Offers an interactive guidance to a systematic and scientifically critical interpretation of optical coherence tomography (OCT) images. The Clinical Atlas of Intravascular OCT consists of eight separate chapters offering the following contents: (i) Principles of OCT, (ii) Artefacts, (iii) Atherosclerosis, (iv) Evaluation of metallic stents, (v) 3D-OCT, (vi) Evaluation of bio-resorbable scaffold,s (vii) Miscellaneous (vein grafts, peripheral vessels, etc.), and (viii) New frontiers in OCT imaging.
A scholarly society for advancing understanding of living systems through computation and for communicating scientific advances worldwide. The ISCB serves its global membership by providing high-quality meetings, publications, and reports on methods and tools; by disseminating key information about bioinformatics resources and relevant news from related fields; and by actively facilitating training, education, employment, career development, and networking. We advocate and provide leadership for resources and policies in support of scientific endeavors and to benefit society at large.
Provides interactive modules to help students and researchers understand key bioinformatics concepts. TeachEnG is an interactive online educational tool for reinforcing key concepts in sequence alignment and phylogenetic tree reconstruction. It proposes instructional games which allow students to align sequences by hand, fill out the dynamic programming matrix in the Needleman-Wunsch global sequence alignment algorithm, and reconstruct phylogenetic trees via the maximum parsimony and Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithms. With an easily accessible interface and instant visual feedback, TeachEnG will help promote active learning in bioinformatics.
Interactively calculates the Dynamic Programming (DP) matrix in real time. SAT also visually illustrates the consequences of tweaking the various parameters of the algorithm. This simple software tool will not only be useful for teachers and students of bioinformatics courses but also to future bioinformatics developers as an error check tool when they start implementing this algorithm for the first time.
Provides a web platform for simulations and modelling tools, and other resources like online courses, short courses and full-fledged tool-powered curricula. nanoHUB.org hosts over 3000 content items and more than 260 tools and proposes a list of tools selected for their efficiency and other quality criteria. Each tool is displayed on the platform with some data like numbers of its users, community’s reviews and questions, classroom usage or citations in the literature.
Stores code and certain raw materials for a detailed RNA-seq tutorial. Informatics for RNA-seq is an educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.
Offers wide range of services and repositories widely used in genomic research as well as documentation and material for training. eBiokit is a portable bioinformatics educational platform reducing dependences on the internet. It allows students to connect to the system by accessing to local internet protocol (IP) address or a known uniform resource locator (URL). The platform provides computing platform and database system containing up to 6 terabytes of biological data and software tools of relevance to bioinformatics researching.
Allows students to learn infectious disease concepts by using a modern computational and modeling approach while not requiring students to read or write computer code. DSAIDE permits users to explore different topics in infectious disease epidemiology. The package is structured in a modular way allowing users to directly interact with and modify the underlying simulations.
Allows the investigation of visualization methods in intuitive ways based on filtering. BioVis Explorer is a web application informing users about visualization techniques. This method assists users in studying biological data sets proposed in publications from top-tier journals and conferences within a time range from 2000 to 2016. It also proposes taxonomy of various aspects of the data and visualization methods.
Allows creation of clinical decision aids. DECIDE facilitates supportive functions of a genetic counsellor through patient-centred education and enhanced decision-making. It enables users to work individually, as a couple or family, or with a relative or friend, allowing patients to make decisions in ways that they find most comfortable and supportive. This tool provides an opportunity to make a decision about pharmacogenomics incidental findings or carrier status for recessive diseases.
Clusters big data and interactive visualizations including 3D views, cluster selection and zoom features. ClusterEnG aims at educating the user about the similarities and differences between various clustering algorithms and provides clustering tutorials that demonstrate potential pitfalls of each algorithm. The user can choose the clustering method used by the tool. It implements seven algorithms include k-means, k-medoids, affinity propagation, spectral clustering, Gaussian mixture model, hierarchical clustering and DBSCAN.
Informs about text visualization techniques. Text Visualization Browser is a web application that can be used for getting an overview of the field, teaching purposes, and finding related work based on various categories defined in a survey taxonomy. It classifies about 30 text visualization methods with regard to data source, underlying text representation and processing method, temporal aspects, and supports user interactions.
Presents a list of visualization technique thumbnails organized in a grid. SentimentVis Browser is a web application allowing users to access to category statistics and a summary table with an overview of the complete categorization. It assists users in monitoring of public opinion in social media, literature analysis for digital humanities, or support for research of sentiment and stance in linguistics and natural language processing (NLP). Users can submit additional entries thanks to a form available from the top panel.
Offers the opportunity to perform controlled crosses with model organisms. CGS provides populations of Drosophila, Arabidopsis or mice with unknown patterns of inheritance and gives students the tools to design and perform experiments to discover these patterns. It allows biology students to apply lessons in Mendelian genetics to real-world situations. The tool can be used as a primary laboratory module for introductory biology or genetics courses, or as a supplement to a hands-on genetics module with real organisms.
Provides a virtual laboratory class for undergraduate students of Genetics in Biology. Mutate emulates the so-called fluctuation test whose aim is to distinguish between spontaneous and adaptive mutation hypotheses in bacteria. It permits to train students in some multidisciplinary aspects of current genetics as sequence databases, DNA mutations and hypothesis testing, while introducing the fluctuation test.
