Coding with variable block maps. - Vicente Acuña; Gilles Didier; Alejandro Maass (Theor. Comput. Sci., 2006)

Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. - Ludovic Cottret; Paulo Vieira Milreu; Vicente Acuña; Alberto Marchetti-Spaccamela; Fábio Viduani Martinez; Marie-France Sagot; Leen Stougie (WABI, 2008)

Modes and cuts in metabolic networks: Complexity and algorithms. - Vicente Acuña; Flavio Chierichetti; Vincent Lacroix; Alberto Marchetti-Spaccamela; Marie-France Sagot; Leen Stougie (Biosyst., 2009)

Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms. - Paulo Vieira Milreu; Vicente Acuña; Etienne Birmelé; Pierluigi Crescenzi; Alberto Marchetti-Spaccamela; Marie-France Sagot; Leen Stougie; Vincent Lacroix (WABI, 2010)

A note on the complexity of finding and enumerating elementary modes. - Vicente Acuña; Alberto Marchetti-Spaccamela; Marie-France Sagot; Leen Stougie (Biosyst., 2010)

The biclique k-clustering problem in bipartite graphs and its application in bioinformatics. - Vicente Acuña; Carlos Eduardo Ferreira; Alexandre S. Freire; Eduardo Moreno 001 (Electron. Notes Discret. Math., 2010)

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata. - Ludovic Cottret; Paulo Vieira Milreu; Vicente Acuña; Alberto Marchetti-Spaccamela; Leen Stougie; Hubert Charles; Marie-France Sagot (PLoS Comput. Biol., 2010)

Models and algorithms for metabolic networks: elementary modes and precursor sets. - Vicente Acuña (2010)

Minimum Ratio Cover of Matrix Columns by Extreme Rays of Its Induced Cone. - Alexandre S. Freire; Vicente Acuña; Pilu Crescenzi; Carlos Eduardo Ferreira; Vincent Lacroix; Paulo Vieira Milreu; Eduardo Moreno 001; Marie-France Sagot (ISCO, 2012)

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. - Vicente Acuña; Paulo Vieira Milreu; Ludovic Cottret; Alberto Marchetti-Spaccamela; Leen Stougie; Marie-France Sagot (Bioinform., 2012)

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. - Vicente Acuña; Etienne Birmelé; Ludovic Cottret; Pierluigi Crescenzi; Fabien Jourdan; Vincent Lacroix; Alberto Marchetti-Spaccamela; Andrea Marino 001; Paulo Vieira Milreu; Marie-France Sagot; Leen Stougie (Theor. Comput. Sci., 2012)

Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic Approach. - Vicente Acuña; Andrés Aravena; Alejandro Maass; Anne Siegel (VMCAI, 2014)

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. - Paulo Vieira Milreu; Cecilia Coimbra Klein; Ludovic Cottret; Vicente Acuña; Etienne Birmelé; Michele Borassi; Christophe Junot; Alberto Marchetti-Spaccamela; Andrea Marino 001; Leen Stougie; Fabien Jourdan; Pierluigi Crescenzi; et al. (Bioinform., 2014)

Solving the maximum edge biclique packing problem on unbalanced bipartite graphs. - Vicente Acuña; Carlos Eduardo Ferreira; Alexandre S. Freire; Eduardo Moreno 001 (Discret. Appl. Math., 2014)

Enumeration of minimal stoichiometric precursor sets in metabolic networks. - Ricardo Andrade; Martin Wannagat; Cecilia Coimbra Klein; Vicente Acuña; Alberto Marchetti-Spaccamela; Paulo Vieira Milreu; Leen Stougie; Marie-France Sagot (Algorithms Mol. Biol., 2016)

Deciphering transcriptional regulations coordinating the response to environmental changes. - Vicente Acuña; Andrés Aravena; Carito Guziolowski; Damien Eveillard; Anne Siegel; Alejandro Maass (BMC Bioinform., 2016)

A Family of Tree-Based Generators for Bubbles in Directed Graphs. - Vicente Acuña; Leandro Lima; Giuseppe F. Italiano; Luca Pepè Sciarria; Marie-France Sagot; Blerina Sinaimeri (IWOCA, 2020)

On Bubble Generators in Directed Graphs. - Vicente Acuña; Roberto Grossi; Giuseppe Francesco Italiano; Leandro Lima; Romeo Rizzi; Gustavo Sacomoto; Marie-France Sagot; Blerina Sinaimeri (Algorithmica, 2020)

A family of tree-based generators for bubbles in directed graphs. - Vicente Acuña; Leandro Ishi Soares de Lima; Giuseppe F. Italiano; Luca Pepè Sciarria; Marie-France Sagot; Blerina Sinaimeri (J. Graph Algorithms Appl., 2021)

METACONE: A scalable framework for exploring the conversion cone of metabolic networks. - Álvaro Altamirano; Ignacio Tapia; Vicente Acuña; Daniel Garrido; Pedro A. Saa (Comput. Biol. Chem., 2026)