A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems
Budinich, Marko, Bourdon, Jérémie, Larhlimi, Abdelhalim, Eveillard, Damien
Published in PloS one (10.02.2017)
Published in PloS one (10.02.2017)
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Journal Article
Community metabolic modeling of host-microbiota interactions through multi-objective optimization
Lambert, Anna, Budinich, Marko, Mahé, Maxime, Chaffron, Samuel, Eveillard, Damien
Published in iScience (21.06.2024)
Published in iScience (21.06.2024)
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Journal Article
Environmental vulnerability of the global ocean epipelagic plankton community interactome
Chaffron, Samuel, Delage, Erwan, Budinich, Marko, Vintache, Damien, Henry, Nicolas, Nef, Charlotte, Ardyna, Mathieu, Zayed, Ahmed A, Junger, Pedro C, Galand, Pierre E, Lovejoy, Connie, Murray, Alison E, Sarmento, Hugo, Acinas, Silvia G, Babin, Marcel, Iudicone, Daniele, Jaillon, Olivier, Karsenti, Eric, Wincker, Patrick, Karp-Boss, Lee, Sullivan, Matthew B, Bowler, Chris, de Vargas, Colomban, Eveillard, Damien
Published in Science advances (01.08.2021)
Published in Science advances (01.08.2021)
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Journal Article
Stoichiometric modeling of oxidation of reduced inorganic sulfur compounds (Riscs) in Acidithiobacillus thiooxidans
Bobadilla Fazzini, Roberto A., Cortés, Maria Paz, Padilla, Leandro, Maturana, Daniel, Budinich, Marko, Maass, Alejandro, Parada, Pilar
Published in Biotechnology and bioengineering (01.08.2013)
Published in Biotechnology and bioengineering (01.08.2013)
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Journal Article
Niche partitioning and plastisphere core microbiomes in the two most plastic polluted zones of the world ocean
Jacquin, Justine, Budinich, Marko, Chaffron, Samuel, Barbe, Valérie, Lombard, Fabien, Pedrotti, Maria-Luiza, Gorsky, Gabriel, ter Halle, Alexandra, Bruzaud, Stéphane, Kedzierski, Mikaël, Ghiglione, Jean-François
Published in Environmental science and pollution research international (01.06.2024)
Published in Environmental science and pollution research international (01.06.2024)
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Journal Article
Contribution of genome‐scale metabolic modelling to niche theory
Régimbeau, Antoine, Budinich, Marko, Larhlimi, Abdelhalim, Pierella Karlusich, Juan José, Aumont, Olivier, Memery, Laurent, Bowler, Chris, Eveillard, Damien, Jordan, Ferenc
Published in Ecology letters (01.06.2022)
Published in Ecology letters (01.06.2022)
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Journal Article
The bioleaching potential of a bacterial consortium
Latorre, Mauricio, Cortés, María Paz, Travisany, Dante, Di Genova, Alex, Budinich, Marko, Reyes-Jara, Angélica, Hödar, Christian, González, Mauricio, Parada, Pilar, Bobadilla-Fazzini, Roberto A., Cambiazo, Verónica, Maass, Alejandro
Published in Bioresource technology (01.10.2016)
Published in Bioresource technology (01.10.2016)
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Journal Article
A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment
Travisany, Dante, Cortés, María Paz, Latorre, Mauricio, Di Genova, Alex, Budinich, Marko, Bobadilla-Fazzini, Roberto A., Parada, Pilar, González, Mauricio, Maass, Alejandro
Published in Research in microbiology (01.11.2014)
Published in Research in microbiology (01.11.2014)
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Journal Article
Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals
Latorre, Mauricio, Ehrenfeld, Nicole, Cortés, María Paz, Travisany, Dante, Budinich, Marko, Aravena, Andrés, González, Mauricio, Bobadilla-Fazzini, Roberto A., Parada, Pilar, Maass, Alejandro
Published in Bioresource technology (01.01.2016)
Published in Bioresource technology (01.01.2016)
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Journal Article
OPINION PAPER Evolutionary Constraint-Based Formulation Requires New Bi-level Solving Techniques
Budinich, Marko, Bourdon, Jérémie, Larhlimi, Abdelhalim, Eveillard, Damien
Published in Computational Methods in Systems Biology (01.01.2015)
Published in Computational Methods in Systems Biology (01.01.2015)
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Book Chapter
Conference Proceeding
Priorities for ocean microbiome research
Abreu, Andre, Bourgois, Etienne, Gristwood, Adam, Troublé, Romain, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, Budinich, Marko, Chaffron, Samuel, de Vargas, Colomban, Delmont, Tom O., Eveillard, Damien, Guidi, Lionel, Iudicone, Daniele, Kandels, Stephanie, Morlon, Hélène, Lombard, Fabien, Pepperkok, Rainer, Karlusich, Juan José Pierella, Piganeau, Gwenael, Régimbeau, Antoine, Sommeria-Klein, Guilhem, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Zablocki, Olivier, Arendt, Detlev, Bilic, Josipa, Finn, Robert, Heard, Edith, Rouse, Brendan, Vamathevan, Jessica, Casotti, Raffaella, Cancio, Ibon, Cunliffe, Michael, Kervella, Anne Emmanuelle, Kooistra, Wiebe H. C. F., Obst, Matthias, Pade, Nicolas, Power, Deborah M., Santi, Ioulia, Tsagaraki, Tatiana Margo, Vanaverbeke, Jan
