SSbio - Publications


Publications


Articles:
  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.

  2. 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.

  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
Books/Book Chapters:
  1. Islam, M. M. and R. Saha (2018). Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design. Methods Mol Biol. 1671: 63-82.
Conference Proceedings:
  1. Saha, R., Suresh, S., Park, W., Lee, D.Y. and Karimi, I.A., “Microbial fuel cell in perspective of strain improvement and mediator selection”, Joint third AOHUPO and fourth structural biology and functional genomics conference, 2006, pp 290.
  2. Saha, R., Park, W, Lee., D.Y. and Karimi, I.A., “Comparison on web-based simulation tools of biochemical and cellular model in systems biology”, International conference on modeling in chemical and biological engineering sciences, 2006, pp. 10.
Oral Presentations
  1. Islam, M. M., Schroeder, W., Fernando, S. C., and Saha, R., "Microbiome-Virome Interactions in Bovine Rumen: Elucidating Metabolic Transactions Through Mathematical Modeling ", 255th ACS National Meeting and Exposition, New Orleans, Louisiana, March 18-22, 2018
  2. Saha, R., "Design Biological Systems: The "LEGO way", Science Cafe, University of Nebraska State Museum, Morrill Hall, Lincoln, Nebraska, November 16, 2017
  3. Islam, M. M., Saha, R., Chaudhuri, S., and Thomas, V. C., " Elucidating the Physiological Significance of Nitric Oxide Synthase (NOS) in Staphylococcus aureus through Metabolic Modeling", AIChE Annual Meeting 2017, Minneapolis, MN, October 28-November 2, 2017.
  4.  Schroeder, W., and Saha, R., "K-Ath - Towards a Multi-Tissue Kinetic Model of Arabidopsis thaliana ", AIChE Annual Meeting 2017, Minneapolis, MN, October 28-November 2, 2017.
  5. Islam, M. M., Schroeder, W., Fernando, S. C., and Saha, R., "Microbiome-Virome Interactions in Bovine Rumen: The Role of Auxiliary Metabolic Genes in Relaxing Metabolic Bottlenecks ", AIChE Annual Meeting 2017, Minneapolis, MN, October 28-November 2, 2017.
  6.  Schroeder, W., Kumar, J., and Saha, R., "Computation-Driven Mechanistic Understanding of the Cellular Cost and Regulation of Melanin Production ", AIChE Annual Meeting 2017, Minneapolis, MN, October 28-November 2, 2017.
  7. Saha, R., "Plant Metabolic Models: From Model Building to 'Omics Data Integration and Answering Important Biological Questions", Nebraska Research and Innovation Conference on Predictive Crop Design: Genome to Phenome, Lincoln, NE, April 6-7, 2017.
  8. Saha, R., "Modeling of Metabolism: From Individual Microorganisms to Plant and Microbial Community", UNL Plant Science Retreat, Nebraska City, NE, October 14-15, 2016.
  9. Saha, R, Liu, D., Hoynes-O’Connor, A.G., Liberton, M., Yu, J., Bhattacharyya, M., Balassy, A., Moon, T.S., Maranas, C.D., Pakrasi, H.B., “Synechocystis Sp. PCC 6803: Light Plus Endogenous Regulation Governing Gene Expression Patterns in the Diurnal Cycle”, AIChE annual meeting, Salt Lake City, UT, Nov 8-13, 2015.
  10. Saha, R., Berla, B.M., Pakrasi, H.B. and Maranas, C.D., “Computations-driven optimization of alkane production in Synechocystis sp. PCC 6803”, AIChE annual meeting, Atlanta, GA, Nov 16-21, 2014.
  11. Saha, R., Simons, M., Kumar, A., Guillard, L., Hirel, B and Maranas, C.D., “Towards multi-tissue type metabolic modeling of maize”, AIChE annual meeting, San Francisco, CA, Nov 3-8, 2013.
  12. Saha, R., Berla, B.M., Mueller, T.J., Welkie, D.J., Sherman, L., Pakrasi, H.B. and Maranas, C.D., “Comparative genome-scale modeling of the metabolic potential of cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC6803”, 11th workshop on cyanobacteria, St. Louis, MO, Aug 7-11, 2013.
  13. Saha, R., Verseput, A.T., Mueller, T.J. and Maranas, C.D., “Contrasting the metabolic capabilities of cyanobacterial strains for assessing bio-production platform selection”, AIChE annual meeting, Pittsburgh, PA, Oct 28-Nov 2, 2012.
  14. Saha, R., Berla, B.M., Mueller, T.J., Elvitigala, T., Page, L.E., Pakrasi, H.B. and Maranas, C.D., “Contrasting the metabolic capabilities of cyanobacterial species for assessing bio-production platform selection”, ACS annual meeting, San Diego, CA, Mar 25-29, 2012.
  15. Saha, R., Berla, B.M., Elvitigala, T., Page, L.E., Pakrasi, H.B. and Maranas, C.D., “Contrasting the Metabolic Capabilities of Multiple Cyanobacterial Species”, AIChE annual meeting, Minneapolis, MN, Oct 16-21, 2011.