Simplifies the recognition of the proteins encoded within a DNA sequence. StarORF transcribes the DNA sequence into RNA. It translates the RNA into all the potential open reading frames (ORFs). This tool offers a solution to recognize the translation frame that results in the longest protein coding sequence.
Mimics mating experiments between organisms that are genetically different across a range of traits. StarGenetics permits researchers to investigate the nature of the traits in question. It is useful for students that want to learn genetic experimental design and genetic concepts. This tool serves for the construction of exercises for genetic experiments and for the simulation of crosses between non-model organisms.
Offers free, open and online courses in DNA design. Synthetic Biology One addressed first-year master’s students in a life science background. It provides serious games, courses, lessons, units and quizzes around DNA knowledge. Lessons offered on the platform are designed to be as modular as possible and are classified by subject.
Makes statistics more accessible to a wider range of students through interactive visualizations. Seeing Theory is a web app that visualizes the fundamental concepts covered in an introductory college statistics or Advanced Placement statistics class. This resource can be used by students as an additional resource to textbook, professor and peers. It permits to realize basic probability, compound probability, distributions, statistical inference, linear regression.
Assists users in obtaining genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq). scRNA-seq analysis course allows users to detect scRNA-seq data. This tool presents several advantages such as the possibility for researchers to address issues that are intractable with other methods, permitted thanks to the cellular resolution and the genome wide scope.
Delivers information about biology of proteins. StarBiochem consists of an interactive platform that permits students to learn major concepts in this field. It displays protein structural information based on the four different levels of protein structure.
Permits to learn bioinformatics and program through problem solving. Rosalind offers problems that grows in biological and computational complexity and provides teaching aid and a central homework resource. It aims to attract biologists wanting to develop vital programming skills at their own pace and programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology.
Bise is a bio image information index with several software for bio imaging analysis as Angiogenesis/Sprout Analyzer; SOAX; CLEM; Spot Detector; Matlab; JACoP; ImageJ; Super-Resolution Radial Fluctuations (SRRF).
Maps the landscape of initiatives and activity in the development of Research Objects. Research Objects also aims to exchange of scholarly information on the Web. It improves the potential for understanding and reuses of research by making sure that the information that is needed to make a published resource useful is associated with it, and shared as a whole. The tool is a community site aimed at gathering together information, ideas, and interest around the topic of scholarly publication.
Many resources offer a 10,000-foot view of the current trends in the field, reviews of various technologies, and guidelines on how to effectively design, analyze, and interpret experiments in human genetics and bioinformatics research. By comparison very few resources focus on the mundane, yet critical know-how for those on the ground actually doing the science. Getting Genetics Done aims to fill that gap by featuring software, code snippets, literature of interest, workflow philosophy, and anything else that can boost productivity and simplify getting things done in human genetics research.
Offers provision of storage facility to contain users sequence and results files. BioManager provides a seamless workstation for bioinformatics analyses. It is designed as an online interface that allows the students to access the interface from their home computer, facilitating further study or the completion of assignments outside the class room. This tool facilitates creation of tutorials using a series of standard bioinformatic programs incorporated into a web interface.
A collaborative next-generation sequencing (NGS) resource. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.
Allows users to explore, analyze, and gain insight into such data. This online database contains several analytical and interactive visual methods allowing users to study multifaceted scientific data. The database purposes are exploration and analysis of single facets of such data. Then it transmits results from data analysis to users. One of its functions is to synthesize different types of information from different sources into a unified representation of the data.
Informs users on the various existing visualization techniques. This online library brings a meaningful overview of graph structures, to highlight central objects, to show similar objects, and to reveal outliers. It includes different filters to assist users in their query: a timeline, a keywords table, or color selectors. For each user request, this database provides a list of results containing publications related to a visualization technique.
Annotates and explains available next-generation sequencing (NGS) techniques and their data analysis methods. SequencEnG is an web resource that contains about 60 NGS techniques organized into a knowledge tree based on genetic or epigenetic information being assayed. Interactive data analysis pipelines are available for RNA-seq, ChIP-seq, Hi-C, and Whole Genome Bisulfite Sequencing (WGBS), with lists of major bioinformatics tools for each analysis step in the pipelines. It can be useful for students and researchers entering bioinformatics and the NGS field.
Supplies techniques that assists users in development of software. Performance Visualization is an online library that classifies different technique of visualization and categorizes them. This resource is useful to better understand how different software is run on such machines and optimize their performance. It supplies a context-based classification and survey of existing performance visualizations.
Informs users about visualization techniques. SetViz is an online platform providing information and classifying set visualization techniques into six categories. The techniques in each category exhibit similar scalability and readability properties as well as design considerations. This resource proposes software implementations, demos and videos about the surveyed techniques.
Classifies existing visualization techniques. Dynamic Graph Visualization covers the evolution of relationship between effective diagrams, entities in readable and scalable. This online library contains several publication references that are tag and categorize thanks to a hierarchical taxonomy. Each graph is represented as static graphs based on a timeline or animated diagrams.
Provides a survey of the literature in a format which facilitates easy scanning. ALTBIB includes citations from published articles, books, book chapters, and technical reports. It can be easy searchable through a friendly-user interface. The user can limit the search to a particular field. Users seeking a finer degree of precision in retrieval than available through either ALTBIB's standard Basic Search screen or Limits option searching can use the advanced searching features.
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/).