BIOINFORMATICS SPECIALIST (JUNIOR, ASSISTANT, ASSOCIATE, or FULL Rank) - ULLIAN LAB

About the role

The Department of Ophthalmology at the University of California, San Francisco (UCSF) is looking to hire a full-time Bioinformatics Specialist to focus on bioinformatics and data analysis for various research projects. The Specialist will work with Vision researchers to provide comprehensive bioinformatics support to users of the Department of Ophthalmology’s NIH-funded Vision Core Grant.

Responsibilities

• Provide expertise in the design, execution, data management, and analysis of a variety of genomics projects from start to finish including but not limited to, typical sequencing techniques, such as single-cell/bulk RNA-seq, ATAC-seq, spatial transcriptomics (MERFISH/Visium), proteomics, metabolomics, and other omics data across modalities.
• Develop bioinformatics tools used for whole genome sequencing, targeted sequencing, RNA sequencing, and single cell sequencing to analyze sequence data and provide bioinformatics and data science support to various research projects in understanding mammalian eye diseases.
• Design and implement state-of-the-art analysis pipelines using best software engineering practices, including benchmarking, quantitative assessment, adaptation, and parameter optimization of emerging bioinformatic pipelines and algorithms.

Requirements

• Specialist appointment at the Junior rank must possess Baccalaureate degree (or equivalent degree) or at least four years of research experience.
• Specialist appointed at the Assistant rank must possess a Master’s degree or a baccalaureate degree with 3 or more years of research experience.
• Specialists appointed at the Associate rank must possess a Master's degree (or equivalent degree) or five to ten years of experience in the relevant specialization.
• Specialists appointed at the full rank must possess a terminal degree (or equivalent degree) or ten or more years of experience in the relevant specialization.
• Specialists appointed at the full rank must possess postdoctoral level training in bioinformatics and a strong research background in vision neuroscience with a biological, theoretical and practical application of a body of highly specialized knowledge in the human, primate and non-human primate visual system.
• The candidate must have organizational and collaborative skills.
• Must be adaptable, reliable, and willing to learn.
• Excellent communication, organizational and time management skills are essential.

Qualifications

• Background knowledge of genomics, genetics, molecular biology, data science, and statistical modeling.
• Proficiency with R, Unix, Bash, Python. SLURM for on HPC. Version control such as Github.
• Single-cell omics analysis pipelines and tools such as Seurat, Signac, Monocle, Harmony, Liger, FastMNN, Limma, RNA-velocity, SCENIC(plus), Scanpy, GSVA, GO-PCA, Clustering Trees, Encode-ATAC-seq, NicheNet, CellPhoneDB, CellChat, Infercnv, Metascape etc.
• Knowledge with whole genome sequencing (WGS) and typical NGC analysis pipelines and tools such as Fastqc, samtools, bwa, bedtools, freebayes, GATK, SOILoCo, Lep-Map3, HAWK, AFLAP.
• Experience in statistical modeling for neural recordings, imaging and behavioral data.
• Experience with data science projects encountered in vision and ophthalmology research, such as large electronic health records, epidemiology datasets, neural recordings, imaging, and behavioral data.
• Ability to coordinate and mentor people with non-bioinformatics background.
• Ability to prioritize and multi-task is necessary.
• Experience and track record in leading the construction and comparison of single cell retinal atlas of marmoset, and/or other non-human primate, human, as well as probing postnatal development mechanisms of the fovea.

Benefits

Salary and Rank will be commensurate with the applicant’s experience and training. See Table 24B for the salary range for this position. A reasonable estimate for this position is $55,000 - $194,800.

Contact Information

Please direct any questions to Erik.Ullian@ucsf.edu.