BIOINFORMATICS

Bioinformatics

Our research in bioinformatics  involves functional annotation of genomes, creation of databases, comparative genomics and experimental approaches for validating computational predictions. In collaboration with the Institute of Bioinformatics, Bangalore, India; we have developed various databases and tools to curate data from published literature. We promote the use of Distributed Annotation System to enable further annotation of our database by individual researchers at any location. Our other interests include protein domain identification and clustering, identification and annotation of genes, cataloging alternate splice forms and single nucleotide polymorphisms (SNPs).

Databases

  • Human Protein Reference Database (HPRD)

    HPRD is a novel comprehensive protein information resource depicting relevant information of proteins such as protein-protein interactions, Post Translational Modifications, domain architecture  expression and cellular localization. It contains information for over 27000 human proteins and disease genes. This  is the first database to implement the standardization protocol put forward by the Proteomics Standards Initiative for Molecular Interactions (PSI-MI). Data from published literature is curated manually and reviewed by scientists working at IOB. This project is in collaboration between the PandeyLab at Johns Hopkins University and the Institute of Bioinformatics.

  • Human Proteinpedia

    Human Proteinpedia is a community portal for sharing and integration of human protein data through the use of a distributed annotation system. It allows research laboratories to contribute and maintain protein annotations which are also mapped to the corresponding proteins through the Human Protein Reference Database.All the public data contributed to Human Proteinpedia can be queried, viewed and downloaded. This is a joint project between Pandey lab and Institute of Bioinformatics.

  • Plasma Proteome Database (PPD)

    The Plasma Proteome Database, the first of its kind ensures a comprehensive resource for all human plasma proteins along with their isoforms. The database includes information pertaining to isoform specific expression, disease, localization, post translational modification and single nucleotide polymorphism. The information provided in this database is through manual annotation done by exhaustive literature research.

  • NetPath

    'NetPath' is a curated resource of signal transduction pathways in humans. It is a collaboration between the PandeyLab at Johns Hopkins University and the Institute of Bioinformatics. Currently, 10 cancer and 10 immune signaling pathways are freely available in GenMAPP, PSI-MI and BioPaX formats at this website.. The 10 cancer signaling pathways were developed in collaboration with the Computational Biology Center at Memorial Sloan-Kettering Cancer Center and with Gary Bader's lab at the University of Toronto for the 'Cancer Cell Map'.

  • Breast Cancer Database

    BCD contains all the “Known molecular alterations related to Breast Cancer”. Includes information related to known molecular alterations at the chromosome, mRNA and protein levels. The data includes information on differential regulation of all the reported genes and its proteins related to breast cancer. This database is linked to the HPRD for manually curated protein annotations, ONCOMINE, Geneontology, Unigene, and Genecard, where the user can have a comparative account of cancerous and normal state for a particular gene of their interest.

Tools

  • PathBuilder

    PathBuilder is an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. This tool enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events either manually or through automated methods. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets.
    This is a joint project between Pandey lab and Institute of Bioinformatics.

  • BioBuilder

    A content management system, designed for easy modifications and management of HPRD, using web interface. The administration of annotation process and a built-in review system permits a global team of scientists to coordinate their annotation efforts. This user friendly tool is created using Python and Zope. This is a joint project between Pandey lab and Institute of Bioinformatics.

  •  TAGmapper

    TAGmapper is a comprehensive web-based tool used to perform tag-to-gene mapping, based on mapping experimentally derived tags to a gene in the UniGene cluster or an EST. It provides a comprehensive and accurate mapping of SAGE tags to genes. This is a joint project between Pandey lab and Institute of Bioinformatics.