Bioinformatician (Open Rank)

University of Colorado Anschutz Medical Campus

Department of Pediatrics Section of Genetics & Metabolism

Job Title: Bioinformatician (Open Rank)

Position #:Requisition #:37106

Job Summary:

The Breuss laboratory () at the University of Colorado Anschutz Medical Campus welcomes applications for a Bioinformatician at the intermediate or senior level. The Breuss laboratory is focused on employing and developing statistical machine learning bioinformatic algorithms and related approaches for the detection of genomic mosaicism and the assessment of cellular states. We aim to use large-scale genomics of individuals or populations to discover general principles of genomic mosaicism and its impact on human health. The hired talented Bioinformatician will employ and develop approaches to further the research of the laboratory under the guidance of the principal investigator.

The Intermediate and Senior Bioinformatician will utilize applied or computational mathematical analyses for a wide array of different applications and to solve complex problems. Experiments may include text interpretation coding grounded theory methodology for the analysis of certain data and quantum state analyses. Intermediate and Senior Bioinformaticians may also perform duties in labs that use primarily electronic equipment. For Senior Bioinformaticians some assignments will not move beyond this level.

Key Responsibilities:

• Develop retrain and apply advanced computational pipelines including data simulation machine learning and convolutional neural networks to further innovative genomic research (60%).
  • Develop retrain and implement machine-learning-based (e.g. MosaicForecast) and convolutional neural network-based (e.g. DeepMosaic) classifiers on genomic data in an HPC environment.
  • Develop and employ machine-learning-based tools (e.g. UMAP for dimension reduction) to visualize functional states of cells measured by e.g. single-cell RNA-Seq or single-nucleus ATAC-Seq.
  • Develop and employ simulation frameworks for mosaic data.
  • Write (i.e. code) and optimize high-performance computing (HPC) pipelines (e.g. Slurm scripts Snakemake processes) to enable large-scale data processing and integrate the developed tools with toolkits to process genomic data.
  • Write and apply customized scripts (e.g. shell scripts Python algorithms) to support the aforementioned work.
• Manage/maintain the laboratorys raw and processed data documentation of pipelines (internally and externally e.g. GitHub) and access to these resources (20%).
  • Maintain the internal and external computational pipeline repositories (e.g. GitHub) and SOPs related to HPC usage and data processing.
  • Develop scientifically rigorous data management strategies for all projects that are run within the HPC environment.
  • Perform regular checks of the HPC infrastructure (e.g. PetaLibrary storage Blanca nodes) to ensure that adequate resources are available for the laboratorys current and projected needs.
• Contribute to manuscripts for publication and participate in regular lab meetings and scientific activities (10%).
  • Provide overview and quality control figures data tables and publishable pipelines for ongoing projects and scientific manuscripts.
  • Present updates on the computational pipelines and data processing progress to the lab members in lab meetings.
  • At the Senior level: Lead technical and bioinformatic projects within the laboratory.
• Communicate with the investigator other team members and external collaborators. Train and supervise junior lab members (10%).
  • Collaborate with and support Principal Investigators (PIs) and other stakeholders in bioinformatics and data analysis.
  • At the Senior Level: Serve as a resource for PIs and other stakeholders.
  • Participate in meetings that discuss data processing and pipeline development with the principal investigator and team members.
  • Communicate with external collaborators (and service providers) about issues regarding the HPC infrastructure and collaborations that employ it.
  • Train junior lab members in the use of the HPC infrastructure.

This description is a summary only and describes the general level of work being performed; it is not intended to be all-inclusive. The duties of this position may change from time to time based on business needs. We reserve the right to add or delete duties and responsibilities at the discretion of the supervisor and/or hiring authority.

Work Location:

Onsite this role is expected to work onsite and is located in Aurora CO.

Why Join Us:

The Breuss laboratory is located in the Department of Pediatrics in the Section of Genetics and Metabolism on the Anschutz Medical Campus. We are part of a thriving research environment and are working at the cutting edge of genome biology and genetic mosaicism.

Why work for the University

We haveAMAZINGbenefits and offerexceptional amounts of holiday vacation and sick leave! The University of Colorado offers an excellent benefits package including:

• Medical: Multiple plan options
• Dental: Multiple plan options
• Additional Insurance: Disability Life Vision
• Retirement 401(a) Plan: Employer contributes 10% of your gross pay
• Paid Time Off: Accruals over the year
• Vacation Days: 22/year (maximum accrual 352 hours)
• Sick Days: 15/year (unlimited maximum accrual)
• Holiday Days: 10/year
• Tuition Benefit: Employees have access to this benefit on all CU campuses
• ECO Pass: Reduced rate RTD Bus and light rail service

There are many additional perks & programs with the CU Advantage.

