resume.json

{
  "basics": {
    "name": "Benjamin Lewis",
    "label": "Scientist",
    "image": "",
    "email": "benlewis.biology @ gmail.com",
    "phone": "",
    "url": "https://megadesk.github.io/",
    "summary": "I am a biological data scientist, with a strong wet lab prior.",
    "location": {
      "address": "Torrey Pines",
      "postalCode": "CA 92037",
      "city": "San Diego",
      "countryCode": "US",
      "region": "California"
    }

  },
  "work": [
    {
      "name": "Actio Biosciences",
      "position": "Bioinformatics Scientist II",
      "url": "https://actiobiosciences.com/",
      "startDate": "2024-04-01",
      "endDate": "present",
      "summary": "Single cell transcriptomics/multiomics",
      "highlights": ["Single cell transcriptomics/multiomics, Target Triage, Biomarker Discovery"]
    },
    {
      "name": "Aspen Neuroscience",
      "position": "Scientist I, R&D",
      "url": "https://aspenneuroscience.com/",
      "startDate": "2022-04-25",
      "endDate": "2024-03-29",
      "summary": "Single cell transcriptomics/multiomics",
      "highlights": ["Single cell transcriptomics/multiomics"]
    },
    {
      "name": "Hardy Diagnostics,",
      "position": "Research and Development Intern",
      "url": "https://hardydiagnostics.com/",
      "startDate": "2013-06-01",
      "endDate": "2013-12-01",
      "summary": "Designed and developed chromogenic diagnostic media formulations"
    }
  ],
  "education": [
    {
      "institution": "University of California, San Diego",
      "location": "San Diego, California, USA",
      "url": "https://www.ucsd.edu/",
      "area": "Molecular Biology",
      "studyType": "PhD",
      "startDate": "2016-09-01",
      "endDate": "2022-03-14",
      "summary": "PhD research focused on RNA-binding protein functions in mitochondrial regulation. Conducted under the mentorship of Gene Yeo and Tony Hunter.",
      "courses": ["Quantitative Methods in Genetics and Genomics", "Statistical Methods in Bioinformatics"]
    },
    {
      "institution": "California Polytechnic State University",
      "location": "San Luis Obispo, California, USA",
      "url": "https://www.calpoly.edu/",
      "area": "Stem Cell Research",
      "studyType": "Master of Science (MS)",
      "startDate": "2013-09-01",
      "endDate": "2015-06-01",
      "summary": "Master's degree focused on stem cell research, with extensive laboratory experience in molecular biology techniques and stem cell-based disease modeling."
    },
    {
      "institution": "California Polytechnic State University",
      "location": "San Luis Obispo, California, USA",
      "url": "https://www.calpoly.edu/",
      "area": "Biochemistry and Microbiology (Double Major)",
      "studyType": "Bachelor of Science (BS)",
      "startDate": "2008-09-01",
      "endDate": "2013-06-01",
      "summary": "Completed a double major in Biochemistry and Microbiology with an emphasis on foundational research methods, molecular biology, and analytical techniques."
    }
  ],
  "publications": [
    {
      "name": "Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs",
      "publisher": "Cell Reports",
      "releaseDate": "2015-09-01",
      "url": "https://doi.org/10.1016/j.celrep.2015.07.062",
      "summary": "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."
    },
    {
      "name": "Autologous and Heterologous Cell Therapy for Hemophilia B toward Functional Restoration of Factor IX",
      "publisher": "Cell Reports",
      "releaseDate": "2018-05-01",
      "url": "https://doi.org/10.1016/j.celrep.2018.03.121",
      "summary": "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."
    },
    {
      "name": "LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function",
      "publisher": "RNA",
      "releaseDate": "2024-02-16",
      "url": "https://doi.org/10.1261/rna.079799.123",
      "summary": "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."
    }
  ],
  "skills": [
    {
      "name": "Bioinformatics and Statistical Analysis",
      "keywords": [
        "Multiomic data analysis (Single-cell transcriptomics, Proteomics, ATAC-seq, CLIP-seq)",
        "Predictive machine learning model design and implementation",
        "Data visualization and statistical analysis"
      ]
    },
    {
      "name": "Programming and Computational Skills",
      "keywords": [
        "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"
      ]
    },
    {
      "name": "Molecular Biology",
      "keywords": [
        "Viral vector design and production",
        "Gene cloning and DNA assembly techniques",
        "NGS/qPCR analysis",
        "RNA manipulation and analysis techniques",
        "Immunoblotting"
      ]
    },
    {
      "name": "Cellular Biology and Analysis",
      "keywords": [
        "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"
      ]
    },
    {
      "name": "Microscopy and Imaging",
      "keywords": [
        "Immunofluorescence microscopy",
        "Confocal microscopy",
        "Brightfield microscopy",
        "Plate scanning"
      ]
    }
  ],
  "certificates": [
    {
      "name": "IBM Data Science Professional Certificate",
      "date": "2023-06-15",
      "issuer": "IBM",
      "url": "https://coursera.org/verify/professional-cert/Y9M6RFY4NCCY"
    },
    {
      "name": "IBM AI Engineering Professional Certificate",
      "date": "2024-01-19",
      "issuer": "IBM",
      "url": "https://coursera.org/verify/professional-cert/7NMH5QT7Q4XF"
    },
    {
      "name": "DeepLearning.AI TensorFlow Developer Professional Certificate",
      "date": "2024-05-14",
      "issuer": "DeepLearning.AI",
      "url": "https://coursera.org/verify/professional-cert/U96RULUPAKP6"
    }
  ],
  "languages": [
    {
      "language": "English",
      "fluency": "Native speaker",
      "icon": ""
    }
  ]
}