Senior Scientist - Stanford Clinical Genomics Service

Stanford Health Care
Job Location
Palo Alto, CA
Job Description

Stanford Clinical Genomics Service (SCGS) is a joint effort between Stanford Health Care (Stanford Hospital & Lucile Packard Children’s Hospital) and Stanford School of Medicine to provide best-in-class clinical genomics sequencing service for patients with unexplained heritable diseases and inherited cancer predisposition. As a member of SCGS, you will be joining a large team of Clinical Lab Scientists, BioInformaticians, Clinical Data Scientists, Curators, Genetic Counselors and Physicians working together to help provide genomics driven Precision/Personalized Medicine to patients. SCGS provides a unique opportunity to do both Clinical Genomics and research in Translational Genomics through collaborations with research labs within Stanford School of Medicine.  SCGS is fully funded and is not dependent on Grants for its operations. We offer competitive salaries (even by Bay Area industry standards), generous benefits and a collaborative work culture with mutual respect.

Sr. Scientist – Algorithms will be responsible for evaluating current algorithms used in NGS analysis workflows and determine their suitability for use in a clinical 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.

Essential Functions
Evaluate third-party NGS algorithms and tools for suitability of use in a Clinical setting.

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 help improve the overall solve rate of cases.

Keep up to date with latest developments in applications of NGS in clinical diagnostics.

Maintain a high profile in the NGS and Bioinformatics community through publications, conference presentations and collaborations.



Graduate Degree (Ph.D/M.S) in a work-related field/discipline from an accredited college or university.


Ph.D plus Two (2) or M.S plus Six (6) years of experience developing algorithms for next generation sequencing. 

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, Django/Ruby, Perl/Python, R, and Hadoop. Proficient in Unix/Linux.

Strong analytical abilities and communication skills.




How to Apply,

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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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