Niaz Bahar Chowdhury

This study profiles multi-omics data in Picochlorum celeri under CO2 limitation, revealing a CO2-dependent switch in Rubisco subunits and extensive post-translational modifications.

RealKcat predicts enzyme kinetics from sequence using a curated dataset and embeddings, showing sensitivity to catalytic mutations and robustness across evaluations.

The paper identifies genetic variants in the shikimate dehydrogenase gene Sad1 that affect enzyme activity and homoserine accumulation in maize kernels through integrated metabolite profiling and genome-scale modeling.

ChatGEM enables interactive simulation of genome-scale metabolic models via natural language, improving performance and reducing execution time for complex tasks.

PathwaySeeker uses AI to reason about organism-specific metabolic networks using proteomic and metabolomic data, distinguishing confirmed reactions from hypotheses.

This study investigates lignin degradation mechanisms in Rhodopseudomonas palustris using multi-omics and CRISPRi to identify essential pathways and improve sustainable valorization of lignin.

The paper integrates a rice grain metabolic model with transcriptomics data to identify histidine as a marker for grain chalkiness under warmer night temperatures.

This paper develops a genome-scale metabolic model for Treponema pallidum, identifies glycerol-3-phosphate dehydrogenase as an alternative electron sink, and validates its predictive accuracy with proteomics data.

This paper uses artificial neural networks to predict growth rates of Rhodopseudomonas palustris on lignin breakdown products by analyzing transcriptomics and proteomics data, identifying key transport proteins as critical predictors.

This study identifies a thermodynamic bottleneck in the TCA cycle of S. aureus that favors acetate overflow metabolism for bioenergetic efficiency.

This study enhances PHB and 3HV production in Paraburkholderia sacchari by overexpressing key pathway genes, achieving 162% and 145% increases respectively, while identifying thermodynamic limitations for 3HV.

The paper uses machine learning and metabolic modeling to show phosphoglycerate mutase is critical for Chlamydia trachomatis persistence under nutrient starvation.

The paper shows that optimal protein allocation in Neisseria gonorrhoeae enhances GltA and AcnB activity, delaying acetate overflow for ATP production.

This paper reconstructs the first genome-scale metabolic and expression model for Rhodopseudomonas palustris to study anaerobic-photoheterotrophic growth and identify key regulatory mechanisms.

This study develops a genome-scale metabolic model for maize root to analyze metabolic reprogramming under nitrogen stress, identifying key metabolites involved in biomass growth and stress tolerance.