Bioinformatician II

abbott; Alabama; On-site; USD 68,000 - 136,000; Full time

Job summary

Abbott's OncO Cancer Diagnostics unit seeks a Bioinformatician II to support clinical reporting by monitoring variant calls, QC issues, and assay validation in a regulated setting. You will mentor junior staff, collaborate with PIs and cross-functional teams, and help manage NGS data and pipelines.

The role is based in Madison, WI with a Tuesday–Saturday schedule, contributing to pipeline development, data management, and customer delivery.

Qualifications

• Bachelor's or Master's degree in Bioinformatics/CS/Bioengineering or related field; 2 years of job-related experience in biomedical data analysis.
• Proficiency in multiple programming languages (Python/Java) and building workflows; ability to download/learn/apply software and database resources.

Responsibilities

• Implement, test, maintain, and customize bioinformatics resources and software across languages.
• Develop front ends for analysis tools and build project workflows for automated analysis steps.
• Collaborate across teams to align bioinformatics activities with project objectives.
• Mentor junior staff and manage multiple collaborations.

Skills

Python/Java

Linux/UNIX

NGS data handling

Data visualization

Regulated environment

Education

Bachelor's or Master's in Bioinformatics/CS/Bioengineering

Tools

Cromwell/WDL

Snakemake

AWS

DNAnexus

Job description

JOB DESCRIPTION:

Position Overview

The Bioinformatician II is a mid-level role responsible for supporting clinical reporting through the monitoring and review of variant calls and other pipeline outputs, investigation of quality control issues, and participation in assay validation and regulatory inspections. This role involves conducting case investigations, supporting CAP proficiency testing, and documenting variant-level changes. In addition, the role is responsible for monitoring existing bioinformatic NGS pipelines, data management and delivery to customers. This individual builds on foundational knowledge to handle a broader range of bioinformatics assignments, contributes to tool and pipeline development, and collaborates across teams to meet project objectives. The ideal candidate will have a strong background in managing and working with NGS data, experience working in a regulated environment, and the ability to mentor junior staff.

This position is onsite at our Madison location, with a Tuesday to Saturday work schedule.

Essential Duties

• Implement, test, maintain, and customize available bioinformatics resources and scientific software/data sources in multiple programming languages and platforms for research support.
• Develop front ends for analysis tools, visualize and compile results, facilitate routine data processing, migration, organization, and management tasks, and build project-specific workflows that implement automated analysis steps.
• Investigate, customize, and prototype new bioinformatics resources and scientific software for biomedical data processing. This requires skills in multiple programming languages, databases, computational methods, scientific computing, large-scale data analysis, and working with heterogeneous biomedical data from multiple sources.
• Apply software engineering principles to create reusable, modular, tested, version-controlled, repository-based, professional-quality informatics, software, and database resources.
• Design, prototype, and evaluate innovative computational algorithms, data analysis techniques, and statistical methods for biomedical data processing, interpretation and knowledge discovery. Explore and recommend alternative data processing approaches as appropriate.
• Follow scientific literature and manuscripts, investigate emerging biomedical data processing methods, technologies, trends, and paradigms relevant to biomedical informatics, and contribute to manuscripts, grants, research proposals, and research planning activities.
• Attend, contribute to, and present at internal and external scientific meetings and conferences.
• Manage multiple bioinformatics collaborations and projects, while mentoring junior staff.
• Support strategic planning, organization, management, utilization, and optimization of current and future bioinformatics resources, skills, and capabilities.
• Collaborate with principal investigators (PIs), researchers, and fellow bioinformaticians to align bioinformatics activities with organizational objectives and maximize competitive advantage in biomedical research.
• Interact with other research divisions, computing infrastructure teams, and external academic and industry partners.
• Demonstrate excellent communication skills and a strong desire to collaborate with researchers conducting cutting-edge biomedical research.
• Uphold company mission and values through accountability, innovation, integrity, quality, and teamwork.
• Support and comply with the company's Quality Management System policies and procedures. Maintain regular and reliable attendance. Ability to act with an inclusion mindset and model these behaviors for the organization. Ability to work designated schedule. Ability to work nights and/or weekends, as needed. Ability to work on a mobile device, tablet, or in front of a computer screen and/or perform typing for approximately 95% of a typical working day. Ability to travel 5% of working time away from work location, may include overnight/weekend travel.
• Contributes to internal knowledge sharing, standard operating procedure (SOP) updates, and cross-training.

Minimum Qualifications

• Bachelor's Degree/Master's Degree in Bioinformatics/Computer Science/Bioengineering/Computational Biology or related field. 2 years of job related experience in academic/industrial applied research environment in biomedical data analysis.
• Demonstrated ability to understand and implement computational algorithms, statistical analysis methods, custom data analysis software. Demonstrated proficiency in software development in multiple programming languages, such as Python/Java, and derivatives. Demonstrated proficiency in downloading/learning/applying software and database resources for custom analysis and building workflows.
• Demonstrated proficiency with Linux/UNIX based systems and shell scripting. Demonstrated ability in analyzing gene expression, genotyping, sequencing, CGH, or in specific field needed by the duties, and various biomedical databases.
• Demonstrated proficiency with scientific computing and data visualization tools, such as MATLAB/R, and understanding of basic statistics. Demonstrated proficiency in software engineering processes, such as version control, backup, documentation, testing, validation.
• Demonstrated familiarity with large-scale data analysis and utilization of high-performance computing systems, parallel programming. Demonstrated proficiency with NGS workflow processes and languages (e.g., Cromwell/WDL, Snakemake).
• Demonstrated proficiency with cloud computing (e.g., DNAnexus). Demonstrated ability to perform the essential duties of the position with or without accommodation. Authorization to work in the United States without sponsorship.

Preferred Qualifications

• Master's Degree in Bioinformatics/Computer Science/Bioengineering/Computational Biology or related field. 2+ years in large scale NGS operations industry environments. Proficiency in Linux based systems, Python and AWS.
• Experience working in a regulated environment under CLIA/CAP and/or FDA guidelines.

JOB FAMILY:

Research and Discovery

DIVISION:

ONCO Cancer Diagnostics

LOCATION:

United States > Madison : 1 Exact Lane

WORK SHIFT:

Standard

TRAVEL:

Yes, 5 % of the Time

MEDICAL SURVEILLANCE:

No

SIGNIFICANT WORK ACTIVITIES:

Continuous sitting for prolonged periods (more than 2 consecutive hours in an 8 hour day), Keyboard use (greater or equal to 50% of the workday)Abbott is an Equal Opportunity Employer of Minorities/Women/Individuals with Disabilities/Protected Veterans.EEO is the Law link - English: http://webstorage.abbott.com/common/External/EEO_English.pdfEEO is the Law link - Espanol: http://webstorage.abbott.com/common/External/EEO_Spanish.pdf

The base pay for this position is

$68,000.00 - $136,000.00

In specific locations, the pay range may vary from the range posted.