Karthik Raman
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- Computational Approaches to Understand and Manipulate Biological Networks
- Biological Big Data Analysis
- High-performance Computing for Systems Biology
- In silico metabolic engineering
- Theoretical investigations into biological networks
Articles (31)
- (2019) Evolutionary design principles in metabolism Proc Biol Sci 286(1898):20190098-20190098
- (2019) Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks Frontiers in Genetics 10 , Frontiers Media SA
- (2019) Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma FEBS Lett 593(1):23-41
- (2019) Rational metabolic engineering for enhanced alpha-tocopherol production in Helianthus annuus cell culture Biochemical Engineering Journal:107256
- (2019) Assessment of network module identification across complex diseases Nature Methods 16(9):843-852
- (2019) Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation Processes 7(6)
- (2018) Network-based features enable prediction of essential genes across diverse organisms PLOS ONE 13(12):1-13 , Public Library of Science
- (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) Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL. Methods in molecular biology (Clifton, N.J.) 1716:315-336
- (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 , Oxford University Press
- (2015) Critical assessment of genome-scale metabolic networks: the need for a unified standard Briefings in Bioinformatics 16(6):1057-1068 , Oxford University Press
- (2014) Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces PLoS ONE 9(11):e112792+ , Public Library of Science
- (2014) The organisational structure of protein networks: revisiting the centrality–lethality hypothesis Systems and Synthetic Biology 8(1):73-81 , Springer Netherlands
- (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 , The Royal Society of Chemistry
- (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 , The Royal Society of Chemistry
- (2010) Construction and analysis of protein-protein interaction networks Automated Experimentation 2(1):2+
- (2009) Flux balance analysis of biological systems: applications and challenges. Briefings in bioinformatics 10(4):435-449
- (2009) Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis Mol. BioSyst. 5(12):1740-1751 , The Royal Society of Chemistry
- (2008) Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance BMC Microbiology 8:234
- (2008) targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC systems biology 2(1):109+
- (2007) Metabolome Based Reaction Graphs of M. tuberculosis and M. leprae: A Comparative Network Analysis PLoS ONE 2(9):e881+ , Public Library of Science , Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
- (2007) Hallmarks of mycolic acid biosynthesis: A comparative genomics study Proteins: Structure, Function, and Bioinformatics 69(2):358-368 , Bioinformatics Centre and Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India
- (2006) Principles and Practices of Pathway Modelling Current Bioinformatics 1(2):147-160 , Bentham Science Publishers
- (2005) Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs PLoS Computational Biology 1(5):e46+ , Public Library of Science
Books (3)
- (2018) Systems-level modelling of microbial communities : theory and practice , CRC Press
- (2014) A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations , Springer
- (2014) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems , Springer
Book Chapters (3)
- (2016) In Silico Approaches to Metabolic Engineering
- (2011) Systems Biology of Tuberculosis: Insights for Drug Discovery , Springer New York , New York, NY
- (2007) Model Driven Drug Discovery: Principles and Practices , Artech House Publishers
Miscellaneous (3)
- BT 1010: Module on “Big Data in Biology” (Jul 2017)
- BT 2020: Numerical Methods for Biology (Jan 2018, 2019)
- BT 3051: Data Structures and Algorithms for Biology (Jul 2014–2019)
- BT 3240: Metabolic Regulation (Jul 2011–2013)
- BT 4110: Computational Biology Lab (Jul 2015–2017)
- BT 4310: Current Topics in Synthetic Biology (Jul 2014, 2019)
- BT 5240: Computational Systems Biology (Jan 2013–2019, Winter 2017)
- Young Faculty Recognition Award (IIT Madras), for excellence in teaching and research (2015)
- Sir Vithal N. Chandavarkar Memorial Medal for the best Ph.D. thesis in the Supercomputer Education and Research Centre, Indian Institute of Science (2011)