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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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