Bioinformatics Scientist I

The Work Unit: 

What You Will Do: 

The Bioinformatics Scientist within the public health laboratory performs analysis of next generation sequencing (NGS) data produced by the Genomic Surveillance Program. The position is expected to apply state-of-the-art computational methods developed within the unit or by other trusted sources to perform NGS data analysis. This includes but is not limited to pathogen identification, mapping drug- resistance determinants, variant analysis, genome assembly and annotation, and submission of NGS data to public repositories. The analysis may involve bactieral, viral, fungal, parasites and human NGS data. An intermediate level of coding experience, effective communication skills, basic knowledge of microbiology and bioinformatics are necessary requirements for this position. This position has been designated as a safety-sensitive position for purposes of impairment and employment screening policies due to its direct access to and handling of biohazardous materials for analysis. Mishandling biohazards and failure to closely follow standard operating procedures and regulatory requirements, could result in significant risk or threat of a dangerous incident involving exposure to biohazards or erroneous test results that adversely impact the health and safety of the employee, coworkers, or the public.
 

Data Analysis and Pipeline Construction

Performs bioinformatics data analysis on NGS data generated in the lab and submission of NGS data to public repositories. Responsible for the implementation and optimization of bioinformatics pipelines within our cloud-based analysis platform.
 
Data Quality Assessment
 Responsible for data quality assessment of all NGS data, both the raw data obtained from the NGS instrumentation and bioinformatics results derived from the data.

Residency Requirement: 

MINIMUM QUALIFICATIONS: 

Five (5) years of relevant experience in an occupation related to the work assigned to this position

A combination of related education and/or relevant experience in an occupation related to the work assigned equal to five (5) years

NOTE: An applicant may meet the minimum qualifications for this job in one of two ways: They may qualify through their work experience alone or through a combination of education and work experience.

**This experience must be substantiated within the Work Experience section of your application. "See Resume" will not be accepted. In addition, part-time work will be prorated.**

PREFERRED QUALIFICATIONS:

In addition to the minimum requirements, the successful candidate in this position will have the following highly desirable experience and competencies:  

• Demonstrated experience in high-throughput sequencing data analysis and pipeline development for viral, bacterial, and/or fungal pathogens.
• Basic knowledge of the Python and/or R programming languages and shell scripting.
• Demonstrated experience performing quality control of sequencing data for short read (e.g. Illumina) and/or long read (e.g. Oxford Nanopore or PacBio) technologies, including raw reads and downstream analysis results.
• Experience working in a Unix/Linux development environment.
• Experience with cloud computing environments (e.g. Google Cloud) and/or high-performance computing clusters.
• Demonstrated experience with bioinformatics applications such as Spade, Skesa, iVar, samtools, bwa, minimap2, bedtools, Prokka, Mash, Kraken, AMRFinderPlus.
• Demonstrated experience with submitting sequencing data to public repositories, such as GISAID and/or NCBI
• Ability to effectively communicate both orally and in writing with a wide range of customers
• Excellent critical thinking and problem-solving skills
• Excellent interpersonal and customer service skills
• Ability to interpret regulations and statutes
• Ability to interpret and analyze data
• Keen attention to detail
• Ability to self-motivate
• Ability to work well independently as well as in/with a team
• Ability to collaborate and achieve consensus across work units and programs

CONDITIONS OF EMPLOYMENT: 

• A pre-employment background check will be conducted as part of the selection process.

• Must be available in the event of an emergency, (e.g., bio-terrorist attack, chemical attack, disease outbreak or all hazards) and be required to report to work immediately at the regular or alternate location. During this time, travel restrictions may be in place.
• Must be available in the event of the activation of the Continuity of Operations Plan (COOP) and be required to report to work immediately at the regular or alternate location. During this time, travel restrictions may be in place.
• Location: Hybrid

• TRAVEL: Travel to conferences to present posters/paper

Appeal Rights: 

An applicant who has been removed from an employment list or removed from consideration during the selection process may request a review by the State Personnel Director.

As an applicant directly affected by the results of the selection or comparative analysis process, you may file a written appeal with the State Personnel Director.

Review of the completed, signed and submitted appeal will be timely on the basis of written material submitted by you, using the official appeal form signed by you or your representative. This form must be completed and delivered to the State Personnel Board by email at dpa_state.personnelboard@state.co.us within ten (10) calendar days from your receipt of notice or acknowledgment of the Department’s action.

