Karthik Raman

Metagenomic profiling of municipal drinking water microbiomes in an Indian city: Insights into diversity, water quality, and AMR potential
STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies
Harnessing machine learning for metagenomic data analysis: trends and applications
Microbial Communities Facilitate Pathogen Persistence in Hospital Environments
Genome-scale metabolic model guided metabolic flux analysis in the endophyte Alternaria burnsii NCIM1409
Plasmidome, resistome, and virulence-associated genes characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting
Decoding microbial diversity, biogeochemical functions, and interaction potentials in red sea hydrothermal vents
Deciphering Global Patterns of Marine Microbial Community Assembly and Network Stability
An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection
GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations
PURE: Policy-guided Unbiased REpresentations for structure-constrained molecular generation
COmmunity and Single Microbe Optimisation System (COSMOS)
Extensive Benchmarking of Community Detection Algorithms
Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms
Mapping genetic diversity with the GenomeIndia project
Microbial communities on station and train surfaces in Chennai Metro: Insights into urban transit microbiome
UNFOLDing Robustness, Plasticity, Evolvability and Canalisation of Biological Function
An improved framework for grey-box identification of biological processes
Investigating the impact of carbamazepine on tomato plant metabolism using genome-scale metabolic modelling
Metagenomic Profiling of Drinking Water Microbiomes: Insights into Microbial Diversity and Antimicrobial Resistance
Unveiling Hidden Microbial Diversity in Mars 2020 Mission Assembly Cleanrooms with Molecular Insights into the Persistent and Perseverance of Novel Species Defying Metagenome Sequencing
An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in Candida albicans during host infection
Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus
Integrating Model‐Informed Drug Development With AI: A Synergistic Approach to Accelerating Pharmaceutical Innovation
Tumor-Infiltrating Lymphocytes Display Prognostic Signatures Associated with Chemotherapy Response in TNBC Patients
FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models
Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models
Understanding flux switching in metabolic networks through an analysis of synthetic lethals
Functional Insights into Novel Extremophilic Bacteria Isolated from the NASA Phoenix Mission Spacecraft Assembly Cleanrooms
Modeling Microbial Communities: Perspective and Challenges
Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics
Panera: An innovative framework for surmounting uncertainty in microbial community modeling using pan-genera metabolic models
Designing function-specific minimal microbiomes from large microbial communities
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures
Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov
Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov
Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station
Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes
Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes
Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes
Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes
Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models
Genome-scale metabolic model led engineering of Nothapodytes nimmoniana plant cells for high camptothecin production
COWAVE: A labelled COVID-19 wave dataset for building predictive models
COWAVE: A labelled COVID-19 wave dataset for building predictive models
Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes
Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes
On biological networks capable of robust adaptation in the presence of uncertainties: A linear systems-theoretic approach
On biological networks capable of robust adaptation in the presence of uncertainties: A linear systems-theoretic approach
Sloppiness: Fundamental study, new formalism and its application in model assessment
Sloppiness: Fundamental study, new formalism and its application in model assessment
Probing patterning in microbial consortia with a cellular automaton for spatial organisation
Probing patterning in microbial consortia with a cellular automaton for spatial organisation
Discovering design principles for biological functionalities: Perspectives from systems biology
Discovering design principles for biological functionalities: Perspectives from systems biology
iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data
iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data
Metabolic modeling of the International Space Station microbiome reveals key microbial interactions
Metabolic modeling of the International Space Station microbiome reveals key microbial interactions
Effect of dormant spare capacity on the attack tolerance of complex networks
A strategy to make networks more resilient to attacks
Multi-Omic Data Improve Prediction of Personalized Tumor Suppressors and Oncogenes
Multi-Omic Data Improve Prediction of Personalized Tumor Suppressors and Oncogenes
Designing Biological Circuits: From Principles to Applications
Designing Biological Circuits: From Principles to Applications
CAMP: The perfect bacterial matchmaker
It takes two to tango — making bio-production more economical
Learning systems biology, the computational way
Discovering adaptation-capable biological network structures using control-theoretic approaches
Discovering adaptation-capable biological network structures using control-theoretic approaches
