Publications

Janaina Rigonato, Marko Budinich, Alejandro A. Murillo, Manoela C. Brandão, Juan J. Pierella Karlusich, Yawouvi Dodji Soviadan, Ann C. Gregory, Hisashi Endo, Florian Kokoszka, Dean Vik, Nicolas Henry, Paul Frémont, Karine Labadie, Ahmed A. Zayed, Céline Dimier, Marc Picheral, Sarah Searson, Julie Poulain, Stefanie Kandels, Stéphane Pesant, Eric Karsenti, Peer Bork, Chris Bowler, Samuel Chaffron, Colomban de Vargas, Damien Eveillard, Marion Gehlen, Daniele Iudicone, Fabien Lombard, Hiroyuki Ogata, Lars Stemmann, Matthew B. Sullivan, Shinichi Sunagawa, Patrick Wincker, Olivier Jaillon (2021). Insights into biotic and abiotic modulation of ocean mesopelagic communities. bioRxiv.

PDF DOI

S Chaffron, E Delage, M Budinich, D Vintache, N Henry, C Nef, M Ardyna, Aa Zayed, PC Junger, Pe Galand, C Lovejoy, A Murray, H Sarmento, Tara Oceans coordinators, S Acinas, M Babin, D Iudicone, O Jaillon, E Karsenti, P Wincker, L Karp-Boss, MB Sullivan, C Bowler, C de Vargas, D Eveillard (2021). Environmental vulnerability of the global ocean epipelagic plankton community interactome. Science Advances.

PDF DOI

Marko Budinich, Jeremie Bourdon, Abdelhalim Larhlimi, Damien Eveillard (2017). A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PloS one.

PDF DOI

Mauricio Latorre, Maria Paz Cortés, Dante Travisany, Alex Di Genova, Marko Budinich, Angélica Reyes-Jara, Christian Hödar, Mauricio González, Pilar Parada, Roberto A Bobadilla Fazzini (2016). The bioleaching potential of a bacterial consortium. Bioresource technology.

Mauricio Latorre, Nicole Ehrenfeld, Maria Paz Cortés, Dante Travisany, Marko Budinich, Andrés Aravena, Mauricio González, Roberto A Bobadilla Fazzini, Pilar Parada, Alejandro Maass (2016). Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals. Bioresource technology.

Marko Budinich, Jeremie Bourdon, Abdelhalim Larhlimi, Damien Eveillard (2015). OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques. International Conference on Computational Methods in Systems Biology.

Marko Budinich, Jeremie Bourdon, Damien Eveillard (2015). Impact of the species compartment definition on quantitative modeling of microbial communities. bioRxiv.

Mauricio Latorre, Jessica Galloway-Peña, Jung Hyeob Roh, Marko Budinich, Angélica Reyes-Jara, Barbara E Murray, Alejandro Maass, Mauricio González (2014). Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels. Metallomics.

Dante Travisany, Maria Paz Cortés, Mauricio Latorre, Alex Di Genova, Marko Budinich, Roberto A Bobadilla Fazzini, Pilar Parada, Mauricio González, Alejandro Maass (2014). A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment. Research in microbiology.

Roberto A Bobadilla Fazzini, Maria Paz Cortés, Leandro Padilla, Daniel Maturana, Marko Budinich, Alejandro Maass, Pilar Parada (2013). Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans. Biotechnology and bioengineering.

Patricio Martínez, Sebastián Gálvez, Norimasa Ohtsuka, Marko Budinich, Mar\á Paz Cortés, Cristián Serpell, Kenji Nakahigashi, Akiyoshi Hirayama, Masaru Tomita, Tomoyoshi Soga (2013). Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay. Metabolomics.

Marko Budinich, Damien Eveillard, Jeremie Bourdon, Abdelhalim Larhlimi (2013). MeDUSA: a sage-based tool for computing the stoichiometric capacitance of a metabolic network.

PDF