| f | Job Description: | f | Job Description: |
| t | The University of California, San Francisco is seeking a Bioinformatics Programmer to join the bioin | t | The University of California, San Francisco is seeking a Bioinformatics Programmer to join the bioin |
| formatics team supporting the Clinical Cancer Genomics Laboratory (CCGL). Involves developing and ut | | formatics team supporting the Clinical Cancer Genomics Laboratory (CCGL), the Genomic Medicine Labor |
| ilizing computational tools and systems to analyze and interpret biological or other research data. | | atory (GML), and the Institute for Human Genetics Sequencing Core (IHG Core). Responsibilities for C |
| Utilizes and develops algorithms, computational techniques, and statistical methodologies. Helps in | | CGL: In this role, this individual will be part of a bioinformatics team responsible for design, con |
| the design of new experiments. Implements end-user needs in database searching and integration. Main | | struction, and maintenance of a genomic analysis pipeline supporting the UCSF500 Cancer Gene Panel a |
| tains the computational infrastructure and tracks the flow of samples and information for large-scal | | ssay, a molecular test profiling DNA from tumor and normal tissue to identify mutations that may dri |
| e studies. Provides web-based bioinformatics and access to public and proprietary databases. | | ve a patient’s cancer and aid in diagnosis and treatment, and a related RNAseq pipeline to identify |
| | | gene fusions. Our internally developed cloud-based genomic analysis pipelines detect single nucleoti |
| | | de variants, small and medium indels, structural rearrangements, copy number variants, and microsate |
| | | llite instability, and communicate with sequencing core services, laboratory information management |
| | | systems and clinical reporting software. Under the general direction of the Associate Director of Bi |
| | | oinformatics for the Clinical Cancer Genomics Laboratory, the Bioinformatics Programmer will design |
| | | and develop new components and pipelines to support new and enhanced clinical testing. New features |
| | | slated for development include tumor methylation- and whole transcriptome-based classifiers and AI |
| | | tools to assist in clinical signout. Other new software developed will provide support for automatin |
| | | g aspects of sample analysis and error reporting and integration with other clinical systems. Additi |
| | | onal responsibilities will include supporting the development of new target capture panels and test |
| | | validation as well as quarterly data analysis to improve QC and support clinical annotation. In this |
| | | role, the Bioinformatics Programmer will interface with molecular pathologists, laboratory and admi |
| | | nistrative staff, medical researchers, technical teams for related clinical systems and data reposit |
| | | ories, and research consortia. Responsibilities for GML: The individual will be part of the bioinfor |
| | | matics team responsible for building and maintaining pipelines to support genomic analysis for the c |
| | | linical tests performed by GML including: Rapid Whole Genome Sequencing, Exome Sequencing, Hereditar |
| | | y Cancer Panel, and exome subpanels. New features slated for development include long-read sequencin |
| | | g platforms to complement existing short-read whole genome sequencing. The individual will build inf |
| | | rastructure to route data to, from, and between numerous 3rd party platforms, kick off appropriate a |
| | | nalyses, and manage data storage. New pipelines will also be built to support auto verification of n |
| | | egative cases, QC analyses, and retrospective studies. The individual will also perform ad hoc analy |
| | | ses and processing of clinical data to support lab initiatives and special cases that must be handle |
| | | d outside of the standard pipelines. Responsibilities for IHG Core: The individual will work as part |
| | | of the bioinformatics team responsible for building and maintaining an end-to-end automated pipelin |
| | | e to transport raw sequencing data from sequencing machines to UCSF Amazon Web Services Secure Enter |
| | | prise Cloud, convert raw sequencing data to sequencing reads, route clinical data to downstream syst |
| | | ems, perform individual analyses for custom research projects, return data to customers, and manage |
| | | data storage. Other responsibilities: The individual will be required to be on call nights and weeke |
| | | nds for a minimum of 13 weeks of the year, to quickly react to any situations that may arise to ensu |
| | | re prompt data transfer and processing for CCGL, GML, and the IHG Core. Maintenance of pipelines, ap |
| | | plications, and servers must often be performed outside of standard business hours to minimize disru |
