The Ye lab at Department of Medicine, Rheumatology, Institute for Human Genetics, CoLabs and the Baker ImmunoX at UCSF is seeking a highly motived computational biologist (bioinformatics specialist) with backgrounds in computational biology, computer science or other related areas. The individual will have a unique opportunity to work with the Ye lab and two recently established initiatives at UCSF: CoLabs and ImmunoX to lead the development of analysis pipelines for population scale single-cell genomics projects. The incumbent will work closely with an interdisciplinary team of computational biologists, geneticists, and computer scientists to characterize the natural variability in immune response and map the genetic and environmental drivers of that diversity.
The specialist will be responsible for developing data analysis pipelines, implementing state-of-the-art computational methods, and bringing together diverse multiparameter high-throughput genomic datasets to enable deep data integration and knowledge discovery including (but not limited to) single-cell transcriptomics (scRNA-seq and single nuclei RNA-seq), immune repertoire sequencing (TCR), proteomics (scCITE-seq) and epigenomics (scATAC-seq). The qualified applicant should be comfortable with the analyses of 104 – 106 cells and have expertise in integrating multimodal data to arrive at biological insights.
Required qualifications: • Specialists appointed at the Junior rank must possess a baccalaureate degree (or equivalent degree) in bioinformatics, biostatics, computational biology, computer science or related discipline or at least 4 years of research experience. • Specialists appointed at the Assistant rank must possess a master’s degree (or equivalent degree) in bioinformatics, biostatics, computational biology, computer science or related discipline or at least 5 years of experience in the relevant specialization. • Specialists appointed at the Associate rank must possess a master’s degree (or equivalent degree) in bioinformatics, biostatics, computational biology, computer science or related discipline or at least 5-10 years of experience in the relevant specialization. • Specialists appointed at the Full rank must possess a terminal degree (or equivalent degree) in bioinformatics, biostatics, computational biology, computer science or related discipline or at least 10 or more years of experience in the relevant specialization. • Minimum two years of experience in bioinformatics/programming. • Proficiency in C/C++, PERL, Python, R. • Experience with NGS analysis pipelines (e.g. alignment, variant calling and genome annotation) • Experience analyzing large-scale single-cell datasets (i.e. scRNA-seq, scATAC-seq or CITE-seq) • Strong knowledge of statistical methods including Cox models, logistic regression, linear regression, and elastic net regression. • Strong knowledge of parametric and non-parametric statistics. • Strong background in computational methods development and application. • Experience working in the cloud or on local compute clusters. • Experience with code, data and analysis management including github and jupyter. • Knowledge of genomics and immunology is a plus. • Strong verbal and written communication skills. • Able to work independently and collaboratively as a member of an interdisciplinary team. • Ability to multitasking and tracking projects.
Preferred qualifications: • Experience managing other large and complex datasets. • Experience with machine learning techniques, such as random forest models, support vector machines and deep learning. • Familiarity with clinical study design. • Proficiency in a high performance computing language such as C++, Julia and C. • Experience with collaborative projects with biologists and domain experts.
UC San Francisco seeks candidates whose experience, teaching, research, or community service has prepared them to contribute to our commitment to diversity and excellence.
The University of California is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age or protected veteran status.
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 high-quality patient care. It is the only UC campus in the 10-campus system dedicated exclusively to the health sciences.