Environment
Synthetic biology is an emerging field focused on the rational design of DNA molecules that meet user specifications in different segments of the biotechnology market.
The Abell Chair in Synthetic Biology interacts with a vibrant synthetic biology community at Colorado State University that includes more than 25 faculty members on campus in many different academic departments, from mathematics and biology to computer science and veterinary medicine. The Chair is also interacting with a broad range of external partners including academic and industrial collaborators, funding agencies, and scientific journals. The Chair is located in the new, state-of-the-art Suzanne and Walter Scott, Jr. Bioengineering Building, which houses the Systems and Synthetic Biology (SSB) Research Pod. The SSB research pod is a collaborative research environment that promotes research and innovation among students and postdoctoral scholars.
Opportunity
We are looking for a research assistant with a strong interest in bioinformatics to work on an NIH-funded research project aiming at developing digital certificates for engineered DNA molecules.
Plasmids are engineered pieces of DNA that are used for biological research and for manufacturing biologic drugs and therapeutics. Despite the central importance of plasmids to biomedical research and development, the scientific community does not have a standardized, validated and secure infrastructure for associating the physical DNA molecules with the electronic records that describe them. We are proposing to develop a new digital certificate technology that will permanently label the DNA molecules themselves with an identifier that will connect them to standardized electronic documents describing their sequence, function, history, and other essential information allowing scientists to use them in a reproducible, safe, and secure manner.
The research assistant will work in close collaboration with laboratory manager and graduate students. They will be responsible for developing bioinformatics pipeline to analyze plasmid sequencing data collected on different platforms (Sanger, Nanopore, Illumina) as well as assist with running sequencing experiments using various types of automated instruments and sequencing technologies. See https://pubs.acs.org/doi/full/10.1021/acssynbio.0c00401 for additional information.
Responsibilities
- Work with an industrial partner to move the existing algorithms to a production server
- Develop new bioinformatics pipelines to handle different sequencing strategies.
- Assist laboratory manager with running sequencing experiments on different sequencing platforms
- Attend research group meetings
Required Qualifications
- Be enrolled in a graduate program in computer science, engineering, mathematics, or life science.
- Familiarity with basic concepts of bioinformatics including sequence annotation, assembly of sequencing reads, and sequence alignment algorithms.
- Outstanding communication skills in different formats.
- Genuine interest for interdisciplinary research at the interface between computer and life sciences.
- Working knowledge of Python
Preferred Qualifications
- Prior experience in bioinformatics.
- Working knowledge of source control in Git
- Understanding of distributed software architectures
- Prior experience using agile development
- Understanding of AWS and other cloud technologies
Point of Contact: jean.peccoud@colostate.edu
Financial support: NIH Award / NSF Award