Research

My research interests involve developing diagnostic and treatment applications using Systems Biology and Clinomics. Currently, my projects focus on developing multi-omics integration tools and models for the treatment and diagnosis of Neurofibromatosis Type 1 and its associated cancers.

Projects

Statistical Enrichment Analysis of Samples (SEAS)

SEAS is an online interactive software tool to help users characterize specific sample subsets (cohorts). SEAS enables users to explore all available clinotypes (clinical attributes) within a sample subset or cohort, from which they can identify which clinotypes are enriched against all the samples in a data set. SEAS is useful not only for balancing case and control cohorts in traditional case-control studies, but also for profiling samples and sample subsets in cross-sectional studies.

https://aimed-lab.github.io/SEAS/
Pathways, Annotated list, and Gene-sets (PAGs) electronic repository (PAGER)

PAGER database and enrichment analysis

http://discovery.informatics.uab.edu/PAGER/
PAGER WEB APP

A R Shiny based web application to perform PAGER analysis with user-defined and pre-loaded case studies.

https://github.com/aimed-uab/PAGER-Web-APP
SMAP

An R Shiny educational app to guide users through an interactive transcriptomics pipeline.

https://bi-stem-away.github.io/sMAP/
GlucoKinaseDB

GlucoKinaseDB (GKDB) is a manually curated database of glucokinase modulators. The data included in GKDB were retrieved from published articles, chemical data repositories and patent literature. Different classes of modulators are included in GKDB such as; Glucokinase activators (GKAs), GK-GKRP disruptors and Glucokinase inhibitors (GKIs). The database currently provides bioactivity and chemical information on a total of 1723 modulators. GKDB provides several features such as advanced search criteria, downloadable structures in multiple formats, in-browser visualization, cross-links to other chemical databases etc.

https://glucokinasedb.in/
Pepengine

PepEngine is a manually curated database containing detailed structural information of synthetic peptides having the non-standard amino acids α, β-Dehydrophenylalanine (ΔF) and α-Aminoisobutyric acid (Aib).

https://pepengine.in/
VIRdb 2.0

The ultimate vitiligo research database. With differentially expressed genes, curated protein targets, natural compounds, and network visualizations, it’s a powerful tool for advancing vitiligo research and drug development.

https://vitiligoinfores.com/

Publications

Siddharth Yadav, Samuel Bharti, Puniti Mathur (2023). GlucoKinaseDB: A comprehensive, curated resource of glucokinase modulators for clinical and molecular research. Computational Biology and Chemistry https://doi.org/10.1016/j.compbiolchem.2023.107818

Samuel Bharti, Nikita Krishnan, Arian Veyssi, Maryam Momeni, Sneha Raj (2022). sMAP: An interactive microarray data analysis tool for early-stage researchers. bioRxiv https://doi.org/10.1101/2022.05.27.492984

Zongliang Yue, Radomir Slominski, Samuel Bharti and Jake Y Chen (2021). PAGER Web APP: An interactive, online gene set and network interpretation tool of high-throughput functional genomics results. Frontiers in Genetics https://www.frontiersin.org/articles/10.3389/fgene.2022.820361/abstract

Siddharth Yadav, Samuel Bharti, Priyansh Srivastava & Puniti Mathur (2022). PepEngine: A Manually Curated Structural Database of Peptides Containing α, β- Dehydrophenylalanine (ΔPhe) and α-Amino Isobutyric Acid (Aib). International Journal of Peptide Research and Therapeutics. https://doi.org/10.1007/s10989-022-10362-9

Nguyen, T. M., Bharti, S., Yue, Z., Willey, C. D., & Chen, J. Y. (2021). Corrigendum: Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. Frontiers in Big Data, 4, 804141. https://doi.org/10.3389/fdata.2021.804141

Bharti, S., Sengupta, A., Chugh, P., & Narad, P. (2020). PluriMetNet: A dynamic electronic model decrypting the metabolic variations in human embryonic stem cells (hESCs) at fluctuating oxygen concentrations. Journal of Biomolecular Structure and Dynamics, 1–9. https://doi.org/10.1080/07391102.2020.1860822

Srivastava, P., Talwar, M., Yadav, A., Choudhary, A., Mohanty, S., Bharti, S., Narad, P., & Sengupta, A. (2021). VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach. F1000Research, 9, 1055. https://doi.org/10.12688/f1000research.25713.2

Bharti, S., Narad, P., Chugh, P., Choudhury, A., Bhatnagar, S., & Sengupta, A. (2020). Multi-parametric disease dynamics study and analysis of the COVID-19 epidemic and implementation of population-wide intrusions: The Indian perspective. MedRxiv, 2020.06.02.20120360. https://doi.org/10.1101/2020.06.02.20120360