Research Interests:

My primary research interest is on understanding design principles and adaptive dynamics of regulatory networks, particularly of transcriptional regulatory networks, in the cellular context (or systems level) through an integrated approach. This involves collective analyses of the following distinct sets of experimental data:

Assembled genome scale regulatory interaction network for an organism and combinatorial properties of its regulatory proteins.
Protein sequence and structural information, which provides a platform for inferring selective constraints placed on components of the network.
Gene expression data providing clues about dynamics displayed by the organism.
Other kinds of genome-scale information, like protein interaction network, which helps to glean potential interfacing of regulatory pathways with other cellular process.

Brief Bio:

Post-doctoral fellow in the group of Dr.L. Aravind, NCBI, NLM, NIH since June 2004.

Research associate, sponsored by The Wellcome Trust grant, in Dr. N. Srinivasan's group at Indian Institute of Science, Bangalore, India (Sep 2003 to May 2004).

Ph. D. (Computational Biology), Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India (1998-2004).

M. Sc. in Physics (specialization in Quantum electronics and photonics), SSSIHL, Prashanti Nilayam, Andhra Pradesh, India (1996-1998).

B. Sc. (Honours) in Physics , SSSIHL, Prashanti Nilayam, Andhra Pradesh, India (1993-1996).

Selected Recent Publications:

S. Balaji* , M. Madan Babu* and Aravind, L (2007) Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli, J Mol Biol (in press)

S. Balaji and Aravind, L (2007) The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins, Nucleic Acids Research (in press).

S. Balaji* and Aravind, L (2007) The two faces of short-range evolutionary dynamics of regulatory modes in bacterial transcriptional regulatory networks, Bioessays 29(7):625-9.

Madan Babu M, S. Balaji , Iyer, L.M. and Aravind, L. (2006) Estimating the Prevalence and Regulatory Potential the Telomere Looping Effect in Yeast, Cell Cycle 20(5).

S. Balaji* , Madan Babu, M* Iyer, L.M., Luscombe, N.M., and Aravind, L. (2006) Principles of combinatorial regulation in the yeast transcriptional regulatory network, J Mol Biol. 360(1):213-27.

S. Balaji , Iyer, L.M., Aravind, L and Madan Babu, M. (2006) Uncovering distributed robustness in protein regulatory networks, J Mol Biol. 360(1):204-12.

S. Balaji , Madan Babu, M., Iyer, L.M., Aravind, L. (2005). Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains, Nucleic Acids Research, 33(13):3994-4006.