Bioinformatics Analyst with Biomedical Science Background

********@*****.** • +1-857-***-**** • Davie, FL

Linkedin.com/in/alexander-bontempo

Publications: ORCID Profile

Code Samples: GitHub

Alexander Bontempo

Bridging Biomedical Research & Bioinformatics to Drive Discovery 1

PhD-trained biomedical researcher with 10+ years of wet lab expertise in oncology, virology, and immunology, now advancing a career in bioinformatics through both hands-on projects and a Master’s in Bioinformatics (Feb 2026). Adept at bridging bench science with computational analysis, independently building bioinformatics pipelines, and delivering high-quality results for publications and grant proposals. Skilled at applying statistical rigor and biological insight to transform large datasets into meaningful discoveries.

Core Competencies:

Bioinformatics & Computational Analysis (scRNA-seq, GATK variant calling, Python and R), nextflow, docker and HPC

10+ years biochemistry & molecular biology

laboratory experience

Machine Learning & Predictive Analytics Experimental Design & Data Integration

Project Leadership & Collaboration Publication Support

Statistical Modeling & Data Interpretation Mentorship & Training Technical Proficiencies:

Programming & Tools: R Python Perl (fundamentals) MySQL HPC slurm scripting

Statistics: Linear & Nonlinear Regression Multivariate Analysis ANOVA Factorial & Mixed Models

Machine Learning: caret keras PyTorch (in progress) TensorFlow (in progress)

Genomic & Proteomic Databases: BLAST OMIM PDB UniProt Ensembl IGV UCSC Genome Browser GEO

Bioinformatics: RNA-seq scRNA-seq Proteomics Microbiome (QIIME2) GATK variant calling Nextflow Docker

Laboratory Expertise: routinely executed Biochemical & Molecular Biology Protocols Education

Master of Science – Bioinformatics INTERNATIONAL UNIVERSITY OF LA RIOJA (Expected Feb 2026) PhD - Biomedical Sciences NATIONAL AUTONOMOUS UNIVERSITY OF MEXICO Bachelor of Science – Molecular Biology UNIVERSITY OF PADUA Career Highlights

Built End-to-End scRNA-seq Pipeline: Developed and deployed a working single-cell RNA-seq pipeline integrating Harmony, SoupX, scrublet, CellChat, enrichGO in just two weeks; integrated Scanpy analysis starting from Seurat normalized dataset. Now finalizing the Nextflow pipeline. Published a Docker image for Seurat 5.3.1 (docker hub bontix77/sc_rna:v1.0). Uploaded to GitHub, enabling cell-cell communication analysis, batch and ambient RNA normalization and doublets removal and more.

Delivered Publication-Ready Proteomics Analysis: Conducted clustering, volcano plots, and pathway enrichment analysis independently, autonomously providing figures for peer-reviewed publication.

Bridged Wet Lab and Computational Biology: Translated raw datasets into biologically relevant insights, directly supporting publications and NIH grant proposals.

Professional Experience

NOVA SOUTHEASTERN UNIVERSITY Ft. Lauderdale, FL

Private research university specializing in health, biological, and biomedical sciences. Researcher 2023 – Present

Lead independent and collaborative research projects spanning HIV latency, proteomics, and computational biology. Manage project design, execution, and publication readiness while mentoring technicians and students.

Independent projects: scRNA-seq pipeline integrating Seurat and Scanpy. Containerized using a custom Docker image based on Seurat 5.3.1 (published on docker hub). Pipeline coded in Nextflow. Coded and tested the HPC slurm script. Now concluding a end-to-end pipeline from fastq to .vcf using GATK for variant calling. Hisat2 alignment for transcriptomic analysis.

Advanced HIV Latency Research: Directed proteomics analysis (dimensionality reduction, clustering, GO), differential gene expression, and pathway analysis; managed project end-to-end with article under review.

Mentorship & Training: Supervised and trained lab staff and students in virology and computational workflows.

Interdisciplinary Collaboration: Partnered with Kawai Lab on viral vectors and BLI assays. ********@*****.** • +1-857-***-**** • Davie, FL

Linkedin.com/in/alexander-bontempo

Publications: ORCID Profile

Code Samples: GitHub

Alexander Bontempo

Bridging Biomedical Research & Bioinformatics to Drive Discovery 2

COVID-19 Research: Led study on P. gingivalis and SARS-CoV-2 interactions; published findings.

