Ethan Oksen

Ethan Oksen

About

I am an experienced biotechnology researcher and bioprocess engineer with graduate training in biotechnology and bioinformatics. I thrive on solving difficult technical challenges and pushing myself to continuously improve and learn. I am currently seeking opportunities to apply my skills and experience in a new role. For a detailed overview of my qualifications and work experience, please check out my resume.

In my previous role at Lawrence Berkeley National Laboratory, I identified data management as a key bottleneck for early-stage biotechnology company momentum. Many companies struggled to find relevant data from previous experiments within their own department because it was sioled in Excel spreadsheets, leading to duplicated work and wasted time. This experience and conversations with colleagues inspired me to develop fermPlot, a bioprocess web application designed to simplify data parsing, normalization, and visualization. fermPlot allows scientists and engineers to upload the unnormalized data they would usually parse and visualize in Excel and get publication-quality interactive visualizations, replicate statistics [beta], and normalized tables [beta] that can be added to a SQL database. If you have questions, suggestions, bug reports, or want to participate in beta testing for fermPlot, please reach out at [email protected].

I’ve also developed a freely available Nextflow pipeline for aligning and calling variants from next-generation sequencing data.

I have experience using a variety of technologies, programming languages and packages for data analysis, modeling, visualization, bioinformatics, molecular biology, and process engineering. I am always eager to learn new skills and technologies - finding the most effective tool for the work at hand. Here’s a list of some of the tools I’ve used in my work:

  • Software and Technologies
    • Programming Languages and Scripting: Python, R, JavaScript, Bash
    • Dashboards, Visualization, and Notebooks: Dash/Plotly, R Shiny, Matplotlib/Seaborn, ggplot2, Jupyter Notebook
    • Data Analysis and Processing: Python — Pandas, NumPy, SciPy; R — dplyr, tidyr, base R
    • Containerization and Version Control: Docker, Git, GitHub
    • Database Management: PostgreSQL, MySQL
    • Cloud Services and Application Orchestration: AWS (EC2, S3, ECR), Terraform, Ansible, Nginx, Gunicorn
    • Operating Systems and Environment: Linux/Unix, macOS, Windows
  • Bioinformatics:
    • Workflow Management: Nextflow
    • Guide RNA Design: Benchling, CHOPCHOP
    • Cloning, Primer Design, and Codon Optimization: Benchling
    • Bioinformatics Libraries for R and Python: Bioconductor, BioPython
    • Genome Alignment and Assembly: bbmap, BWA, Bowtie2, SPAdes
    • RNA-seq Analysis: Cufflinks, DESeq2, HISAT2, HTSeq, TopHat
    • Pre-processing and Quality Control: FastQC, fastp, MultiQC, Trimmomatic
    • Variant Calling and Genotyping: Delly, FreeBayes, GATK
    • Variant Annotation: Annovar, SnpEff, SnpSift
    • Data Handling and File Conversion: bcftools, bedtools, samtools
  • Laboratory:
    • Laboratory Information Systems: LabKey, Benchling
    • Molecular Biology: DNA/RNA extraction and purification; PCR, qPCR; Illumina NGS; cloning workflows; Protein expression and purification; Flow Cytometry and cell sorting
    • Lab Automation: Hamilton/Eppendorf liquid handlers, Sartorius AMBR 250 and Biolector for high throughput screening
    • Data Collection and Integration: LabView
    • Analytical Instrumentation: GC-MS, LC-MS/RI/UV, UV-Vis spectrometers

P.S. I love hiking and backpacking. You can see some of my photos of my trips on my photography page.