Qualifications:

Minimum Qualifications:

Intermediate Level:

• Bachelors degree in Bioinformatics Biostatistics Computational Biology Data Science Computer Science or a related field.
• One (1) year of data management and bioinformatic analyses experience.

Senior Level:

• Bachelors degree in Bioinformatics Biostatistics Computational Biology Data Science Computer Science or a related field.
• Two (2) years of data management and bioinformatic analyses experience.

Preferred Qualifications:

Intermediate Level:

• Masters degree in Bioinformatics Biostatistics Computational Biology Data Science Computer Science or a related field.
• Experience with genomic data processing at scale.
• Experience with genomic mosaicism analysis.
• Two (2) years of experience analyzing data using high-performance computing.
• Two (2) years of data management and bioinformatic analyses experience.
• Two (2) years of experience with machine learning methods.
• Two (2) years of experience employing Python packages.
• Two (2) years of experience working with Linux including shell scripting.
• Two (2) years of experience working in an HPC environment.

Senior Level:

• Masters degree in Bioinformatics Biostatistics Computational Biology Data Science Computer Science or a related field.
• Experience with genomic data processing at scale.
• Experience with genomic mosaicism analysis.
• Three (3) years of data management and bioinformatic analyses experience employing specific competencies.
• Three (3) years of experience analyzing data using high-performance computing.
• Three (3) years of data management and bioinformatic analyses experience.
• Three (3) years of experience with machine learning methods.
• Three (3) years of experience employing Python packages.
• Three (3) years of experience working with Linux including shell scripting.
• Three (3) years of experience working in an HPC environment.

Knowledge Skills and Abilities:

Understanding of basic and advanced concepts in genetics and genomics.

Demonstrated fluency in one or more programming languages (e.g. R Python C) and willingness to learn new ones as necessary.

Ability to communicate effectively both in writing and orally.

Ability to establish and maintain effective working relationships with employees at all levels throughout the institution.

How to Apply:

For full consideration please submit the following document(s):

1. A letter of interest describing relevant job experiences as they relate to listed job qualifications and interest in the position

2. Curriculum vitae / Resume

3. Three to five professional references including name address phone number (mobile number if appropriate) and email address

Questions should be directed to:

Screening of Applications Begins:

Immediately and continues until the position is filled. For best consideration apply by July 1 2025.

Anticipated Pay Range:

The starting salary range (or hiring range) for this position has been established as:

Intermediate Level: $56700 to $72123

Senior Level: $61298 to $77971

The above salary range (or hiring range) represents the Universitys good faith and reasonable estimate of the range of possible compensation at the time of posting. This position may be eligible for overtime compensation depending on the level.

Your total compensation goes beyond the number on your paycheck. The University of Colorado provides generous leave health plans and retirement contributions that add to your bottom line.

Total Compensation Calculator

Equal Employment Opportunity Statement:

CU is an Equal Opportunity Employer and complies with all applicable federal state and local laws governing nondiscrimination in employment. We are committed to creating a workplace where all individuals are treated with respect and dignity and we encourage individuals from all backgrounds to apply including protected veterans and individuals with disabilities.

ADA Statement:

The University will provide reasonable accommodations to applicants with disabilities throughout the employment application process. To request an accommodation pursuant to the Americans with Disabilities Act please contact the Human Resources ADA Coordinator at .

Background Check Statement:

The University of Colorado Anschutz Medical Campus is dedicated to ensuring a safe and secure environment for our faculty staff students and visitors. To assist in achieving that goal we conduct background investigations for all prospective employees.

Vaccination Statement:

CU Anschutz strongly encourages vaccination against the COVID-19 virus and othervaccine-preventable diseases. If you work visit or volunteer in healthcare facilities or clinics operated by our affiliated hospital or clinical partners or by CU Anschutz you will be required to comply with the vaccination and medical surveillance policies of the facilities or clinics where you work visit or volunteer respectively. In addition if you work in certain research areas or perform certain safety-sensitive job duties you must enroll in theoccupational health medical surveillance program.