| | | ptions to the labs. |
| | | |
| Qualifications: | | Qualifications: |
| Required Qualifications: - In-depth knowledge of bioinformatics methods and data structures - In-dep | | Required Qualifications: - In-depth knowledge of bioinformatics methods and data structures - In-dep |
| th knowledge of bioinformatics programming design, modification and implementation - In-depth knowle | | th knowledge of bioinformatics programming design, modification and implementation - In-depth knowle |
| dge of genetics, genomics, and cancer biology - Advanced interpersonal skills in order to work with | | dge of genetics, genomics, and cancer biology - Advanced interpersonal skills in order to work with |
| both technical and non-technical personnel at all levels in the organization, including senior proje | | both technical and non-technical personnel at all levels in the organization, including senior proje |
| ct leadership - Ability to communicate technical information in a clear and concise manner - Minimum | | ct leadership - Ability to communicate technical information in a clear and concise manner - Minimum |
| 5 years of experience with Illumina sequencing data, genetic variant calling, variant analysis, ann | | 5 years of experience with Illumina sequencing data, genetic variant calling, variant analysis, ann |
| otation and filtering - Proficiency with Python, R, Unix/Linux OS and shell scripting, and associate | | otation and filtering - Proficiency with Python, R, Unix/Linux OS and shell scripting, and associate |
| d libraries - Strong knowledge of statistics and experience working with large genomics datasets - M | | d libraries - Strong knowledge of statistics and experience working with large genomics datasets - M |
| inimum 3 years of experience with clinical pipelines, procedures, implementation, and documentation | | inimum 3 years of experience with clinical pipelines, procedures, implementation, and documentation |
| - Strong experience with APIs - Advanced skills in data migration and data conversion Preferred Qual | | - Strong experience with APIs - Advanced skills in data migration and data conversion Preferred Qual |
| ifications: - Advanced understanding of relational databases, web interfaces and operating systems. | | ifications: - Advanced understanding of relational databases, web interfaces and operating systems. |
| - Advanced project management skills - Advanced ability to interface with management on a regular ba | | - Advanced project management skills - Advanced ability to interface with management on a regular ba |
| sis - Ability to lead a team, meet deadlines and demonstrate advanced problem solving skills - In-de | | sis - Ability to lead a team, meet deadlines and demonstrate advanced problem solving skills - In-de |
| pth knowledge of web, application and data security concepts and methods - In-depth knowledge of web | | pth knowledge of web, application and data security concepts and methods - In-depth knowledge of web |
| , application and data security concepts and methods - Working knowledge of Amazon Web Services, inc | | , application and data security concepts and methods - Working knowledge of Amazon Web Services, inc |
| luding AWS Batch - Experience developing, evaluating, or deploying machine learning models for genom | | luding AWS Batch - Experience developing, evaluating, or deploying machine learning models for genom |
| ics, biomedical, or healthcare applications - Ability to critically evaluate emerging AI technologie | | ics, biomedical, or healthcare applications - Ability to critically evaluate emerging AI technologie |
| s and identify opportunities for implementation in clinical genomics workflows - Familiarity with la | | s and identify opportunities for implementation in clinical genomics workflows - Familiarity with la |
| rge language models (LLMs), retrieval-augmented generation (RAG), prompt engineering, and generative | | rge language models (LLMs), retrieval-augmented generation (RAG), prompt engineering, and generative |
| AI applications in healthcare or life sciences Education, Licenses/Certifications: - Bachelor's deg | | AI applications in healthcare or life sciences Education, Licenses/Certifications: - Bachelor's deg |
| ree in biological science, computational / programming, or related area and / or equivalent experien | | ree in biological science, computational / programming, or related area and / or equivalent experien |
| ce/training - Required - Master's Degree and 4 yrs relevant experience in bioinformatics - Required | | ce/training - Required - Master's Degree and 4 yrs relevant experience in bioinformatics - Required |
| - PhD in Bioinformatics or related field - Preferred | | - PhD in Bioinformatics or related field - Preferred |