  16. Saha, R., Suthers, P.F. and Maranas, C.D., “Towards Genome-Scale Metabolic Reconstruction of Plant Metabolism”, AIChE annual meeting, Salt Lake City, UT, Nov 7-14, 2010.
  17. Saha, R., Park, W, Lee, D.Y. and Karimi, D.Y., “Comparison on web-based simulation tools of biochemical and cellular model in systems biology”, International conference on modeling in chemical and biological engineering sciences, Bangkok, Oct 25-27, 2006.
Poster Presentations
  1. Islam, M. M., Thomas, V. C., and Saha, R., "Towards Data-driven Discovery of Novel Therapeutic Targets through Metabolic Modeling of Staphylococcus aureus", UNL Spring Research Fair, Lincoln, NE, April 10, 2018
  2. Islam, M. M., Sandhu, J., Walia, H, and  Saha, R., "Effect of Heat Stress on Rice Seed Development: Discovering Global Regulatory Players and Modeling of Rice Metabolism ", AIChE Annual Meeting 2017, Minneapolis, MN, October 28-November 2, 2017.
  3. Daggumati, S.R., Le, T., Islam, M. M., and Saha, R., "Towards Modeling of Methane Recycling Lake Washington Microbial Community", AIChE Annual Meeting 2017, Minneapolis, MN, October 28-November 2, 2017.
  4. Saha, R., "Implementing Peer Instruction in a Flipped Class: Perspectives from Chemical Engineering Computation", Summer School for Chemical Engineering Faculty, American Society for Engineering Education (ASEE),  North Carolina State University, Raleigh, NC, July 29-August 3 2017.
  5. Le, T., Daggumati, S. R., Islam, M. M., and Saha, R., “Constructing a Genome-Scale Metabolic Modle for Methylobacter tundripaludum", Fall Research Fair 2017, University of Nebraska-Lincoln, Lincoln, NE, August 9, 2017.
  6. Buchanan, K., Schroeder, W., Islam, M. M., and Saha, R., “Computational Modeling of Actinobacillus succinogenes to Optimize Production of Succinic Acid", Fall Research Fair 2017, University of Nebraska-Lincoln, Lincoln, NE, August 9, 2017.
  7. Islam, M. M., Sandhu, J., Walia, H., and Saha, R., “Thermal Stress on Plants: Insights About Global Regulation and Metabolic Model Development", Nebraska Research and Innovation Conference on Predictive Crop Design: Genome to Phenome, Lincoln, NE, April 6-7, 2017.
  8. Schroeder, W., and Saha, R., "k-athaliana-toward a Multi-tissue Kinetic Model of Arabidopsis thaliana", Nebraska Research and Innovation Conference on Predictive Crop Design: Genome to Phenome, Lincoln, NE, April 6-7, 2017.
  9. Islam, M. M., Saha, R., “Modeling of metabolsim: From Individual Microorganism to Whole-Plant and Multi-species Consortia", UNL Plant Science Retreat, Nebraska City, NE, October 14-15, 2016.
  10. Yu, J., Saha, R., Berla, B.M., Mueller, T.J., Kumar, A., Simons, M., Khodayari, A., Whitney Hollinshead, W., Abernathy, M., He, L., Tang, Y.J., Maranas, C.D., Pakrasi, H.B., “Systems Level Study of a Novel Fast-Growing Cyanobacterial Strain for Next- Generation Biofuel Production”, DOE genomic sciences meeting, Tysons, VA, Feb 22-25, 2015.
  11. Saha, R., Simons, M., Kumar, A., Guillard, L., Hirel, B and Maranas, C.D., “Assessing the Metabolic Impact of Nitrogen Availability using a Compartmentalized Maize Leaf Genome-Scale Model”, 3rd COBRA meeting, Winter Green, VA, May 20-23, 2014.
  12. Saha, R., Simons, M., Islam, M.M., Zomorrodi, A.R., Hirel, B and Maranas, C.D., “Metabolic modeling of multi tissue and multi organism systems”, DOE genomic sciences meeting, Crystal City, VA, Feb 10-12, 2014.
  13. Saha, R., Mueller, T.J., Berla, B.M., Pakrasi, B.M. and Marans, C.D., “Construction of metabolic models for a family of cyanobacteria”, DOE genomic sciences meeting, Bethesda, MD, Feb 24-27, 2013.
  14. Saha, R., Berla, B.M., Mueller, T.J., Elvitigala, T., Page, L.E., Pakrasi, H.B. and Maranas, C.D., “Contrasting the metabolic capabilities of Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC6803”, DOE genomic sciences meeting, Bethesda, MD, Feb 26-29, 2012.
  15. Saha, R., Suthers, P.F. and Maranas, C.D., "Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism”, DOE genomic sciences meeting, Crystal City, VA, Apr 10-13, 2011.
  16. Saha, R., Suresh, S., Park, W., Lee, D.Y. and Karimi, I.A., “Microbial fuel cell in perspective of strain improvement and mediator selection”, Joint third AOHUPO and fourth structural biology and functional genomics conference, Singapore, Dec 4-7, 2006.
  17. Saha, R., Park, W, Lee., D.Y. and Karimi, D.Y., “Comparison on web-based simulation tools of biochemical and cellular model in systems biology”, Annual graduate students’ symposium, NUS, Singapore, Sep 24, 2006.