National Institute Of Biomedical Genomics (NIBMG)

Postdoctoral fellow (November, 2008 - June,2011) at Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
Postdoctoral fellow (April, 2008 - October, 2008) Cologne Center for Genomics , University of Cologne, Cologne, Germany
Postdoctoral fellow (July, 2007 - April, 2008) Medical Research Center, University Hospital, Mannheim, University of Heidelberg, Germany

"Summa-cum-laude " for PhD thesis (2007)
"Nehru Memorial Gold Medal" for M.Sc. Computer Application (2003)
1^st ranker of M.Sc Computer Applications at Indian Agricultural Statistics Research Institute, New Delhi (2001-2003).

"Promotionsstipendium an der Medizinische Fakultaet Mannheim der Ruprecht-Karls-Universtitaet Heidelberg (Fellowship of Faculty of Medical Sciences Mannheim, University of Heidelberg, Germany"2007-2008
Fellowship of DFG (German Research Foundation) Graduiertenkollegs 886, "Bildgebende Verfahren zur Expressionsanalytik: vom Gen zum Protein" for Ph.D (2004-2007)
ARS-NET (2004) of the Indian Council for Agricultural Research, New Delhi
Junior Research Fellowship (JRF) of Indian Council for Agricultural Research, New Delhi with All India Rank 4, year (2001-2003)
Member of American Society of Nephrology (ASN)

Role of miRNAs and other small-RNAs in Polycystic Kidney Disease (Talk; Center for Polycystic Kidney Disease Research, Harvard Medical School, Boston, March 2009)
Analysis of MicroRNA microarrays using SAS ( Talk; JMP Genomics Workshop July 12, SAS Institute, Heidelberg, July 2007)
Computational approaches to explore the possible roles of miRNAs in PKD ( Talk; Meeting of the Research Training Group 886, Wissenschaftsforum, Heidelberg, July 2006 )
A New microRNA Database and Sequence Analyses ( Talk; Meeting of the Research Training Group 886, Wissenschaftsforum, Heidelberg, February 2006 )
RNAi: Prediction by self-learning artificial intelligence and validation in vitro ( Talk; Meeting of the Research Training Group 886, Wissenschaftsforum, Heidelberg, February 2005)
Applications of IT tools in Bioinformatics ( Talk; Indian Agriculture Statistical Research Institute, New Delhi, October, 2002)
Voice over Internet Protocol (VoIP) ( Talk; Indian Agriculture Statistical Research Institute, New Delhi, July, 2002)

Bioinformatics and Systems Biology-

I study transcriptional and post-transcriptional mechanisms of gene regulations (such as those by transcription factors and microRNAs (miRNAs)) by integrating computational and experimental tools at systems level. I have special interest in studying the role of miRNAs, for which I extensively use Next-Generation sequencing (NGS; "454/Roche" as well as "Illumina" platform), miRNA- microarrays as well as gene-expression and DNA microarrays (for ChIP-on-chip). A major part of my work demands developing new tools, databases and resources/pipelines for assembly, and analysis of high-throughput data. These computational resources are fairly generic and equally applicable in animal as well as plant biology research. In my present studies in Dr. Kreidberg's laboratory, I am attempting to identify all microRNAs (miRNAs) and other small-RNAs (smRNAs) differentially regulated during Autosomal Dominant Polycystic Kidney Disease (ADPKD) using NGS of the smRNA transcriptome, as well as exploring the functional patterns/signatures of smRNA-mRNA interaction during the course of kidney development and progression of PKD.

In another projects, I developed new pipelines for investigating the transcription factor targets at whole genome level and applied it to identify the targets of WT1-transcription factor in developing kidney using 'Chip-on-chip' data by combining several motif discovery algorithms such as Weeder, MEME, Gibbs sampler and THEME, with statistical measures of significance and also developed pipelines to identify miRNAs that may regulate kidney development.

Summary of PhD thesis : A combinatorial study to identify microRNAs and their targets in Polycystic Kidney Diseases

My PhD work involved two broad aspects: (1) Development of a public resource and information system for miRNA community; and (2) Use of this and other computational and experimental resources, mainly miRNA-microarrays and gene expression arrays to develop a combinatorial method to identify miRNA-targets at pathway level. This pipeline was applied to explore if miRNAs play a role in Polycystic Kidney Disease (PKD). I have developed a relational database called "Argonaute" using PHP and MySQL. The relational database schema based on Entity-Relationship (ER) model was implemented using SQL and then PHP and Perl were used as 3 rd generation host language to implement the external input and output documents. This database was among the top 5 databases as reported by Nucleic Acids Research. For (2), I adopted a combinatorial approach, where I developed a novel approach to identify pathways that may be miRNA-targets using computational predictions and 2-way-microarray analysis for miRNAs (using the Locked Nucleic Acid based miRNA chips) and for targets of miRNAs (using Affymetrix microarrays). This approach was applied for PKD. New miRNAs were discovered, which were previously not reported in kidney. Further, the role of miRNAs in PKD was confirmed and the targets and pathways affected were mapped.

I developed a pipeline for the analysis of the complete small-RNome of an ecological model plant, Nicotiana. attenuata. This was a collaborative project between me and Dr. Shree P. Pandey for the lab of Prof. Ian T. Baldwin, at the Dept of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany. The aim of this project was to sequence and map the changes in the small-RNA portion of the transcriptome during herbivory and silencing of RNA-directed RNA polymerases, the enzymes essential for the production of double-stranded precursor siRNAs.

I developed software, "Survey Data Analysis Package" to analyze two-stage sampling data and "Development Index" to study agricultural development, infra-structural facilities and overall socio-economic development of different regions using Visual Basic 6.0.