John J. Caperella Jr., MS

Bioinformatician & Full-Stack Software Engineer

MS in Bioinformatics with 2+ years computational research experience and full-stack engineering experience building production-ready scientific and business applications.
13 Crotona Avenue, Harrison, NY 10528 914-484-0257 jcaperella@gmail.com GitHub: github.com/jcaperella29
Education
Brandeis University, Waltham, MA
May 2024
Master of Science in Bioinformatics  •  GPA: 4.0
Pace University, Dyson College of Arts and Sciences, Pleasantville, NY
May 2019
Bachelor of Science in Biochemistry; Mathematics Minor
Honors: Biochemistry Excellence Award, Dyson Society of Fellows, Dean’s Scholarship, Dean’s List, Multiple Presentation Awards
Skills
Programming & Deployment
  • R (Bioconductor, ML, Shiny)
  • Python (ML, Biopython, Flask)
  • Bash, SQL Alchemy
  • Docker, Apptainer/Singularity
  • Nextflow, CWL
  • Google Cloud Platform
  • AWS (App Runner, SES, ECR)
  • Basic SQL and web development
Genomics & Genetics
  • PLINK, METAL
  • Variant calling
  • ATAC peak analysis
  • Burden tests, meta-analysis
  • FASTQ pipelines
  • De novo assembly
Transcriptomics
  • RNA-seq, scRNA-seq
  • Microarray processing
  • WGCNA, differential expression
  • PCA/UMAP visualization
Machine Learning & Dimensionality Reduction
  • Regression models
  • Random Forests, neural networks
  • PCA, UMAP
  • Hierarchical clustering, k-means
Structural Biology
  • PyMOL
  • AlphaFold
  • AutoDock
Databases & Data Sources
  • Genebass, Ensembl, UCSC, NCBI
  • PDB, Open Targets, UniProt
  • Gene Ontology
Data Visualization Tools
  • Flourish Studio — interactive bar, bubble, and treemap charts using Perturb-seq enrichment data; storytelling dashboards.
  • Tableau — interactive dashboards combining bar charts and volcano plots; parameter-driven Top-N filters; custom calculated fields; cross-sheet highlight actions; dynamic tooltips; dashboard containers and layout control.
  • Power BI — built cross-filtered dashboards using Country/Product/Discount slicers; created DAX measures for revenue, profit, and margins; implemented treemaps and comparative bar charts to analyze product and regional performance.
Projects
Independent / Self-Directed
Bioinformatics Tools Hub — Multi-Species Analysis Platform
Ongoing
Creator & Full-Stack Developer  •  R, Shiny, Python, Docker/Singularity, HTML/CSS/JS, GA4, Looker Studio
jcaperella29.github.io/JC_BIOINFORMATICS_HUB
  • Engineered a unified platform of interactive multi-species analysis tools supporting human, mouse, fly, and zebrafish for RNA-seq, scRNA-seq, Perturb-seq, ATAC-seq, miRNA-seq, and GWAS workflows.
  • Built consistent UIs for differential expression, QC, PCA/UMAP, clustering, metadata handling, and machine learning (RF/NN-based) analysis.
  • Containerized all tools for HPC deployment using Docker, Singularity, and Apptainer, ensuring reproducibility and minimal setup.
  • Added a dedicated Analytics Tab featuring an embedded Looker Studio iframe dashboard, GA4 event tracking, interactive time-series usage charts, auto-updating event tables, and “Last Checked” timestamps.
  • Designed a central navigation portal improving accessibility for programmers and non-programmers.
Client / Production Work
Inflection Point Portal — Full-Stack Flask Application
2025
Sole Developer (Client Project)  •  AWS, Python/Flask, SQL Alchemy, HTML/CSS/JS, CometChat, AWS SES
  • Built a production multi-page portal for a small business (The Inflection Point) as the sole full-stack developer.
  • Implemented user authentication, and secure file uploading (general + private).
  • Embedded a CometChat real-time messaging widget for user-to-user communication.
  • Built an email sending interface using AWS SES, with UI forms for subject/body and backend API handling.
  • Developed a goal-tracking dashboard with cumulative progress entries and user-specific tracking.
  • Deployed on AWS with containerization, environment variables, and secure secrets management.
Relevant Experience
Independent / Consulting
Independent Software Engineer
2024–Present
  • Designed and deployed full-stack applications integrating scientific workflows, business logic, and real-time communication tools.
  • Built Flask portals, Shiny apps, APIs, and containerized workflows ready for production use.
  • Implemented reproducible deployment patterns using Docker/Apptainer, environment variables, and secrets management.
Inflection Point — Contract Web Developer
2025
  • Owned end-to-end delivery of a production portal (AWS + Flask) for a small business, from requirements through deployment.
  • Implemented authentication, file upload flows, real-time chat integration, and an AWS SES email interface.
  • Built and shipped user-facing dashboards for structured goal tracking and progress history.
Academic Research
Computational Research Assistant — Department of Biology
Pace University, Pleasantville, NY  •  2021–2024
  • Automated zebrafish hair-cell counting with a Python GUI to streamline image-based quantification.
  • Used ML + AlphaFold to predict Cxcr4b receptor partners.
  • Provided computational and lab support; introduced the team to text-mining workflows.
Research Assistant — Department of Biology
Pace University, Pleasantville, NY  •  2020–2021
  • Zebrafish husbandry and experimental support.
  • RNA extraction, RT-PCR, gel electrophoresis.
  • EdU labeling, confocal microscopy, sequence analysis.
Biology & Chemistry Tutor
Pace University, New York, NY  •  2019–2020
  • Tutored General Biology and General & Organic Chemistry students.
  • Supported exam preparation, concept reinforcement, and study strategy.