Bioinformatics Programmer 3

University of California San Francisco • San Francisco, CA

3d

About The Position

The Kidney Genetics, Genomics, and Advanced Models Laboratory at the UCSF Mission Bay campus is recruiting an individual with expertise in computational biology. The general responsibilities of this position are as follows: Independent analysis of single cell and bulk genomics data including from CRISPR screens, kidney organoid models, and primary cell models. Datasets generated and used by the laboratory include single cell and bulk RNA-seq, single cell and bulk ATAC-sequencing, ChiP-sequencing, and HiC. Analysis of biobank scale human genetics data to identify novel genotype-phenotype and gene-environment interactions. Figure generation and writing for publications and grant proposals Coordination and management of laboratory compute resources Candidates will be expected to work independently and in a collaborative multidisciplinary team. Opportunities for career development will be provided and encouraged. The candidate will report to Gabriel Loeb, MD, PhD, the Principal Investigator of the Kidney Genetics, Genomics, and Advanced Models Laboratory. The final salary and offer components are subject to additional approvals based on UC policy. Your placement within the salary range is dependent on a number of factors including your work experience and internal equity within this position classification at UCSF. For positions that are represented by a labor union, placement within the salary range will be guided by the rules in the collective bargaining agreement. The salary range for this position is $101,300 - $216,700(Annual Rate). To learn more about the benefits of working at UCSF, including total compensation, please visit: https://ucnet.universityofcalifornia.edu/compensation-and-benefits/index.html The Nephrology Division spans multiple campuses with faculty and staff located at the UCSF Health, San Francisco Veterans Affairs Medical Center, and Zuckerberg San Francisco General The Nephrology Division consists of faculty, fellows, and staff whose work is grounded in deep commitment to and respect for patients with kidney disease. The Nephrology Division has employed and trained leaders in academic nephrology, superb clinical research scientists and basic scientists, and outstanding clinical nephrologists. Our faculty are leading experts in adult nephrology: including acute kidney injury, chronic kidney disease, hypertension, electrolyte disorders, and kidney transplantation. Our mission continues in this tradition: expanding the frontiers of basic and clinical investigation in nephrology, training the next generation of academic nephrology leaders and providing the highest level of patient care. Our division within and the UCSF School of Medicine overall provides a premier academic environment for faculty and trainees to provide outstanding clinical care and to be at forefront of kidney research worldwide. The Kidney Genetics, Genomics, and Advanced Models Laboratory is located in the UCSF Cardiovascular Research Institute at UCSF’s Mission Bay Campus. The UCSF Cardiovascular Research Institute (CVRI) is at the forefront of discovery science, with innovative investigators in the fields of cell biology, genetics, genomics, structural biology, developmental biology, and translational science. The University of California, San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It is the only campus in the 10-campus UC system dedicated exclusively to the health sciences. We bring together the world’s leading experts in nearly every area of health. We are home to five Nobel laureates who have advanced the understanding of cancer, neurodegenerative diseases, aging and stem cells. UCSF is a diverse community made of people with many skills and talents. We seek candidates whose work experience or community service has prepared them to contribute to our commitment to professionalism, respect, integrity, diversity and excellence – also known as our PRIDE values. In addition to our PRIDE values, UCSF is committed to equity – both in how we deliver care as well as our workforce. We are committed to building a broadly diverse community, nurturing a culture that is welcoming and supportive, and engaging diverse ideas for the provision of culturally competent education, discovery, and patient care. Additional information about UCSF is available at diversity.ucsf.edu Join us to find a rewarding career contributing to improving healthcare worldwide.

Requirements

• Bachelor’s degree in Bioinformatics/ Systems Biology/ Math/ Statistics/ Computer / Computational / Data Science, or Domain Sciences with computer / computational / data specialization or equivalent experience / training.
• 3 or more years of directly relevant programming experience
• Proficiency in at least one programming language used for single-cell analysis (e.g., R or Python), including use of established single-cell analysis frameworks.
• Thorough knowledge of bioinformatics methods, applications programming, web development and data structures.
• Thorough knowledge of bioinformatics programming design, modification and implementation.
• Independently design and execute end-to-end single-cell analysis pipelines.
• Strong project management skills.
• Ability to generate publication-quality figures and clearly communicate analytical results in writing.
• Demonstrated ability to work independently and collaboratively within a multidisciplinary research team.
• Thorough knowledge of modern biology and applicable field of research.
• Communication skills to work with both technical and non-technical personnel in multiple fields of expertise and at various levels in the organization.
• Ability to communicate technical information in a clear and concise manner.
• Ability to interface with management on a regular basis.
• Self motivated, work independently or as part of a team, able to learn quickly, meet deadlines and demonstrate problem solving skills.
• Thorough knowledge of web, application and data security concepts and methods.

Nice To Haves

• PhD degree in Bioinformatics/ Systems Biology/ Math/ Statistics/ Computer / Computational / Data Science, or Domain Sciences with computer / computational / data specialization or equivalent experience.
• Strong preference for those with experience in advanced single cell sequencing and genomewide association data analyses.
• Substantial experience with single-cell data integration, batch correction, and multi-modal analysis.
• Experience analyzing perturbation-based single-cell datasets, including CRISPR or pooled screens.
• Experience working with organoid or disease-model single-cell datasets.
• Familiarity with scalable or high-performance computing environments for large single-cell datasets.
• Experience with bulk genomics and human genetics data

Responsibilities

• Independent analysis of single cell and bulk genomics data including from CRISPR screens, kidney organoid models, and primary cell models.
• Datasets generated and used by the laboratory include single cell and bulk RNA-seq, single cell and bulk ATAC-sequencing, ChiP-sequencing, and HiC.
• Analysis of biobank scale human genetics data to identify novel genotype-phenotype and gene-environment interactions.
• Figure generation and writing for publications and grant proposals
• Coordination and management of laboratory compute resources
• Work independently and in a collaborative multidisciplinary team.
• Make and defend methodological choices for normalization, integration, and statistical testing
• Partner closely with experimentalists to shape data generation and interpret biological findings.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level