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Vicente Ernesto Acuña Aguayo

Scientist researcher

UNIVERSIDAD DE CHILE

Santiago, Chile

Mathematical modelling, optimization, algorithms, machine learning, constraint-based models, linear programming, integer programming, graphs, networks, enumeration, bioinformatics, hypergraphs, metabolic networks, flux balance analysis.

Bioinformatics, Université de Lyon. Francia, 2010
Computer Science, Universidad de Chile. Chile, 2004
Ingeniero Civil Matemático, Universidad de Chile. Chile, 2002

Postdoctoral position Full Time

Université de Lyon

Lyon, Francia

2010 - 2011
Postdoctoral position Full Time

Universidad de Chile

FCFM

Santiago, Chile

2012 - 2013
Investigador - Scientist Full Time

Universidad de Chile

FCFM

Santiago, Chile

2013 - A la fecha
Profesor Adjunto Part Time

UNIVERSIDAD DE CHILE

Ciencias Físicas y Matemáticas

Santiago, Chile

2016 - A la fecha

Research engineer Full Time

CMM, Universidad de Chile

Santiago, Chile

2004 - 2005

Tutor of Benjamín Ruiz, course of Introduction to Mathematical Modelling (July-December 2014). Center for Mathematical Modeling and Escuela de Ingeniería (Universidad De Chile).

Teaching graduate and postgraduate course "Modeling and Analysis of Biological Networks" (March-July 2014). Doctoral School of Complex Systems (Universidad Adolfo Ibañez) and Escuela de Ingeniería (Universidad De Chile). Jointly with Alejandro Maass and Eric Goles.

Teaching regular course of Probability and Statistics (March-July 2014). Escuela de Ingeniería (Universidad de Chile).

Organization of regular seminar MOAI-Bio (2013-2014). Center for Mathematical Modeling (Universidad de Chile).

Organization of mini course BioASP (2013-2014). Main exposer Santiago Videla. Center for Mathematical Modeling (Universidad de Chile).


Unveiling abundance-dependent metabolic phenotypes of microbial communities Acuna, Vicente; Cortes, Maria Paz; Eveillard, Damien; Maass, Alejandro Eduardo Article ISI MSYSTEMS (2023)
Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways Article SCOPUS Frontiers in Molecular Biosciences (2020)
On Bubble Generators in Directed Graphs Article SCOPUS Algorithmica (2019)
Deciphering transcriptional regulations coordinating the response to environmental changes Acuña V; Aravena, A.; Guziolowski, C; Eveillard D.; Siegel A.; Maass A. Article ISI SCOPUS BMC BIOINFORMATICS (2016)
Enumeration of minimal stoichiometric precursor sets in metabolic networks. Andrade, Ricardo; Wannagat, Martin; Klein, Cecilia C; Acuña, Vicente; Marchetti-Spaccamela, Alberto; Milreu, Paulo V; Stougie, Leen; Sagot, Marie-France Article Algorithms for Molecular Biology (2016)
Solving the maximum edge biclique packing problem on unbalanced bipartite graphs Acuna V., Ferreira C.E.; Freire A.S., Moreno E. Article DISCRETE APPLIED MATHEMATICS (2014)
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure Cottret, L.; Acuña V; Birmelé, E.; Borassi, M.; Junot, C.; Marchetti-Spaccamela, A; Marino, A.; Stougie, L; Jourdan F.; Crescenzi, P.; et al. Article ISI BIOINFORMATICS (2014)
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks Acuña V; Milreu, P.V.; Cottret, L.; Marchetti-Spaccamela, A; Stougie, L; Sagot M. Article ISI SCOPUS Bioinformatics (2012)
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets Acua V.; Birmel E.; Cottret, L.; Crescenzi, P.; Jourdan F.; Lacroix, V.; Marchetti-Spaccamela, A; Marino, A.; Milreu, P.V.; Sagot, M.-F.; et al. Article ISI SCOPUS Theoretical Computer Science (2012)
A note on the complexity of finding and enumerating elementary modes Acuña V; Marchetti-Spaccamela, A; Sagot, M.-F.; Stougie, L Article BIOSYSTEMS (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 Cottret, L.; Milreu, P.V.; Acuña V; Marchetti-Spaccamela, A; Stougie, L; Charles, H.; Sagot, M.-F. Article PLOS COMPUTATIONAL BIOLOGY (2010)
The biclique k-clustering problem in bipartite graphs and its application in bioinformatics Acuna V., Ferreira C.E.; Freire A.S., Moreno E. Article Electronic Notes in Discrete Mathematics (2010)
Modes and cuts in metabolic networks: Complexity and algorithms Acuña V; Chierichetti, F.; Lacroix, V.; Marchetti-Spaccamela, A; Sagot, M.-F.; Stougie, L Article BIOSYSTEMS (2009)
Coding with variable block maps Acuña V; Didier, G; Maass A. Article ISI SCOPUS THEORETICAL COMPUTER SCIENCE (2006)


Modeling parsimonious putative regulatory networks: complexity and heuristic approach Acuña V; Aravena, A.; Maass A.; Siegel A. BookSection (2014)
Enumerating chemical organisations in consistent metabolic networks: Complexity and algorithms Milreu, P.V.; Acuña V; Birmelé, E.; Crescenzi, P.; Marchetti-Spaccamela, A; Sagot, M.-F.; Stougie, L; Lacroix, V. BookSection (2010)
The biclique k-clustering problem in bipartite graphs and its application in bioinformatics Acuña V; Ferreira C.E.; Moreno E. BookSection (2010)
Enumerating precursor sets of target metabolites in a metabolic network Cottret, L.; Milreu, P.V.; Acuña V; Marchetti-Spaccamela, A; Martinez, F.V.; Sagot, M.-F. BookSection (2008)


Minimum ratio cover of matrix columns by extreme rays of its induced cone Acuña V; Crescenzi, P.; Ferreira C.E.; Lacroix, V.; Milreu, P.V.; Moreno E.; Sagot, M.-F. ConferencePaper SCOPUS Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (2012)


Methodological Approaches Investigated as Accurately as possible for applications to biology- MAIA PCI (16STIC-09) Proyecto 2016-2018 Inv. Responsable
ENUMERATING FUNCTIONAL SUBSTRUCTURES IN GENOME WIDE METABOLIC NETWORKS FONDECYT (1140631) Proyecto 2014-2018 Inv. Responsable