# Samuel Bharti

> Computational biologist building tools that make omics data easier to explore, trust, and share. PhD candidate at UAB, recently a Shiny SWE intern at Posit.

Machine-readable index of https://www.samuelbharti.com/ · PhD candidate @ UAB · previously Posit (Shiny), Genentech (human genetics). The complete site text is at https://www.samuelbharti.com/llms-full.txt.

## About
- [Home](https://www.samuelbharti.com/): who I am and what I build
- [Now](https://www.samuelbharti.com/now): what I'm focused on right now
- [Experience](https://www.samuelbharti.com/experience): roles, education, teaching, and honors
- [Skills](https://www.samuelbharti.com/skills): the tools I use and the work they add up to
- [NF1](https://www.samuelbharti.com/nf1): my PhD research on Neurofibromatosis Type 1
- [Ask an AI](https://www.samuelbharti.com/ai): how to point an assistant at this site
- [Claude Science Hackathon](https://www.samuelbharti.com/claude-science-hackathon): the story behind genescout and biobouncer
- [NF Conference 2026 poster](https://www.samuelbharti.com/nf-conference-2026): NF1-associated breast cancer in novel rat models

## Work
- [All work](https://www.samuelbharti.com/work): the full catalog with the work-to-skill matrix
- [genescout](https://www.samuelbharti.com/work/genescout): app: An agentic evidence-review workbench. Give it a candidate list and a disease context, get back a plausibility-ranked, cited shortlist. Research use only.
- [tahoe-explorer](https://www.samuelbharti.com/work/tahoe-explorer): app: Filter and subset Tahoe-100M perturbation metadata, 100.6 million rows, and leave with a reproducible pull recipe. Summaries push down to DuckDB.
- [Plotomics Live](https://www.samuelbharti.com/work/plotomics-live): app: 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.
- [variant-reviewer](https://www.samuelbharti.com/work/variant-reviewer): app: One gene, one variant, one page. Eighteen cards fan out asynchronously across public APIs, with a 3D structure viewer and a ClinVar typeahead.
- [plotomics](https://www.samuelbharti.com/work/plotomics): package: Seventeen GPU-accelerated visualizations from one TypeScript core, wrapped three ways: npm for React, htmlwidgets for R, anywidget for Python. The same core drops into all three unchanged.
- [biobouncer](https://www.samuelbharti.com/work/biobouncer): package: 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.
- [bioclients](https://www.samuelbharti.com/work/bioclients): package: 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.
- [biohttp](https://www.samuelbharti.com/work/biohttp): package: Normalized HTTP transport. Calls return a result value rather than raising, so transport failure, a bad status code and an unreadable body stay distinct outcomes. Circuit breaking, retry and caching are defaults.
- [recount-explorer](https://www.samuelbharti.com/work/recount-explorer): app: Shiny app to browse, analyze, and export recount3 RNA-seq studies: 18,998 datasets, quality checks, and PCA.
- [R Shiny Template](https://www.samuelbharti.com/work/r-shiny-template): template: Reusable, public starter kit for quickly building reproducible bioinformatics and data apps in R Shiny.
- [R for Beginners](https://www.samuelbharti.com/work/r-for-beginners): teaching: 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.
- [AWS R Shiny Deployment Workshop](https://www.samuelbharti.com/work/aws-r-shiny-deployment-workshop): teaching: Workshop on deploying a Dockerized R Shiny bioinformatics app on an AWS EC2 instance, using sMAP as the example. Hosted with STEM-Away.
- [peacock](https://www.samuelbharti.com/work/peacock): package: Streamlines project initialization and workflow management.
- [GlucoKinaseDB](https://www.samuelbharti.com/work/glucokinasedb): database: Manually curated database of 1,700+ glucokinase modulators with bioactivity and chemical data, in-browser 3D structure visualization, and API endpoints.
- [PepEngine](https://www.samuelbharti.com/work/pepengine): database: Manually curated structural database of synthetic peptides containing the non-standard amino acids α,β-dehydrophenylalanine (ΔF) and α-aminoisobutyric acid (Aib).
- [gene-list-builder](https://www.samuelbharti.com/work/gene-list-builder): app: 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.
- [draft-reviewer](https://www.samuelbharti.com/work/draft-reviewer): app: 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.
- [Multi-Omics Locus Viewer (MOLV)](https://www.samuelbharti.com/work/multi-omics-locus-viewer-molv): app: 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.
- [RAPTOR](https://www.samuelbharti.com/work/raptor): app: 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.
- [Pediatric Thyroid Cancer (PTC) Explorer](https://www.samuelbharti.com/work/pediatric-thyroid-cancer-ptc-explorer): app: Interactive genomics and clinical-analysis app for whole-exome and bulk RNA-seq pediatric thyroid cancer data.
- [Statistical Enrichment Analysis of Samples (SEAS)](https://www.samuelbharti.com/work/statistical-enrichment-analysis-of-samples-seas): app: Online tool to characterize sample subsets (cohorts) and find enriched clinotypes, handy for balancing case/control cohorts and profiling samples in cross-sectional studies.
- [NF1 scRNA-seq Integration App](https://www.samuelbharti.com/work/nf1-scrna-seq-integration-app): 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.
- [NF1 Rat Exome Data Explorer](https://www.samuelbharti.com/work/nf1-rat-exome-data-explorer): app: Interactive explorer that combines nf-core whole-exome outputs with variant tools and AI-assisted analysis for NF1-associated tumor models.
- [sMAP (Standard Microarray Analysis Pipeline)](https://www.samuelbharti.com/work/smap-standard-microarray-analysis-pipeline): app: R Shiny educational app that walks users through an interactive transcriptomics pipeline with quality control, statistics, and biomarker discovery.
- [VIRdb 2.0](https://www.samuelbharti.com/work/virdb-2-0): database: Vitiligo research database with differentially expressed genes, curated protein targets, natural compounds, and co-expression network visualizations.
- [PAGER 3.0 & PAGER Web App](https://www.samuelbharti.com/work/pager-3-0-and-pager-web-app): app: Pathways, Annotated-lists and Gene-signatures Electronic Repository, with an R Shiny web app for pathway and gene-set enrichment and network interpretation.
- [BioDivPortal](https://www.samuelbharti.com/work/biodivportal): app: R Shiny app that maps and visualizes species occurrences across Poland, using Leaflet for geospatial mapping and dygraphs for time-series exploration.
- [ondemand-html-renderer](https://www.samuelbharti.com/work/ondemand-html-renderer): app: 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.

