Senior Staff Scientist

Stanford Health Care
Job Location
Palo Alto, CA 94111
Job Description


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.

Minimum Requirements

Education: Graduate Degree (Ph.D, M.S with considerable experience will be considered) in Computer Science/Engineering, Bioinformatics, Mathematics, Statistics and other related fields.

Experience: Six (6) years of experience with increasing responsibilities, developing algorithms for next generation sequencing (preferably in a Clinical setting).

Knowledge, Skills, and Abilities

  • Knowledge of algorithmic techniques common to bioinformatics (e.g., dynamic programming and graph algorithms), machine learning and statistical analysis methods (e.g., Bayesian inference, Hidden Markov Models, Principal Component Analysis).

  • Experience in developing one or more of the algorithms used in NGS analysis - Sequence alignment, Variant Calling (SNVs), Local-Assembly (De-bruijn graph), and Fusion Detection etc.

  • Extensive experience handing error modes in NGS data (preferably Illumina) within STR, long homo-polymers, high GC and other troublesome regions of the human genome.

  • Experience in bioinformatics resources such as BLAST, BWA, GATK, dbGaP, Clustalw, NCBI, EBI, Pfam, COG, GO, KEGG, etc.

  • Experience in Biomarkers/Genomic markers discovery is a big plus.

  • Proficiency in either C/C++ or Java and Linux.

  • Familiarity with Perl, Python and R.

  • Strong analytical abilities and communication skills.

About Our Organization

Healing humanity through science and compassion, one patient at a time.

At Stanford Health Care, we seek to provide patients with the very best in diagnosis and treatment, with outstanding quality, compassion and coordination. With an unmatched track record of scientific discovery, technological innovation and translational medicine, Stanford Medicine physicians are pioneering leading edge therapies today that will change the way health care is delivered tomorrow.

As part of our spirit of discovery, we also leverage our deep relationships with luminary Silicon Valley companies to develop new ways to deliver preeminent patient care. 

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