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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.
Milreu PV, Klein CC, Cottret L, Acuña V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF. Milreu PV, et al. Among authors: marchetti spaccamela a. Bioinformatics. 2014 Jan 1;30(1):61-70. doi: 10.1093/bioinformatics/btt597. Epub 2013 Oct 27. Bioinformatics. 2014. PMID: 24167155 Free PMC article.
MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network.
Pusa T, Ferrarini MG, Andrade R, Mary A, Marchetti-Spaccamela A, Stougie L, Sagot MF. Pusa T, et al. Among authors: marchetti spaccamela a. Bioinformatics. 2020 Jan 15;36(2):514-523. doi: 10.1093/bioinformatics/btz584. Bioinformatics. 2020. PMID: 31504164 Free PMC article.
Modes and cuts in metabolic networks: complexity and algorithms.
Acuña V, Chierichetti F, Lacroix V, Marchetti-Spaccamela A, Sagot MF, Stougie L. Acuña V, et al. Among authors: marchetti spaccamela a. Biosystems. 2009 Jan;95(1):51-60. doi: 10.1016/j.biosystems.2008.06.015. Epub 2008 Aug 3. Biosystems. 2009. PMID: 18722501 Review.
Enumeration of minimal stoichiometric precursor sets in metabolic networks.
Andrade R, Wannagat M, Klein CC, Acuña V, Marchetti-Spaccamela A, Milreu PV, Stougie L, Sagot MF. Andrade R, et al. Among authors: marchetti spaccamela a. Algorithms Mol Biol. 2016 Sep 19;11:25. doi: 10.1186/s13015-016-0087-3. eCollection 2016. Algorithms Mol Biol. 2016. PMID: 27679654 Free PMC article.
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 PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF. Cottret L, et al. Among authors: marchetti spaccamela a. PLoS Comput Biol. 2010 Sep 2;6(9):e1000904. doi: 10.1371/journal.pcbi.1000904. PLoS Comput Biol. 2010. PMID: 20838465 Free PMC article.
A Combinatorial Algorithm for Microbial Consortia Synthetic Design.
Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF. Julien-Laferrière A, et al. Among authors: marchetti spaccamela a. Sci Rep. 2016 Jul 4;6:29182. doi: 10.1038/srep29182. Sci Rep. 2016. PMID: 27373593 Free PMC article.