VARIANT ANALYST – GENOMICS

Come join our team as we use cutting edge analyses to make medicine and healthcare more accessible for everyone and especially to those burdened by rare genetic diseases. Our Variant Analysts are involved in all aspects of analysis work from project inception to reporting our findings to physicians, researchers, and clinics on discovery of molecular variation in DNA and RNA sequences and the consequences of those variations. We strive to help pediatric and adult patients facing diagnostic odysseys as they search for answers and therapeutic treatments that may impact their clinical management and/or their overall quality of life. Our Center works toward the goal of improving medical and scientific understanding of diseases to assist patients and healthcare providers. 

Projects in our Center typically require team analysis of DNA and RNA variation alongside evaluation of symptoms and phenotypes collected by our collaborators. Opportunities abound to collaborate cross-functionally with highly specialized subject matter experts in biology, genetics, molecular analysis, and computer programmers including examination of single cases to larger cohort analyses to development of new software to facilitate and analyze unique data. Our CGDS group shares software openly to promote the advancement of science and medicine.

Using their accumulated medical, biological, genomics, and/or genetics expertise, the successful candidate will use a variety of software, to independently and as part of a team, analyze and interpret genetic variation to identify causal variants. Candidates with good analytical, communication, and organization skills will excel in this position. Additionally, individuals with a keen attention to technical detail and the ability to mentor others will stand out as candidates. 

To learn more about us, visit the Center for Computational Genomics and Data Science (CGDS) website https://sites.uab.edu/cgds/, and read our mission statement at https://tinyurl.com/v62ywom. If interested, please reach out to Donna Brown at donnabrown@uabmc.edu to learn more. Apply for this position here  https://uab.taleo.net/careersection/ext/jobdetail.ftl?job=T194069

ANNUAL SALARY RANGE:  $57,940 – $94,150

REQUIREMENTS

Master’s degree in genetics, pathology, medical laboratory science or a related field and one (1) year of related experience required. Work experience may NOT substitute for education requirement. 

DUTIES AND RESPONSIBILITIES

  • Use internal and external software to perform analysis and interpretation of panel, exome, and whole genome data for the purpose of identification of disease-causing variants.
  • Perform clinical correlation of gene/variant candidates with patient phenotype using external knowledge repositories, scientific literature review, and expert knowledge.
  • Perform variant classification using CAP/AMP/ACMG criteria.
  • Manage interactions and collaborations with research and clinical colleagues within and external to UAB to facilitate information exchange to help diagnose cases and to define the path for confirmation and validation of novel candidate variants and genes.
  • Participate in training and mentorship of trainees and collaborators through direct interaction and presentations
  • Summarize and present results and progress at team and other relevant meetings.
  • Contribute to the preparation of abstracts, figures, grant applications, and manuscript and variant/data submissions.
  • Present findings at local, national, and international conferences.
  • Perform other duties as assigned

DESIRED

  • Knowledge of molecular genetics techniques
  • Familiarity with omics data and molecular diagnostic use cases
  • Familiarity with medical terms
  • Experience with publicly available biological databases
  • Experience in project management
  • Familiarity with R or Python, and computer scripting experience 

INTERVIEW PROCESS

Phase 1 – A 30-minute screen with the analysis team manager to get acquainted and learn more about the Center for Computational Genomics and Data Sciences (CGDS)

Phase 2 Virtual ‘Onsite’ – About 2 hours and 30 minutes which includes a 10-minute break between each session

  • Introductions and meeting with analysis team members – 30 minutes 
  • A short presentation by the candidate showing previous work in biology, their role in and findings of the work  –20 minutes presentation/10 minutes questions 
  • Meet with other senior team researchers – 30 minutes
  • Introduction to the Director of the Center, Dr. Elizabeth Worthey, wrap-up conversation with analysis team manager – 30 minutes

LEARN MORE ABOUT US

Learn more about our team members by visiting https://sites.uab.edu/cgds/team/.

