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Colorado State University SCS Research Associate II, III, or IV - Microbial Genomics Research in Fort Collins, Colorado

Working Title SCS Research Associate II, III, or IV - Microbial Genomics Research

Position Location Fort Collins, CO

Research Professional Position Yes

Posting Number 202000969AP

Position Type Admin Professional/ Research Professional

Classification Title

Number of Vacancies 1

Work Hours/Week

Proposed Annual Salary Range $52,000-$80,000 commensurate with experience and qualifications.

Employee Benefits

Colorado State University (CSU) and the State of Colorado are committed to providing employees with a strong and competitive benefits package that supports you, your health, and your family. Visit CSU’s Human Resources website for detailed benefit plan information for permanent full-time and part-time classified employees in the following University benefit areas.

Desired Start Date

Position End Date (if temporary)

To ensure full consideration, applications must be received by 11:59pm (MT) on 02/15/2021

Description of Work Unit

This position is affiliated with the CSU microbiome network and the Department of Soil and Crop Sciences. The CSU microbiome network is a community of scholars interested in understanding the functional and structural basis of microbiomes, and their ecological relevance, and applications to host (human, animal, plant) and environmental systems. The Department of Soil and Crop Sciences faculty, staff, and students use cutting-edge computational, laboratory, and field based research to develop solutions to solve the most pressing issues related to Earth and its ecosystems.

Position Summary

This position will perform microbial genomics research using computational and statistical analyses to decipher biological meaning from genome sequences and related data, including both DNA and RNA sequences, as well as other microbiome data. The applicant’s specific efforts will include: 1. Contribute to the development of DRAM, the laboratory genome annotation software, and new computation tools and frameworks for microbiome data science 2. Establish pipelines and create software for analyzing next generation DNA and RNA sequencing methods, and benchmark and validate these sequence analysis pipelines and approaches 3. Analysis of internally generated microbiome data using standard pipelines as well as innovative approaches 4. Work alongside microbiologists, computational biologists, environmental scientists in a team project environment, with the end goal of contributing to the discovery of functions and interactions encoded in microbial community genomic data 5. Develop data management and server operations protocols for within and outside the laboratory 6. Contribute data and figures for the public dissemination of the research output via scientific publications and presentations

Required Job Qualifications

Research Associate II • B.S. in bioinformatics, computational biology, statistics, computer science, or closely related field + 3 years related experience, or a Master’s degree in computational biology, bioinformatics, or related field Research Associate III • B.S. in bioinformatics, computational biology, statistics, computer science, or closely related field + 5 years related experience or a Master’s + 2 years exp. or PhD degree in computational biology, bioinformatics, or similar field or equivalent field Research Associate IV • B.S. in bioinformatics, computational biology, statistics, computer science, or closely related field + 10 years related experience or a Master’s + 5 years exp. or PhD degree + 2 years exp. in computational biology, bioinformatics, or similar field or equivalent field All candidates: • A strong background in working with genomic and gene expression data including NGS analyses (mapping, variant calling, etc.) • Proficiency in Python, adept at developing software and scripts for genome-enabled bioinformatics analyses • Experience using Linux command-line tools and relational databases (SQL). • Proven ability in software development, including best practices in testing, version control using git and continuous integration • Excellent written communication skills, including the capacity to work independently to author software with clearly established protocols, and including coding best practices and reproducible research • Ability and desire to communicate in cross functional teams with members from varying backgrounds

Preferred Job Qualifications

• Demonstrated experience applying genome analyses to microbial systems, especially working with multi-omic data • Experience with multivariate statistics in a scientific programming environment like R, with a focus on microbial ecology analyses • Background education or training in molecular biology, biochemistry, or microbiology • Experience with developing web-based front-end interfaces is preferred • Strong quantitative background (machine learning, Bayesian inference, etc.) • Experience with workflow management tools (Snakemake, nextflow, etc.) • System administration experience

Diversity Statement

Reflecting departmental and institutional values, candidates are expected to have the ability to advance the Department’s commitment to diversity and inclusion.

Essential Duties

Job Duty Category Data Analysis


Analysis of metagenomic, metatranscriptomic, proteomic and metabolite data sets.

Percentage Of Time 40

Job Duty Category Software Design


Development of existing software in the Wrighton laboratory and create software for analyzing DNA and RNA sequencing data.

Percentage Of Time 40

Job Duty Category Mentoring


Providing assistance to laboratory members in microbiome bioinformatics pipelines (graduate students, post-doctoral researchers and research associates).

Percentage Of Time 20

Special Instructions to Applicants

For full consideration, complete application materials must be submitted online by 02/15/2021. Applicants should upload the following: (1) a cover letter addressing qualifications; (2) curriculum vitae; and (3) contact information of three professional references, one of who is/was an immediate supervisor, who has firsthand knowledge of the applicant’s profession abilities. References will not be contacted without prior notification of candidates. For inquiries about the position, contact Reb Daly For additional information about the Wrighton laboratory, visit

Conditions of Employment Pre-employment Criminal Background Check (required for new hires)

Search Contact

EEO Statement

Colorado State University is committed to providing an environment that is free from discrimination and harassment based on race, age, creed, color, religion, national origin or ancestry, sex, gender, disability, veteran status, genetic information, sexual orientation, gender identity or expression, or pregnancy and will not discharge or in any other manner discriminate against employees or applicants because they have inquired about, discussed, or disclosed their own pay or the pay of another employee or applicant. Colorado State University is an equal opportunity/equal access/affirmative action employer fully committed to achieving a diverse workforce and complies with all Federal and Colorado State laws, regulations, and executive orders regarding non-discrimination and affirmative action. The Office of Equal Opportunity is located in 101 Student Services.

The Acting Title IX Coordinator is the Vice President for Equity, Equal Opportunity and Title IX, 123 Student Services Building, Fort Collins, CO. 80523-0160, (970) 491-1715,

The Section 504 and ADA Coordinator is the Vice President for Equity, Equal Opportunity and Title IX, 101 Student Services Building, Fort Collins, CO 80523-0160, (970) 491-5836.

Background Check Policy Statement

Colorado State University strives to provide a safe study, work, and living environment for its faculty, staff, volunteers and students. To support this environment and comply with applicable laws and regulations, CSU conducts background checks. The type of background check conducted varies by position and can include, but is not limited to, criminal history, sex offender registry, motor vehicle history, financial history, and/or education verification. Background checks will also be conducted when required by law or contract and when, in the discretion of the University, it is reasonable and prudent to do so.

References Requested

Minimum Requested 3

Maximum Requested 3

Supplemental Questions

Required fields are indicated with an asterisk (*).

Applicant Documents

Required Documents

  • Cover Letter

  • Curriculum Vitae

Optional Documents