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Bioinformatician

Job Description


MED-CORE-RHEU

Full Time

68632BR


Job Summary

The Ye lab at the Department of Medicine, Rheumatology Institute for Human Genetics at UCSF seeks a highly motivated computational biologist with a background in computational biology, computer science, or other related areas. The individual will have a unique opportunity to lead the development of cloud-based analysis pipelines in the AWS environment 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.
Under the supervision of the principal investigator, the qualified candidate will be responsible for developing data analysis pipelines, maintaining and implementing computational methods to the AWS platform, 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 and BCR), proteomics (scCITE-seq), epigenomics (scATAC-seq), and spatial sequencing. 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:

  • Bachelor/Master’s degree in bioinformatics, biostatics, computational biology, computer science, or related discipline.
  • Minimum one year 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)
  • Experience working on AWS including data storage on S3 and compute on EC2
  • 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.
  • Strong verbal and written communication skills.
  • Able to work independently and collaboratively as a member of an interdisciplinary team.
  • Ability to multitask and track projects.
Preferred qualifications:
  • Knowledge of genomics and immunology is a plus.
  • 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 high-performance computing language such as C++, Julia, and C.
  • Experience with collaborative projects with biologists and domain experts.

Department Description

The Division of Rheumatology is a part of the Department of Medicine (DOM) at UCSF. The mission of the Rheumatology Division includes research, teaching and patient care. The Division has activities at multiple sites including Parnassus, Laurel Heights and Mission Bay. The Division runs several clinical practices, conducts basic and clinical research, and educates medical students, residents, clinical fellows and postdoctoral scholars. In addition, the Division has significant and complex financial and administrative relationships with DOM and the UCSF Medical Center, as well as large patient care programs, large clinical, federal, and privately supported research programs and seven faculty laboratories. The Rheumatology Division has 17 full-time faculty, nine clinical fellows, seven post-doctoral research fellows, seven WOS faculty, and 23 research and administrative staff. The Division has a sponsored research portfolio of $10+ million per year including over 40 sponsored awards, as well at the Russell Engleman Rheumatology Research Center which has an endowment principal of $30 million and generates income of $1.3 million per year in support of its clinical, research, training, and service missions. The PREMIER Center is a P30 resource-based core center funded by NIH / NIAMS. Its mission is to promote research in precision medicine across the UCSF campus through the provision of specific services, consultations, educational activities, and pilot funding.


Required Qualifications

  • Bachelor's degree in bioinformatics, biostatistics, computational biology, computer science, or related discipline with 2+ years of experience or an equivalent combination of education and experience. 
  • 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)    
  • Proficiency in C/C++, PERL, Python, R    
  • Strong background in computational methods development and application    
  • Experience with working in the cloud or on local compute clusters, experience with code, data, and analysis management including Github and Jupyter    
  • Strong verbal and written communication skills    
  • Able to work independently and collaboratively as a member of an interdisciplinary team  
  • Ability to multitask and track projects

Preferred Qualifications

  • Knowledge of genomics and immunology
  • 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 high-performance computing language such as C++, Julia, and C.    
  • Experience with collaborative projects with biologists and domain experts.    
  • Master’s degree in bioinformatics, biostatistics, computational biology, computer science or related discipline

About UCSF

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.


Pride Values

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.


Equal Employment Opportunity

The University of California San Francisco 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, age, protected veteran or disabled status, or genetic information.


Job Code and Payroll Title

009402 BIOINFORMATICS PROGR 2


Job Category

Research and Scientific


Bargaining Unit

99 - Policy-Covered (No Bargaining Unit)


Location

Parnassus Heights (SF)


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