cv
Basics
Name | Benjamin Lewis |
Label | Scientist |
benlewis.biology @ gmail.com | |
Url | https://gitbenlewis.github.io/ |
Summary | I am a biological data scientist, with a strong wet lab prior. |
Work
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2024.04 - present Bioinformatics Scientist II
Actio Biosciences
Single cell transcriptomics/multiomics
- Single cell transcriptomics/multiomics, Target Triage, Biomarker Discovery
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2022.04 - 2024.03 Scientist I, R&D
Aspen Neuroscience
Single cell transcriptomics/multiomics
- Single cell transcriptomics/multiomics
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2013.06 - 2013.12 Research and Development Intern
Hardy Diagnostics,
Designed and developed chromogenic diagnostic media formulations
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 |