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Karthik Raman's Lab @ IIT Madras

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Publications

Compact

2025

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Metagenomic profiling of municipal drinking water microbiomes in an Indian city: Insights into diversity, water quality, and AMR potential

Vikas Kumar†, Shradha Sharma†, Kaomud Tyagi, Barathi Lenin, Aarti Ravindran, Karthik Raman*, Inderjeet Tyagi*,

Journal of Environmental Chemical Engineering

13:119959

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Decoding microbial diversity, biogeochemical functions, and interaction potentials in Red Sea hydrothermal vents

Sharifah Altalhi, Júnia Schultz, Tahira Jamil, Isabel Diercks, Shradha Sharma, Jörg Follmann, Intikhab Alam, Karthik Raman, Nico Augustin, Froukje M. van der Zwan, Alexandre Soares Rosado_,

Environmental Microbiome

20:118

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PURE: Policy-guided Unbiased REpresentations for structure-constrained molecular generation

Abhor Gupta*, Barathi Lenin, Sean Current, Rohit Batra, Balaraman Ravindran, Karthik Raman*, Srinivasan Parthasarthy*,

Journal of Cheminformatics

17:156

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Harnessing machine learning for metagenomic data analysis: trends and applications

Shradha Sharma, Hari Priya Narahari, Karthik Raman*,

mSystems

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An integrated systems biology approach establishes arginine biosynthesis as a metabolic weakness in *Candida albicans* during host infection

Shuvechha Chakraborty, Indumathi Palanikumar, Yash Gune, K.V. Venkatesh, Karthik Raman*, Susan Idicula-Thomas*,

Cell Communication and Signaling

23:362

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COSMOS: COmmunity and Single Microbe Optimisation System

Lavanya Raajaraam, Karthik Raman*,

npj Systems Biology and Applications

11:51

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GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations

Venkatesh Kamaraj, Ayam Gupta, Karthik Raman*, Manikandan Narayanan*, Himanshu Sinha*,

Nucleic Acids Research: Genomics and Bioinformatics

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Functional Insights into Novel Extremophilic Bacteria Isolated from the NASA Phoenix Mission Spacecraft Assembly Cleanrooms

Júnia Schultz, Tahira Jamil, Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Anamika Rawat, Niketan Patel, Srinivasan Krishnamurthy, Intikhab Alam, Nitin Kumar Singh, Karthik Raman, Alexandre Soares Rosado*, Kasthuri Venkateswaran*,

Microbiome

13:117

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Mapping genetic diversity with the GenomeIndia project

Chandrika Bhattacharya, ..., Himanshu Sinha, Manikandan Narayanan, Karthik Raman, Raghu Padinjat, Radhakrishnan Sabarinathan, GenomeIndia Consortium, Yadati Narahari, Vijayalakshmi Ravindranath, Kumarasamy Thangaraj, Divya Tej Sowpati, & more

Nature Genetics

57:767

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Integrating Model-Informed Drug Development With AI: A Synergistic Approach to Accelerating Pharmaceutical Innovation

Karthik Raman*, Rukmini Kumar, Cynthia J. Musante, Subha Madhavan,

Clinical and Translational Science

13:e70124

2024

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Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus

Asif Hameed, Francesca McDonagh, Pratyay Sengupta, Georgios Miliotis, Shobhan Karthick Muthamilselvi Sivabalan, Lukasz Szydlowski, Anna Simpson, Nitin Kumar Singh, Punchappady Devasya Rekha, Karthik Raman*, Kasthuri Venkateswaran*,

Microbiology Spectrum

13:e01376-24

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Understanding flux switching in metabolic networks through an analysis of synthetic lethals

Sowmya Manojna Narasimha†, Tanisha Malpani†, Omkar S. Mohite, J. Saketha Nath, Karthik Raman*,

npj Systems Biology and Applications

10:104

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Modeling Microbial Communities: Perspective and Challenges

Lavanya Raajaraam, Karthik Raman*,

ACS Synthetic Biology

13:2260-2270

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Panera: A novel framework for surmounting uncertainty in microbial community modelling using Pan-genera metabolic models

Indumathi Palanikumar, Himanshu Sinha, Karthik Raman*,

iScience

27:110358

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Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics

