Senior Staff 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. Staff Scientist – Algorithms will be responsible for leading the algorithm development efforts within SCGS. This position will be responsible for evaluating current algorithms and develop a "best-practice" set of algorithms for use in a clinical diagnostics setting.  This position will be responsible for guiding and mentoring other junior members of the algorithm development team. 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

Lead the algorithm development group and efforts with the goal of developing NGS algorithms that serve as NGS community standards.

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 algorithms for novel fusion detection.

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.

Perform other related duties as assigned.





Graduate Degree (Ph.D, M.S with considerable experience will be considered) in a work-related field/discipline from an accredited college or university.


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-Brn 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.




How to Apply,

and reference job number 35415 in "Keywords" field

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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