Ph.D., Biomedical Engineering & Bioinformatics
University of Alabama at Birmingham
Samuel Bharti
Doctoral Researcher, Biomedical Engineering and Bioinformatics, University of Alabama at Birmingham
- email sbharti@uab.edu
- web samuelbharti.com
- github github.com/samuelbharti
- orcid orcid.org/0000-0003-4190-7058
- scholar Google Scholar
- linkedin linkedin.com/in/samuelbharti
I am a doctoral researcher in Biomedical Engineering and Bioinformatics at the University of Alabama at Birmingham, in the Center for Genomics and Data Science. My research turns single-cell and multi-omics data from Neurofibromatosis Type 1 (NF1) tumor models into testable hypotheses for drug repurposing and prioritization.
Alongside the research I build software for omics data: Shiny applications, R and Python packages, and reproducible workflows that make data easier to explore, trust, and share. In 2026 I was a software engineering intern on the Shiny team at Posit (formerly RStudio); in 2025 I built a locus-centered multi-omics visualization platform in Genentech's Human Genetics group. I also teach R, Git, Bash, and Python as a certified Carpentries instructor.
Education
Certificate, Translation of Biomedical Innovation to Clinical Practice
University of Alabama at Birmingham
B.Tech., Bioinformatics
Amity University
Experience
Software Engineering Intern, Posit
- Software engineer on the Shiny team in Posit's Open Source group.
- Built more than ten apps and four packages across R, Python, and JavaScript, mostly for computational biology and bioinformatics.
- Contributed to Shiny and shinyreact.
Human Genetics gRED Intern, Genentech
- Designed and built a modular scientific software platform and supporting R package for locus-centered visualization across 11,000+ GWAS, eQTL, pQTL, single-cell, and ATAC-seq datasets in Alzheimer's disease.
- Developed reusable components and reproducible workflows for interactive cross-dataset exploration and hypothesis review.
- Collaborated with scientists and engineers to integrate the platform within secure internal systems and presented the work to the Human Genetics department.
Graduate Research Assistant, Center for Genomics and Data Science, UAB
- Single-nuclei and multi-omics analysis of NF1-associated tumor models to generate testable hypotheses for drug repurposing.
- Built and deployed 5+ Shiny applications and internal tools on UAB research infrastructure for interactive visualization, sample tracking, QC review, and multi-omics exploration.
- Developed reproducible workflows and interfaces that help researchers explore complex experimental data and share results.
- Caught and validated sample contamination in 3′ datasets through QC analysis and validation with 10x Genomics.
Business Development Fellow, Bill L. Harbert Institute for Innovation & Entrepreneurship (HIIE), UAB
- Assessed the commercial potential of 12 UAB technologies and prepared licensing materials.
- Automated internal workflows with Power Automate and the Microsoft Graph API.
- Conducted technical and market research supporting commercialization.
Chief Technical Officer, FundU Games Pvt. Ltd.
- Led an 8-person team building a FinTech product with React, Node.js, R Shiny, MongoDB, and Docker.
- Managed the company's AWS infrastructure and helped secure initial funding.
Bioinformatics Engineer, STEM-Away
- Mentored international student teams.
- Developed bioinformatics course materials and app templates for scalable deployment.
Software
browse interactively →1.
Filter and subset Tahoe-100M perturbation metadata, 100.6 million rows, and leave with a reproducible pull recipe. Summaries push down to DuckDB.
2.
Shiny app to browse, analyze, and export recount3 RNA-seq studies: 18,998 datasets, quality checks, and PCA.
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One gene, one variant, one page. Eighteen cards fan out asynchronously across public APIs, with a 3D structure viewer and a ClinVar typeahead.
4.
Twenty-six pages of GPU-accelerated visualization through shinyreact, in 476 lines of R, one of which is the UI. Precomputed .f32 blobs go straight to the GPU.
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A gate for biological inputs. Validate gene symbols, ontology terms, variant formats and accessions through one API, offline or live. R and Python share a conformance corpus, so the two cannot disagree.
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One client per biological database, each split into a request half and a pure parser half that needs no network to test. Transport and caching are left to biohttp.
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Reusable, public starter kit for quickly building reproducible bioinformatics and data apps in R Shiny.
10.
Interactive R lessons with paired slide decks, built on the Gapminder dataset for workshops and self-paced learning. Adapted from Software Carpentry's R novice course.
11.
Workshop on deploying a Dockerized R Shiny bioinformatics app on an AWS EC2 instance, using sMAP as the example. Hosted with STEM-Away.
