Laboratory Research Associate - 135132

The Department of Pediatrics is one of the largest departments within the School of Medicine with approximately 171 Faculty, 60 post- doctoral fellows (both MDs and PhDs) along with over 300 support staff (not including hospital staff). In addition, the Department has 57 clinical residents and fellows distributed across the Divisions. The missions of research, education and patient care are intertwined, and are integral to the goals of the department.

The Department has undergone significant growth in recent years with a consolidated budget of approximately $106 million including sponsored projects expenditures of approximately $54 million and clinical revenue of over $ 52 million. This expansion of the Department's research and clinical portfolio is expected to continue in the next few years.

The Department's 18 divisions include Academic General Pediatrics, Child Development & Community Health; Allergy, Immunology and Rheumatology; Cardiology; Dermatology; Dysmorphology; Emergency Medicine; Endocrinology; Gastroenterology; Genetics; Genome Information Sciences; Hospital Medicine; Infectious Diseases; Neonatology; Nephrology; Pharmacology & Drug Discovery; Rehabilitation Medicine; and Respiratory Medicine.

In 2001, physicians and leadership of the University of California, San Diego (UCSD), Rady Children's, and Children's Specialists of San Diego (CSSD) unified pediatric patient care, research, education and community service programs, creating a university-affiliated children's health system to serve the region. Over the past two decades, an extensive list of joint programs has developed, with many physicians and researchers playing a role at both institutions.

This affiliation has consolidated the clinical, teaching, research and public service programs of the UCSD School of Medicine's Department of Pediatrics with San Diego's only health care system dedicated to the health and well-being of children. In 2009, this partnership was furthered by the creation of Rady Children's Specialists of San Diego, a Medical Foundation, and is now recognized as having global leaders in research, technology, translational medicine, education and clinical excellence.

Under general supervision, the incumbent will independently perform primary computational biology analysis for the laboratory, including sequencing analysis of single cell RNA sequencing experiments. Chromatin immunoprecipitation-sequencing experiments, bulk RNA-sequencing experiments, and assay of transposase accessibility sequencing experiments. Will perform these analyses using both the R and Python programming languages, and will have to be able to download and implement software packages from, but not limited to, BioConductor, BioStars, ScanPy, and Seurat. Contributes original and innovative ideas related to experiments and data interpretation. The incumbent will also be in charge of management of lab-related supercomputing cluster access and dataframe management and lab server file storage. Maintains and prepares accurate records of all experiments. Assist in the preparation of data for publication. Responsible for deposition of sequencing data into open access databases. Provides training, work direction and supervision in areas of computational expertise as needed to all students and postdoctoral fellows. Performs other duties as assigned including primary analysis for collaborations with other research groups requiring analysis of sequencing experiments.

• Theoretical knowledge of chemistry, biochemistry, genetics, immunology, microbiology, molecular biology or related field, as typically attained with an advanced degree, and/or an equivalent combination of education and experience.

• Must be highly proficient expertise in Unix, Linux, R, Python, Bash, and Command Line.

• Must have prior expertise with Seurat and ScanPy environments. Demonstrated experience performing single cell analysis with Seurat and ScanPy packages.

• Must be highly proficient in cluster and cloud computing as well as cloud storage with Amazon Web Services.

• Demonstrated strong experience and knowledge in coordinating computational analysis through cloud computing and cloud storage.

• Demonstrated expertise in single cell RNA-sequencing and single cell-Multiomic sequencing analysis.

• Demonstrated experience performing independent analysis of published and publicly available datasets.

• Demonstrated ability to follow verbal and/or written instructions, including follow-up on previously begun procedures. Demonstrated accurate record data and enter into appropriate medium.

• Demonstrated experience mentoring and overseeing undergraduates and postdoctoral fellows.

• Experience with computer software such as Excel and Prism to analyze data, store results and compute raw data.

• Strong communication skills (both verbal and written) needed to interact professionally and effectively in the work environment, as well as to effectively and accurately document research procedures. Demonstrated ability to read, comprehend and discuss research materials.

• Demonstrated experience managing UCSD Universal Scaled Storage cloud data storage.

• Demonstrated experience establishing and maintaining cluster computing on the UCSD research computing cluster.

• Demonstrated experience to adhere to established UCSD guidelines and policies.

• Employment is subject to a criminal background check.

• Occasional evenings and weekends may be required.