Research Data Analyst I- Hybrid - 136928

The UC San Diego Department of Neurological Surgery is among the leading neurosurgical centers in the country. The Department offers challenging career opportunities in the diverse areas of state-of-the-art clinical services, advanced educational programs, and cutting-edge research. The Department is committed to offering a dynamic learning environment and growing opportunities to its talented and dedicated employees.

The research work in the Beaumont lab investigate brain tumor epigenomics with a specific focus on chromatin remodeling complexes, tumor dependencies and precision oncology. We utilize new high-throughput epigenomic sequencing techniques and computational biology methods to achieve a deeper understanding of the chromatin landscape in human tumor tissues and tumor-derived cancer stem cells. Leveraging multimodal data from 3D chromatin conformation, DNA methylation and epigenomics studies, the lab performs in vitro tumorigenesis and clonogenic studies using human tumor stem cell lines, and directly assess the role of critical candidate regulators by genome editing using CRISPR gene editing. By harnessing computational tools, these studies promise significant advances in the development of precision therapeutics in neuro-oncology, and importantly, improvement in patient outcomes. Similarly, the primary focus of The Furnari lab is to study fundamental pathways that drive initiation and progression of glioblastoma, as well as the multiple malignant phenotypes of this aggressive brain cancer. Studies in the lab range from classical tumor biology, biochemistry, cell biology, signal transduction and bioinformatic analyses, to orthotopic glioma models and preclinical investigations.

Under supervision of the Principal Investigators, the Research Data Analyst 1 will assist with the development and implementation of computational pipelines for epigenomic data analysis in cancer research. The work associated with this position will be part of the dynamic research environments of the Beaumont/Kfoury-Beaumont (MCC) and Furnari (SSCI) labs, which focus on the etiology and treatment of adult and pediatric brain cancers. Key responsibilities include assisting with computational support for biologists and clinicians in multidisciplinary translational cancer research projects, developing bioinformatics tools and computational methodologies for the analysis of multimodal epigenomic data, and assisting with the preparation of data and results for publication or dissemination as part of databases, web sites, electronic notebooks and other resources. Assist with analysis of next generation sequence data (bulk RNAseq, scRNAseq, ChIPseq, ATACseq) using applications such as Python and R, together with local supercomputer facilities. Involve in the management and archiving of large scale datasets, creating figures for publications, depositing of data to public servers (GEO), and creating graphical user interfaces (GUI) for data analysis. Collaborate with spatial computing experts to create architectural epigenomic maps in human brain reference space. Perform other duties as assigned.

CT: Entry-level professional with limited prior experience; learns to use professional concepts to resolve problems of limited scope and complexity; works on assignments that are initially routine in nature, requiring limited judgment and decision making. Employees at this level are expected to acquire the skills and knowledge to perform more advanced work following an agreed upon time in position, through defined training and development planning.

• Five years (5) of related experience, education/training, OR a Bachelor's degree in Bioinformatics, Physics, Engineering, Math, Computer Science, Quantitative Biology or related area plus one (1) year of related experience/training

• Programming experience including Python through undergraduate courses or equivalent experience.

• Practical experience with scientific and statistical computing environments such as R, Python, and Jupyter.

• Practical experience with programming languages including Python and R.

• Knowledge of bioinformatics methods, applied mathematics, computer science and statistics. Knowledge of computational biology approaches and tools.

• Acquiring knowledge of research function. Acquiring ability to perform research analysis duties.

• Acquiring statistical analysis, systems programming, and database design skills to perform research analysis duties.

• Ability to effectively manage time and see assigned parts of projects through to completion on deadline.

• Basic consultation and communication skills.

• Knowledge of operating systems such as MS Windows, MAC, UNIX and Linux, with a willingness and ability to update and increase computer skills and knowledge as needed.

• Ability to design, develop and test algorithms.

• Demonstrated excellent organizational skills including ability to keep clear and accurate records, document computer programs and analysis methodologies, organize a varied workload, meet deadlines, follow written and oral protocols and give oral presentations on the progress of research.

• Demonstrated successful, positive interpersonal communication skills needed to interact well with others to facilitate communication about project requirements, including the ability to discuss and understand day-to-day analysis team's affairs, research plans, results and ideas with PI and other team members and collaborators in a constructive, professional and pleasant manner.

• Excellent skill and ability to conduct web/online resource and literature searches.

• Master's degree in Bioinformatics or equivalent preferred, with prior experience in genomic and epigenetics analysis.

• Experience in genomic sequence processing and alignment.

• Oncology experience.

• Must be able to work various hours and locations based on business needs.

• Employment is subject to a criminal background check.