CGDS representing at ACMG 2022

From left to right – Donna Brown, Shaurita Hutchins, Tarun Mamidi, James Scherer, Angelina Uno-Antonison, Manavalan Gajapathy, Deeptha Srirangam

Several members of CGDS (Center for Computational Genomics and Data Science) attended annual ACMG (American College of Medical Genetics) conference held in Nashville, TN. This is the first in-person conference for people at CGDS since the pandemic.

Dr. Manavalan Gajapathy presented a poster titled “QuaC: Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Data”. Please use the below link to download the poster.

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, and read our mission statement at

To apply please email a copy of your your resume to Angelina Uno-Antonison at For the official job requisite, visit

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


  • 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


  • 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


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


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 our team members by visiting

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


  • 🩺 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)


  • ✨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


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:

Hackin’ it at the Hackathon

Recently, members of CGDS participated in the UAB hosted AI Against Cancer Data Science Hackathon with not just one team, but two teams. Their aim was at “solving cancer-related research, prevention, and healthcare practice problems using Artificial Intelligence (AI) and data science.” Both teams were formed of a diverse range of skilled individuals bringing together capabilities and experience from areas of genetics, genomics, transcriptomics, bioinformatics, machine learning, molecular biology, developmental biology, and clinical genomics.

Team Ditto, comprised of the same members that’d placed third in the 2020 UAB COVID-19 Hackathon ( Tarun Mamidi, doctoral trainee in Genetics, Genomics and Bioinformatics; Dr. Ryan Melvin, Data Scientist in Anesthesiology; Dr. Thi K. Tran-Nguyen, Postdoctoral Fellow in PMI; Dr. Liz Worthey formed a new collaboration with Dr. Rati Chkheidze from Neuropathology. They presented work on “AI Guided Multiomics Data Mapping on Pathology Whole Slide Images of Glioblastoma”. For more information on their project, please watch their presentation recording here.

The new team this year, entered as Team BirthSeq-AI, was comprised of: Dr. Gurpreet Kaur, Postdoctoral Fellow in CGDS; Shaurita Hutchins, doctoral trainee in Genetics, Genomics and Bioinformatics; Brandon Wilk, doctoral trainee in Genetics, Genomics and Bioinformatics; Kristen Coutinho, doctoral trainee in Genetics, Genomics and Bioinformatics & Cortes Brain Aging and Physiology Lab; and mentored by Dr. Liz Worthey. Their focus on was on “Development of an AI-based Approach to Better Understand Chorangiomas by Studying Placental Heterogeneity”. For more information on their project, please watch their presentation recording here.

Team Ditto winning Second prize and Team BirthSeq-AI winning Health Equity Award

Both teams had stellar presentations and work performed in their respective areas with Team Ditto taking Second Place and Team BirthSeq-AI taking the Health Equity Award. See more at

My Gene Counsel Selected by Foundation for Prader-Willi Research to Enable Responsible Return of Results for Genome Sequencing Project

My Gene Counsel
, a digital health company that provides innovative genetic counseling solutions, today announced it is partnering with the Foundation for Prader-Willi Research (FPWR) on the first Prader-Willi syndrome (PWS) Genome Project. Through this partnership, My Gene Counsel will support FPWR in the responsible return of select genetic test results to research participants with PWS who undergo whole genome sequencing.

The study, which began enrolling participants in May 2021, will use whole genome and RNA sequence analysis to identify how variations in patients’ DNA influence the range and severity of PWS symptoms and response to treatments.

“We are excited to take the first steps towards harnessing the knowledge of the genome to better understand and optimize individual outcomes for those with Prader-Willi syndrome,” said Theresa Strong, Director of Research Programs at the Foundation for Prader-Willi Research.

Analysis of the DNA sequences will be performed at the University of Alabama at Birmingham (UAB). Liz Worthey, who leads the Center for Computational Genomics and Data Science at the UAB School of Medicine stated, “PWS patients are burdened with a highly complex array of symptoms. By using both whole genome sequencing and RNAseq, we’ll be working to discover and understand the molecular mechanisms that underlie those symptoms, and potentially lead to new therapies. Aiding patient cohorts and individual patients with rare, undiagnosed, or misdiagnosed disease is the primary focus of our expert team. We’re honored that FPWR chose our team for this study.”

As part of the initiative, FPWR will return pathogenic variants in genes on the American College of Medical Genetics and Genomics Secondary Findings list (ACMG SF v3.0) to participants and has enlisted health technology company My Gene Counsel to help return these results in a safe and responsible way.

To that end, My Gene Counsel will ensure that patients who undergo whole genome testing as part of the PWS Genome Project have access to comprehensive genetic counseling information designed to enhance participant understanding. Each participant who chooses to have their results returned will receive an electronic Living Lab Report® from My Gene Counsel that is personalized to the individual’s genetic test results and covers topics related to disease risk, medical management options, relevance to family, emotional support, and available resources.

“Offering rare disease communities, like PWS, genetic testing will push research forward,” said Ellen Matloff, President and CEO of My Gene Counsel. “We are proud to enter the rare disease space by partnering with the Foundation for Prader-Willi Research to return genetic test results that are paired with updating genetic counseling information.”

The Living Lab Reports are written and continuously updated by a network of top certified genetic counselors and medical experts and are vetted by patient advocates. In addition to delivering complex genomic information in a patient-friendly format, the reports will update and notify participants automatically by text and/or email as new risk information, management guidelines, and variant reclassifications become available. Living Lab Reports can also be used to update participants on study progress and findings over time. The PWS Genome Project is currently enrolling participants, ages 10 to 65 and residing in the U.S., with a genetically confirmed diagnosis of Prader-Willi syndrome. Additional requirements can be found here. Those interested in joining the study should contact Caroline Vrana-Diaz, Research Project Coordinator for the Foundation for Prader-Willi Research, at

About My Gene Counsel
My Gene Counsel was created to address the need for an automated, scalable solution to meet the growing demand for accurate and timely genetic counseling information. With its industry-leading database of proprietary genetics content organized by gene and variant, My Gene Counsel’s HIPAA-compliant SaaS solution delivers continuously updating genetic counseling information to patients and providers via Living Lab Reports® in many areas of genomics, including hereditary and somatic cancer testing, hereditary cardiovascular disease, noninvasive prenatal testing, and more. Founded by certified genetic counselors with 30+ years of clinical experience, My Gene Counsel helps partners save resources, retain patients, and efficiently deliver on the promise of precision medicine. For more information, visit

About Foundation for Prader-Willi Research
Prader-Willi syndrome is a genetic disorder that typically causes low muscle tone, short stature, incomplete sexual development, cognitive disabilities, behavior problems, and a chronic hunger that can lead to excessive eating and life-threatening obesity. The Foundation for Prader-Willi Research is a non-profit organization dedicated to eliminating the challenges of Prader-Willi syndrome through the advancement of research and therapeutic development. It was founded and is maintained by parents and other relatives of persons with the syndrome. For more information, visit

Senior Bioinformatician

For application details, please contact Dr. Elizabeth Worthey ( 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:

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.


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.

Inaugural face to face meeting of the hackathon collaborators

Left to right: Elizabeth Worthey, Tarun Karthik Kumar Mamidi, Thi Kim Tran-Nguyen, Ryan Melvin

Mentored by Dr. Worthey, this team won 3rd place in the UAB COVID Hackathon that took place in 2020. Soon after, this project was accepted and published in Frontiers in Big Data. Please find the article here.

Now, they’re gearing up for another Hackathon AI against Cancer taking place in August 2021.