UAB BENEFITS

https://www.uab.edu/humanresources/home/images/Benefits/2022Summary_UAB.pdf

Including but not limited to:

  • Medical/Dental/Vision Healthcare plans
  • Flexible Spending Account
  • 15 Accrued PTO Days, 3 Additional Floating Holidays
  • Separate Sick Leave – 10 Days
  • Teachers Retirement System of Alabama (pension plan)
  • 403b Plan (the non-profit version of 401k) with up to 5% matching by UAB
  • UAB Tuition Assistance
    • For employee, 100% in-state tuition to UAB for all undergraduate, graduate, and professional program courses at UAB.
    • For children (50% for all undergraduate courses) and spouses (50% for up to 18 credit hours)

ADDITIONAL PERKS

  • Opportunities to present at professional and academic conferences
  • Extending your professional network through collaborations
  • Participate in publications and presentations
  • Mentoring students

Software Developer III – Genomics

Come join our team as we work on cutting edge techniques to make medicine and healthcare more accessible and affordable for all. Our software developers are involved in the design and execution of projects related to studies investigating variants in DNA sequences and the changes identified from these sequences, with the goal of improving our understanding of disease and better serving patients and healthcare providers. We also strive to help pediatric and adult patients facing diagnostic odysseys as they search for answers and therapeutic treatments that may impact their clinical management and/or overall quality of life.

Projects in the Center often require contributing to front and backend development in a full-stack environment, mentoring alongside pair programming, and regularly supervising projects. Opportunities to collaborate cross-functionally with highly specialized subject matter experts in biology and genetics using, but not limited, to Nodejs, Vuejs, Apache Kafka, Terraform, Ansible, and High-Performance Computing, are also common. We aim to make our software openly available and deployable for everyday use in clinics and research institutions.

Someone with excellent to self-evaluation skills and who seeks to continually improve software development will excel in this position. Additionally, individuals with a keen attention to technical detail and the ability to mentor others will stand out as candidates. No prior experience in the fields of biology, genetics, or genomics is required.

To learn more about us, visit the Center for Computational Genomics and Data Science (CGDS) website https://sites.uab.edu/cgds/, and read our mission statement at https://tinyurl.com/v62ywom.

To apply please email a copy of your your resume to Angelina Uno-Antonison at aeunoantonison@uabmc.edu. For the official job requisite, visit https://uab.taleo.net/careersection/ext/jobdetail.ftl?job=T188111.

ANNUAL SALARY RANGE:  $81,525 – $132,475

REQUIREMENTS

  • Bachelor’s degree in Software Engineering, Computer Science, or a related field and five (5) years of related experience are required. Work experience may not substitute for education requirements. 
  • Experience with agile development practices along with continuous integration
  • Programming proficiency with two of the following languages: Javascript, Python, Java, C++, C#, Ruby, Go, Rust
  • Proficient with modern testing methodologies in unit, integration, and system testing
  • Attention to detail, including an interest in delivering high-quality code iteratively that is easy to maintain and scale
  • Familiarity with database technologies
  • Experience in developing web applications or micro-services
  • Proficient working in a Unix, Mac, or Windows environment
  • Experience with containers and container orchestration
  • Highly collaborative and able to work well in a co-located team
  • Ability to initiate and work on several projects at a time with minimal supervision; motivation to follow through to completion while adhering to deadlines and maintaining accurate records

DESIRED

  • Knowledge of Architectural modeling, domain-driven design
  • Interest in microbiology, genetics, healthcare, or patient care
  • Familiarity with omics data and molecular diagnostic use cases
  • Familiarity with Infrastructure-as-Code
  • Familiarity with continuous deployment
  • Familiarity with Test-Driven-Development (TDD)
  • Experience in data management of large data sets

INTERVIEW PROCESS

Phase 1 – A 30-minute screen with the engineering manager to get acquainted and learn more about the Center for Computational Genomics and Data Sciences (CGDS)

Between Phase 1 & 2 – Provided a take-home packet with a coding exercise and supporting documentation. You can pick to prepare one of the two coding exercises. During the ‘Virtual Onsite,’ time is dedicated to sharing the prepared code and the opportunity for the development team to ask questions about it. This activity evaluates the ability to teach and mentor teammates. These exercises are the same for entry-level candidates, not requiring too much time to prepare. The coding exercise also allows learning about types of data and work CGDS does.