Priyan Bhattacharya, Karthik Raman*, Arun K. Tangirala*,

Bulletin of Mathematical Biology

86:100

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Designing function-specific minimal microbiomes from large microbial communities

Aswathy Raghu, Indumathi Palanikumar, Karthik Raman*,

npj Systems Biology and Applications

10:46

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Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station

Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Nitin Kumar Singh, Karthik Raman*, Kasthuri Venkateswaran*,

Microbiome

12:62

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Novel spore-forming species exhibiting intrinsic resistance to third- and fourth-generation cephalosporins and description of Tigheibacillus jepli gen. nov., sp. nov.

Georgios Miliotis, Pratyay Sengupta, Asif Hameed, Maria Chuvochina, Francesca McDonagh, Anna Simpson, Ceth Parker, Nitin Singh, Punchappady Rekha, Dearbháile Morris, Karthik Raman, Nikos Kyrpides, & more

mBio

15:e00181-24

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Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob*, Tomiko T. Oskotsky*, ..., The Preterm Birth DREAM Community, ..., James C. Costello, Marina Sirota*,

Cell Reports Medicine

5:101350

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Design Principles for Biological Adaptation: A Systems and Control-Theoretic Treatment

Priyan Bhattacharya, Karthik Raman*, Arun Tangirala,

Methods Mol Biol

2760:35-56

2023

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Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes

Anna C. Simpson†, Pratyay Sengupta†, Flora Zhang, Asif Hameed, Ceth W. Parker, Nitin K. Singh, Georgios Miliotis, Punchappady D. Rekha, Karthik Raman, Christopher E. Mason*, Kasthuri Venkateswaran*,

Scientific Reports

13:19207

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Genome-scale metabolic model led engineering of Nothapodytes nimmoniana plant cells for high camptothecin production

Sarayu Murali, Maziya Ibrahim, Hemalatha Rajendran, Shagun Shagun, Shyam Kumar Masakapalli, Karthik Raman, Smita Srivastava*,

Frontiers in Plant Science

14:1207218

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BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures

Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Issac Hecht, Aarthi Ravikrishnan, Rafael S. Gonçalves, & more

Nature Biotechnology

42:709--804

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Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes

Dinesh Kumar Kuppa Baskaran, Shreyansh Umale, Zhichao Zhou, Karthik Raman*, Karthik Anantharaman*,

ISME Communications

3:42

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COWAVE: A Labelled COVID-19 Wave Dataset for Building Predictive Models

Melpakkam Pradeep, Karthik Raman*,

PLoS ONE

18:e0284076

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Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes

Pratyay Sengupta, Shobhan Karthick Muthamilselvi Sivabalan, Amrita Mahesh, Indumathi Palanikumar, Dinesh Kumar Kuppa Baskaran, Karthik Raman*,

Journal of the Indian Institute of Science

103:891-907

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Sloppiness: fundamental study, new formalism and its application in model assessment

Prem Jagadeesan, Karthik Raman*, Arun K. Tangirala*,

PLoS ONE

18:e0282609-108984

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On biological networks capable of robust adaptation in the presence of uncertainties: A linear systems-theoretic approach

Priyan Bhattacharya, Karthik Raman*, Arun K. Tangirala*,

Mathematical Biosciences

358:121-126

2022

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Bayesian Optimal Experiment Design for Sloppy Systems

Prem Jagadeesan, Karthik Raman*, Arun K. Tangirala*,

IFAC-PapersOnLine

55:

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Probing patterning in microbial consortia with a cellular automaton for spatial organisation

Sankalpa Venkatraghavan†, Sathvik Anantakrishnan†, Karthik Raman*,

Scientific Reports

12:17159

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Anjana Anilkumar Sithara, Devi Priyanka Maripuri, Keerthika Moorthy, Sai Sruthi Amirtha Ganesh, Philge Philip, Shayantan Banerjee, Malvika Sudhakar, Karthik Raman*,

Nucleic Acids Research: Genomics and Bioinformatics

3:lqac053

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Discovering design principles for biological functionalities: perspectives from systems biology

