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Niaz Bahar Chowdhury
Data Scientist

Niaz Bahar Chowdhury is a data scientist at the Environmental Molecular Sciences Laboratory (EMSL), focusing on integrating multi-omics data with genome-scale metabolic models (GSMs) to understand microbial and plant metabolism. His expertise spans transcriptomics, proteomics, and metabolomics integration with GSMs, with applications in the predictive modeling of metabolic phenotypes. His work has advanced the understanding of metabolic networks in diverse biological systems, including bacteria (Chlamydia trachomatis, Neisseria gonorrhoeae, Staphylococcus aureus), archaea (Methanosarcina acetivorans), and plants (Zea mays, Oryza sativa). Leveraging computational tools such as constraint-based modeling and machine learning, Chowdhury aims to bridge genotype–phenotype relationships to drive systems biology research forward.

Google Scholar: https://scholar.google.com/citations?user=LmGuJxEAAAAJ&hl=en&oi=ao

Research Interests

  • Genome-scale metabolic modeling
  • Multi-omics data integration with genome-scale metabolic modeling
  • Machine learning applications in systems biology
  • Metabolic engineering and synthetic biology
  • Predictive modeling of microbial and plant metabolism

Education

Awards and Recognition

  • University of Nebraska-Lincoln (UNL) Distinguished Doctoral Dissertation Award, 2025
  • UNL College of Engineering Teaching Fellowship, 2024
  • Center for the Integration of Research, Teaching, and Learning Associate Degree in STEM Education, 2024
  • Professional Development Fellowship, 2023
  • School of Graduate Studies Travel Fellowship, 2023
  • Milton Mohr Fellowship for Excellence in Biotechnology Research, 2023
  • 2nd Prize Winner, UNL College of Engineering Graduate Symposium, 2022
  • 1st Prize Winner, UNL College of Engineering Graduate Symposium, 2021

Publications

2025

Chowdhury, R., W. Schroeder, D. Sarkar, N. B. Chowdhury, S. Dey, and R. Saha. 2025. “Fermi Calculations Enable Quick Downselection of Target Genes and Process Optimization in Photosynthetic Systems.” Plant Physiology kiaf103. https://doi.org/10.1093/plphys/kiaf103.

2024

Shahreen, N., J. Ahn, A. Alsiyabi, N. B. Chowdhury, D. Shinde, S. S. Chaudhari, K. W. Bayles, V. C. Thomas, and R. Saha. 2024. “A Thermodynamic Bottleneck in the TCA Cycle Contributes to Acetate Overflow in Staphylococcus aureus.” mSphere 10 (1): e00883-24. https://doi.org/10.1128/msphere.00883-24.

Chowdhury, N. B., N. Pokorzynski, E. A. Rucks, S. P. Ouellette, R. A. Carabeo, and R. Saha. 2024. “Metabolic Model Guided CRISPRi Identifies a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence.” mSystems 9 (7): e00717-24. https://doi.org/10.1128/msystems.00717-24.

Shahreen, N., N. B. Chowdhury, and R. Saha. 2024. “Optimal Protein Allocation Controls the Inhibition of GltA and AcnB in Neisseria gonorrhoeae.” Pathogens and Disease 82: ftae023. https://doi.org/10.1093/femspd/ftae023.

2023

Chowdhury, N. B., M. Simons-Senftle, B. Decouard, I. Quillere, M. Rigault, K. A. Sajeevan, B. Acharya, R. Chowdhury, B. Hirel, A. Dellagi, C. Maranas, and R. Saha. 2023. “A Multi-organ Maize Metabolic Model Connects Temperature Stress with Energy Production and Reducing Power Generation.” iScience 26 (12): 108400. https://doi.org/10.1016/j.isci.2023.108400.

Samuelson, D. R., D. R. Smith, K. C. Cunningham, S. Haq, D. N. Villageliú, C. M. Ellis, N. B. Chowdhury, A. E. Ramer-Tait, J. D. Price, and D. L. Knoell. 2023. “The Inherited Intestinal Microbiota from Myeloid-Specific ZIP8KO Mice Impairs Pulmonary Host Defense Against Pneumococcal Pneumonia.” Pathogens 12 (5): 639. https://doi.org/10.3390/pathogens12050639.

Morris, D. S., N. B. Chowdhury, M. Kathol, and R. Saha. 2023. “Opening the Door to Nitrogen Fixation in Oxygenic Phototrophs.” Trends in Biotechnology 41 (3): 283–285. https://doi.org/10.1016/j.tibtech.2023.01.005.

Salvi, A. M., N. B. Chowdhury, R. Saha, and N. R. Buan. 2023. “Supplementation of Sulfide or Acetate and 2-Mercaptoethane Sulfonate Restores Growth of the Methanosarcina acetivorans ΔhdrABC Deletion Mutant During Methylotrophic Methanogenesis.” Microorganisms 11 (2): 327. https://doi.org/10.3390/microorganisms11020327.

2022

Chowdhury, N. B., A. Alsiyabi, and R. Saha. 2022. “Characterizing the Interplay of Rubisco and Nitrogenase Enzymes in Anaerobic-Photoheterotrophically Grown Rhodopseudomonas palustris CGA009 Through a Genome-Scale Metabolic and Expression Model.” Microbiology Spectrum 10 (4): e01463-22. https://doi.org/10.1128/spectrum.01463-22.

Chowdhury, N. B., W. L. Schroeder, D. Sarkar, N. Amiour, I. Quilleré, B. Hirel, C. D. Maranas, and R. Saha. 2022. “Dissecting the Metabolic Reprogramming of Maize Root Under Nitrogen-Deficient Stress Conditions.” Journal of Experimental Botany 73 (1): 275–291. https://doi.org/10.1093/jxb/erab435.

Alsiyabi, A., N. B. Chowdhury, D. Long, and R. Saha. 2022. “Enhancing In Silico Strain Design Predictions Through Next Generation Metabolic Modeling Approaches.” Biotechnology Advances 54: 107806. https://doi.org/10.1016/j.biotechadv.2021.107806.