Senior Scientist

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

Senior Scientist

Sr. 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 is responsible for developing novel algorithms for DNASeq and RNASeq for use in a diagnostics setting.  This position, as part of the algorithm development team will help with benchmarking of bioinformatics tools and with rapid prototyping of new methods/tools. This position will interface with the Curation team to identify gaps in variant detection and annotation and develop novel algorithms and methods to fill those gaps.


  • Benchmark community NGS algorithms and tools against NIST/GiaB truth sets.
  • Develop an extensive regression suite consisting of reference genomes (GA4GH/NIST) against which the various algorithms will be benchmarked.
  • Help with rapid prototyping of novel algorithms using R, Matlab.
  • Develop best protocols for analysis of NGS data including optimization of parameters, and consensus approaches across various tools.
  • Work closely with the data curators and genetic counselors to identify gaps in variant detection and annotation algorithms in current pipeline and suggest novel approaches to improve diagnosis.
  • Keep up to date with latest developments in applications of NGS in clinical diagnostics.
  • Help algorithms team participate in PrecisionFDA challenges.
  • Maintain a high profile in the NGS and Bioinformatics community through publications, conference presentations and collaborations.

Education: Graduate Degree (Ph.D/M.S) in a Computer Science/Engineering, Bioinformatics, Mathematics, Statistics or other related fields is preferred.

Experience: Ph.D plus 2 years of experience (fresh graduates with research directly related to NGS algorithms will be considered) or M.S plus four (4) years of experience developing algorithms for NGS platforms (preferably for Illumnia).

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 with developing vectorized code and multi-threading is desired.

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

  • Demonstrated ability in data analysis and understanding of NGS data.

  • Experience using public annotation sources such as ClinVar, Exome Variant Server, 1000 Genomes, TCGA and DGV.

  • Knowledge of one or more of C/C++/Java, SQL, Perl/Python and R. Proficient in Unix/Linux.

  • Experience deploying bioinformatics pipelines in Cloud Platforms such as AWS or Google Cloud is desirable.

  • 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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