Other

• Shahreen, N., Thomas, VC., and Saha, R., “Omics-Informed Metabolic Modeling of Staphylococcus Aureus Reveals Underlying Principles of Overflow Metabolism”, BMES Annual Meeting, Oct 11–14, 2023
• Osinuga, A., Solis, A. G., Cahoon, R., Cahoon, E., Alsiyabi, A., and Saha, R., “Advancing Metabolic Understanding with a Refined Dynamic Metabolic Flux Analysis (r-DMFA) Framework: A Case Study on Sphingolipid Biosynthesis and Homeostasis in Arabidopsis Thaliana” Oral Presentation,  5^th Annual UNL College of Engineering Graduate Student Symposium, February 23, 2024.
• Long, D., and Saha, R., “The Green Machine: Bacterial strain design for kids” College of Engineering Graduate Symposium, Keynote, February 26th, 2021.
• Alsiyabi, A., Brown, B., Immethun, C., and Saha R., “Harnessing sunlight to convert CO2 into biodegradable plastic” College of Engineering Graduate Symposium, February 26th, 2021
• Brown, B. and Saha, R., “Conversion of Lignin into Biodegradable Plastic by Rhodopseudomonas palustris CGA009,” Proceedings of World Biomaterials Congress, Dec 11-15, 2020.
• Lamarre, Y., A. Aich, M. Islam, J. M. Scianni, A. C. S. Pinto, A. M. C. Tavassi, J. Elion, W. E. Nemer, R. Saha, S. Kashima, and D. T. Covas, “Leveraging plasma-derived exosomes for biomarker discovery in sickle cell disease: preparation for a large prospective study”, Hematology, Transfusion and Cell Therapy, 2020, 42:S2.
• Brown, B.. and Saha, R., “Conversion of Lignin into Biodegradable Plastic by Rhodopseudomonas palustris CGA009,” Proceedings of World Biomaterials Congress, Dec 11-15, 2020.
• Brown, B.. and Saha, R., “Conversion of Lignin into Bioplastic by Rhodopseudomonas palustris,” Proceedings of ASABE International Meeting, Jul 13-15, 2020.
• [People’s choice Award winner] Islam, M. M., “Metabolic Modeling and Analysis of Microbes, Plants, and Microbial Ecosystems: Discovery and Redesign”, College of Engineering Graduate Research Symposium, University of Nebraska-Lincoln, February 21, 2020.
• Saha, R., “Metabolic Modeling and ‘Omics’ Data Integration in the Context of Plant Systems Biology”, Agronomy & Horticulture Seminar, University of Nebraska-Lincoln, November 22, 2019
• 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
• Saha, R., “Design Biological Systems: The “LEGO way”, Science Cafe, University of Nebraska State Museum, Morrill Hall, Lincoln, Nebraska, November 16, 2017
• 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.
• Saha, R., “Modeling of Metabolism: From Individual Microorganisms to Plant and Microbial Community”, UNL Plant Science Retreat, Nebraska City, NE, October 14-15, 2016.
• 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.
• 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.
• 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

• Shahreen, N., Thomas, VC., and Saha, R., “Rethinking Metabolic Strategies: Staphylococcus aureus‘s Unique Approach to Energy Generation”, UNL Student Research Days, March 26, 2024.
• Tabibian, M. and Saha, R., “Deciphering the Metabolic Signature of Lung Mast Cells in Health and Cancer: A Genome-Scale Metabolic Modeling and Machine Learning Study”, UNL Student Research Days, March 26, 2024.
• Razmpour, R. and Saha, R., “Exploring Pancreatic Ductal Adenocarcinoma (PDAC) through the Lens of Genome-Scale Metabolic Modeling and Machine Learning”, UNL Student Research Days, March 26, 2024.
• Shahreen, N., Thomas, VC., and Saha, R., “Rethinking Metabolic Strategies: Staphylococcus aureus‘s Unique Approach to Energy Generation”, 5th Annual UNL College of Engineering Graduate Student Symposium, February 23, 2024.
