Systems Biology
Sloppiness: Fundamental study, new formalism and its application in model assessment
Computational modelling of biological processes poses multiple challenges in each stage of the modelling exercise. Some significant challenges include identifiability, precisely estimating parameters from limited data, …
Multi-Omic Data Improve Prediction of Personalized Tumor Suppressors and Oncogenes
The progression of tumorigenesis starts with a few mutational and structural driver events in the cell. Various cohort-based computational tools exist to identify driver genes but require multiple samples to identify …
Designing Biological Circuits: From Principles to Applications
Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits─the repressilator and the toggle switch─were designed and implemented, many advances have been made in this …
Novel ratio-metric features enable the identification of new driver genes across cancer types
Abstract An emergent area of cancer genomics is the identification of driver genes. Driver genes confer a selective growth advantage to the cell. While several driver genes have been discovered, many remain undiscovered, …
A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites
Microbial production of chemicals is a more sustainable alternative to traditional chemical processes. However, the shift to bioprocess is usually accompanied by a drop in economic feasibility. Co-production of more than …
NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
Essential gene prediction models built so far are heavily reliant on sequence-based features, and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using …
Two-species community design of lactic acid bacteria for optimal production of lactate
Microbial communities that metabolise pentose and hexose sugars are useful in producing high-value chemicals, resulting in the effective conversion of raw materials to the product, a reduction in the production cost, and …
Systems-Theoretic Approaches to Design Biological Networks with Desired Functionalities
SBML Level 3: an extensible format for the exchange and reuse of biological models
MINREACT: an efficient algorithm for identifying minimal metabolic networks
Abstract Genome-scale metabolic models are widely constructed and studied for understanding various design principles underlying metabolism, predominantly redundancy. Metabolic networks are highly redundant and it is …
A priori parameter identifiability in models with non-rational functions
Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma
Retinoblastoma (RB) is a childhood eye cancer. Currently, chemotherapy, local therapy, and enucleation are the main ways in which these tumors are managed. The present work is the first study that uses constraint‐based …
Systems-Level Modelling of Microbial Communities: Theory and Practice
Systems-Level Modelling of Microbial Communities: Theory and Practice introduces various aspects of modelling microbial communities and presents a detailed overview of the computational methods which have been developed …
Sridharakumar Narasimhan
Dr. Sridharakumar Narasimhan received his M.Tech (Integrated course) degree in Chemical Engineering from IIT Bombay in 1998. Subsequently, he worked for 2 years as a process engineer in the mineral process group of the …