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells. - Selivanov, Vitaly A.; Meshalkina, Ludmilla E.; Solovjeva, Olga N.; Kuchel, Philip W.; Ramos-Montoya, Antonio; Kochetov, German A.; Lee, Paul W.-N.; Cascante, Marta (Bioinform., 2005)

An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites. - Selivanov, Vitaly A.; Puigjaner, Joaquim; Sillero, Antonio; Centelles, Josep J.; Ramos-Montoya, Antonio; Lee, Paul W.-N.; Cascante, Marta (Bioinform., 2004)