About Us:

We are located at School of Computational Sciences, Jawaharlal Nehru University (JNU), New Delhi. JNU is a prestigious Indian university, recently ranked at no. 3 in the country as per the Government instituted committee for this purpose. School of Computational and Integrative Sciences is a relatively young institution with JNU with its thrust research areas being Bioinformatics, Complex Systems and Big data analytics.

We are interested in developing data-driven algorithms and applications for biological data with an integrative perspective. We aim to leverage on our past and ongoing works in the field of sequence and structural analysis of protein-DNA and other biomolecular interactions, particularly their modelling through machine learning algorithms. We also draw from our experience in studying patterns of global and condition-specific gene expression, miRNA and NGS data analysis for Intestinal Bowel Syndrome, Influenza vaccination response, Uni-parental disomy and other critical problems in the field of Biomedical research. Our technical research interests are in machine learning, big data analytics and novel architectures and training methods for deep learning through neural networks.

As a Principal Investigator of this group: Science, poetry and pretentious thinking are all my passions, of which I chose the first as a profession. I do science for the artist's vanity and a decent career it can paradoxically combine to offer. It is delusional enough to make me lose sight of the trivial world, and useful enough so I can pay my bills and lead a happy life. This website is a public and semi-personal portal, to advertise myself and my group (under development) and put together a summary of our achievements in the course of our random walk across the beautiful and unusual forays offered by our deliberate and chance encounters with knowledge.

Shandar Ahmad

Recently completed activities

  • Collaborative project

    Whole exome sequencing data analysis in UPD14-like diseases

    In collaboration with Dr Kagami, Dr Sekita and Dr Mizuguchi, we are trying to find the cause of a severe group of congenital diseases which show the same symptoms as Uni-parental disomy. Currently, the whose exome sequencing of several patients has been completed and a disease signature is being established.

  • Collaborative project completed

    Pose prediction optimization

    Philip Prathipati (NIBIOHN, Japan) has published a paper on

    accurate pose prediction,

    in protein-ligand docking

    in which I contributed in

    data analysis and discussions.

    Read the paper here

Ongoing and upcoming activities

  • Genome-wide DNA conformational dynamics:

    A genome-wide analysis of conformational dynamics of transcription factor targets has been completed. This study highlights how chromatin specificity of transcription factors is related to the intrinsic dynamics of DNA sequences. The same has been submitted for publication.

  • Novel DNA-binding proteins in human genome

    We are developing a machine learning method to identify novel DNA-binding proteins, by integrating gene expression profiles and sequence-based annotations. We show that global gene expression patterns may significantly alter biological function of proteins with week binding site level signals.

  • Genome-phenome diversity analysis of microbial genomes

    A number of bacterial and viral genomes have been sequenced and their genetic diversity documented. Different microbial strains show different virulence and phenotypic profiles, but a functional association is poorly understood. We are developing novel Bioinformatics strategies to decode how small genetic changes in microbes lead to big phenotypic variations.

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© 2016 Shandar Ahmad

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