For further information on the Board Rules, you can refer to 4 Colorado Code of Regulations (CCR) 801-1, State Personnel Board Rules and Personnel Director's Administrative Procedures, Chapter 8, Resolution of Appeals and Disputes, at spb.colorado.gov/board-rules.

E-Verify: 

CDPHE uses e-Verify, an Internet-based system, to confirm the eligibility of all newly hired employees to work in the United States. Learn more about E-Verify, including your rights and responsibilities.

ADAAA Accommodations:

The State of Colorado believes that equity, diversity, and inclusion drive our success, and we encourage candidates from all identities, backgrounds, and abilities to apply. The State of Colorado is an equal opportunity employer committed to building inclusive, innovative work environments with employees who reflect our communities and enthusiastically serve them. Therefore, in all aspects of the employment process, we provide employment opportunities to all qualified applicants without regard to race, color, religion, sex, disability, age, sexual orientation, gender identity or expression, pregnancy, medical condition related to pregnancy, creed, ancestry, national origin, marital status, genetic information, or military status (with preference given to military veterans), or any other protected status in accordance with applicable law. The Colorado Department of Public Health and Environment is committed to the full inclusion of all qualified individuals. As part of this commitment, our agency will assist individuals who have a disability with any reasonable accommodation requests related to employment, including completing the application process, interviewing, completing any pre-employment testing, participating in the employee selection process, and/or to perform essential job functions where the requested accommodation does not impose an undue hardship. If you have a disability and require reasonable accommodation to ensure you have a positive experience applying or interviewing for this position, please direct your inquiries to our ADAAA Coordinator at cdphe_benefits@state.co.us or call 303-692-2060, option 5.

For further information on the Board Rules, you can refer to 4 Colorado Code of Regulations (CCR) 801-1, State Personnel Board Rules and Personnel Director's Administrative Procedures, Chapter 8, Resolution of Appeals and Disputes, at spb.colorado.gov/board-rules.

A complete application packet must include:

• Completed State of Colorado application.

• If using education to qualify for this position a copy of your transcripts (unofficial acceptable) or diploma must be provided with application. Transcripts must be attached to your colorado.gov/jobs application.

• If you are a veteran, a copy of your DD214 must be attached to your colorado.gov/jobs application.

The Selection Process:

All applications that are received by the closing of this announcement will be reviewed against the Minimum Qualifications in this announcement. Candidates who meet the minimum qualifications proceed to the next step.

Colorado Revised Statutes require that state employees are hired and promoted based on merit and fitness through a comparative analysis process.

Part of, or all of, the comparative analysis for this position may be a structured application review, which involves a review of the information you submit in your application materials by Subject Matter Experts (SMEs) against the preferred qualifications.

A top group, up to six candidates, will be invited to schedule an interview with the hiring manager.

E-Verify: 

CDPHE uses e-Verify, an Internet-based system, to confirm the eligibility of all newly hired employees to work in the United States. Learn more about E-Verify, including your rights and responsibilities.

ADAAA Accommodations:

The State of Colorado believes that equity, diversity, and inclusion drive our success, and we encourage candidates from all identities, backgrounds, and abilities to apply. The State of Colorado is an equal opportunity employer committed to building inclusive, innovative work environments with employees who reflect our communities and enthusiastically serve them. Therefore, in all aspects of the employment process, we provide employment opportunities to all qualified applicants without regard to race, color, religion, sex, disability, age, sexual orientation, gender identity or expression, pregnancy, medical condition related to pregnancy, creed, ancestry, national origin, marital status, genetic information, or military status (with preference given to military veterans), or any other protected status in accordance with applicable law. The Colorado Department of Public Health and Environment is committed to the full inclusion of all qualified individuals. As part of this commitment, our agency will assist individuals who have a disability with any reasonable accommodation requests related to employment, including completing the application process, interviewing, completing any pre-employment testing, participating in the employee selection process, and/or to perform essential job functions where the requested accommodation does not impose an undue hardship. If you have a disability and require reasonable accommodation to ensure you have a positive experience applying or interviewing for this position, please direct your inquiries to our ADAAA Coordinator at cdphe_benefits@state.co.us or call 303-692-2060, option 5.