Bioinformatician Molecular Genetics

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Job description

Description:

To develop, optimize, and implement NGS pipelines for clinical diagnostic tests. These include proficiency in one or several commonly used computer languages in the bioinformatics field (such as python, Unix, R, C++). To facilitate writing algorithms as they needed, ability to design and create, or adapt and modify software that are suited to process and analyze the sequencing data, considering the current regulatory requirements as they pertain to an NGS pipeline validation and maintenance (i.e., version control) and various publicly available or vendor developed tools as they pertain to NGS data visualization and data processing.

Essential Responsibilities:

Provides general bioinformatics analysis support for NGS projects and mainly responsible for data analysis and software compilations including next generation sequence alignment, polymorphism identification, expression analysis, and visualization tools and browsers.Summarizes data analyses results in the form suitable as the basis for the first draft of written reports and makes preliminary interpretations of the data.Assists in development, testing, and maintenance of modular software pipelines for genome sequencing, assembly, annotation, metagenomic analysis, and genotyping using high-throughput sequencing platforms such as Illumina, Thermo-Fisher, and Pacific Biosciences.Manages data including loading and querying data from database systems, downloading data from public repositories, and transforming data to the necessary formats.Helps to identify, evaluate, and incorporate relevant algorithms and software pipelines by reviewing pertinent literatures in bioinformatics and computational biology.The primary focus will be on bioinformatics data analysis, software development and systems administration.Evaluation and selection of commercial or open-source software required in assisting the proteomics database analysis may be requiredProvides general bioinformatics analysis support and assist in development, testing and maintenance of software pipelines such as NGA or mass spectrometry data, network analysis, and visualization tools and browsers.Coordinating with fellow programmers, scientists and technicians for providing support programming for analysis of genomic and proteomic data sequencing in various therapeutic areas and providing quality control instructions in programmingDevelopment of scripts to move data from one analysis module to another, typically as part of the management of large data sets (loading, transformation, report generation, quality checks, etc.).Aiding in software training for the scientists and technicians, maintaining the in-house tools and databases and supporting the bioinformatics team with their on-going efforts.Ensures compliance/ regulatory and accreditation agencies' rules and regulations.Implements effective risk control process.Researches/resolves problems/issues.Oversees and coordinates startup, implementation and maintenance activities resulting from new bioinformatics services or transfer of services.Participates in department, inter-department, inter-facility and inter-regional projects which help the Regional Laboratory achieve its goal of providing quality service and client support in a cost effective manner.Other duties as necessary

Basic Qualifications:

Experience

* Minimum five (5) years of experience in laboratory data analysis required.
* Minimum three (3) years of experience in a clinical data analysis required.

Education

* MA/MS degree Bioinformatics or related field required.

License, Certification, Registration

* N/A

Additional Requirements:

* Experience with NGS pipelines in the clinical setting including in-depth knowledge of sequence alignment and variant filtering algorithms (including but not limited to samtools, verdict, pindel, Picard)
* Expertise in building data analysis/bioinformatics pipelines to support NGS data analysis
* Skillful in one (or more) commonly used computer languages such as Python, C++, Unix, and R.
* Experience with high performance and parallel computing
* Experience with various NGS platforms and sequencing technologies
* Familiarity with genomics concepts and experience in clinical data analysis (such as variant prioritization and annotation)
* Must be able to work in a Labor/Management Partnership environment.

Preferred Qualifications:

* Positive attributes include excellent organizational skills, a strong interest in learning, the ability to multi-task, and an ability to work independently.
* Familiarity with Microarray technology. (Direct experience with these technologies in a diagnostic setting a plus)
* Must be comfortable using a variety of databases such as Atlas of cancer disorders, ISCN database, the UCSC genome browser, COSMIC, etc., to aid in the interpretation of genomic variants
* Knowledge of federal, state, local, and accreditation agency regulations.
* Working knowledge of laboratory protocols relevant to sequence analysis
* Familiarity with current professional guidelines as they pertain to design, development, and maintenance of an NGS bioinformatics pipeline
* Extensive experience with the analysis of Next Generation Sequencing data and data handling of sequence files generated on the Illumina platform
* Expertise in NGS data quality assessment, visualization and NGS assay validation
* Strong interpersonal, and written/oral communication skills
* Ability to both work independently and as part of a multi-disciplinary team
* Excellent problem-solving skills
* Excellent troubleshooting skills
* Any Clinical Laboratory Licensure from State of California
* PhD in Genetics/Bioinformatics, Molecular Genetics/Bioinformatics, or a related field.

Notes:

* Weekend work optional

Primary Location: California,Los Angeles,Regional Service Center Scheduled Weekly Hours: 40 Shift: Day Workdays: Mon, Tue, Wed, Thu, Fri, Sat, Sun Working Hours Start: 08:00 AM Working Hours End: 05:00 PM Job Schedule: Full-time Job Type: Standard Employee Status: Regular Employee Group/Union Affiliation: NUE-SCAL-01|NUE|Non Union Employee Job Level: Individual Contributor Department: Regional Service Center - Molecular Oncology - 0806 Travel: No Kaiser Permanente is an equal opportunity employer committed to a diverse and inclusive workforce. Applicants will receive consideration for employment without regard to race, color, religion, sex (including pregnancy), age, sexual orientation, national origin, marital status, parental status, ancestry, disability, gender identity, veteran status, genetic information, other distinguishing characteristics of diversity and inclusion, or any other protected status.

External hires must pass a background check/drug screen. Qualified applicants with arrest and/or conviction records will be considered for employment in a manner consistent with federal and state laws, as well as applicable local ordinances, including but not limited to the San Francisco and Los Angeles Fair Chance Ordinances.

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