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Ali Zomorrodi, Ph.D.

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Mentoring
Available: 07/01/20, Expires: 06/30/21

The goal of this project is to construct the next-generation of biological network models for macrophages (one of the major innate immune cells) through integrating models of metabolism and gene expression.

Having a keen interest in computational research is the only requirement and no mathematical or programming skills are needed. Interested candidates are, however, expected to learn Python or MATLAB during the course of this project.

This project can be performed entirely remotely during the pandemic.

Available: 07/01/20, Expires: 06/30/21

The goal of this project is to reconstruct species-resolved metabolic network models of the gut microbiota using metagenomic data collected from IBD patients and healthy subjects during the Human Microbiome Project (HMP).

Having a keen interest in computational research is the only requirement and no mathematical or programming skills are needed. For students who are particularly interested in computational modeling or computer programming there are ample opportunities to tailor the projects toward their interests.

This project can be performed entirely remotely during the pandemic.

Available: 07/01/20, Expires: 06/30/21

The goal of this project is to computationally assess how the gut microbiota affects the host metabolic phenotypes in celiac and non-celiac children by using genome-scale metabolic network models.
Having a keen interest in computational research is the only requirement and no mathematical or programming skills are needed.

For students who are particularly interested in computational modeling or computer programming there are ample opportunities to tailor the projects toward their interests.

This project can be performed entirely remotely during the pandemic.


Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Zomorrodi AR, Segrè D. Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities. Nat Commun. 2017 11 16; 8(1):1563. PMID: 29146901.
    Citations:    
  2. Zomorrodi AR, Segrè D. Synthetic Ecology of Microbes: Mathematical Models and Applications. J Mol Biol. 2016 Feb 27; 428(5 Pt B):837-61. PMID: 26522937.
    Citations:    
  3. Chowdhury A, Zomorrodi AR, Maranas CD. Bilevel optimization techniques in computational strain design. Computers & Chemical Engineering. 2015; 72:363-372. View Publication.
  4. Zomorrodi AR, Maranas CD. Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. European Journal of Operational Research. 2014; 237(2):665-676. View Publication.
  5. 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 Sep; 25:50-62. PMID: 24928774.
    Citations:    
  6. Zomorrodi AR, Islam MM, Maranas CD. d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. ACS Synth Biol. 2014 Apr 18; 3(4):247-57. PMID: 24742179.
    Citations:    
  7. Chowdhury A, Zomorrodi AR, Maranas CD. k-OptForce: integrating kinetics with flux balance analysis for strain design. PLoS Comput Biol. 2014 Feb; 10(2):e1003487. PMID: 24586136.
    Citations:    
  8. 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 Sep; 8(9):1090-104. PMID: 23450699.
    Citations:    
  9. 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 Nov; 14(6):687-704. PMID: 23036703.
    Citations:    
  10. Zomorrodi AR, Suthers PF, Ranganathan S, Maranas CD. Mathematical optimization applications in metabolic networks. Metab Eng. 2012 Nov; 14(6):672-86. PMID: 23026121.
    Citations:    
  11. 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. PMID: 22761798.
    Citations:    
  12. Zomorrodi AR, Maranas CD. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comput Biol. 2012 Feb; 8(2):e1002363. PMID: 22319433.
    Citations:    
  13. Zomorrodi AR, Maranas CD. Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol. 2010 Dec 29; 4:178. PMID: 21190580.
    Citations:    
  14. Suthers PF, Zomorrodi A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol. 2009; 5:301. PMID: 19690570.
    Citations:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.