13.
Manually curated database of 1,700+ glucokinase modulators with bioactivity and chemical data, in-browser 3D structure visualization, and API endpoints.
14.
Manually curated structural database of synthetic peptides containing the non-standard amino acids α,β-dehydrophenylalanine (ΔF) and α-aminoisobutyric acid (Aib).
15.
Resolve a disease name to an EFO/MONDO term, query seven gene-disease sources in parallel, and dedupe to one row per gene. Re-ranks live as you tune the source weights.
16.
Local Shiny app for reviewing Markdown drafts in the browser: paragraph-anchored comments that survive edits, reviews saved as plain YAML, and an optional bring-your-own-key AI assistant. No server, no database, everything is a file.
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Multi-Omics Locus Viewer (MOLV)internal
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.
19.
RAPTORinternal
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.
20.
Interactive genomics and clinical-analysis app for whole-exome and bulk RNA-seq pediatric thyroid cancer data.
21.
Online tool to characterize sample subsets (cohorts) and find enriched clinotypes, handy for balancing case/control cohorts and profiling samples in cross-sectional studies.
22.
NF1 scRNA-seq Integration Appinternal
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.
23.
NF1 Rat Exome Data Explorerinternal
Interactive explorer that combines nf-core whole-exome outputs with variant tools and AI-assisted analysis for NF1-associated tumor models.
24.
R Shiny educational app that walks users through an interactive transcriptomics pipeline with quality control, statistics, and biomarker discovery.
25.
Vitiligo research database with differentially expressed genes, curated protein targets, natural compounds, and co-expression network visualizations.
26.
Pathways, Annotated-lists and Gene-signatures Electronic Repository, with an R Shiny web app for pathway and gene-set enrichment and network interpretation.
27.
R Shiny app that maps and visualizes species occurrences across Poland, using Leaflet for geospatial mapping and dygraphs for time-series exploration.
28.
Chrome extension that restores HTML report viewing in OnDemand v2+. It detects report output and opens it in a clean preview tab instead of the broken in-app rendering.
Publications
view on the research page →Siddharth Yadav, Samuel Bharti, Puniti Mathur (2023). GlucoKinaseDB: A comprehensive, curated resource of glucokinase modulators for clinical and molecular research. Computational Biology and Chemistry
Samuel Bharti, Nikita Krishnan, Arian Veyssi, Maryam Momeni, Sneha Raj (2022). sMAP: An interactive microarray data analysis tool for early-stage researchers. bioRxiv
Zongliang Yue, Radomir Slominski, Samuel Bharti and Jake Y Chen (2022). PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics. Frontiers in Genetics
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.
Nguyen, T. M., Bharti, S., Yue, Z., Willey, C. D., & Chen, J. Y. (2021). Statistical Enrichment Analysis of Samples: A General-Purpose Tool to Annotate Metadata Neighborhoods of Biological Samples. Frontiers in Big Data, 4, 725276.
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.
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.
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.
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.
Presentations
Mapping the Genomic Landscape and Tumor Heterogeneity of NF1-Associated Breast Cancer Using Novel Rat Models.
Application of a Multi-Omics Approach in NF1-Deficient Tumors and Controls can Highlight Novel Associations and Therapeutic Targets.
Exploratory Analysis of Cancer Clinical Samples using the new Web-based SEAS Software.
Exploratory Analysis of Cancer Clinical Samples using the new Web-based SEAS Software.
PluriMetNet: A dynamic electronic model deciphering the metabolic profiling of human embryonic stem cells (hESCs) and its applications.
Honors and awards
- Google Cloud Research Credit Award, Google (2026)
- Elected Member, Tau Beta Pi Engineering Honor Society, UAB (2025)
- Student Member, American Association for Cancer Research (AACR) (2024 to present)
- Blazer Graduate Research Fellowship, UAB (2022 to 2023)
- Professional Development & Travel Awards, UAB CCTS & UAB GSG (2022 to 2024)
Teaching and leadership
- Certified Instructor, The Carpentries (2024 to present). Taught workshops on R, Git, Bash, and Python at UAB's Biological Data Science Core.
- President, Informatics Club, UAB (2023 to 2025). Grew computational training across departments through workshops, peer-learning sessions, and professional-development seminars.
- Mentor, STEM-Away. Gave a talk and live demo on containerized bioinformatics and deploying R Shiny apps on AWS.
Last updated 2026-08-29