Database Engineer – Principal/Senior Bioinformatics Research Scientist

M. Madan Babu’s Group at the Center of Excellence for Data-Driven Discovery and the Department of Structural Biology is seeking a highly driven, full-time Principal Bioinformatics Research Scientist to serve as a Database Engineer to support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35 million in institutional funding (more information in the  St. Jude Strategic Plan 2022–2027 (pp 62-63). This is a joint project between the Kalodimos Lab and the Babu Group at St Jude.

The project will extend the ultra-high field NMR spectroscopy and biochemistry approaches developed recently by the Kalodimos lab (Science 370, eabc2754, 2020) to study the human kinome. This is a large-scale project that aims to detect and structurally characterize the distinct conformational states populated by kinases, and to dissect the mechanisms of allosteric regulation and those underpinning oncogenic and drug-resistance mutations. This strategy will be integrated with and complemented by data-science and computational approaches developed by the Babu lab (Nature 587, 650, 2020), to systematically characterize the conformational landscape of the human kinome. 

This position is for a senior-level database engineer who will employ a variety of languages and tools to develop, construct, test and maintain data pipelines to organize multimodal biological information, and work with data scientists and visualization specialists to make biological discoveries and reveal fundamental principles of biological systems. The ideal candidate will have strong experience working in data warehouse environments and developing data marts to help scientists query, visualize and understand high-dimensional biological data.  This role requires a strong background in computer science, data architecture and database management. You will work with an interdisciplinary team of 40 scientists including biochemists, spectroscopists, data scientists and bioinformaticians; exceptional communication (written and verbal), training experience and critical thinking skills are a must. When submitting your application, please include your CV and a cover letter. St Jude offers a well-defined career ladder with potential for growth and advancement. Industry-competitive salaries are based on your degree and years of experience.

Ranked #1 in the U.S. in Pediatric Cancer, St. Jude Children’s Research Hospital is a NCI-designated Comprehensive Cancer Center, and home to the Pediatric Cancer Genome Project. The St. Jude campus is a truly unique research environment, encompassing state-of-the-art HPC facilities, world-leading oncology basic research, outstanding Shared Resources and Core Facilities and a dedicated translational Chemical Biology and Therapeutics department. The $412M Advanced Research Center, opened in 2021, doubles the campus’ research space and adds support for an additional 1000 employees. There is a vibrant Data Science community at St. Jude, with opportunities to interact with researchers in the Biostatistics and Computational Biology Departments, and tremendous support from the Center for Applied Bioinformatics.

The Department of Structural Biology is building one of the world’s most comprehensive research center for defining molecular structures to understand health and disease at the molecular level. The Department is home to multiple Technology Core Centers (Cryo-EM and Tomography, X-ray, NMR, Single-Molecule Imaging, and Protein Technologies) ready to characterize Data Driven Discoveries.

St. Jude Children’s Research Hospital is consistently named as one of Fortune magazine and Glassdoor.com’s “Best Places to Work,” as well as “Best Workplace for Women” and “Best Workplace for Diversity.” We are in the heart of Memphis, Tennessee, a vibrant and friendly city at the historic American crossroads of music, trade, food, and culture. Mild winters and beautiful green outdoor spaces are part of the reasons why Forbes recently named Memphis the 4th happiest city in which to work. Low cost of living and high quality of life are other attractions; Money magazine listed Memphis as one of the least expensive cities in which to raise a child. St. Jude facilities and salaries are highly competitive. The Kalodimos and Babu Groups strive to build and maintain a culture of respect, diversity, and inclusion and we strongly feel these values directly contribute to the dynamic and intellectually stimulating scientific environment we can provide.

As a Database Engineer you will work as a part of a team and contribute to ongoing projects on the Blue Sky Kinase Project. You will be expected to work efficiently to manage concurrent projects, collaborate extensively, and meticulously document work and code.

• Developing and maintaining MySQL databases
• Writing proposals to secure access to large consortium datasets
• and overseeing Extract-Load-Transform (ELT) scripts to incorporate large volumes of biological omics data and metadata from disparate sources into Data Warehouse using common file transfer protocols and RESTful APIs
• Communicating with experimentalists to understand how to incorporate new biological information into the data warehouse
• Prepare results and support the development of advanced querying, analysis and visualization projects through thoughtful data structuring and configuring tables for easy visualization
• Drafting and enforcing policies for data backup, version control, documentation, functionality testing and security

• A minimum of five (5) years of relevant experience in development, management and querying of relational databases preferred
• Demonstrated project leadership and self-directed work experience
• Demonstrated proficiency in MySQL database development and administration
• Ability to work with next-gen ORMs that abstract MySQL datasets (SQLAlchemy, GraphQL, Prisma, Apollo, etc.)
• Proficiency with knowledge Graphs and Graph Databases (e.g. Neo4j)
• Demonstrated proficiency in web application development support
• Proficiency with semantic Web technologies (e.g. SPARQL)
• Expertise in Python and/or R

Preferred Skills and Experience

• SQL Developer Certification
• Hands-on experience with Azure or AWS cloud computing platforms and database specialty certifications
• Knowledge of biological / omics or clinical data formats, eg VCF, FASTQ, BAM, SDTM, etc
• Expertise working with biological data (structural data, sequences, genomic data, etc.) and understand how auxiliary/reference data (e.g. reference genome sequences) are used in the analysis and interpretation of omics data
• Our preference is for candidates who have demonstrated proficiency working with large biological datasets. However, we will be happy to other consider candidates if they can demonstrate experience working with large datasets from multiple fields outside of biology
• Ability to contribute new ideas to solve difficult scientific problems on collaborative technical teams. May also participate in manuscript preparation at project’s conclusion
• Drive and enthusiasm to stay current with technological advances in the field, apply them to the Team’s workflows, and teach team members
• Experience working in HPC and parallel computing environments as well as familiarity using UNIX-like systems, shell scripting

Principal Bioinformatics Research Scientist

• Thirteen (13) years of relevant post-degree work experience is required
• Eleven (11) years of relevant post-degree work experience is required with a Master’s degree
• Eight (8) years of relevant post-degree work experience is required with a PhD

Senior Bioinformatics Research Scientist

• Ten (10) years of relevant post-degree work experience is required
• Eight (8) years of relevant post-degree work experience is required with a Master’s degree
• Five (5) years of relevant post-degree work experience is required with a PhD 

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