A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites
A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites
Novel ratio-metric features enable the identification of new driver genes across cancer types
Novel ratio-metric features enable the identification of new driver genes across cancer types
Bayesian Optimal Experiment Design for Sloppy Systems
Bayesian Optimal Experiment Design for Sloppy Systems
NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
The art of molecular computing: Whence and whither
The art of molecular computing: Whence and whither
Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes
Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes
CASTLE: A database of synthetic lethal sets predicted from genome-scale metabolic networks
How COVID-19 impacts population movement: A data-driven analysis to study population behavior during a pandemic
Bio-surveillance of Antimicrobial Resistance (AMR) and COVID-19 prevalence in Chennai: A MetaSUB approach using metagenomic
Predicting Essential Genes through Network Approach: Deciphering basis of Life
Modelling microbial communities: Harnessing consortia for biotechnological applications
Modelling microbial communities: Harnessing consortia for biotechnological applications
Systems-Theoretic Approaches to Design Biological Networks with Desired Functionalities
Systems-Theoretic Approaches to Design Biological Networks with Desired Functionalities
Two-species community design of lactic acid bacteria for optimal production of lactate
Two-species community design of lactic acid bacteria for optimal production of lactate
MinReact : a systematic approach for identifying minimal metabolic networks
MinReact : a systematic approach for identifying minimal metabolic networks
SBML Level 3: an extensible format for the exchange and reuse of biological models
SBML Level 3: an extensible format for the exchange and reuse of biological models
Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut
Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut
Mycobacterium tuberculosis (Mtb) lipid mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival
Mycobacterium tuberculosis (Mtb) lipid mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival
Machine Learning Applications for Mass Spectrometry-Based Metabolomics
Machine Learning Applications for Mass Spectrometry-Based Metabolomics
Novel ratio-metric features enable the identification of new driver genes across cancer types
MINREACT: an efficient algorithm for identifying minimal metabolic networks
A new index for information gain in the Bayesian framework⁎
A new index for information gain in the Bayesian framework⁎
Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments
Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models
Rational metabolic engineering for enhanced alpha-tocopherol production in Helianthus annuus cell culture
Rational metabolic engineering for enhanced alpha-tocopherol production in Helianthus annuus cell culture
Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation
Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation
Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks
Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks
Evolutionary design principles in metabolism
Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma
Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma
Network-based features enable prediction of essential genes across diverse organisms
Network-based features enable prediction of essential genes across diverse organisms
Systems-Level Modelling of Microbial Communities: Theory and Practice
Understanding the evolution of functional redundancy in metabolic networks
Understanding the evolution of functional redundancy in metabolic networks
Enumerating all possible biosynthetic pathways in metabolic networks
A systems-theoretic approach towards designing biological networks for perfect adaptation
A systems-theoretic approach towards designing biological networks for perfect adaptation
Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL
Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL
Predicting novel metabolic pathways through subgraph mining
Elucidating the biosynthetic pathways of volatile organic compounds in Mycobacterium tuberculosis through a computational approach
Elucidating the biosynthetic pathways of volatile organic compounds in Mycobacterium tuberculosis through a computational approach
A General Mechanism for the Propagation of Mutational Effects in Proteins
A General Mechanism for the Propagation of Mutational Effects in Proteins
In Silico Approaches to Metabolic Engineering
Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks
Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks
Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces
The organisational structure of protein networks: revisiting the centrality–lethality hypothesis
Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach
The evolvability of programmable hardware
Evolvability and robustness in a complex signalling circuit
Systems biology
A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis
Construction and analysis of protein–protein interaction networks
Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis
PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways
Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance
Hallmarks of mycolic acid biosynthesis: A comparative genomics study
Metabolome Based Reaction Graphs of M. tuberculosis and M. leprae: A Comparative Network Analysis
Principles and Practices of Pathway Modelling
Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs