Provides a standard for recording and reporting microarray-based gene expression data. MIAME is a standard that includes (i) the normalization strategy (spiking, housekeeping genes, total array, other approach), (ii) the normalization and quality control algorithms used, (iii) the identities and location of the array elements serving as controls, as well as their type, and (iv) hybridization extract preparation, detailing how the control samples are included in sample targets prior to hybridization.
Provides open-source packages implementing the MAGE Object Model (MAGE-OM) in several programming languages. MAGE-STK is a suite of software developed to facilitate adoption of MAGE. The toolkit aims to provide an intermediate object layer that can then be used to export data to MAGE-ML, to store data in a persistent data store such as a relational database, or as input to software-analysis tools.
Aims to provide a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems. MAGE is a microarray data standard. The spreadsheet-based format, MAGE-TAB, is part of the standard and can be used for annotating and communicating microarray data in a Minimum Information About a Microarray Experiment (MIAME) compliant fashion.
Permits an intuitive writing and collaboration, with the rigor and power of LaTeX. Typeset is a writing and collaboration tool for research papers and thesis documents. This editor comes with in-built tools for research related actions, removing all unwanted complexity in the research writing process. It enables with powerful tools to easily perform actions like adding and citing references, creating scientific expressions, cross referencing tables/equations/figures.
A Java application for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. ProCon converts Sequest.out, ProteinScape® and ProteomeDiscoverer® identification results, and outputs semantically enriched annotation of data in mzIdentML data format. ProCon can assist in preparing data submission to public repositories as recommended in the paper publication guidelines of major proteomics journals.
Furnishes a LaTeX document class corresponding to a standard document format for SBML Level 3 package. SBMLPkgSpec contains a wide range of features such as: (i) define SBML package version and SBML validation rules; (ii) format the names of common SBML object classes and XML primitive data types (iii) create new package-specific definitions (iv) use customized commands for cross-referencing sections, tables and figures.
Enables the open sharing of research outputs and educational materials. SPARC aims to democratize access to knowledge, accelerate discovery, and increase the return on our investment in research and education. It places a premium on collaboration and collective action, and works to advance this mission through the development and leadership of active coalitions. SPARC focuses on collaborating with other stakeholders to build on the opportunities created by the Internet, promoting changes to both infrastructure and culture needed to make open the default for research and education.
Provides information about high-throughput nucleotide sequencing experiments. MINSEQE avoids ambiguous interpretation and facilitates reproducibility of the results of experiments. Its utilization permits users to improve integration of multiple experiments across different modalities. This guideline contains: (1) the description of the biological system, samples, and the experimental variables, (2) the sequence read data for each assay, (3) the summary data for the set of assays, (4) general information about the experiment and sample-data relationships, and (5) essential experimental and data processing protocols.
Facilitates the development of software for reading and writing flow cytometry data. The goal of the Flow Cytometry Standard (FCS) is to provide a uniform file format that allows files created by any type of acquisition hardware to be analyzed by any third party data analysis tool. The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Finally, it includes simplified support for international characters and improved support for storing compensation.
Provides a list of verified ciliary genes, which can be used as a reference dataset of cilia genes. SCGS facilitates determination of objective cut-off thresholds via receiver operator characteristic (ROC) curves. It was constructed by collecting 27 ciliary studies from Cildb, which holds a large collection of ciliary datasets. The database can be used to train and evaluate bioinformatics tools, and can be considered as a reference resource.
A community-developed standard to functionally describe cell phenotypes with contextual information from the microenvironment. MultiCellDS is a library of over 200 digital cell lines contained a hierarchical, standardized yet extensible representation of a biological cell line’s phenotype in one or more microenvironmental contexts. Ultimately, MultiCellDS aspires to promote data sharing in computational and experimental biology and medicine, particularly cancer.
Gene fusion detection in Plants
Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants.
Whole genome and transcriptome sequencing data analysis of Plants
In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants.
Development of webservers, databases and computational pipelines for plant research
Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research.
Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies.
Professional & Academic Background
Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India
Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA
Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India
PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India
M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India
B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India
Awards and Fellowships
Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India
GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009
Scientific Contributions/ Recognitions
Associate editor: Journal of Translational Medicine.
Editorial Board Member of Journal: Theoretical Biology and Medical Modelling.
Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals.
Web Resources/ Databases (Developed/ Contributed)
A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/)
GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/).
Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/).
Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/).
Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/).
Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/).
Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/).
Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/)
Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/).
A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).