A biologist with a deep interest in computational analysis of proteins and gene sequences. I analyze protein sequences in an evolutionary context to recognize their in-built signatures, that dictate their overall structure and function in the cellular context. Detectable relationships between proteins that harbor such signatures provide the evolutionary perspective to how proteins perform such a diverse array of functions. I am interested in using a comparative approach to decode these signatures and to understand this in the light of large milieu of interactions within a cell.
Qualifications
B.Sc. Zoology
Stella Maris College for Women, University of Madras
M.Sc. Biotechnology
Pondicherry University
Adv Diploma in Bioinformatics
University of Pune
PhD- Bioinformatics
Manipal University
Experience
Total Years of Experience: 23
Academic Experience: Indian Institute of Science, National Centre for Biological Sciences –21
Industry Experience: Monsanto R&D, Astra Zeneca R&D, DSQ Biotech Ltd- 2 years
Computational Biology, Bioinformatics, Protein function, Protein evolution, Protein-protein interactions, Protein structure prediction, Molecular modelling and docking, Data analysis — All-omics platforms
National Journal Papers
- Influence of protein structural similarities in adding value to genome data. Ind J Biotech. 2004
- Influence of genomic and other biological data sets in the understanding of protein structures, functions and interactions. Int J Knowledge Discovery Bioinf. 2011
International Journal Papers
- Computational tools to study RNA-protein complexes. Front Mol Biosci. 2022
- Profiles of Natural and Designed Protein-Like Sequences Effectively Bridge Protein Sequence Gaps: Implications in Distant Homology Detection. Methods Mol Biol. 2022
- Sequence Divergence and Functional Specializations of the Ancient Spliceosomal SF3b: Implications in Flexibility and Adaptations of the Multi-Protein Complex. Front Genet. 2022
- Identification, functional characterization, assembly and structure of ToxIN type III toxin-antitoxin complex from E. coli. Nucleic Acids Res. 2022
- Rewards of divergence in sequences, 3‑D structures and dynamics of yeast and human spliceosome SF3b complexes. Curr Res in Str Biol. 2021
- Signatures of conserved and unique molecular features in Afrotheria. Sci Rep. 2021
- Comparative analysis of structural and dynamical features of ribosome upon association with mRNA reveals potential role of smaller ribosomal subunit. Front Mol Biosci. 2021
- Molecular and structural basis of cross-reactivity in M. tuberculosis toxin-antitoxin systems. Toxins. 2020
- Artificial protein sequences enable recognition of vicinal and distant protein functional relationships. Proteins. 2020
- Bioinformatic and mutational studies of related toxin-antitoxin pairs in M.tuberculosis predict and identify key functional residues. J Biol Chem. 2019
- Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. Sci Rep. 2019
- Use of designed sequences in protein structure recognition. Biol Direct. 2018
- Domain architecture of BAF250a reveals the ARID and ARM-repeat domains with implication in function and assembly of the BAF remodeling complex. PLOS One. 2018
- Protein design and its applications. Curr Opin Str Biol. 2016
- De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods. Biol Direct. 2015
- ChExVis: A tool for molecular channel extraction and vizualization. BMC Bioinformatics. 2015
- Bridging the islands of protein families in sequence space using artificial sequences. J Biomol Struct Dyn. 2015
- NrichD database: sequence databases enriched with computationally designed protein-like sequences aid in remote homology detection. Nucleic Acids Res. 2015
- Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure. J Proteome Res 2014
- Filling-in void and sparse regions in protein sequence space by protein-like artificial sequences enables remarkable enhancement in remote homology detection capability. J. Mol Biol. 2014
- Structural Annotation of the Mycobacterium tuberculosis Proteome. Microbiol Spectr. 2014
- Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage. PLOS One. 2013
- Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins. Mol Biosyst. 2012
- Structural Annotation of M. tuberculosis Proteome. PLOS One. 2011
- Influence of genomic and other biological data sets in the understanding of protein structures, functions and interactions. Int J Knowledge Discovery Bioinf. 2011
- Length variations amongst protein domain superfamilies and consequences on structure and function. PLOS One. 2009
- CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations. BMC Struct Biol. 2008
- Gadkari RA, Sandhya S et al, The antigen binding sites of various hCG monoclonal antibodies show homology to different domains of LH receptor. Mol Cell Endocrinol. 2007
- Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. NAR. 2006
- Recent trends in remote homology detection: an Indian medley. Bioinformation. 2006
- Assessment of a rigorous transitive profile-based search method to detect remotely similar proteins. J Biomol Struct Dyn. 2005
- Effective detection of remote homologues by searching in sequence dataset of a protein domain fold. FEBS Lett. 2003
Books / Chapter Published
- Relating protein families in sequence space through multiple intermediates. In Mathematical Biology, edited by P.Chandra & B.V.R.Kumar, Anamaya Publishers, New Delhi
- Structural annotation of Mycobacterium tuberculosis proteome. Molecular Genetics of Mycobacteria, 2nd Edition, Microbiology Spectrum, ASM journals, 2014
- 2022: Seed grant, Bioinformatics research- Ramaiah University of Applied Sciences
- 2011 – 2014: DST post-doctoral grant in the Women Scientist scheme (WosA)
- 2004 – 2007: CSIR award of Senior Research fellowship towards PhD
- 1998 – 1999: DBT fellowship towards Adv. Diploma Course in Bioinformatics
- 1998: Ranked State IV (All India XI) and in top 0.1 percentile in GATE, DoE, Govt. of India
- UGC-NET qualification for Lectureship
- 1996 – 1998: DBT fellowship towards M.Sc. Biotechnology, Pondicherry University, India
- 1995- 1996: Recipient of Dr. Shiranee Pereira, Dr. Eileen Riordan, Dr. Dharmarajan awards for excellence in Zoology and Genetics-Stella Maris College for Women, University of Madras