PUBLICATIONS
Books
Maranas, CD and Zomorrodi AR, Optimization Methods in Metabolic Networks, Wiley, 2016
Papers
See the latest list of publications in Google Scholar.
21. Zomorrodi AR, Hemez C, Arranz-Gibert P, Wu T, Isaacs FJ, Segrè D. Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. iScience. 2022;25(7):104562. PMID: 35789833.
20. Mehrotra I, Serena G, Cetinbas M, Kenyon V, Victoria MM, Harshman SG, Zomorrodi AR, Sadreyev RI, Fasano A, Leonard MM. Characterization of the blood microbiota in children with Celiac Disease. Current Research in Microbial Sciences. 2021;2:100069
19. Olshan KL, Zomorrodi AR, Pujolassos M, Troisi J, Khan N, Fanelli B, Kenyon V, Fasano A, Leonard MM. Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet. Nutrients. 2021;13(7), PMID: 34210038
18. Leonard MM, Valitutti F, Karathia H, Pujolassos M, Kenyon V, Fanelli B, Troisi J, Subramanian P, Camhi S, Colucci A, Serena G, Cucchiara S, Trovato CM, Malamisura B, Francavilla R, Elli L, Hasan NA, Zomorrodi AR, Colwell R, Fasano A, CDGEMM Team. Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study. Proc Natl Acad Sci U S A. 2021;118(29). PMID: 34253606
17. Colarusso AV, Goodchild-Michelman I, Rayle M, Zomorrodi AR. Computational modeling of metabolism in microbial communities on a genome-scale. Curr Opin Syst Biol. 2021;26:46-57
16. Olshan KL, Leonard MM, Serena G, Zomorrodi AR, Fasano A. Gut Microbiota in Celiac Disease: Microbes, Metabolites, Pathways and Therapeutics. Expert Rev Clin Immunol. 2020. Epub 2020/10/26. doi: 10.1080/1744666X.2021.1840354. PubMed PMID: 33103934.
15. Leonard MM, Karathia H, Pujolassos M, Troisi J, Valitutti F, Subramanian P, Camhi S, Kenyon V, Colucci A, Serena G, Cucchiara S, Montuori M, Malamisura B, Francavilla R, Elli L, Fanelli B, Colwell R, Hasan N, Zomorrodi* AR, Fasano* A, Team C-G. Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease. Microbiome. 2020;8(1):130. Epub 2020/09/11. doi: 10.1186/s40168-020-00906-w. PubMed PMID: 32917289. (*Co-corresponding authors)
14. Zomorrodi AR, Segrè D. Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities. Nat Commun. 2017;8(1):1563. Epub 2017/11/16. doi: 10.1038/s41467-017-01407-5. PubMed PMID: 29146901.
13. Zomorrodi AR, Segrè D. Synthetic Ecology of Microbes: Mathematical Models and Applications. J Mol Biol. 2016;428(5 Pt B):837-61. Epub 2015/11/11. doi: 10.1016/j.jmb.2015.10.019. PubMed PMID: 26522937.
12. Chowdhury A, Zomorrodi AR, Maranas CD. Bilevel optimization techniques in computational strain design. Computers & Chemical Engineering. 2015;72:363-72. doi: 10.1016/j.compchemeng.2014.06.007.
11. Zomorrodi A, Maranas C. Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. European Journal of Operational Research. 2014;237(2):665-76. doi: 10.1016/j.ejor.2014.01.054.
10. Khodayari* A, Zomorrodi* AR, Liao JC, Maranas CD. A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. Metab Eng. 2014;25C:50-62. doi: 10.1016/j.ymben.2014.05.014. PubMed PMID: 24928774. (*Joint first authors)
9. Zomorrodi AR, Islam MM, Maranas CD. d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol. 2014;3(4):247-57. doi: 10.1021/sb4001307. PubMed PMID: 24742179.
8. Chowdhury A, Zomorrodi AR, Maranas CD. k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput Biol. 2014;10(2):e1003487. doi: 10.1371/journal.pcbi.1003487. PubMed PMID: 24586136.
7. Zomorrodi AR, Lafontaine Rivera JG, Liao JC, Maranas CD. Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. Biotechnol J. 2013;8(9):1090-104. doi: 10.1002/biot.201200270. PubMed PMID: 23450699.
6. Ranganathan* S, Tee*; TW, Chowdhury# A, Zomorrodi# AR, Yoon JM, Fu Y, Shanks JV, Maranas CD. An integrated computational and experimental study for overproducing fatty acids in Escherichia coli. Metab Eng. 2012;14(6):687-704. doi: 10.1016/j.ymben.2012.08.008. PubMed PMID: 23036703. (*Joint first authors, #Joint second authors)
5. Zomorrodi AR, Suthers PF, Ranganathan S, Maranas CD. Mathematical optimization applications in metabolic networks. Metab Eng. 2012;14(6):672-86. doi: 10.1016/j.ymben.2012.09.005. PubMed PMID: 23026121.
4. Wang N, Eckert KA, Zomorrodi AR, Xin P, Pan W, Shearer DA, Weisz J, Maranus CD, Clawson GA. Down-regulation of HtrA1 activates the epithelial-mesenchymal transition and ATM DNA damage response pathways. PLoS One. 2012;7(6):e39446. doi: 10.1371/journal.pone.0039446. PubMed PMID: 22761798.
3. Zomorrodi AR, Maranas CD. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol. 2012;8(2):e1002363. doi: 10.1371/journal.pcbi.1002363. PubMed PMID: 22319433.
2. Zomorrodi AR, Maranas CD. Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol. 2010;4:178. doi: 10.1186/1752-0509-4-178. PubMed PMID: 21190580.
1. Suthers* PF, Zomorrodi* A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol. 2009;5:301. doi: 10.1038/msb.2009.56. PubMed PMID: 19690570. (*Joint first authors)