## Research
- [Research & publications](https://www.samuelbharti.com/research): peer-reviewed papers, preprints, and talks
- [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 (2022). PAGER Web APP: An Interactive, Online Gene Set and Network Interpretation Tool for Functional Genomics. Frontiers in Genetics](https://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.](https://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.](https://doi.org/10.3389/fdata.2021.725276)
- [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.](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)
- [ORCID](https://orcid.org/0000-0003-4190-7058): 0000-0003-4190-7058
- [ResearchGate](https://www.researchgate.net/profile/Samuel-Bharti): Samuel-Bharti
- [Google Scholar](https://scholar.google.co.in/citations?user=GT1IKEoAAAAJ&hl=en): GT1IKEoAAAAJ

## Writing
- [All posts](https://www.samuelbharti.com/blog): the blog listing with topic filters and search
- [R Shiny Template v2.0](https://www.samuelbharti.com/posts/r-shiny-template-v2-0/): A reproducible and container-ready R Shiny template with renv, Docker, and Zenodo citation support. (2026-05-02)
- [R Shiny Template](https://www.samuelbharti.com/posts/r-shiny-template/): Here's why you need a template for your next R Shiny app. (2024-09-25)
- [Introduction to GlucoKinaseDB](https://www.samuelbharti.com/posts/intro-to-gkdb/): A Centralized Resource for Diabetes Drug Target Information (2023-05-10)
- [Introduction to SEAS](https://www.samuelbharti.com/posts/intro-to-seas/): Understanding your sample subsets: an introduction to SEAS (2022-11-06)
- [Introduction to PepEngine](https://www.samuelbharti.com/posts/intro-to-pepengine/): A database of synthetic peptides with the non-standard amino acids (2022-04-12)
- [Enrichment analysis and annotation using PAGER](https://www.samuelbharti.com/posts/intro-to-pager/): A database of annotations to enrich gene lists or identify cell types. (2022-04-06)
- [Microarray analysis for non-coders using sMAP](https://www.samuelbharti.com/posts/intro-to-smap/): An R Shiny application enabling researchers to analyze microarray datasets. (2022-02-20)
- [Deploy your Shiny App on AWS](https://www.samuelbharti.com/posts/aws-r-shiny-deploy/): Learn how to deploy your R shiny app on AWS instance. (2021-11-21)
- [Introduction to Vitiligo Information Resource (VIRdb 2.0)](https://www.samuelbharti.com/posts/intro-to-virdb/): A database for vitiligo biomarkers and its comorbidities. (2021-10-06)

## Optional
- [Blog RSS feed](https://www.samuelbharti.com/blog.xml)
- [NF1 field-notes RSS feed](https://www.samuelbharti.com/nf1.xml)
- [Résumé (PDF)](https://www.samuelbharti.com/files/Resume_SamuelBharti_Apr2026_SB.pdf)
- [GitHub](https://github.com/samuelbharti)
- [LinkedIn](https://www.linkedin.com/in/samuelbharti/)
- [Bluesky](https://bsky.app/profile/samuelbharti.com)
- [Email](mailto:samuelbharti.io@gmail.com)
- [Full text for LLMs](https://www.samuelbharti.com/llms-full.txt): the entire site as one document