Phase 2 Virtual ‘Onsite’ – About 3 hours and 15 minutes including 10-minute break in between each session

  • Development team interview –1 hour
  • Meet with some of the Center’s senior researchers –30 minutes
  • Prepared Code review session and Follow up Team discussion session –1 hour
  • Introduction to the Director of the Center, Dr. Elizabeth Worthey, wrap-up conversation with engineering manager – 30 minutes

GENERAL RESPONSIBILITIES

Software Developer III – Genomics, will design and execute projects to analyze molecular variation from next-generation sequencing and other omics or related technologies. Collaborate with the Software Architect in situation analysis conceiving novel software.

  • Engage in user experience, system design and specifications, development, testing, debugging, documentation, and support. Develop tools including APIs and web interfaces used to interpret omics datasets. Implement solutions to improve analysis workflow efficiency
  • Improve standardization of data resources of various types, including genomic, other omics, phenotype, and associated metadata—review results and feedback to implement continuous development.
  • Participate in grant proposal submission providing technical expertise. Contribute to collaborative informatics and data science projects in the field of human disease research. Present results and progress at the team and other meetings
  • Partner with Software Architect and Principal Investigator to communicate with internal and external clients. Work to build the team and meet deadlines and goals.
  • Mentor other software developers.
  • Perform other duties as assigned.

LEARN MORE ABOUT US

Learn more about our team members by visiting https://sites.uab.edu/cgds/team/.

The Center of Computational Genomics and Data Science teammates within the Gather Town, interactive virtual space, to have a virtual afternoon get together to have fun and play games

BENEFITS

https://www.uab.edu/humanresources/home/images/Benefits/2021Summary_UAB.pdf

  • 🩺 Medical/Dental/Vision Healthcare plans
  • 💵Flexible Spending Account
  • 🧳15 Accrued PTO Days, 3 Additional Floating Holidays
  • 🌡️Separate Sick Leave – 10 Days
  • 💰Teachers Retirement System of Alabama (Like 401(k))
  • 🧮UAB Tuition Assistance
    • For employee, 100% in-state tuition to UAB for all undergraduate, graduate, and professional program courses at UAB
    • For children (50% for all undergraduate courses) and spouses (50% for up to 18 credit hours)

PERKS

  • ✨Mentoring students
  • 🧬Collaborating with seasoned genomic scientists
  • 💻Opportunities to present at professional and academic conferences
  • 📜Participate in publications

Diversity & Inclusion

CGDS is dedicated to being an inclusive and diverse workplace. To us, this means that our teammates are open to being the most authentic versions of themselves and can feel safe to express their thoughts, feelings, and emotions in a way that allows them to grow and thrive both personally and professionally. Our team currently consists of several members from diverse racial, ethnic, cultural, and religious backgrounds and we pride ourselves in being accepting of the unique differences and perspectives that contribute to the overall success of our team. Understanding that our diversity is our strength, we make intentional and conscious efforts to foster an inclusive work environment which include:

  • Screening our job posting and other messaging for biased or outdated language
  • Deliberate efforts to promote psychological safety, mental health, wellness and personal growth
  • A clearly defined mission and set of core values in our manual of operations that outlines our commitment to a diverse and welcoming work environment
  • A standardized set of interview questions that are used for all candidates interviewed for a position
  • Making conscious efforts and financial investments in posting open positions to job boards dedicated to reaching marginalized communities
  • Support staff with training in diversity and inclusion, mental health support, and gender studies
  • Collaborations with researchers focused on bettering minority health, health accessibility, and inclusion in research

MISSION, VISION & VALUES

UAB serves students, patients, the community, and the global need for discovery, knowledge dissemination, education, creativity, and the application of groundbreaking solutions. We are a leader among comprehensive public urban research universities with academic medical centers. We expect all employees to adhere to our shared values of Integrity, Respect, Diversity, Inclusiveness, Collaboration, Excellence and achievement, Stewardship, and Accountability. UAB’s Vision, Mission & Shared Values can be found here: https://www.uab.edu/plan/the-plan/mission-vision-shared-values/

Senior Bioinformatician

For application details, please contact Dr. Elizabeth Worthey (eworthey@peds.uab.edu) with your CV.

