Hi, I'm Austin Marshall.
A
Wet-lab scientist with a passion for bridging the gap between biology and computer science.
About
I am postdoctoral fellow at Houston Methodist Research Institute. My efforts are focused on defining the relationship between the brain and periphery using culture-independent workflows. I've worked with many different nucleic acid sequencing technologies like Sanger, Illumina, and ONT Nanopore MinION. I am passionate about applying third generation sequencing and novel bioinformatic workflows to determine how the microbiome impacts other systems and vice versa.
- Languages: R, C++, Bash
- Sequencing platforms: Sanger, Illumina, ONT Nanopore
- Microbiomes: Bioaerosols, Water, Gut, Anaerobic digestate, Dust
- Techniques: Bioaerosol collection, DNA and RNA extraction, Nanopore sequencing, RT-PCR, Metagenome-assembled genome construction
Experience
- Performed sequencing experimentation and analysis on gut microbiome samples to study connection with neurological conditions.
- Developed bioinformatic pipelines to process Oxford Nanopore Technologies sequencing data.
- Introduced upperclassmen biology majors to human anatomy through the use of PT, PA and OT cadavers.
- Effectively taught students how to perform physiological measurements and how to execute high level research studies with those same measurements.
- Tools: AD Instruments hardware and software
- Performed DNA extraction and long-read sequencing on dust samples returned from the International Space Station for microbiome analysis.
- Aided in the development of bioinformatic pipelines to process Oxford Nanopore Technologies sequencing data.
- Developed antibody nanoparticle conjugates for rapid mycotoxin detection assays.
- Worked on a few different mycotoxin targets as well as aiding with protein production from mammalian cell cultures.
- Improved the detection limits of current assays through implmentation of novel nanoparticle technology.
- Tools: Monoclonal antibodies, Nanoparticle chemistry, Hybridoma transfer technology
Skills
Wet-Lab Techniques
Bioaerosol Collection
DNA and RNA Extraction
RT-PCR
mRNA Isolation
Nanopore Sequencing
Bioinformatic Tools
Guppy Basecalling
16S rRNA Classification
Metagenomic Classification
Metagenome-assembled Genomes
Metatranscriptomic Studies
Education
Department of Biology, Clarkson University Graduate School
Potsdam, NY, USA
Degree: PhD in Interdisciplenary Bioscience and Biotechnology
Completion Date: December 2023
Department of Chemistry and Biomolecular Science, Clarkson University
Potsdam, NY, USA
Degree: B.Sc. in Biomolecular Science with a Minor in Biomedical Engineering
Completion Date: May 2020
Publications
Marshall, A. et al. Application of nanopore sequencing for accurate identification of bacterial colonies. bioRxiv (2023) doi:10.1101/2023.01.03.522650.
Banerjee, G. et al. Application of advanced genomic tools in food safety rapid diagnostics: challenges and opportunities. Curr Opin Food Sci 100886 (2022) doi:10.1016/j.cofs.2022.100886.
Presentations
American Association of Aerosol Research
2021: Application of Long-read Nanopore Sequencing for the Analysis of Airborne Microbes
2022: Estimation of Direct Human Contribution to the Aerobiome Composition of Indoor Environments
Microbiology of the Built Environment GRC
2022: Application of Nanopore Sequencing in Low Concentration Airborne Microbe Surveillance
Projects
The first ever nanopore-only MAG from an ISS sample!