• Shahreen, N., Thomas, VC., and Saha, R., “Omics-Informed Metabolic Modeling of Staphylococcus Aureus Reveals Underlying Principles of Overflow Metabolism”, 3rd Annual UNL Microbiology Research Symposium, December 1, 2023.
• Razmpour, T. and Saha, R., “Identifying PDAC Diagnostic Biomarkers Utilizing Machine Learning Combined with Genome-Scale Metabolic Modeling”, BMES Annual Meeting, OCT 11-14, 2023
• Osinuga, A., Cahoon, R., Cahoon, E., and Saha, R., “Embracing Variability in Dynamic Metabolic Modeling: Novel Insights into Arabidopsis thaliana’s Sphingolipid Biosynthesis” Poster Presentation, Graduate Student Poster Sessions, UNL Student Research Days, March 26, 2024.
• Osinuga, A., Cahoon, R., Cahoon, E., and Saha, R., “Modeling Sphingolipid Metabolism and Prediction of orosomucoid (ORM) Proteins’ Regulatory Roles: ¹⁵N Stable Isotope Labeling Studies” Poster Presentation, Nebraska Plant Science Symposium, April 25, 2023.
• Osinuga, A., Cahoon, R., Cahoon, E., and Saha, R., “Modeling Sphingolipid Metabolism and Prediction of orosomucoid (ORM) Proteins’ Regulatory Roles: ¹⁵N Stable Isotope Labeling Studies” Poster Presentation, Graduate Student Poster Sessions, UNL Student Research Days, March 28, 2023.
• Shahreen, N., Thomas, VC., and Saha, R., “Omics-Informed Metabolic Modeling of Staphylococcus Aureus Reveals Underlying Principles of Overflow Metabolism”, UNL Student Research Days, March 28, 2023.
• Osinuga, A., Cahoon, R., Cahoon, E., and Saha, R., “Sphingolipid Metabolism Modeling and Prediction of orosomucoid (ORM) Proteins’ Regulatory Roles: N¹⁵ Stable Isotope Labeling Studies” Poster Presentation, 4^th Annual UNL College of Engineering Graduate Student Symposium, February 24, 2023.
• Shahreen, N., Thomas, VC., and Saha, R., “Omics-Informed Metabolic Modeling of Staphylococcus Aureus Reveals Underlying Principles of Overflow Metabolism”, 4th Annual UNL College of Engineering Graduate Student Symposium, February 24, 2023.
• Osinuga, A., Cahoon, R., Cahoon, E., and Saha, R., “Understanding ORM Protein Regulation via Sphingolipid Metabolism Modeling: N¹⁵ Stable isotope Labeling Studies” Poster Presentation, UNL Center for Plant Science Innovation, Plant Science Retreat, November 10-11, 2022.
• Chowdhury, N., Schroeder, W., Zhang, D., Simons, M., Hirel, B., Cahoon, E., Maranas, C., and Saha, R., “Stress Response Study of Zea mays by Incorporating Omics Information into its Genome-Scale Metabolic Model”, COnstraint-Based Reconstruction and Analysis (COBRA) Conference, virtual, March 1-2, 2021.
• Islam, M. M., Thomas, V. C., and Saha, R., “Optimization-Based Analysis of Comparative Metabolomic Data Identifies Regulatory Mechanisms in Staphylococcus Aureus Mutants”, COnstraint-Based Reconstruction and Analysis (COBRA) Conference, virtual, March 1-2, 2021.
• Schroeder, W. L., and Saha, R., “Introducing and Optimization- and Explicit Runge-Kutta- Based Approach to Perform Dynamic Flux Balance Analysis”, COnstraint-Based Reconstruction and Analysis (COBRA) Conference, virtual, March 1-2, 2021.
• Alsiyabi, A., Brown, B., Immethun, C., and Saha R., “Metabolic Modeling and Fluorometry Elucidate the Interplay between Electron Sources and Sinks in a Purple Non-Sulfur Bacterium”, COnstraint-Based Reconstruction and Analysis (COBRA) Conference, virtual, March 1-2, 2021.