Priyan Bhattacharya, Karthik Raman*, Arun K. Tangirala*,

Journal of Biosciences

47:56

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Effect of Dormant Spare Capacity on the Attack Tolerance of Complex Networks

Sai Saranga Das, Karthik Raman,

Physica A

598:127419

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Metabolic modeling of the International Space Station microbiome reveals key microbial interactions

Rachita K Kumar, Nitin Singh, Sanjaay Balakrishnan, Ceth W. Parker, Karthik Raman*, Kasthuri Venkateswaran*,

Microbiome

10:102

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Multi-omic data improve prediction of personalized tumor suppressors and oncogenes

Malvika Sudhakar, Raghunathan Rengaswamy*, Karthik Raman*,

Frontiers in Genetics

13:854190

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Designing Biological Circuits: From Principles to Applications

Debomita Chakraborty, Raghunathan Rengaswamy, Karthik Raman*,

ACS Synthetic Biology

11:1377-1388

2021

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Discovering adaptation-capable biological network structures using control-theoretic approaches

Priyan Bhattacharya, Karthik Raman*, Arun K. Tangirala*,

PLoS Computational Biology

18:e1009769

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Novel ratio-metric features enable the identification of new driver genes across cancer types

Malvika Sudhakar, Raghunathan Rengaswamy*, Karthik Raman*,

Scientific Reports

12:5

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A Computational Framework to Identify Metabolic Engineering Strategies for the Co-Production of Metabolites

Lavanya Raajaraam, Karthik Raman*,

Frontiers in Bioengineering and Biotechnology

9:779405

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Synthetic biology beyond borders

Karthik Raman, Himanshu Sinha, Claudia E Vickers, Pablo Ivan Nikel,

Microbial Biotechnology

14:2254-2256

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Two-species community design of lactic acid bacteria for optimal production of lactate

Maziya Ibrahim, Karthik Raman*,

Computational and Structural Biotechnology Journal

19:6039-6049

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Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd

Attila Gabor†, Marco Tognetti†, Alice Driessen, Jovan Tanevski, Baosen Guo, Wencai Cao, He Shen, Thomas Yu, Verena Chung, Single Cell Signaling in Breast Cancer DREAM Consortium members, Bernd Bodenmiller*, Julio Saez-Rodriguez*,

Molecular Systems Biology

17:e10402

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NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks

Vimaladhasan Senthamizhan, Balaraman Ravindran, Karthik Raman*,

Frontiers in Genetics

12:722198

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Modelling microbial communities: Harnessing consortia for biotechnological applications

Maziya Ibrahim†, Lavanya Raajaraam†, Karthik Raman*,

Computational and Structural Biotechnology Journal

19:3892-3907

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The art of molecular computing: whence and whither

Sahana Gangadharan, Karthik Raman*,

BioEssays

43:202100051

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Sequence Neighborhoods Enable Reliable Prediction of Pathogenic Mutations in Cancer Genomes

Shayantan Banerjee, Karthik Raman*, Balaraman Ravindran*,

Cancers

13:2366

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An Introduction to Computational Systems Biology

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2020

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Systems-Theoretic Approaches to Design Biological Networks with Desired Functionalities

Priyan Bhattacharya, Karthik Raman*, Arun Tangirala,

Methods Mol Biol

2189:133-135

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SBML Level 3: an extensible format for the exchange and reuse of biological models

Sarah M. Keating*, Dagmar Waltemath*, ..., Karthik Raman, ..., Henning Hermjakob, John C. Doyle, Michael Hucka*, SBML Community members,

Molecular Systems Biology

16:e91110

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A new index for information gain in the Bayesian framework

Prem Jagadeesan, Karthik Raman, Arun K. Tangirala*,

IFAC-PapersOnLine

53:634-639

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Metagenome-Wide Association Analysis Identifies Microbial Determinants of Post-Antibiotic Ecological Recovery in the Gut

Kern Rei Chng, Tarini Shankar Ghosh, Yi Han Tan, Tannistha Nandi, Ivor Russel Lee, Amanda Hui Qi Ng, Chenhao Li, Aarthi Ravikrishnan, Kar Mun Lim, David Lye, Timothy Barkham, Karthik Raman, & more

