1. Computational and Bioinformatics experience:
T-Lex Web Interfacing and Data Generation and Analysis: (Internship at Stanford University, CA)
Designed a sample Web-Interface for T-Lex tool and generated, annotated the data using the tool and
worked on Drosophila data of 12 different species and also testing on different platforms using the T-Lex
Tool.
(Please refer to webpage : http://petrov.stanford.edu/cgi-bin/Tlex_databases/home.cgi! ).
Large-Scale Data Analysis of p53 Gene Expression in Embryonic Stem Cell Populations (Master’s Thesis)
To explore sets of genes that are correlated with the p 5 3 expression within and between different
groups of embryonic stem cells using A g i l e n t W o r k B e n c h T o o l , and also predicted if p53 might
be regulating one single set of genes in all different stem cell populations or whether its expression is
different in different populations. This was then combined to determine which genes actually are
similar using ChIP-seq data and those which bind to p53 and also measured their expression profile
across different populations.
A re-analysis of previously available microarray dataset followed by analysis of the ChIP-seq data was
done and comparison of these two datasets provided appropriate expression profile of p53 and also
detection of a new pathway which was the Ca+2 Signaling Pathway.
To depict an ideal target site for prevention of African Sleeping Sickness caused by T.Brucei
An ideal target site was detected to prevent the growth of the parasite. Glycolytic Pathway is
considered to be an important source of energy for the parasite survival especially in Trypanosomes
and Leishminia. Enzymes are considered to be the best targets thereby GAPDH enzyme in this pathway
was chosen as a target and worked on.
Genome assembly using short reads, its challenges, methods and future of de novo assembly
A next generation genomics review of data on short reads generated by high sequencing technology
was made and methods which were put to use, the challenges faced in handling the short read data
and appropriate solutions to overcome these challenges along with future technologies like de novo
assembly was studied.
Knowledge about usage of Mapping Reads and worked with Velvet algorithm for assembly.
To map illumine reads of E.coli on to a reference genome and exam the data for single nucleotide
polymorphisms, insertions and deletions. BWA was used to align the reads and Genome Viewer was used
to view the aligned reads.
Velvet was also used to assembly of the short reads.
Modeling generation and Evaluation of the protein (TbAUK1)
TbAUK1 is a protein kinase which is concentrated in the mitotic phase of the cell cycle of blood
stream form of
Trypanosoma Brucei and can act as an important target site for production of anti-parasitic drug. This

2. required model development and validation of the model using SAVES server and also considering the
Ramachandran Plot and generation of ligands using LIDUEAS tool and further by checking the binding of
the ligand with human and that of the modelled protein and a presentation on the work was also done.
RevTrans Tool Creation
Developed RevTrans tool using NetBeans (BioJava packages) and HTML. This tool helps in providing a
reverse complement of an input sequences, and can be majorly used in the areas of Bioinformatics for
the exploring DNA sequences to find reverse complement.
Protein Structure Prediction and Database creation
A Protein database for Human X chromosome proteins whose structures have not been published in
the public databases were modelled and fully annotated data was created.