Computational Systems Biology Lab

Design Principles for Perfect Adaptation in Biological Networks with Nonlinear Dynamics

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

Bulletin of Mathematical Biology

86:100

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

Priyan Bhattacharya, Karthik Raman*, Arun Tangirala,

Methods Mol Biol

2760:35-56

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

Discovering design principles for biological functionalities: perspectives from systems biology

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

Journal of Biosciences

47:56

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

Sai Saranga Das, Karthik Raman,

Physica A

598:127419

Designing Biological Circuits: From Principles to Applications

Debomita Chakraborty, Raghunathan Rengaswamy, Karthik Raman*,

ACS Synthetic Biology

11:1377-1388

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

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

PLoS Computational Biology

18:e1009769

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

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

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

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

Karthik Azhagesan, Balaraman Ravindran*, Karthik Raman*,

PLoS ONE

13:e0208722

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

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

IFAC-PapersOnLine

51:307-312

Enumerating all possible biosynthetic pathways from metabolic networks

Aarthi Ravikrishnan, Meghana Nasre, Karthik Raman*,

Scientific Reports

8:9932

Predicting Novel Metabolic Pathways through Subgraph Mining

Aravind Sankar, Sayan Ranu*, Karthik Raman*,

Bioinformatics

33:3955-3963

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

Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces

Raghavendran Partha, Karthik Raman*,

PLoS ONE

9:e112792

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

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

Karthik Raman, Rohit Vashisht, Nagasuma Chandra,

Molecular BioSystems

5:1740-1751

Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance

Karthik Raman, Nagasuma Chandra,

BMC Microbiology

8:234

targetTB: A target identification pipeline for Mycobacterium tuberculosis

Karthik Raman, Yeturu Kalidas, Nagasuma Chandra,

BMC Systems Biology

2:109

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