Bioinformatics Scientist I
Salary: $69,024.00 - $75,926.40 Annually
Location : Denver Metro, CO
Job Type: Full Time
Job Number: FAA00523-04/28/26
Department: Department of Public Health & Environment
Division: Division of Disease Control and Public Health Response
Opening Date: 05/06/2026
Closing Date: 5/14/2026 11:59 PM Mountain
FLSA: Determined by Position
Type of Announcement: This position is open only to Colorado state residents.
Primary Physical Work Address: 8100 E Lowry Blvd., Denver, CO 80230
Department Contact Information: [click to reveal email address]
Salary Note: Although the full salary range for this position is provided, appointments are typically made at or near the range minimum.
How To Apply: Please submit an online application for this position at [click to reveal website link]. Reach out to the Department Contact to apply using a paper application, including any supplemental questions. Failure to submit a complete and timely application may result in the rejection of your application. Applicants are responsible for ensuring that application materials are received by the appropriate Human Resources office before the closing date and time listed.
Department Information
ABOUT US:
At The Colorado Department of Public Health and Environment (CDPHE) we are dedicated to the Colorado for All philosophy - working toward a Colorado where everyone has the opportunity to succeed.
We support the basic human rights of our neighbors regardless of gender, race, ethnicity, religion, national origin, age, sexual orientation, gender identity, citizenship status, education level, disability, socio-economic status, or any other visible or invisible identity. We are committed to increasing the diversity of our staff and providing culturally responsive programs and services. Therefore, we strongly encourage individuals from diverse backgrounds to apply.
IMPORTANT INFORMATION:
- TERM LIMIT: THIS POSITION IS TERM LIMITED AND FUNDING CANNOT BE GUARANTEED BEYOND 06/30/2027. THE INCUMBENT IN THIS POSITION MUST BE WILLING AND ABLE TO RESIGN ON THIS DATE OR WHEN FUNDS RUN OUT, WHICHEVER COMES FIRST.
Be BOLD.....Make a REAL difference . . . join us in serving our communities advancing Colorado's health and protecting the places we live, work, learn, and play, to create a healthy and sustainable Colorado where current and future generations thrive.
Mission - To advance Colorado's health and protect the places we live, work, learn, and play.
Vision - To create a healthy and sustainable Colorado where current and future generations thrive.
CDPHE offers:
- Free parking and access to RTD bus lines.
- Flexible working arrangements
- Retirement ( PERA options), Medical and dental health plans
- Defined Benefit Plan or the PERA Defined Contribution Plan, plus optional 401K and 457 plans
- Paid life insurance
- Short- and long-term disability coverage
- 11 paid holidays per year and generous personal time off
- Tuition assistance
- Wellness programs
- Professional development opportunities on a wide variety of subjects
- Career advancement opportunities throughout the State system
Some positions may qualify for the Public Service Loan Forgiveness (PSLF) Program. For more information, go to: [click to reveal website link]
Description of Job
The Work Unit:
Genomic Surveillance work unit exists to provide accurate scientific data and test results about detection, identification, and characterization of microorganisms by current molecular, genomic, and bioinformatics methods in clinical and environmental specimens from culture independent diagnostic tests (CIDTs), as well as following extraction of nucleic acid targets from live cultures of bacteria, fungi, parasites, viruses, and other agents of public health concern isolated from source specimens. These data are used in timely support of patient diagnosis and management, epidemiological investigations of disease outbreaks, rapid response to bioterrorism events, and identification of agents affecting public health and environment.
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.
Minimum Qualifications, Substitutions, Conditions of Employment & Appeal Rights
Residency Requirement:
This posting is only open to residents of the State of Colorado at the time of submitting your application.
MINIMUM QUALIFICATIONS:
Experience Only:
Five (5) years of relevant experience in an occupation related to the work assigned to this position
OR
Education and Experience:
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 [click to reveal email address] 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
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 [click to reveal email address] or call [click to reveal phone number], 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.
Supplemental Information
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 [click to reveal email address] or call [click to reveal phone number], option 5.
The State of Colorado offers permanent employees a variety of benefits including medical, dental, life and disability insurance, as well as a comprehensive leave program. Please click the following link for detailed information:
Please note that each agency's contact information is different; therefore, we encourage all applicants to view the full, official job announcement which includes contact information and class title. Select the job you wish to view, then click on the "Print" icon.
01
Are you willing to submit to a pre-employment background check?
- Yes
- No
02
This position requires educational transcripts or diplomas to be submitted if you are using education to meet the minimum qualifications for this position or for the substitution of education for some experience. If you are using education to meet the minimum qualifications or substitution for this position, a copy of your unofficial (or official) transcript/diploma is required please attach to your application by the application deadline.
- Yes
- No
03
This is a term-limited position and employment cannot be guaranteed beyond June 30, 2026. Employees who are in term-limited positions are eligible to apply for other positions within the state personnel system, including transfer opportunities. The incumbent in this position must be willing and able to resign on this date or when funds run out, whichever comes first. As a condition of employment, do you agree?
- Yes
- No
04
This is a critical position and can be expected to work and/or remain at their worksite in delayed start, early release, or closure situations. 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. Are you willing to comply with these requirement?
- Yes
- No
05
CDPHE--This position requires Critical Status: As condition of employment, candidates must be willing to 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. Are you willing and able to comply with this requirement?
- Yes
- No
06
Describe your experience in assembly and annotating genomes from raw sequencing reads?
07
List what programming languages you have had training and experience on.
08
How do you approach pathogen identification and variant analysis using NGS data?
Required Question