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Basics
| Name | Benjamin Lewis |
| Label | Senior Scientist | Multi-Omic Discovery |
| benlewis.biology @ gmail.com | |
| Url | https://gitbenlewis.github.io/ |
| Summary | Neuro-data scientist specializing in multi-omic biomarker discovery, integrative transcriptomics, and therapeutic target identification in biotech R&D. |
Work
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2026.01 - Present San Diego, CA
Senior Scientist - Bioinformatics, Research and Development
Actio Biosciences
Promoted to Senior Scientist in January 2026 in recognition of scientific leadership, cross-program impact, and strategic contributions to portfolio advancement.
- Partnered with biology, translational, and executive stakeholders to guide data-driven portfolio decisions.
- Led multi-omic biomarker discovery and novel target identification across therapeutic programs.
- Drove target identification efforts resulting in multiple assets advancing to nomination and portfolio prioritization.
- Scientific lead for single-cell and bulk transcriptomic strategy across multiple therapeutic programs.
- Designed and deployed a production-grade RNA-seq pipeline (Nextflow, Python, AWS), reducing turnaround time from 2 weeks to <48 hours and standardizing analytics across R&D.
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2024.04 - 2025.12 San Diego, CA
Bioinformatics Scientist II, Research and Development
Actio Biosciences
Multi-omic biomarker discovery and integrative transcriptomics supporting early-stage therapeutic programs.
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2022.04 - 2024.03 San Diego, CA
Scientist I, Research and Development
Aspen Neuroscience
Cross-functional single-cell and multiomic discovery supporting pipeline and IND-enabling programs.
- Single-cell transcriptomics/multiomics: project design and data analysis lead.
- Functional genomics for pipeline development: project design and data analysis lead.
- Contributed to preclinical and IND-enabling studies to support regulatory filings and clinical progression.
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2013.06 - 2013.12 Santa Maria, CA
Research and Development Intern
Hardy Diagnostics
Developed chromogenic diagnostic media formulations and authored protocols for 510(k) validation studies.
Education
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2016.09 - 2022.03 San Diego, California, USA
PhD
University of California, San Diego
Molecular Biology
- Quantitative Methods in Genetics and Genomics
- Statistical Methods in Bioinformatics
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2013.09 - 2015.06 San Luis Obispo, California, USA
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2008.09 - 2013.06 San Luis Obispo, California, USA
Bachelor of Science (BS)
California Polytechnic State University
Biochemistry and Microbiology (Double Major)
Publications
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2024.02.16 LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function
RNA
The study identifies LARP4 as a critical RNA-binding protein that regulates nuclear-encoded mitochondrial mRNAs, ensuring proper mitochondrial biogenesis and function by maintaining the expression of respiratory chain complex proteins.
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2018.05.01 Autologous and Heterologous Cell Therapy for Hemophilia B toward Functional Restoration of Factor IX
Cell Reports
This research explores cell-based therapies for Hemophilia B, including the use of corrected iPSCs differentiated into hepatocyte-like cells and the transplantation of cryopreserved human hepatocytes, offering a potential long-term cure for the disease.
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2015.09.01 Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs
Cell Reports
This study highlights the use of CRISPR technology to correct the CFTR gene mutation in induced pluripotent stem cells (iPSCs) derived from cystic fibrosis patients. The corrected cells were differentiated into airway epithelial cells, restoring normal CFTR expression and function.
Skills
| Bioinformatics and Statistical Analysis | |
| Multiomic data analysis (Single-cell transcriptomics, Proteomics, ATAC-seq, CLIP-seq) | |
| Predictive machine learning model design and implementation | |
| Data visualization and statistical analysis |
| Programming and Computational Skills | |
| Python (pandas, matplotlib, seaborn, scikit-learn, scanpy/adata, scvi-tools, PyTorch) | |
| Linux | |
| AWS and Cloud/High-Performance Computing Environments | |
| GitHub | |
| R | |
| Nextflow-based RNAseq pipelines |
| Molecular Biology | |
| Viral vector design and production | |
| Gene cloning and DNA assembly techniques | |
| NGS/qPCR analysis | |
| RNA manipulation and analysis techniques | |
| Immunoblotting |
| Cellular Biology and Analysis | |
| CRISPR/Cas9 gene editing in iPSCs and cell lines | |
| Stem cell-based disease modeling | |
| Extracellular flux analysis | |
| Flow cytometry techniques and analysis (FACS) | |
| Live cell imaging |
| Microscopy and Imaging | |
| Immunofluorescence microscopy | |
| Confocal microscopy | |
| Brightfield microscopy | |
| Plate scanning |
Certificates
| DeepLearning.AI TensorFlow Developer Professional Certificate | ||
| DeepLearning.AI | 2024-05-14 |
| IBM AI Engineering Professional Certificate | ||
| IBM | 2024-01-19 |
| IBM Data Science Professional Certificate | ||
| IBM | 2023-06-15 |
Languages
| English | |
| Native speaker |