Clinical Genomics Pipeline Engineer

UCSF Health, AG; Oakland (CA); Sur place; USD 120 000 - 180 000; Plein temps

Résumé du poste

University of California, San Francisco (UCSF) seeks a Bioinformatics Programmer to join the bioinformatics team supporting CCGL, GML, and IHG Core. The role designs and maintains genomic analysis pipelines for UCSF500 and related RNAseq workflows, interfacing with pathology, lab staff, researchers, and clinical systems.

The position emphasizes development of new classifiers, AI tools, sample analysis automation, and data integration across platforms, with on-call duties and collaboration with

Qualifications

• In-depth knowledge of bioinformatics methods and data structures.
• In-depth knowledge of bioinformatics programming design, modification and implementation.
• In-depth knowledge of genetics, genomics, and cancer biology.
• Advanced interpersonal skills to work with technical and non-technical staff.
• Ability to communicate technical information clearly.
• Minimum 5 years of experience with Illumina sequencing data, variant calling, annotation and filtering.
• Proficiency with Python, R, Unix/Linux OS and shell scripting.
• Strong knowledge of statistics and large genomics datasets.
• Minimum 3 years of experience with clinical pipelines, procedures, implementation, and documentation.
• Strong experience with APIs.
• Advanced skills in data migration and data conversion.

Responsabilités

• Design and develop new components and pipelines for clinical testing.
• Support tumor methylation and whole transcriptome classifiers and AI tools.
• Automate sample analysis and error reporting.
• Collaborate with pathologists, staff, researchers, and clinical systems teams.
• Maintain and improve QC and clinical annotation pipelines.
• Interface with data repositories and research consortia.
• Build infrastructure to route data to/from multiple platforms.
• Perform ad hoc analyses for special cases outside standard pipelines.

Connaissances

Python

R

Unix/Linux

Shell scripting

Illumina sequencing data

Variant calling

Data analysis

APIs

Statistics

Communication

Formation

Bachelor's degree in biological science / computational field

Master's degree with 4+ years of bioinformatics experience

PhD in Bioinformatics or related field

Outils

AWS Batch

Relational databases

Description du poste

University of California, San Francisco (UCSF) seeks a Bioinformatics Programmer to join the bioinformatics team supporting CCGL, GML, and IHG Core. The role designs and maintains genomic analysis pipelines for UCSF500 and related RNAseq workflows, interfacing with pathology, lab staff, researchers, and clinical systems.

The position emphasizes development of new classifiers, AI tools, sample analysis automation, and data integration across platforms, with on-call duties and collaboration with