Publications
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Articles (62)
- (2023) BugSigDB Captures Patterns of Differential Abundance across a Broad Range of Host-Associated Microbial Signatures Nature Biotechnology:1-13 , Nature Publishing Group
- (2023) Genome-scale metabolic model led engineering of Nothapodytes nimmoniana plant cells for high camptothecin production Frontiers in Plant Science 14:1207218
- (2023) COWAVE: A labelled COVID-19 wave dataset for building predictive models PLoS ONE 18(7):e0284076
- (2023) Metagenome-Based Metabolic Modelling Predicts Unique Microbial Interactions in Deep-Sea Hydrothermal Plume Microbiomes ISME Communications 3(1):1-14 , Nature Publishing Group
- (2023) Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes Journal of the Indian Institute of Science
- (2023) Sloppiness: Fundamental study, new formalism and its application in model assessment PLoS ONE 18(3):e0282609
- (2023) On Biological Networks Capable of Robust Adaptation in the Presence of Uncertainties: A Linear Systems-Theoretic Approach Mathematical Biosciences 358:108984
- (2022) Bayesian Optimal Experiment Design for Sloppy Systems IFAC-PapersOnLine 55(23):121-126
- (2022) Probing patterning in microbial consortia with a cellular automaton for spatial organisation Scientific Reports 12(1):17159
- (2022) iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data NAR Genomics and Bioinformatics 4(3):lqac053
- (2022) Discovering design principles for biological functionalities: Perspectives from systems biology Journal of Biosciences 47(4):56
- (2022) Effect of Dormant Spare Capacity on the Attack Tolerance of Complex Networks Physica A: Statistical Mechanics and its Applications 598:127419
- (2022) Metabolic Modeling of the International Space Station Microbiome Reveals Key Microbial Interactions Microbiome 10(1):102
- (2022) Multi-Omic Data Helps Improve Prediction of Personalised Tumor Suppressors and Oncogenes Frontiers in Genetics 13:854190
- (2022) Designing Biological Circuits: From Principles to Applications ACS Synthetic Biology 11(4):1377-1388
- (2022) Discovering adaptation-capable biological network structures using control-theoretic approaches PLoS Computational Biology 18(1):e1009769
- (2022) Novel Ratio-Metric Features Enable the Identification of New Driver Genes across Cancer Types Scientific Reports 12(1):5
- (2022) A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites Frontiers in Bioengineering and Biotechnology 9:1330
- (2021) Two-Species Community Design of Lactic Acid Bacteria for Optimal Production of Lactate Computational and Structural Biotechnology Journal 19:6039-6049
- (2021) NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks Frontiers in Genetics 12:1666
- (2021) Modelling Microbial Communities: Harnessing Consortia for Biotechnological Applications Computational and Structural Biotechnology Journal 19:3892-3907
- (2021) The Art of Molecular Computing: Whence and Whither BioEssays 43(8):2100051
- (2021) Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes Cancers 13(10):2366
- (2020) SBML Level 3: An Extensible Format for the Exchange and Reuse of Biological Models Molecular Systems Biology 16(8):e9110
- (2020) A New Index for Information Gain in the Bayesian Framework IFAC-PapersOnLine 53(1):634-639
- (2020) Metagenome-Wide Association Analysis Identifies Microbial Determinants of Post-Antibiotic Ecological Recovery in the Gut Nature Ecology & Evolution 4(1256-1267):1-12
- (2020) Machine Learning Applications for Mass Spectrometry-Based Metabolomics Metabolites 10(6):243
- (2020) Mycobacterium Tuberculosis (Mtb) Lipid–Mediated Lysosomal Rewiring in Infected Macrophages Modulates Intracellular Mtb Trafficking and Survival Journal of Biological Chemistry 295:9192-9210
- (2020) MinReact: A Systematic Approach for Identifying Minimal Metabolic Networks Bioinformatics (Oxford, England) 36(15):4309-4315
- (2020) Investigating Metabolic Interactions in a Microbial Co-Culture through Integrated Modelling and Experiments Computational and Structural Biotechnology Journal 18:1249-1258
- (2019) Deciphering the Metabolic Capabilities of Bifidobacteria Using Genome-Scale Metabolic Models Scientific Reports 9(1):18222
