Research

My research develops diagnostic and treatment applications using systems biology and clinomics. Right now I’m focused on multi-omics integration tools and models for diagnosing and treating Neurofibromatosis Type 1 (NF1) and its associated cancers, turning single-cell and multi-omics data into insights that are useful in the clinic.

Projects

Featured

Multi-Omics Locus Viewer (MOLV): Shiny application and R package I built for the Human Genetics team at Genentech for locus-first, integrative visualization across 11,000+ GWAS, eQTL, pQTL, single-cell, and ATAC-seq datasets in Alzheimer’s disease. Deployed internally.
RAPTOR: Record-based Abstraction of Phenotypes, Terms, Ontologies, and Disease Relations. An agentic AI system that pulls phenotypes, genes, diseases, and ontology-linked concepts out of unstructured patient records. Deployed in-house.
NF1 scRNA-seq Integration App: Shiny app that brings nf-core outputs together with Seurat, pseudobulk, and CellChat for end-to-end single-cell and single-nuclei RNA-seq exploration in one place. Deployed in-house.
NF1 Rat Exome Data Explorer: Interactive explorer that combines nf-core whole-exome outputs with variant tools and AI-assisted analysis for NF1-associated tumor models. Deployed in-house.
Pediatric Thyroid Cancer (PTC) Explorer: Interactive genomics and clinical-analysis app for whole-exome and bulk RNA-seq pediatric thyroid cancer data.
Statistical Enrichment Analysis of Samples (SEAS): Online tool to characterize sample subsets (cohorts) and find enriched clinotypes, handy for balancing case/control cohorts and profiling samples in cross-sectional studies. https://aimed-lab.github.io/SEAS/
R Shiny Template: Reusable, public starter kit for quickly building reproducible bioinformatics and data apps in R Shiny. Read the post

Earlier work

PAGER 3.0 & PAGER Web App: Pathways, Annotated-lists and Gene-signatures electronic repository, with an R Shiny web app for pathway and gene-set enrichment and network interpretation. http://discovery.informatics.uab.edu/PAGER/ and https://github.com/aimed-uab/PAGER-Web-APP
sMAP (Standard Microarray Analysis Pipeline): R Shiny educational app that walks users through an interactive transcriptomics pipeline with quality control, statistics, and biomarker discovery. https://bi-stem-away.github.io/sMAP/
GlucoKinaseDB: Manually curated database of 1,700+ glucokinase modulators with bioactivity and chemical data, in-browser 3D structure visualization, and API endpoints. https://glucokinasedb.in/
PepEngine: Manually curated structural database of synthetic peptides containing the non-standard amino acids α,β-dehydrophenylalanine (ΔF) and α-aminoisobutyric acid (Aib). https://pepengine.in/
VIRdb 2.0: Vitiligo research database with differentially expressed genes, curated protein targets, natural compounds, and co-expression network visualizations. https://vitiligoinfores.com/
BioDivPortal: R Shiny app that maps and visualizes species occurrences across Poland, using Leaflet for geospatial mapping and dygraphs for time-series exploration.
PluriMetNet: Genome-scale metabolic model of human embryonic stem cells that decodes metabolic variation under fluctuating oxygen concentrations.

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

Presentations

Poster: “Application of a Multi-Omics Approach in NF1-Deficient Tumors and Controls can Highlight Novel Associations and Therapeutic Targets.” CCTS Translational Training Symposium, Biloxi, MS (Sep 2023).
Poster: “Exploratory Analysis of Cancer Clinical Samples using the new Web-based SEAS Software.” O’Neal Research Retreat, UAB (Oct 2022).
Poster: “Exploratory Analysis of Cancer Clinical Samples using the new Web-based SEAS Software.” CCTS Translational Training Symposium, Mobile, AL (Sep 2022).
Poster: “PluriMetNet: A dynamic electronic model deciphering the metabolic profiling of human embryonic stem cells (hESCs) and its applications.” RECOMB 2020, Italy (Jun 2020).