SENIOR STAFF SCIENTIST
Sr. Staff Scientist – Algorithms will be part of a growing Clinical Genomics team of Bioinformaticians, Lab Scientist, Data Curation Scientists, Clinicians and Medical Fellows. Clinical Genomic Service (CGS) is a collaboration between Stanford Hospitals and Stanford School of Medicine to deliver best-in-class genomics service to Stanford community. CGS plans to use multi-omics (Whole Exome and Transcriptome) analysis approach to diagnosis. This position will be responsible for leading the algorithm development efforts within CGS. Evaluate current algorithms and develop a “best-practice” set of algorithms for use in a clinical diagnostics setting. Guide and mentor other junior members of the algorithm development team. Interface with the Curation team to identify gaps in variant detection and annotation and develop novel algorithms and methods to fill those gaps.
- Lead the algorithm development group and efforts with the goal of developing NGS algorithms that serve as NGS community standards.
- Develop novel algorithms for DNASeq and RNASeq for use in a diagnostics setting.
- Develop new and/or improve upon existing algorithms for genome assembly, variant detection (SNPs and InDels) and Structural Variant detection (CNVs, Inversions and Translocations) for clinical grade genomic analysis pipeline.
- Develop and maintain a knowledge database of variants and annotations discovered in processing of samples.
- Develop and maintain a database of public annotation sources such as ClinVar, Exome Variant Server, 1000 Genomes, TCGA and DGV.
- Develop efficient protocols and tools to upload WGS/WES data from internal servers to Cloud Storage (AWS S3/Google Cloud Storage).
- Establish new and leverage existing collaborations with research groups within Stanford and other pre-eminent research institutions.
- Maintain a high public profile within the Clinical and Translational Genomics community through publications and presentations in high impact journals and conferences.
- Help mentor other junior-level bioinformaticians in the group.
- Work closely with the data curators and genetic counselors to help improve the overall solve rate of cases.