HIV Immunogen Project: Coordinated with Duke, Cornell, and Bioqual on ADCC and neutralization assays; manuscript under review.

Machine Learning: Deployed Machine Learning pipeline to support marker analysis of a RNASeq dataset.

Other Collaborations: Coauthored a paper describing the role of Piezo1 in the context of osteoclast physiology. Post-Doctoral Researcher 2020 – 2023

Conducted independent postdoctoral research focused on virology and immunology, with emphasis on viral-host interactions and SARS-CoV-2 infection mechanisms. Integrated wet lab experimentation with bioinformatics analysis.

SARS-CoV-2 Infection Studies: Designed and executed experiments on gingival epithelial cells and CD147; published results.

Computational Integration: Applied bioinformatics tools to connect transcriptomic datasets with biological findings, supporting publication-quality results.

FORSYTH INSTITUTE / HARVARD SCHOOL OF DENTAL MEDICINE Cambridge, MA World-renowned research institute focused on oral biology, immunology, and infectious disease. Post-Doctoral Researcher 2018 – 2020

Served as the first and only researcher on a newly funded HIV immunogen project. Established protocols and infrastructure independently, advancing research readiness and enabling downstream studies.

Built Research Infrastructure from Scratch: Established new protocols in protein production, purification, and electron microscopy for a new establishing laboratory.

Designed Novel HIV Immunogen: Produced and characterized 1086.c SOSIP; conducted BLI, Negative Stain EM images acquisition, RELION images processing and AlphaFold2 comparative analysis.

Accelerated Project Launch: Generated structural and antigenicity data within four months, enabling antigenicity studies.

Recognition: Awarded Careers in Immunology Fellowship from the American Association of Immunologists (2019). NATIONAL AUTONOMOUS UNIVERSITY OF MEXICO Queretaro, Mexico Largest university in Latin America, leading biomedical and molecular biology research across oncology and public health. Researcher 2011-2018

Conducted PhD-level research in oncology, with a focus on breast cancer chemoresistance. Combined molecular biology, biochemistry, and bioinformatics to explore therapeutic pathways.

Breast Cancer Resistance Studies: Developed MCF-7 chemoresistant cell line; applied Western blot, RT-qPCR, and confocal microscopy.

Bioinformatics Foundation: Completed intensive RNA-seq dataset analysis course, establishing core computational skills.

Recognition: Received Premio a la Innovación Farmacéutica for pharmaceutical innovation (2018). Recent Publications

1. Bontempo A., Heidari A., Pastore M.R., Madonia R., Sadik A., Schweizer M., Cayabyab M. (2025). Yoda1, a Piezo1 agonist, induced latent HIV reactivation associated with upregulation of CD3/TCR complex and HLA genes. Preprint. DOI: 10.21203/rs.3.rs-6208371/v1 2. Bontempo A., Chirino A., Heidari A., Lugo A., Shindo S., Pastore M.R., Madonia R., Antonson S.A., Godoy C., Nichols F.C., et al.

(2024). Inhibition of SARS-CoV-2 infection by Porphyromonas gingivalis and the oral microbiome. Microbiology Spectrum. DOI: 10.1128/spectrum.00599-24

3. Shindo S., Nakamura S., Rawas-Qalaji M., Heidari A., Pastore M.R., Okamoto M., Suzuki M., Salinas M., Minond D., Bontempo A., et al.

(2024). Piezo1 protects against inflammatory bone loss via a unique Ca2+-independent mechanism in osteoclasts. Front immunol. DOI: 10.3389/fimmu.2025.1661538

Latest Independent Projects

Latest Independent Projects Reproducible Single-Cell Analysis Pipeline (GitHub: bontix-77/scRNAseq)

Engineered a containerized Nextflow pipeline integrating Seurat (R) and Scanpy (Python) for flexible, scalable analysis.

Implemented SoupX for ambient RNA removal, CellChat for cell–cell communication, and enrichGO for pathway analysis.

Published custom Docker images (bontix77/sc_rna:v1.1) to resolve dependencies and ensure full reproducibility.

Automated data ingestion and Quarto HTML reporting to streamline communication.

Deployed a Machine Learning pipeline using Caret algorithms to identify predictive markers on bulk RNA-seq dataset .

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