Come join a diverse and growing team of computational biologists working to develop and apply computational biology, bioinformatics, and data science methods to identify the molecular underpinnings of disease and to generate knowledge of the functional impact of molecular variation to better understand disease onset, progression, and outcome, response to therapeutics, and relationship to human health. This individual will have the opportunity to work with world class researchers and clinicians and to work on a variety of pediatric and adult diseases. Current projects are focused on gaining knowledge and understanding of disease mechanisms and outcomes for Mendelian disorders and more common complex diseases including cancer, neurodegenerative diseases, and immune disorders.

Mission, Vision & Values

UAB serves students, patients, the community and the global need for discovery, knowledge dissemination, education, creativity and the application of groundbreaking solutions. We are a leader among comprehensive public urban research universities with academic medical centers. We expect all employees to adhere to our shared values of Integrity, Respect, Diversity and inclusiveness, Collaboration, Excellence and achievement, Stewardship, and Accountability. UAB’s Vision, Mission & Shared Values can be found here: https://www.uab.edu/plan/the-plan/mission-vision-shared-values/

General Responsibilities

To participate in research activities involved in the analysis of Next Generation Sequencing such as data derived from genomics and transcriptomics (bulk and single-cell sequencing) to the UAB Biological Data Science institutional core. To support research services such as study design, data management, data analysis, pipeline development and to aid in the generation of training guides and documentation. To stay abreast of recent literature and other new developments, incorporating new techniques into existing data analysis protocols and pipelines in support of the institutional core’s mission of high quality, reproducible computational biology research.

Key Duties & Responsibilities

  1. Performs computational data analysis of transcriptomics and genomics studies.
  2. Designs, develops and implements software tools and analytical procedures supporting bioinformatics analysis.
  3. Participates in projects related to the core sustainability including but not limited to pipeline development, web application development, maintenance of documentation and training guides and other services to support the needs of UAB investigators.
  4. Provides computational support services such as study design, data management and data migration.
  5. Offers bioinformatics consultation services to UAB investigators.
  6. Evaluates and identifies new technologies for implementation.
  7. Performs other duties as assigned.

Minimum Requirements

Doctorate in a related field OR Master’s degree in a related field and two (2) years of related experience OR Bachelor’s degree in related field and four (4) years of related experience OR Associate’s degree in related field and six (6) years of related experience required. Work experience may NOT substitute for education requirements.

Knowledge / Skills / Abilities

  • Knowledge of the biological sciences
  • Experience in computational biology analysis
  • Experience in Linux and using a command-line environment
  • Knowledge of scripting languages such as, Python, shell scripts, and R
  • Knowledge of best practices of reproducible and scalable research such as version control (git) and environment managing systems (e.g.: conda, Docker, Singularity)
  • Proficiency in the visualization of omics data
  • Experience in High Performance Computing environment is preferable
  • Ability to work as part of a team
  • Knowledge of theoretical and applied statistics, and molecular biology, as demonstrated through previous work or academic experience
  • Problem-solving skills
  • Attentive to detail
  • Organizational skills
  • Excellent written and verbal communication skills

An ideal candidate will follow best practices described to ensure reproducible and scalable research and be proficient in the analysis of transcriptomics data (e.g.: differential expression analysis, enrichment analysis, single-cell or nuclei data visualization and analysis, gene set annotation and contribute to upstream data analysis through the development of pipelines). An ideal candidate should also be familiar with managing virtual computational environments and be familiar with high performance computing clusters.

Disclaimer

Please Note: The duties and responsibilities described are not a comprehensive list and additional tasks may be assigned to the employee as necessitated by business demands. This job description does not constitute a contract of employment or otherwise limit UAB’s employment-at-will rights at any time. Employees are expected to comply with all UAB policies and procedures during their employment.