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Hadadi, N., Hafner, J., Shajkofci, A., Zisaki, A., Hatzimanikatis, V. ATLAS of Biochemistry, A repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synthetic Biology 5, 1155–1166 (2016). Publisher

Hafner, J., Mohammadi Peyhani, H., Sveshnikova, A. et al. Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power. ACS Synthetic Biology x, xxxx-xxxx (2020). Publisher


 Hadadi, N., MohammadiPeyhani, H., Miskovic, L., Seijo, M. & Hatzimanikatis, V. Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites. Proc. Natl. Acad. Sci. U. S. A. 201818877 (2019). Publisher


Jankowski, M. D., Henry, C. S., Broadbelt, L. J. & Hatzimanikatis, V. Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks. Biophysical Journal 95, 1487–1499 (2008). Publisher


Tokic, M., Hadadi, N., Ataman, M. et al. Discovery and evaluation of biosynthetic pathways for the production of five methyl ethyl ketone precursors. ACS Synthetic Biology 7, 1859-1873 (2018). Publisher

 MohammadiPeyhani, H.,et al. Database for drug metabolism and comparisons,, aids discovery and design. Preprint on BioRxiv. Publisher


 MohammadiPeyhani, H., Hafner, J. et al. ATLASx: a computational map for the exploration of biochemical space. Preprint on BioRxiv. Publisher


Chiappino-Pepe, A., Tymoshenko, S., Ataman, M., Soldati-Favre, D., Hatzimanikatis, V. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. PLoS Comput Biol 13 (3), (2017). Publisher

Stanway, R., et al., Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. Cell 179, 1112-1128.e26 (2019). Publisher

Hatzimanikatis, V. et al. Exploring the diversity of complex metabolic networks. Bioinformatics 21, 1603–1609 (2005). Publisher

Finley, S. D., Broadbelt, L. J. & Hatzimanikatis, V. Computational framework for predictive biodegradation. Biotechnology and Bioengineering 104, 1086–1097 (2009). Publisher

Soh, K. C. & Hatzimanikatis, V. DREAMS of metabolism. Trends in Biotechnology 28, 501–508 (2010). Publisher

Henry, C. S., Broadbelt, L. J. & Hatzimanikatis, V. Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnology and Bioengineering 106, 462–473 (2010). Publisher

Finley, S. D., Broadbelt, L. J. & Hatzimanikatis, V. In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene. BMC Systems Biology 4, 7 (2010). Publisher

Hadadi, N. et al. A computational framework for integration of lipidomics data into metabolic pathways. Metabolic Engineering 23, 1–8 (2014). Publisher

Hadadi, N. & Hatzimanikatis, V. Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Current Opinion in Chemical Biology 28, 99–104 (2015). Publisher

Hadadi, N., Hafner, J., Soh, K. C. & Hatzimanikatis, V. Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites. Biotechnology Journal , (2016). Publisher