Samuel Bharti

Doctoral Researcher, Biomedical Engineering and Bioinformatics, University of Alabama at Birmingham

Summary

I'm a doctoral researcher in Biomedical Engineering and Bioinformatics at the University of Alabama at Birmingham. My research integrates single-nuclei and multi-omics data to find better ways to diagnose and treat Neurofibromatosis Type 1 (NF1) and its associated cancers.

Alongside the research I own six open-source packages for omics data across R, Python, and TypeScript, and I build the apps and agentic AI tools scientists use to explore their own results. I wrote five of those packages in 2026 at Posit (formerly RStudio). The year before, at Genentech, I built MOLV, a locus-first multi-omics visualization platform for Alzheimer's disease.

Skills

Programming & scripting: R, Python, Bash, SQL, TypeScript, JavaScript, PHP, Git, GitHub
Data products & publishing: R Shiny, Quarto, Streamlit, Jupyter, ggplot2, Plotly, D3, Leaflet, interactive reporting
Bioinformatics & multi-omics: single-cell & spatial transcriptomics, bulk RNA-seq, variant & clinical analysis, multi-omics integration, quality control, Seurat, DESeq2, CellChat, Bioconductor, nf-core / Nextflow
Workflows & infrastructure: reproducible workflows, modular development, workflow automation, Docker, REST APIs, Posit publishing, AWS, GCP, HPC / SLURM
Agentic AI & ML: agent systems, tool calling, MCP, A2A, Google ADK, OpenAI APIs, LangChain, LLM apps, Neo4j knowledge graphs, machine learning, network analysis

Education

Ph.D., Biomedical Engineering & BioinformaticsBirmingham, AL · Expected 2027

University of Alabama at Birmingham

Certificate, Translation of Biomedical Innovation to Clinical PracticeBirmingham, AL

University of Alabama at Birmingham

B.Tech., BioinformaticsNoida, India

Amity University

Experience

PhD Candidate, Center for Genomics and Data Science, UABBirmingham, AL · Aug 2022 - Present

Own the single-nuclei and multi-omics analysis of NF1-associated tumor models, from quality control to the shortlist of drugs worth testing.
Built and deployed 5+ Shiny applications and internal tools on UAB research infrastructure for visualization, sample tracking, QC review, and multi-omics exploration.
Caught sample contamination in 3′ datasets that quality control had passed, and had it confirmed by the platform vendor.

Software Engineering Intern, PositBoston, MA (remote) · May 2026 - Aug 2026

Owned five packages end to end, from API design through release: biobouncer, biohttp, bioclients, biocohort, and plotomics.
Contributed seven merged pull requests upstream to the Shiny ecosystem, and the first shinyreact release credits me as a New Contributor.
Built more than ten apps across R, Python, and JavaScript, mostly for computational biology and bioinformatics.

Human Genetics gRED Intern, GenentechSouth San Francisco, CA · Jun 2025 - Aug 2025

Built MOLV, a Shiny platform and R package for locus-first visualization across 11,000+ GWAS, eQTL, pQTL, single-cell, and ATAC-seq datasets in Alzheimer's disease.
Built its components and workflows so the same locus view worked across every dataset.
Integrated it into Genentech's secure internal systems alongside the scientists and engineers who use it, then presented the work to the Human Genetics department.

Software

browse interactively →

apps (21)

tahoe-explorerSubset 100.6M rows and leave with a pull recipe.live app github

recount-explorerBrowse, QC, and export 18,998 recount3 studies.live app github

variant-reviewerOne gene, one variant, one page.live app github

Plotomics LiveTwenty-six GPU-rendered pages in 476 lines of R.live app github

DE ExplorerDifferential expression on TCGA and airway RNA-seq.live app github

Drug PerturbationConnectivity scoring against a perturbation panel.live app github

Signature ScoringScores TCGA-BRCA samples on 50 Hallmark pathways.live app github

Genome ExplorerRecurrent TCGA breast drivers on hg19 via igv.js.live app github

gene-list-builderSeven gene-disease sources, one row per gene.live app github

draft-reviewerMarkdown review with comments that survive edits.github

genescoutAn agentic evidence-review workbench.live app github

MOLVLocus-first views across 11,000+ Alzheimer's datasets.internal

RAPTORPhenotype, ontology, and disease-relation records.internal

PTC ExplorerExome and RNA-seq review of pediatric thyroid cancer.

SEASFinds clinotypes enriched in a sample subset.

NF1 scRNA-seq Appnf-core, Seurat, and CellChat in one single-cell app.internal

NF1 Rat ExomeWhole-exome variants from NF1-associated rat tumors.internal

sMAPTeaches a transcriptomics pipeline, QC to biomarkers.

PAGER 3.0Pathway repository with enrichment and networks.github

BioDivPortalMaps species occurrences across Poland over time.

ondemand-html-rendererRestores HTML report viewing in OnDemand v2+.github

packages (6)

plotomicsSeventeen plots from one core, wrapped three ways.github docs

biobouncerA gate for biological inputs.github doi

bioclientsOne client per database, parsers testable offline.github docs

biohttpNormalized HTTP transport.github docs

peacockProject scaffolding for R and Python.github docs

biocohortHolds a study's subjects and samples in one object.github docs

templates (1)

R Shiny TemplateStarter kit for reproducible Shiny data apps.

teaching (2)

R for BeginnersInteractive R lessons and decks, built on Gapminder.github doi

AWS Shiny WorkshopDeploying a Dockerized Shiny app on AWS EC2.github

databases (3)

GlucoKinaseDB1,700+ curated glucokinase modulators, 3D and API.

PepEngineSynthetic peptide structures containing ΔF and Aib.

VIRdb 2.0Vitiligo genes, targets, compounds, and networks.

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

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

doi.org/10.1101/2022.05.27.492984

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

doi.org/10.3389/fgene.2022.820361

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.

doi.org/10.1007/s10989-022-10362-9

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.

doi.org/10.3389/fdata.2021.725276

Corrigendum: doi.org/10.3389/fdata.2021.804141

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.

doi.org/10.12688/f1000research.25713.2

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.

doi.org/10.1080/07391102.2020.1860822

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.

doi.org/10.1101/2020.06.02.20120360

Presentations

Mapping the Genomic Landscape and Tumor Heterogeneity of NF1-Associated Breast Cancer Using Novel Rat Models.

Children's Tumor Foundation NF Conference 2026, Denver, CO (Jun 2026).

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).

Exploratory Analysis of Cancer Clinical Samples using the new Web-based SEAS Software.

O'Neal Research Retreat, UAB (Oct 2022).

Exploratory Analysis of Cancer Clinical Samples using the new Web-based SEAS Software.

CCTS Translational Training Symposium, Mobile, AL (Sep 2022).

PluriMetNet: A dynamic electronic model deciphering the metabolic profiling of human embryonic stem cells (hESCs) and its applications.

RECOMB 2020, Italy (Jun 2020).

Honors and awards

Claude Science Hackathon, one of 500 participants selected globally (2026)
Google Cloud Research Credit Award, Google (2026)
Elected Member, Tau Beta Pi Engineering Honor Society, UAB (2025)
Blazer Graduate Research Fellowship, UAB (2022 - 2023)
Professional Development & Travel Awards, UAB CCTS & UAB GSG (2022 - 2024)

Professional memberships

American Association for Cancer Research (AACR), Student Member (2024 - Present)

Teaching and leadership

Certified Instructor, The Carpentries (2024 - Present). Taught workshops on R, Git, Bash, and Python at UAB's Biological Data Science Core.
President, Informatics Club, UAB (2023 - 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 2026-10-02