• Chowdhury, N., and Saha, R., “Stress Response Study of Zea mays by Incorporating Omics Information into its Genome-Scale Metabolic Model”, College of Engineering Graduate Research Symposium, University of Nebraska-Lincoln, February 26, 2021.
• Brown, B., and Saha, R., “Hydrogen Biofuel Production from a Versatile Bacterium Using Agricultural Waste.”, 3in 5 pitch competition, College of Engineering Graduate Research Symposium, University of Nebraska-Lincoln, February 26, 2021.
• Kathol, M., Immethun, C., and Saha, R., “Investigating the relaxase behavior and replication functionality of the mobilization protein mobV in the plasmid pBBR1”, 3in 5 pitch competition, College of Engineering Graduate Research Symposium, University of Nebraska-Lincoln, February 26, 2021.
• Islam, M. M., “Optimization in Biological Systems: The Legacy of Engineering Complex Processes”, College of Engineering Graduate Research Symposium, University of Nebraska-Lincoln, February 26, 2021
• Schroeder, W. L., Harris, S. D., and Saha, R., “EuGeneCiD: Toward and Optimization-Based Tool for Synthetic Biology Design”. Poster Presentation. Central US Synthetic Biology Workshop, Online and Video Poster Presentation. Sept. 10, 2020.
• Schroeder, W. L., Harris, S. D., and Saha, R., “Computation-driven mechanistic understanding of the cellular cost and role of defensive pigment production in a polyextremotolerant fungus”. Poster Presentation. Engineering Graduate Student Symposium, Lincoln, NE, USA. Feb. 21, 2020.
• Islam, M. M., Sandhu, J., Walia, H, and Saha, R., “MiReN: An Optimization Tool for Data-Driven Discovery of Global Regulatory Phenomena During Heat Stress in Rice Seed”, Midwest Big Data hub (MBDH) All-hands meeting, Chicago, IL, October 29-30, 2019
• Immethun, C., Changa, T., and Saha, R., “Engineering a purple non-sulfur bacterium to expand symbiotic nitrogen fixation”, Plant Science Symposium, Lincoln, NE, October 17-18, 2019
• [First Place prize winner] Islam, M. M., Sandhu, J., Walia, H, and Saha, R., “MiReN: An Optimization Tool for Data-Driven Discovery of Global Regulatory Phenomena During Heat Stress in Rice Seed”, UNL Plant Sciences Symposium, Nebraska Innovation Campus, March 12, 2019
• Islam, M. M., Fernando, S. C., and Saha, R., “Virome modulate metabolic shiftws in the rumen microbiome: computational predictions based on genome-scale Metabolic Modeling”, 19th Annual Symposium in Virology, University of Nebraska-Lincoln, Lincoln, NE, September 6, 2019
• Islam, M. M., Sandhu, J., Walia, H, and Saha, R., “MiReN: An Optimization Tool for Data-Driven Discovery of Global Regulatory Phenomena Used to Elucidate the Heat Stress Response Mechanism in Rice Seed”, COnstraint-Based Reconstruction and Analysis (COBRA) Conference, Seattle, WA, October 14-16, 2018
• O’Neil, J., Al-Siyabi, A., and Saha, R., “Maximization of Succinic Acid Production on A. succinogenes via Genome-scale Metabolic Modeling”, UNL summer Research Fair, Lincoln, NE, 2018
• Daggumati, S. R., Le, T., Islam, M. M., and Saha, R., “Utilizing Methane-Oxidizing Microbes to Mitigate Trichloroethylene in Soil and Groundwater”, UNL summer Research Fair, Lincoln, NE, 2018
• Maaliao, C., Islam, M. M., and Saha, R., “Understanding Stress Response Mechanism in Rice Seed”, UNL summer Research Fair, Lincoln, NE, 2018
• 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
• 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.
• 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.
• [Best Poster Award winner] 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.