Wet lab and bioinformatics researcher

Alexander Bontempo

Bioinformatician

Bridging Biomedical Research & Bioinformatics to Drive Discovery 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 - Statistical Modeling & Data Interpretation

- Machine Learning & Predictive Analytics - Experimental Design & Data Integration

- Regulatory Documentation & Publication Support

- Project Leadership & Collaboration

- Mentorship & Training - Languages: English Italian Spanish

Technical Proficiencies:

- Programming & Tools: R Python Perl (fundamentals) MySQL (in progress)

- 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)

- Laboratory Expertise: 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 (Seurat, SoupX, scrublet, CellChat, enrichGO) in just two weeks; uploaded to GitHub, enabling cell-cell communication analysis, batch and ambiental RNA normalization and doublets removal.

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.

Publications: ORCID Profile

Code Samples: GitHub

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.

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 20+ new protocols in protein production, purification, and electron microscopy.

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).

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). Mechanosensing by Piezo1 regulates osteoclast differentiation via PP2A-Akt axis in periodontitis. bioRxiv Preprint. DOI: 10.1101/2024.09.04.611049 4. Bontempo A., Chirino A., Heidari A., Boparai S., Arora S., Ruiz S., Antonson S.A., Kawai T., Cayabyab M.J.

(2023). Assessment of SARS CoV 2 entry in gingival epithelial cells expressing CD147. European Journal of Oral Sciences. DOI: 10.1111/eos.12906

5. Bontempo A., Garcia M.M., Rivera N., Cayabyab M.J., Bontempo A. (2020). A Systematic Approach to HIV-1 Vaccine Immunogen Selection. AIDS Research and Human Retroviruses. DOI: 10.1089/aid.2019.0239 6. Bontempo A., Ugalde-Villanueva B., Delgado-González E., Rodríguez Á.L., Aceves C. (2017). Molecular iodine impairs chemoresistance mechanisms, enhances doxorubicin retention and induces downregulation of the CD44+/CD24+ and E-cadherin+/vimentin+ subpopulations in MCF-7 cells resistant to low doses of doxorubicin. Oncology Reports. DOI: 10.3892/or.2017.5934 7. Nava-Villalba M., Nuñez-Anita R.E., Bontempo A., Aceves C. (2015). Activation of peroxisome proliferator-activated receptor gamma is crucial for antitumoral effects of 6-iodolactone. Molecular Cancer. DOI: 10.1186/s12943-015- 0436-8

Projects:

Single-Cell RNA-Seq Analysis Pipeline (GitHub: bontix-77/scRNAseq) Code Samples: GitHub Built an end-to-end scRNA-seq workflow in R (Seurat, SoupX, Scrublet) for preprocessing and quality control.

Applied CellChat and enrichGO to model cell–cell communication and perform gene ontology enrichment.

Automated GEO data ingestion, gene ID conversion, and reproducible analysis pipelines with documentation.

Generated visualizations and HTML reports in RMarkdown to communicate results to cross-disciplinary teams.

Generated ML pipeline deploying Caret algorithms for the determination of predictive markers.

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