Rajib Saha

Thermodynamic Quality Control Reshapes Spatially Resolved Metabolic Flux Predictions in Prostate Cancer

Quality-controlled, cycle-certified E-Flux Human-GEM models of twelve regions from one prostate tumor curb implementation-driven flux inflation and show predicted metabolic similarity tracks spatial region, not histology.

Accessing Enzyme Kinetic Data and Prediction Methods at Scale

OpenKinetics Predictor unifies thirteen enzyme kinetic predictors behind one interface and API; on E. coli iML1515, eight kcat predictors correlate pairwise at r 0.08 to 0.67.

Robust Prediction of Enzyme Variant Kinetics with RealKcat

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

Natural Variation in Maize Shikimate Dehydrogenase Alters Enzyme Activity and Kernel Homoserine Accumulation.

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.

Solute Carrier Transporter Family Modulates Neutrophil Metabolism During Health and Disease

This study identifies metabolic reprogramming in neutrophils under stress conditions and highlights the role of solute carrier transporters in metabolic specialization.

Machine Learning Reveals Proteome-Encoded Growth Predictors of Rhodopseudomonas palustris CGA009 on Lignin Aromatics

The paper uses machine learning on proteomics data to predict growth rates of Rhodopseudomonas palustris on lignin-derived substrates and identifies proteomic features that encode growth potential across environments.

A Closed Computational - Experimental Loop Identifies Metabolic Collapse at the Root of Macrophage Dysfunction due to Zinc Dyshomeostasis

This study identifies metabolic collapse due to zinc dyshomeostasis in macrophages, showing succinate and kynurenic acid can restore immune function.

GAN-Enhanced Machine Learning and Metabolic Modeling Identify Reprogramming in Pancreatic Cancer

This study uses GAN-enhanced machine learning and metabolic modeling to identify metabolic reprogramming in pancreatic cancer, revealing key pathways and potential therapeutic targets.

Pathway Thermodynamic Analysis Postulates Change in Glutamate Metabolism as a Key Factor in Modulating Immune Responses

This study uses MDF analysis to examine how temperature changes affect metabolic pathway thermodynamics, identifying glutamate metabolism as a key factor in immune response modulation.

Diffusion Models vs. DCGANs for Class-Imbalanced Lung Cancer CT Classification: A Comparative Study

This study compares diffusion models and DCGANs for class-imbalanced lung cancer CT classification, finding diffusion models achieve higher accuracy and better recall for benign cases.

Minimal Gene Signatures Enable High-Accuracy Prediction of Antibiotic Resistance in Pseudomonas aeruginosa

This study uses machine learning to identify minimal gene signatures predicting antibiotic resistance in Pseudomonas aeruginosa with high accuracy.

Genome-scale metabolic modeling and machine learning unravel metabolic reprogramming and mast cell role in lung cancer through a multi-level analysis

This study uses genome-scale metabolic modeling and machine learning to analyze metabolic changes in lung cancer and mast cells, identifying key metabolic pathways and potential therapeutic targets.

High Enzyme Promiscuity in Lignin Degradation Mechanisms in Rhodopseudomonas palustris CGA009

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

Transcriptome Enhanced Rice Grain Metabolic Model Identifies Histidine Level as a Marker for Grain Chalkiness

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

Enzyme-constrained Metabolic Model of Treponema pallidum Identified Glycerol-3-phosphate Dehydrogenase as an Alternate Electron Sink

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.

Artificial Neural Network Reveals the Role of Transport Proteins in Rhodopseudomonas palustris CGA009 During Lignin Breakdown Product Catabolism

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.

Crusty-Pinky: A Novel Polyextremotolerant Fungus and its Methylobacterium Symbionts Could be an Essential Symbiosis for the Biological Soil Crust Consortium

The paper describes a novel fungal-symbiont system where Methylobacterium spp. enhance the growth and metabolic capabilities of a polyextremotolerant fungus in biological soil crusts.

Unique Adaptations of a Photosynthetic Microbe Rhodopseudomonas palustris to the Toxicological Effects of Perfluorooctanoic Acid

This study examines Rhodopseudomonas palustris' ability to remove perfluorooctanoic acid (PFOA) and its toxicological response, finding temporary incorporation of PFOA into the cell membrane and diauxic growth patterns at varying concentrations.

AraRoot - A Comprehensive Genome-Scale Metabolic Model for the Arabidopsis Root System.

The paper develops AraRoot, a genome-scale metabolic model for Arabidopsis root system, identifying key metabolic pathways and stress responses.

A thermodynamic bottleneck in the TCA cycle contributes to acetate overflow in Staphylococcus aureus

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

Dissecting Metabolic Landscape of Alveolar Macrophage

This study investigates metabolic shifts in alveolar macrophages during M1 and M2 activation phases, highlighting non-central carbon metabolism pathways and temperature's role in immune response.

Heterologous expression of critical pathway genes leads to complex pattern of increased yield of bioplastic precursors in Paraburkholderia sacchari ITP 101

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.

Quantitative Dynamic Analysis of de novo Sphingolipid Biosynthesis in Arabidopsis thaliana

The paper uses dynamic modeling to analyze sphingolipid biosynthesis in Arabidopsis, identifying key enzymes critical for homeostasis and cell viability.

Machine Learning and Metabolic Model Guided CRISPRi Reveals a Central Role for Phosphoglycerate Mutase in Chlamydia trachomatis Persistence

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

Optimal Protein Allocation Controls the Inhibition of GltA and AcnB in Neisseria gonorrhoeae

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

Characterizing the interplay of rubisco and nitrogenase enzymes in anaerobic-photoheterotrophically grown Rhodopseudomonas palustris CGA009 through a genome-scale metabolic and expression model

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

Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling

This study uses genome-scale metabolic modeling with patient transcriptomic data to identify metabolic vulnerabilities in PDAC and suggest potential therapeutic targets and drug combinations.

Dissecting the Metabolic Reprogramming of Maize Root under Nitrogen Limiting Stress Condition

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.

Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

The paper uses computational modeling to predict regulatory roles of ORM proteins in the plant sphingolipid pathway, identifying both repressive and activating effects on key enzymes.

Investigation of microbial community interactions between lake Washington methanotrophs using genome-scale metabolic modeling

The paper develops genome-scale metabolic models of methanotrophs from Lake Washington to study their interactions and metabolic responses under different environmental conditions.