BIOINFORMATICIAN II

Position Summary:

The primary role is to execute a variety of data management and analysis tasks, ensuring the quality, reproducibility, and efficiency of processes related to high-dimensional data. You will collaborate with study investigators and fellow bioinformatics professionals within the department to contribute to high-quality, reproducible research across various scientific disciplines and diseases.

The ideal candidate will have:   Proficiency in programming languages such as Bash, Python, R, C/C++, or other scripting languages in a Linux/Unix environment is required.  Experience working with large datasets or bioinformatics data is essential.  Proven experience in building and optimizing analysis pipelines for high-throughput next-generation sequence data analysis under Linux/Unix environment is a must.  Familiarity with HPC schedulers (LSF, Slurm, etc.) is necessary.  Competence in working with distributed storage systems (GPFS / Spectrum Scale, Spark, etc.) is required.  Proficiency in database development and SQL is essential.  Prior experience in independent data analyses and project management is preferred.

Duties and Responsibilities:

1. Data Analysis and Pipeline Development:  Develop, optimize, and maintain highly automated analytical pipelines, leveraging GPU technology for the analysis of high-throughput short and long reads next-generation sequence data (e.g., WGS, WES, WGBS, ChIP-Seq, ATAC-Seq, RNA-Seq, Hi-C, CUTRUN-Seq) in a Linux/Unix environment.  Manipulate common genomic file formats (e.g., FASTQ, SAM, BAM) for NGS experiments. Convert study data to and from common genetic file formats (e.g., PLINK, VCF).  Ensure modularity and flexibility in analytical pipelines, allowing the seamless addition or removal of tools as needed.  Establish and maintain reproducibility in pipelines, providing comprehensive documentation for users, including software installation and configuration instructions.  Perform quality control for genome-wide association studies (GWAS) or NGS studies.  Offer best practice recommendations and execute downstream integrative analyses.  Develop, evaluate, and recommend analytic tools and utilize high-performance computing clusters effectively.  Create and maintain local bioinformatics databases and integrate public databases.

2. Research Support and Collaboration:  Assist in the development of grant applications and contribute to the presentation of research results.  Engage in formal and informal training activities, journal clubs, and grant-writing meetings.  Support manuscript preparation and submission, benchmarking results, new pipelines, databases, and scientific discoveries where applicable.

3. Protocol Development and Knowledge Sharing:  Establish best practices and novel protocols for data analysis.  Share protocols and expertise through open documentation and hands-on training.

4. Funding Acquisition:  Assist in securing funding to support methods evaluation, development, and infrastructure.

5. Technical Expertise:  Identify and resolve technical issues, proposing software upgrades and evaluating new technologies for implementation.  Collaborate with high-performance computing staff as required.

6. Software Development and Informatics Projects:  Design, develop, and implement software workflows, pipelines, and tools. Participate in informatics projects, contributing to the evaluation, design, and construction of databases, web applications, and other services that meet investigator and departmental needs.

Perform other duties as assigned

Salary Range: $63,875 – $103,800

Bachelor's degree in Biological Sciences, Computer Science with interest in Biology/Genomics, or a related field required and four (4) years of related experience required. Work experience may NOT substitute for education requirement.