Nature Ecology and Evolution

4:1256-1267

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Mycobacterium tuberculosis (Mtb) lipid–mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival

Kuldeep Sachdeva, Manisha Goel, Malvika Sudhakar, Mansi Mehta, Rajmani Raju, Karthik Raman, Amit Singh, Varadharajan Sundaramurthy*,

Journal of Biological Chemistry

295:9192-9210

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Machine Learning Applications for Mass Spectrometry-Based Metabolomics

Ulf Liebal*, Thuy An Phan Nguyen, Malvika Sudhakar, Karthik Raman, Lars M. Blank,

Metabolites

10:243

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MinReact: a systematic approach for identifying minimal metabolic networks

Gayathri Sambamoorthy, Karthik Raman*,

Bioinformatics

36:4309-4315

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Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

Aarthi Ravikrishnan, Lars M. Blank, Smita Srivastava, Karthik Raman,

Computational and Structural Biotechnology Journal

18:1249-1258

2019

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Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

Devika N T, Karthik Raman*,

Scientific Reports

9:18222

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Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases

Sarvenaz Choobdar, \ldots, The DREAM Module Identification Challenge Consortium, \ldots, Sven Bergmann*, Daniel Marbach*,

Nature Methods

16:843

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Special issue on theory and application of network algorithms in biology

Karthik Raman, A Kalyanaraman,

Int J Adv Eng Sci Appl Math

11:89-90

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Rational engineering of vitamin E metabolism for enhanced alpha-tocopherol production in Helianthus annuus cell culture

Aparajitha Srinivasan, Vijayakumar S, Karthik Raman, Smita Srivastava*,

Biochemical Engineering Journal

151:107256

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Uncovering Novel Pathways for Enhancing Hyaluronan Synthesis in Recombinant Lactococcus lactis: Genome-Scale Metabolic Modeling and Experimental Validation

Abinaya Badri, Karthik Raman*, Guhan Jayaraman*,

Processes

7:343

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Adapting Community Detection Algorithms for Disease Module Identification in Heterogeneous Biological Networks

Beethika Tripathi, Srinivasan Parthasarathy, Himanshu Sinha, Karthik Raman, Balaraman Ravindran*,

Frontiers in Genetics

10:164

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Evolutionary design principles in metabolism

Gayathri Sambamoorthy, Himanshu Sinha*, Karthik Raman*,

Proc Biol Sci

286:20190098

2018

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Network-based features enable prediction of essential genes across diverse organisms

Karthik Azhagesan, Balaraman Ravindran*, Karthik Raman*,

PLoS ONE

13:e0208722

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Metabolite systems profiling identifies exploitable weaknesses in retinoblastoma

Swagatika Sahoo*, Ranjith Kumar R, Brandon Nicolay, Omkar Mohite, Karthikeyan Sivaraman, Vikas Khetan, Pukhraj Rishi, Suganeswari Ganesan, Subramanian Krishnakumar, Karthik Raman, Wayne Miles, Sailaja V Elchuri*,

FEBS Letters

593:23-41

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Systems-Level Modelling of Microbial Communities: Theory and Practice

Aarthi Ravikrishnan, Karthik Raman,

:

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A systems-theoretic approach towards designing biological networks for perfect adaptation

Priyan Bhattacharya, Karthik Raman, Arun K. Tangirala*,

IFAC-PapersOnLine

51:307-312

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Enumerating all possible biosynthetic pathways from metabolic networks

Aarthi Ravikrishnan, Meghana Nasre, Karthik Raman*,

Scientific Reports

8:9932

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Understanding the evolution of functional redundancy in metabolic networks

Gayathri Sambamoorthy, Karthik Raman*,

Bioinformatics

34:i981-i987

2017

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Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL

Karthik Raman*, Aditya Pratapa, Omkar Mohite, Shankar Balachandran,

Methods Mol Biol

1716:315-336

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Predicting Novel Metabolic Pathways through Subgraph Mining

Aravind Sankar, Sayan Ranu*, Karthik Raman*,

Bioinformatics

33:3955-3963

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Elucidating the biosynthetic pathways of volatile organic compounds in Mycobacterium tuberculosis through a computational approach

