Ali R. Zomorrodi

发表

MINLP Fundamentals and Applications

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2016 .

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

Costas D. Maranas, Ali R. Zomorrodi, Anupam Chowdhury, 2014, PLoS Comput. Biol..

Appendix A Coding Optimization Models in GAMS

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2016 .

Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2010, BMC Systems Biology.

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2012, PLoS Comput. Biol..

Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2014, Eur. J. Oper. Res..

Bilevel optimization techniques in computational strain design

Costas D. Maranas, Ali R. Zomorrodi, Anupam Chowdhury, 2015, Comput. Chem. Eng..

Optimization Methods in Metabolic Networks: Maranas/Optimization Methods in Metabolic Networks

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2016 .

Computational Strain Design

Costas D. Maranas, Ali R. Zomorrodi, C. Maranas, 2016 .

Computational modeling of metabolism in microbial communities on a genome-scale

Ali R. Zomorrodi, Analeigha V. Colarusso, Isabella Goodchild-Michelman, 2021, Current Opinion in Systems Biology.

A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data.

Ali R. Zomorrodi, J. Liao, C. Maranas, 2014, Metabolic engineering.

Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks.

Ali R. Zomorrodi, J. Liao, C. Maranas, 2013, Biotechnology journal.

d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities.

Ali R. Zomorrodi, C. Maranas, M. Islam, 2014, ACS synthetic biology.

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

Ali R. Zomorrodi, D. Segrè, 2017, Nature Communications.

Genome-scale gene/reaction essentiality and synthetic lethality analysis

Ali R. Zomorrodi, C. Maranas, P. Suthers, 2009, Molecular systems biology.

Comparison of PID Controller Tuning Methods

Mohammad Shahrokhi, Ali R. Zomorrodi, M. Shahrokhi, 2012 .

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli.

Ali R. Zomorrodi, Anupam Chowdhury, Costas D Maranas, 2012, Metabolic engineering.

Genome-scalegene/reaction essentialityandsynthetic lethality analysis

Ali R. Zomorrodi, C. Maranas, P. Suthers, 2009 .

Mathematical Optimization Fundamentals

Ali R. Zomorrodi, C. Maranas, 2016 .

Down-Regulation of HtrA1 Activates the Epithelial-Mesenchymal Transition and ATM DNA Damage Response Pathways

Ali R. Zomorrodi, K. Eckert, J. Weisz, 2012, PloS one.

Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease

Ali R. Zomorrodi, R. Colwell, P. Subramanian, 2020, Microbiome.

Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine

Farren J. Isaacs, Ali R. Zomorrodi, D. Segrè, 2022, iScience.

Resolving Network Gaps and Growth Prediction Inconsistencies in Metabolic Networks

Ali R. Zomorrodi, C. Maranas, 2016 .

Strategies and Technologies Computing for Systems Biology 230 Standards in Genomic Sciences : Launch of a Standards Compliant Open-Access Journal for the ‘ Omics Community

George A. Khoury, Ali R. Zomorrodi, P. Cirino, 2022 .

Intracellular metabolic circuits shape inter-species microbial interactions

Ali R. Zomorrodi, D. Segrè, 2017, bioRxiv.

Thermodynamic Analysis of Metabolic Networks

Ali R. Zomorrodi, C. Maranas, 2016 .

Flux Balance Analysis and LP Problems

Ali R. Zomorrodi, C. Maranas, 2016 .

Synthetic Ecology of Microbes: Mathematical Models and Applications.

Daniel Segrè, Ali R. Zomorrodi, Ali R Zomorrodi, 2016, Journal of molecular biology.

Mathematical optimization applications in metabolic networks.

Ali R. Zomorrodi, Patrick F Suthers, Sridhar Ranganathan, 2012, Metabolic engineering.

Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study

Ali R. Zomorrodi, P. Subramanian, Nur A. Hasan, 2021, Proceedings of the National Academy of Sciences.

Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet

Ali R. Zomorrodi, A. Fasano, J. Troisi, 2021, Nutrients.

Gut microbiota in Celiac Disease: microbes, metabolites, pathways and therapeutics

Ali R. Zomorrodi, A. Fasano, M. Leonard, 2020, Expert review of clinical immunology.

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities

Ali R. Zomorrodi, D. Segrè, 2017, Nature Communications.

Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease

Ali R. Zomorrodi, P. Subramanian, A. Fasano, 2020, Microbiome.

Comparison of MLP NN Approach with PCA and ICA for Extraction of Hidden Regulatory Signals in Biological Networks

Ali R. Zomorrodi, B. Nasernejad, J. Kabudian, 2006 .

Characterization of the blood microbiota in children with Celiac disease

Ali R. Zomorrodi, R. Sadreyev, A. Fasano, 2021, Current Research in Microbial Sciences.

LP and Duality Theory

Ali R. Zomorrodi, C. Maranas, 2016 .

Computational design and construction of an Escherichia coli strain engineered to produce a non-standard amino acid

Farren J. Isaacs, Ali R. Zomorrodi, D. Segrè, 2022, bioRxiv.

Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities

Ali R. Zomorrodi, 2012 .

Modeling with Binary Variables and MILP Fundamentals

Ali R. Zomorrodi, C. Maranas, 2016 .

Using Systems Engineering to Reconstruct, Analyze and Redesign Metabolism

Ali R. Zomorrodi, C. Maranas, P. Suthers, 2009 .

Mathematical optimization applications in metabolic networks.

Ali R. Zomorrodi, C. Maranas, P. Suthers, 2012, Metabolic engineering.