- Dr. Karthik Raman
- Department of Biotechnology
Karthik was nominated for YFRA on the basis of excellent course evaluations in three different courses over the last three years, well-cited research publications in international journals and an edited book. Karthik is a PI on a DBT-funded project and co-PI on an Indo-Finland initiative in synthetic biology, and has initiated several interdisciplinary collaborative projects at IITM.
Karthik's 17 papers have over 750 citations in all (650+ in the last five years). Some of Karthik's algorithms and models have been instrumental in advancing systems-level understanding of Mycobacterium tuberculosis, the tubercular pathogen. Karthik has also written two well-cited reviews in systems biology and was recently invited to contribute a chapter to the comprehensive 3-volume Handbook on Computational Biology, published by Chapman & Hall/CRC. Karthik's most recent work at IITM, in the area of computational systems biology/biological network analysis has also been published in high-impact journals in the field.
Karthik Raman's research contributions
Karthik Raman has made significant contributions to the field of systems biology and biological network modelling over the last 10 years. During his doctoral research in the lab of Prof. Nagasuma Chandra, Indian Institute of Science, Karthik applied various mathematical modelling techniques to study the metabolic and protein interaction networks of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Karthik published the first ever detailed curated mathematical model of the unique mycolic acid pathway in Mtb. This work has been well cited (150+ citations) and laid an important foundation for the curation of genome-scale metabolic models of Mtb by leading research groups in systems biology. Karthik also performed a systematic analysis of every protein in Mtb, assessing their suitability as drug targets, by means of various computational analyses (130+ citations). Karthik's analyses elucidated the effectiveness of known drug targets, suggested their possible side effects, and also suggested several new targets for anti-TB drugs.
During his post-doctoral stint at the lab of Prof. Andreas Wagner, University of Zürich, Karthik studied the robustness and evolvability of complex biological systems, such as the TOR signalling network in yeast, as well as man-made digital logic circuits. By navigating a very large space (1045) of possible circuits and the functions they compute (≈1019), Karthik and Wagner showed that properties important for the evolvability of biological systems exist in digital logic circuitry as well. Further, they showed that it is possible to design robust and evolvable digital circuits, much in the same way Nature has evolved robust and evolvable signalling, metabolic or regulatory circuits. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry, with applications in synthetic biology as well.
As a principal investigator at the Department of Biotechnology, IIT Madras, Karthik and his group have continued to work in the area of biological network modelling, focusing mostly on metabolic networks, with industrial applications in metabolic engineering and identification of combinatorial drug targets. In a recent study, Karthik and his MS student (in collaboration with Shankar Balachandran, CSE, IITM) devised an efficient algorithm to identify synthetic lethal genes in metabolic networks. Synthetic lethals are combinations of genes that when removed simultaneously abolish the growth of an organism â€" they are important in identifying combinatorial drug targets and novel interactions. Using an elegant extension to the established method of Flux Balance Analysis, they eliminated large portions of the search space for lethals, to rapidly identify synthetic lethals in many pathogenic organisms. Karthik and his PhD student also analysed 99 published metabolic networks, illustrating the shortcomings of various published metabolic networks, and recommended a set of standards to be adhered to in the systems biology community, for more effectively reconstructing metabolic models. Karthik's group comprises 4 PhDs and 2 MS students; he has mentored 15 undergraduates for thesis projects.
In 2014, Karthik co-edited a book on "A Systems Theoretic Approach to Systems and Synthetic Biology" in two volumes, together with Dr. Vishwesh Kulkarni (University of Warwick, UK) and Dr. Guy-Bart Stan (Imperial College, London). Karthik has also written a couple of well cited reviews on flux balance analysis (180 citations) and construction and analysis of proteinâ€"protein interaction networks (50+ citations).