Ethan Oksen

Ethan Oksen

About

My name is Ethan Oksen, and I am an experienced biotechnology researcher and bioprocess engineer with graduate training in biotechnology and bioinformatics. I am a curious and independent thinker with a passion for interdisciplinary research. I thrive on solving difficult technical challenges and pushing myself to improve and learn every day. I am currently seeking opportunities to apply my skills and experience in a new role. For a detailed overview of my qualifications, 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 biotech company momentum. This experience and conversations with colleagues inspired me to develop a bioprocess web application called fermPlot. My ultimate aim is to create a platform that incentivizes scientists and engineers to upload their previously siloed data to a database by providing automated data parsing, statistical analysis, and interactive visualizations. If you have questions, suggestions, or bug reports 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, 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, Bash, Nextflow, Javascript
    • Operating Systems and Environment: Linux/Unix, macOS, Windows
    • Containerization and Version Control: Docker, Git, GitHub
    • Database Management: PostgreSQL, MySQL
    • Cloud Services and Application Orchestration: AWS (EC2, S3, ECR), Terraform, Docker, Nginx, Gunicorn
  • Data Analysis, Visualization Libraries, and Scientific Figure Generation:
    • Visualization and Dashboards: Plotly, Matplotlib, base R; RShiny, Dash
    • Data Analysis: pandas, numpy, tidyverse
    • Scientific Figure Generation: Adobe Illustrator and Photoshop
  • Bioprocess Engineering:
    • Data Collection and Process Control Tools: LabView, Sartorius MFCS and AMBR 250 High Throughput software.
    • Bioreactor Systems: Sartorius AMBR 250 High Throughput and BIOSTAT B, BioLector Pro, ABEC 50L and 300L fermenters.
    • Bioreactor Sensors: pH, DO, biomass, in-line biochemistry analysis (YSI), and process mass spectrometry (Prisma Benchtop).
    • Lab Automation: Hamilton Microlab STAR and Eppendorf epMotion 5073 liquid handling robots.
    • Analytical Instrumentation: GC-MS, LC-MS/RI/UV, UV-Vis spectrometers, DSC/TGA, rheometry, and flow cytometry.
    • Downstream Processes: Tangential flow filtration, depth filtration, disc stack centrifugation, homogenization, distillation, and chromatography.
  • Bioinformatics:
    • Genome Alignment and Assembly Tools: bbmap, BWA, Bowtie2, SPAdes, STAR
    • Pre-processing and Quality Control Tools: FastQC, fastp, MultiQC, Trimmomatic
    • Variant Calling and Genotyping Tools: Delly, FreeBayes, GATK
    • Variant Annotation Tools: Annovar, SnpEff, SnpSift
    • RNA-seq Analysis Tools: Cufflinks, DESeq2, HISAT2, HTSeq, TopHat
    • Data Handling, Manipulation, and Workflow Management Tools: bcftools, bedtools, Nextflow, Picard, samtools
    • Bioinformatics Libraries for R and Python: Bioconductor, BioPython
    • Genomic Data Visualization and Exploration Tool: IGV, UCSC Genome Browser

If you’d like to collaborate, discuss potential opportunities, or simply chat about the world of biotechnology, bioprocess engineering, and/or bioinformatics, please feel free to reach out at [email protected]

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