Summer Intern - Viroinformatics (Qian/Tan)

The J. Craig Venter Institute (JCVI) is a dynamic non-profit research organization using science to impact the world. Our research groups focus on human genomic medicine, infectious disease, plant, microbial and environmental genomics, synthetic biology and biological energy, bioinformatics, and software engineering. We are looking for self-motivated, inquisitive minds to learn with us in asking and finding the answers to questions that progress the field of genomics.
 
 Recent advances in sequencing technologies have generated an unprecedented volume of viral genomic data, opening new avenues for applying advanced data analytics and machine learning techniques to study pathogen evolution. For viral pathogens, however, genotype alone does not fully determine host range, tissue tropism, or antigenicity. Even small deviations in the primary amino acid sequence can lead to minimal or substantial structural changes, depending on the properties of the substituted side chains. Conversely, different primary sequences can sometimes yield structurally similar proteins. 

In this project, the candidate will work closely with researchers from both the Infectious Diseases team (Tan Lab) and the Informatics team (Qian Lab) in La Jolla, CA. The focus will be on developing computational methods to predict and compare the structures of viral glycoproteins, leveraging viral sequence data and correlating with neutralization assay results. The goal is to produce a data-driven structure-informed design approach for optimizing immunogenicity of vaccine candidates based on integration of sequential, structural, and functional characteristics. 

The candidate will learn:

• Cutting-edge machine learning methods used in sequence and structure analysis.
• Fundamentals in virology, immunology, and viroinformatics
• Primary steps in vaccine development 

Skills the intern will acquire:

• Sequence conservation analysis skills.
• Backpropagation and gradient descent optimization
• Application programming interface (API) for data access
• Protein structure visualization
• Software programming skills 

Requirements:

• Current Graduate Student 
• Major in Bioinformatics, Bioengineering, Computer Science, Biostatistics, or related fields
• Excellent software programming skills in Python and/or R
• Experience in computational prediction and comparison of protein structures
• Familiar with the existing protein data repositories including UniProt, GenBank, PDB and software tools including ColabFold, AlphaFold and RoseTTAFold.
• Ability to work independently, while respecting the needs of a larger team 
• A commitment to scientific discovery 
• Strong written and verbal communication skills 
• Full-time attendance (40 hours per week)  

Application Process

Please use the link to review the Application Process and Eligibility Requirements. https://www.jcvi.org/careers#internships 

Work Environment
The work environment characteristics described here are representative of those a teammate encounters while performing the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. 

• Moderate noise (i.e., business offices with computers, phones, printers, and light traffic)
• Ability to work in a confined area.
• Ability to sit at a computer terminal for an extended period.
• Ability to stand and/or sit for an extended period, if working in the lab. 

Physical Demands
The physical demands described here are representative of those that must be met to successfully perform the essential functions of this job. Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. 

• While performing the duties of this job, the employee is regularly required to stand, sit; talk, hear, and use hands and fingers to operate a computer and telephone keyboard reach, stoop kneel to install computer equipment.
• Specific vision abilities required by this job include close vision requirements due to computer and lab work.
• Light to moderate lifting is required. 

J. Craig Venter Institute is an Equal Opportunity Employer. All qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other legally protected characteristic or status.