Articles

2021
  1. Alsiyabi, A., Chowdhury, N.B., Long, D.S., Saha, R., "Enhancing in silico strain design predictions through next generation metabolic modeling approaches", Biotechnology Advances, In press, (2021).
  2. Islam, M.M., Goertzen, A., Singh, P.K., and Saha, R., "Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling", bioRxiv preprint, https://doi.org/10.1101/2021.07.14.452356, (2021).
  3. Schroeder., W., Baber, A.S., and Saha, R.,"Optimization-Based Eukaryotic Genetic Circuit Design (EuGeneCiD) and Modeling (EuGeneCiM) Tools: Computational Approach to Synthetic Biology", bioRxiv preprint, doi: http://dx.doi.org/10.2139/ssrn.3850370, (2021).
  4. Islam, M. M., Schroeder, W., and Saha, R., "Kinetic Modeling of Metabolism: Present and Future", Current Opinion in Systems Biology, 26:72-78, (2021).
  5. Long, D.S.,  Immethun, C.M., Vallecilla-Yepez, L., Wilkins, M.R., and Saha, R. "One step forward, two steps back: transcriptional advancements and fermentation phenomena in Actinobacillus succinogenes 130ZPLoS ONE 16(5): e0245407 (2021).
  6. Chowdhury, N. B.Schroeder, W., Sarkar, D., Amiour, N., Quilleré, I., Hirel, B., Costas, C. D., and Saha, R., "Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition", bioRxiv preprint, doi: https://doi.org/10.1101/2021.04.30.442195, (2021).

  7. Alsiyabi, A., Brown, B., Immethun, C., Wilkins, M., and Saha, R., "Synergistic experimental and computational approach identifies novel strategies for PHB overproduction", Research Square preprint, doi: 10.21203/rs.3.rs-334477/v1, (2021).
  8. Alsiyabi, A., Solis. A.G., Cahoon. E. B., and Saha, R., "Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants", PLoS Comput Biol 17(1): e1008284 (2021).

2020
  1. Zamani, E., Johnson, T. J., Chatterjee, S., Immethun, C., Sarella, A., Saha, R., and Dishari, S. K., "Cationic π-Conjugated Polyelectrolyte Shows Antimicrobial Activity by Causing Lipid Loss and Lowering Elastic Modulus of Bacteria", ACS Applied Materials and Interfaces, (2020).

  2. Islam, M. M., Sandhu, J., Walia, H., and Saha, R., "Transcriptomic data-driven discovery of global regulatory features of rice seeds developing under heat stress", Computational and Structural Biotechnology Journal, 18:2556-2567, (2020).

  3. Schroeder., W., and Saha, R., "Protocol for Genome-scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis", STAR Protocol, (2020).
  4. Islam, M. M., Le, T., Daggumati, S. R., and Saha, R., "Investigation of microbial community interactions between lake Washington methanotrophs using genome-scale metabolic modeling", PeerJ, 8:e9464, (2020).

  5. Brown, B., Immethun, C., Wilkins, M., and Saha, R., "Rhodopseudomonas palustris CGA009 polyhydroxybutyrate production from a lignin aromatic and quantification via flow cytometry", Bioresource Technology Reports, 11:1000474 (2020).
  6. Schroeder., W., and Saha, R., "Introducing an Optimization- and explicit Runge-Kutta- based Approach to Perform Dynamic Flux Balance Analysis", Scientific Reports, 10: 9241 (2020).
  7. Schroeder., W., and Saha, R., "Computation-Driven Analysis of Model Polyextremo- tolerant Fungus Exophiala dermatitidis: Defensive Pigment Metabolic Costs and Human Applications", iScience, 23:100980, (2020).
  8. Islam, M. M., Thomas, V. C., Van Beek, M., Ahn, J., Alqarzaee, A. A., Zhou, C., Fey, P. D., Bayles, K. W., and Saha, R., "An integrated computational and experimental study to elucidate Staphylococcus aureus metabolism", npj Systems Biology and Application 6:3 (202o).
  9. Schroeder., W., and Saha, R., "OptFill: ATool for Infeasible Cycle-Free Gapfilling of Stoichiometric Metabolic Models", iScience 23:1 (2020).

  10. Schroeder., W., and Saha, R., "KOPTIC: A novel approach for in silico prediction of enzyme kinetics and regulation", bioRxiv preprint, doi: https://doi.org/10.1101/807628, (2020).

2019
  1. Zamani, E., Chatterjee, S., Changa, T., Immethun, C., Sarella, A., Saha, R., Dishari, S. K., "Mechanistic Understanding of the Interactions of Cationic Conjugated Oligo- and Polyelectrolytes with Wild-type and Ampicillin-resistant Escherichia coli". Sci Rep 9, 20411 (2019).

  2. Islam, M. M., Fernando, S. C., and Saha, R., "Metabolic Modeling Elucidates Metabolic Transactions in the Rumen Microbiome and the Metabolic Shifts upon virome Interactions",  Frontiers in Microbiology 10, 2412 (2019).

  3. Al-Siyabi, A., Immethun, C., and Saha, R., "Modeling the Interplay Between Photosynthesis, Carbon Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium", Nat Sci Rep, 9 (2019).

  4. Immethun, C. M., Daher, T., and R Saha." Applying Blended Learning Techniques: Perspectives from Chemical Engineering Computation", Chem Eng Educ53:3 (2019)

2018
  1. Islam, M. M., Al-Siyabi, A., Obata, T., and Saha, R., "Dissecting metabolic flux in C4 plants: experimental and theoretical approaches", Phytochemistry Reviews, https://doi.org/10.1007/s11101-018-9579-8 (2018)
2017
  1. Lin, P., Saha, R., Zhang, F., and Pakrasi, H. (2017), "Metabolic Engineering of the Pentose Phosphate Pathway for Enhanced Limonene Production in the Cyanobacterium Synechocystis sp. PCC 6803", Nature Scientific Reports, 7:17503, DOI:10.1038/s41598-017-17831-y.