Discipline and Specialization

Computational Biology, Genomics, Pharmaceutical Science

Training/advance exposure in the area of work

Area: High Performance Computing, Computational Biology and Genome Analysis.
Advanced Faculty Training workshop: THINK PARALLEL: Parallel Programming for Engineers and Scientists. Center for Advanced Computing (CDAC), Bangalore, June 2012

Contribution to the scientific advancement

1. Democratizing and accelerating computational biology through development of new tools (WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing)
2. Building future research highways (PmiRExAt: Plant miRNA Expression Atlas Database and web applications.)
3. Scientific computing enrichment(value addition) to every exploration at NABI (In-house collaborations for scientific computing)

Current area of research:

Theme: Unlocking Genomics Potential for Increased Nutrition and Productivity

Project: Development of advanced algorithms, databases, tools and pipeline for data mining and comparative analysis of food crop genomes, transcriptome and small RNA based regulation:

We are accelerating new gene discovery through annotation of plant genome and transcriptomes (cereals and fruits) and understand its role in enhancing nutrition. To understand the abstract digital transcriptional snapshot at genome-wide scale, we use many open source software tools and algorithms ported on our in-house 'Tera (1012)-scale Supercomputing Cluster'.

Using the available software tools we try to see and unravel complex pathways. There were instances where we landed in no man's land where no algorithm/tools/data was available to resolve some snapshots. My group at NABI grabbed few opportunities to develop our own source codes and databases for integrative analysis and data mining. We are constantly working towards integrating information from high throughput genomics experiments through extensive literature and big-data mining to understand the language of genome (operating system of cell).

We also collaborate with many faculty to provide computational biology consultation and service to accelerate their research. Briefly, these big-data explorations involve i) discovering functional DNA binding transcription factors in plants ii) developing transcriptome resource for improving nutritional (iron bioavailability) and processing quality iii) understanding development pathways of mammalian adipose tissue iv) deciphering genes involved in carotenoid biosynthesis pathway v) studying seed development pathways in fruits. Computational Biology Laboratory acts as a gateway for NABI scientists to use computational methods and databases to deepen and integrate their research.

Publications (best five):

1. Gurjar A.K.S, Panwar A.S, Gupta R. and Mantri S.S. (2016). PmiRExAt: Plant miRNA Expression Atlas Database and web applications. Database ; 2016 baw060. doi: 10.1093/database/baw060

2. Gupta R and Mantri S.S. (2016) Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. Frontiers in Genetics. 7:46. doi: 10.3389/fgene.2016.00046

3. Gupta Y, Pathak AK, Singh K, Mantri SS, Singh SP, Tuli R (2015). De novo assembly and characterization of transcriptomes of early-stage fruit from two genotypes of Annona squamosa L. with contrast in seed number. BMC Genomics 16, 86

4. Baboota, R. K., Sarma, S. M., Boparai, R. K., Kondepudi, K. K., Mantri, S., & Bishnoi, M. (2015). Microarray based gene expression analysis of murine brown and subcutaneous adipose tissue: significance with human. PloS ONE, 10(5), e0127701-e0127701.

5. Sharma, P., and Mantri, S. (2014). WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing. PLoS ONE 9, e101144.

6. Awards and Fellowships

1. Qualified GATE 2005.

2. Indian Institute of Information Technology, Allahabad awarded Gold Medal for M.Tech (2005-2007)

3. University Rank In following Subjects-Pharmaceutics, Computer Application, Biotechnology.

4. Ratan Tata Merit Scholarship for undergraduate studies (B.Pharmacy).