Published in Nature microbiology (01.07.2022)
Published in Nature microbiology (01.07.2022)
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Journal Article
Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay
Martínez, Patricio, Gálvez, Sebastián, Ohtsuka, Norimasa, Budinich, Marko, Cortés, María Paz, Serpell, Cristián, Nakahigashi, Kenji, Hirayama, Akiyoshi, Tomita, Masaru, Soga, Tomoyoshi, Martínez, Servet, Maass, Alejandro, Parada, Pilar
Published in Metabolomics (01.02.2013)
Published in Metabolomics (01.02.2013)
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Journal Article
Ocean-wide comparisons of mesopelagic planktonic community structures
Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A, Brandão, Manoela C, Pierella Karlusich, Juan J, Soviadan, Yawouvi Dodji, Gregory, Ann C, Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A, Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels, Stefanie, Pesant, Stéphane, Karsenti, Eric, Acinas, Silvia G, Boss, Emmanuel, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karp-Boss, Lee, Not, Fabrice, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Bork, Peer, Bowler, Chris, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, Jaillon, Olivier
Published in ISME Communications (01.12.2023)
Published in ISME Communications (01.12.2023)
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Journal Article
Ocean-wide comparisons of mesopelagic planktonic community structures
Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro, Brandão, Manoela, Pierella Karlusich, Juan, Soviadan, Yawouvi Dodji, Gregory, Ann, Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed, Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels, Stefanie, Pesant, Stéphane, Karsenti, Eric, Acinas, Silvia, Boss, Emmanuel, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karp-Boss, Lee, Not, Fabrice, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Bork, Peer, Bowler, Chris, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew, Sunagawa, Shinichi, Wincker, Patrick, Chaffron, Samuel, Jaillon, Olivier
Published in ISME Communications (01.12.2023)
Published in ISME Communications (01.12.2023)
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Journal Article
Enterococcus faecalis reconfigures its transcriptional regulatory network activation at different copper levels
Latorre, Mauricio, Galloway-Peña, Jessica, Roh, Jung Hyeob, Budinich, Marko, Reyes-Jara, Angélica, Murray, Barbara E, Maass, Alejandro, González, Mauricio
Published in Metallomics (01.03.2014)
Published in Metallomics (01.03.2014)
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Journal Article
Insights into biotic and abiotic modulation of ocean mesopelagic communities
Rigonato, Janaina, Budinich, Marko, Murillo, Alejandro A, Brandão, Manoela C, Juan J Pierella Karlusich, Soviadan, Yawouvi Dodji, Gregory, Ann C, Endo, Hisashi, Kokoszka, Florian, Vik, Dean, Henry, Nicolas, Frémont, Paul, Labadie, Karine, Zayed, Ahmed A, Dimier, Céline, Picheral, Marc, Searson, Sarah, Poulain, Julie, Kandels, Stefanie, Pesant, Stéphane, Karsenti, Eric, The Tara Oceans Coordinators, Bork, Peer, Bowler, Chris, Chaffron, Samuel, De Vargas, Colomban, Eveillard, Damien, Gehlen, Marion, Iudicone, Daniele, Lombard, Fabien, Ogata, Hiroyuki, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Jaillon, Olivier
Published in bioRxiv (27.02.2021)
Published in bioRxiv (27.02.2021)
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Paper
Method to increase the production of extracellular polymeric substances (EPS) in a Acidithiobacillus ferrooxidans culture by the inhibition of enzymes of tricarboxilic acid cycle
BUDINICH ABARCA MARKO ANTONIO, PARADA VALDECANTOS PILAR ANGÉLICA, PADILLA IGLESIAS LEANDRO MAURICIO, MORENO CORTÉZ PABLO ANDRÉS, MAASS SEPÚLVED ALEJANDRO EDUARDO, BARRETO ROA MARLEN NAYIBE
Year of Publication 06.01.2015
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Year of Publication 06.01.2015
Patent
METHOD TO INCREASE THE PRODUCTION OF EXTRACELLULAR POLYMERIC SUBSTANCES (EPS) IN A ACIDITHIOBACILLUS FERROOXIDANS CULTURE BY THE INHIBITION OF ENZYMES OF TRICARBOXILIC ACID CYCLE
BUDINICH ABARCA MARKO ANTONIO, PARADA VALDECANTOS PILAR ANGELICA, MAASS SEPULVEDA ALEJANDRO EDUARDO, PADILLA IGLESIAS LEANDRO MAURICIO, MORENO CORTEZ PABLO ANDRES, BARRETO ROA MARLEN NAYIBE
Year of Publication 29.02.2012
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Year of Publication 29.02.2012
Patent