Purva Bhatter, Karthik Raman*, Vani Janakiraman*,

Molecular BioSystems

13:750-755

2016

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A General Mechanism for the Propagation of Mutational Effects in Proteins

Nandakumar Rajasekaran, Swaathiratna Suresh, Soundhararajan Gopi, Karthik Raman, Athi N. Naganathan*,

Biochemistry

56:294-305

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In Silico Approaches to Metabolic Engineering

Abinaya Badri, Aparajitha Srinivasan, Karthik Raman*,

Current Developments in Biotechnology and Bioengineering

:

2015

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Fast-SL: An efficient algorithm to identify synthetic lethal sets in metabolic networks

Aditya Pratapa, Shankar Balachandran, Karthik Raman*,,

Bioinformatics

31:3299-3305

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Critical assessment of genome-scale metabolic networks: the need for a unified standard

Aarthi Ravikrishnan, Karthik Raman*,

Briefings in Bioinformatics

16:1057-1068

2014

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Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces

Raghavendran Partha, Karthik Raman*,

PLoS ONE

9:e112792

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A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems

Vishwesh Kulkarni, Guy-Bart Stan, Karthik Raman,

:

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A Systems Theoretic Approach to Systems and Synthetic Biology I: Models and System Characterizations

Vishwesh Kulkarni, Guy-Bart Stan, Karthik Raman,

:

2013

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The organisational structure of protein networks: revisiting the centrality--lethality hypothesis

Karthik Raman*, Nandita Damaraju, Govind Krishna Joshi,

Systems and Synthetic Biology

8:73-81

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Identification of putative and cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach

Anuja Kulkarni, Laxmi Ananthanarayanan*, Karthik Raman,

Computational Biology \& Chemistry

47:149-155

2011

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Evolvability and robustness in a complex signalling circuit

Karthik Raman, Andreas Wagner,

Molecular BioSystems

7:1081-1092

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The evolvability of programmable hardware

Karthik Raman, Andreas Wagner,

Journal of the Royal Society Interface

8:269-281

2010

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Systems Biology

Karthik Raman, Nagasuma Chandra,

Resonance

15:131-153

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Construction and analysis of protein--protein interaction networks

Karthik Raman*,

Automated Experimentation

2:2

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Systems Biology of Tuberculosis: Insights for drug discovery

Karthik Raman, Nagasuma Chandra,

Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology

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A systems perspective of host--pathogen interactions: prediction of tuberculosis disease outcome

Karthik Raman, Ashwini Gurudas Bhat, Nagasuma Chandra,

Molecular BioSystems

6:516-530

2009

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Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis

Karthik Raman, Rohit Vashisht, Nagasuma Chandra,

Molecular BioSystems

5:1740-1751

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Flux balance analysis of biological systems: applications and challenges

Karthik Raman, Nagasuma Chandra,

Briefings in Bioinformatics

10:435-449

2008

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Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance

Karthik Raman, Nagasuma Chandra,

BMC Microbiology

8:234

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targetTB: A target identification pipeline for Mycobacterium tuberculosis

Karthik Raman, Yeturu Kalidas, Nagasuma Chandra,

BMC Systems Biology

2:109

2007

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Metabolome based reaction graphs of M.~tuberculosis and M. leprae: A comparative network analysis

Ketki Verkhedkar, Karthik Raman, Nagasuma Chandra, Saraswathi Vishveshwara,

PLoS ONE

2:e881

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Hallmarks of Mycolic Acid Biosynthesis: A Comparative Genomics Study

Karthik Raman, Preethi Rajagopalan, Nagasuma Chandra,

Proteins: Structure, Function and Bioinformatics

69:358

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Model Driven Drug Discovery: Principles and Practices

Karthik Raman, Yeturu Kalidas, Nagasuma Chandra,

Biological Database Modeling

:

2006

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Principles and Practices of Pathway Modelling

Karthik Raman, Preethi Rajagopalan, Nagasuma Chandra,

Current Bioinformatics

1:147-160

2005

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Flux Balance Analysis of Mycobacterium tuberculosis: targets for anti-tubercular drugs

Karthik Raman, Preethi Rajagopalan, Nagasuma Chandra,

PLoS Computational Biology

1:e46

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