- (2019) Assessment of network module identification across complex diseases Nature Methods 16(9):843-852
- (2019) Rational metabolic engineering for enhanced alpha-tocopherol production in Helianthus annuus cell culture Biochemical Engineering Journal 151:107256
- (2019) Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation Processes 7(6):343
- (2019) Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks Frontiers in Genetics 10:164
- (2019) Evolutionary design principles in metabolism Proc Biol Sci 286(1898):20190098
- (2018) Network-based features enable prediction of essential genes across diverse organisms PLOS ONE 13(12):1-13
- (2019) Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma FEBS Lett 593(1):23-41
- (2018) Understanding the evolution of functional redundancy in metabolic networks Bioinformatics 34(17):i981–i987
- (2018) Enumerating all possible biosynthetic pathways in metabolic networks. Scientific reports 8:9932+
- (2018) A systems-theoretic approach towards designing biological networks for perfect adaptation IFAC-PapersOnLine 51(1):307-312
- (2017) Predicting novel metabolic pathways through subgraph mining Bioinformatics 33(24):3955-3963
- (2017) Elucidating the biosynthetic pathways of volatile organic compounds in Mycobacterium tuberculosis through a computational approach Mol. BioSyst. 13(4):750-755
- (2017) A General Mechanism for the Propagation of Mutational Effects in Proteins. Biochemistry 56(1):294-305
- (2015) Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks Bioinformatics 31(20):3299-3305
- (2015) Critical assessment of genome-scale metabolic networks: the need for a unified standard Briefings in Bioinformatics 16(6):1057-1068
- (2014) Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces PLoS ONE 9(11):e112792+
- (2014) The organisational structure of protein networks: revisiting the centrality–lethality hypothesis Systems and Synthetic Biology 8(1):73-81
- (2013) Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach Computational Biology and Chemistry 47:149-155
- (2011) Evolvability and robustness in a complex signalling circuit Molecular BioSystems 7(4):1081-1092
- (2010) The evolvability of programmable hardware Journal of The Royal Society Interface 8(55):269-281
- (2010) A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis Molecular BioSystems 6(3):516-530
- (2010) Construction and analysis of protein-protein interaction networks Automated Experimentation 2(1):2+
- (2010) Systems biology Resonance 15(2):131-153
- (2009) Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis Mol. BioSyst. 5(12):1740-1751
- (2009) Flux balance analysis of biological systems: applications and challenges. Briefings in bioinformatics 10(4):435-449
- (2008) targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC systems biology 2(1):109+
- (2008) Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance BMC Microbiology 8:234
- (2007) Metabolome Based Reaction Graphs of M. tuberculosis and M. leprae: A Comparative Network Analysis PLoS ONE 2(9):e881+
- (2007) Hallmarks of mycolic acid biosynthesis: A comparative genomics study Proteins: Structure, Function, and Bioinformatics 69(2):358-368
- (2006) Principles and Practices of Pathway Modelling Current Bioinformatics 1(2):147-160
- (2005) Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs PLoS Computational Biology 1(5):e46+
Books (4)
- (2021) An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks , Chapman and Hall/CRC , Boca Raton, FL
- (2018) Systems-level modelling of microbial communities : theory and practice , CRC Press
- (2014) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems , Springer
- (2014) A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations , Springer
In Books (5)
- (2021) Systems-Theoretic Approaches to Design Biological Networks with Desired Functionalities
- (2018) Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL.
- (2016) In Silico Approaches to Metabolic Engineering
- (2007) Model Driven Drug Discovery: Principles and Practices , Artech House Publishers
- (2011) Systems Biology of Tuberculosis: Insights for Drug Discovery , New York, NY
Miscellaneous (1)
- (2008) PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways Nature Precedings