Articles

2021
  1. Alqarzaee, A. A., Chaudhari, S. S., Islam, M. M., Kumar, V., Zimmerman, M. C., Saha, R., Bayles, K. W., Frees, D., and Thomas, V. C., "Staphylococcal ClpXP protease targets the cellular antioxidant system to eliminate fitness-compromised cells in stationary phase", Proceedings of the National Academy of Sciences of the United States of America, doi: https://doi.org/10.1073/pnas.2109671118, (2021).
  2. Vallecilla-Yepez, L., Ramchandran, D., Long, D., Saha, R., and Wilkins, M. R., "Corn fiber as a biomass feedstock for production of succinic acid", Bioresource Technology Reports, doi: https://doi.org/10.1016/j.biteb.2021.100868, (2021).
  3. 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", Journal of Experimental Botany, doi: https://doi.org/10.1093/jxb/erab435, (2021).
  4. Schroeder., W., Baber, A.S., and Saha, R.,"Using EuGeneCid and EuGeneCim computational tools for synthetic biology", STAR Protocols, doi: https://doi.org/10.1016/j.xpro.2021.100820, (2021).
  5. Alsiyabi, A., Stroh, S., and Saha, R., "Investigating the effect of E30 fuel on long term vehicle performance, adaptability and economic feasibility", Fuel, doi: https://doi.org/10.1016/j.fuel.2021.121629, (2021)
  6. Schroeder., W., Baber, A.S., and Saha, R.,"Optimization-Based Eukaryotic Genetic Circuit Design (EuGeneCiD) and Modeling (EuGeneCiM) Tools: Computational Approach to Synthetic Biology", iSciene, doi: https://doi.org/10.1016/j.isci.2021.103000, (2021).
  7. Alsiyabi, A., Brown, B., Immethun, C., Wilkins, M., and Saha, R., "Synergistic experimental and computational approach identifies novel strategies for PHB overproduction", Metabolic Engineering, doi: https://doi.org/10.1016/j.ymben.2021.08.008, (2021).
  8. Alsiyabi, A., Chowdhury, N.B., Long, D.S., Saha, R., "Enhancing in silico strain design predictions through next generation metabolic modeling approaches", Biotechnology Advances, doi: https://doi.org/10.1016/j.biotechadv.2021.107806, (2021).
  9. 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).
  10. Islam, M. M., Schroeder, W., and Saha, R., "Kinetic Modeling of Metabolism: Present and Future", Current Opinion in Systems Biology, 26:72-78, (2021).
  11. 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).
  12. 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.

                          Prior to joining UNL
  1. Saha, R., Liu, D., O'Connor, A.G., Liberton, M., Yu, J., Bhattacharyya, M., Balassy, A., Zhang, F., Moon, T.S., Maranas, C.D. and Pakrasi, H.B. (2016), “Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. PCC 6803: Insights from Transcriptomic, Fluxomic and Physiological Analyses”, mBio, 7(3), e00464-16.

  2. Liberton, M., Saha, R., Jacobs, J. M., Nguyen, A.Y., Chrisler, W.B., Gritsenko, M.A., Smith, R.D., Koppenaal, D.W. and Pakrasi, H.B. (2016), “Proteomics analysis of isolated plasma membrane and thylakoid membrane from Synechocystis sp. PCC 6803”, Molecular and Cellular Proteomics, 15(6), 2021-2032.

  3. Berla, B.M., Saha, R., Maranas, C.D. and Pakrasi, H.B. (2015), “Cyanobacterial Alkanes Modulate Photosynthetic Cyclic Electron Flow to Assist Growth under Cold Stress”, Nature Scientific Reports, 5, doi: 10.1038/srep14894.

  4. Simons, M., Saha, R., Amiour, N., Kumar, A., Guillard, L, Clément, G., Miquel, M., Zheni, L., Mouille, G., Hirel, B. and Costas D. Maranas (2014), “Assessing the Metabolic Impact of Nitrogen Availability using a Compartmentalized Maize Leaf Genome-Scale Model”, Plant Physiology, 166: 1659-1674.

  5. Simons, M, Saha, R., Guillard, L., Clement, G., Armengaud, P., Canas, R, Maranas, C.D., Lea, P.J. and B. Hirel (2014), “Nitrogen-use efficiency in maize (Zea mays L.): from ‘omics’studies to metabolic modelling”, Journal of Experimental Botany, doi: 10.1093/jxb/eru227.

  6. Saha, R., Chowdhury, A. and C.D. Maranas (2014), "Recent advances in the reconstruction of metabolic models and integration of omics data", Current Opinion in Biotechnology, 29, 39-45.

  7. Berla, B.M., Saha, R., Immethun, C.D., Maranas, C.D., Moon, T.S. and Pakrasi, H.B. (2013), "Synthetic biology of cyanobacteria: unique challenges and opportunities", Frontiers in Microbiology, 4.

  8. Saha, R., A.T. Verseput, B.M. Berla, T.J. Mueller, H.B. Pakrasi and C.D.Maranas (2012), "Reconstruction and comparison of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803," PLoS ONE, 7(10): e48285.

  9. Saha, R., P.F. Suthers and C.D. Maranas (2011), "Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism.," PLoS ONE, 6(7):e21784.

  10. Lee, D.Y., Saha, R., Khan, Y.F.N., Park, W. and Karimi, I.A. (2009), “Web-based applications for building, managing and analyzing kinetic models of biological systems”, Briefings in Bioinformatics, 10(1): 65-74.

  11. Ahn, J., Lee, H., Saha, R., Park, M., Jung, J-K and Lee, D.Y. (2008), “Exploring the effects of carbon sources on the metabolic capacity for shikimic acid production in  Escherichia coli using in silico metabolic predictions”, Journal of microbiology and biotechnology, 18(11): 1773-1784.