Job ID: 43152
Job date: 2017-10-04
End Date:
Company : Stanford Health Care Country : Role : Research Scientist
Job date: 2017-10-04
End Date:
Company : Stanford Health Care Country : Role : Research Scientist
Job Description:
The Stanford Clinical Genomics Service is seeking a qualified individual for the role of "Senior Scientist-Algorithms" to join our growing team. This is an opportunity to improve patients' lives through diagnosis and treatment of genetic conditions, by working together with bioinformaticians, lab scientists, variant interpretation scientists, genetic counselors, clinicians and medical fellows. In this position you will be responsible for developing novel algorithms for DNASeq and RNASeq for use in a diagnostic setting. As part of the algorithm development team, you will critically evaluate existing bioinformatics tools and prototype new methods/tools. You will interface with the variant interpretation team to identify gaps in variant detection and annotation and develop novel algorithms and methods to fill those gaps. Specific responsibilities include:
The Stanford Clinical Genomics Service is seeking a qualified individual for the role of "Senior Scientist-Algorithms" to join our growing team. This is an opportunity to improve patients' lives through diagnosis and treatment of genetic conditions, by working together with bioinformaticians, lab scientists, variant interpretation scientists, genetic counselors, clinicians and medical fellows. In this position you will be responsible for developing novel algorithms for DNASeq and RNASeq for use in a diagnostic setting. As part of the algorithm development team, you will critically evaluate existing bioinformatics tools and prototype new methods/tools. You will interface with the variant interpretation team to identify gaps in variant detection and annotation and develop novel algorithms and methods to fill those gaps. Specific responsibilities include:
- Rapid prototyping of novel algorithms using R, Matlab, or other tools
- Develop best protocols for analysis of NGS data including optimization of parameters, and consensus approaches across various tools
- 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
- 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
- Participate in PrecisionFDA challenges along with the rest of the algorithms team
- Maintain a high profile in the NGS and Bioinformatics community through publications, conference presentations and collaborations
Qualifications
Any combination of education and experience that would likely provide the required knowledge, skills and abilities as well as possession of any required licenses or certifications is qualifying. Minimum Requirements:- 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 Illumina).
- 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.
- M.Sc. or higher Degree in Bioinformatics
- M.Sc. or higher Degree in Computer Science
- M.Sc. or higher Degree in Statistics
- Master's Degree in Engineering
- Bioinformatics
- DNA sequencing
- Lunix/Unix
- Machine Learning
- Next Generation Sequencing
- Programing in C
- Programing in C++
- Programing in Python
- Programing Skills
- Programming in Java
- Programming in Matlab
- Programming in PERL
- Programming in R
- RNA-seq
- SQL
- Statistics
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Additional Info:
All qualified applicants will receive consideration for employment without regard to race, sex, color, religion, national origin, protected veteran status or on the basis of disability.[Click Here to Access the Original Job Post]