CGDS Trainee Presents at the UAB Cystic Fibrosis Research Center Symposium

On October 4, 2023, Tarun Mamidi, a doctoral candidate in CGDS, showcased his research at the UAB Cystic Fibrosis Research Center Symposium, focusing on the use of neural networks to identify modifier variants in Cystic Fibrosis (CF).

His work aims to improve our understanding of how these variants can change how CF affects individuals and their response to treatments. By applying advanced neural network techniques, Tarun’s research offers potential pathways for more precise and effective therapeutic strategies.

Congratulations to Tarun!

CGDS Trainee Attends the CAGI⁕⁕ Workshop in Boston

Tarun Mamidi, a doctoral candidate in CGDS, recently participated in the Critical Assessment of Genome Interpretation (CAGI⁕⁕) Workshop from September 29 to October 1, 2023, in Boston, Massachusetts.

His presentation, “DITTO: Automated tertiary rare disease diagnosis pipeline using explainable Machine Learning,” highlighted innovative approaches to rare disease diagnosis.

The CAGI⁕⁕ Workshop is a gathering aimed at advancing genome interpretation techniques and addressing ethical, methodological, and technological challenges in the field. Through discussions on variant impact prediction and clinical genome interpretation, the event fosters collaboration among experts to enhance diagnosis and treatment strategies.

Tarun’s contribution to this forum underscores our lab’s commitment to leveraging technology for meaningful advancements in genome interpretation.

CGDS Trainee Attends 2023 CCTS Training Symposium

Samuel Bharti, a doctoral trainee in CGDS, attended the 2023 CCTS Training Symposium in Biloxi, MS from September 27th to September 29th. Thanks to his outstanding work, Samuel received a $300 travel award to present his latest research on Neurofibromatosis Type 1 (NF1).

In his poster presentation titled “Application of a Multi-Omics Approach in NF1 Deficient Tumors and Controls can Highlight Novel Associations and Therapeutic Targets,” Samuel shared how his research approach could open new pathways for understanding and treating NF1.

The CCTS Training Symposium is a gathering of some of the brightest minds in clinical and translational science, offering a platform for sharing cutting-edge research.

Congratulations to Samuel on his well-deserved recognition!

Rabab Fatima Embarks on a Journey at Georgia Tech

We’re excited to announce that Rabab Fatima, a Software Developer II at CGDS, has been accepted into the Master’s in Computer Science (Online) program at the Georgia Institute of Technology, starting Spring 2024.

Rabab’s decision to pursue this advanced degree stems from her commitment to deepening her expertise in Computer Science and Software Engineering, with a keen focus on the Interactive Intelligence specialization. This specialization aligns with her passion for exploring the intersection of Artificial Intelligence, Human-Computer Interaction, and Cognitive Science.

Rabab’s goal is to harness the knowledge and skills acquired through the OMSCS program to innovate and create cutting-edge technical products and tools. She aims to develop solutions that are not only technologically advanced but also intelligent and human-centered, reflecting a deep understanding of cognitive science alongside the latest developments in AI and Machine Learning. Rabab’s journey into this prestigious program is a testament to her dedication to her professional growth and her vision for contributing meaningful advancements in the tech world.

We congratulate Rabab on this significant achievement and look forward to the innovative contributions she will undoubtedly make to our field with the insights gained from her studies at Georgia Tech.

CGDS Trainee Receives Inclusive Campus Commitment Award

CGDS trainee, Shaurita Hutchins, received the Inclusive Campus Commitment Award in April at UAB’s Student Excellence Awards.

The award recognizes a student who embodies UAB Inclusive Campus Commitment by ensuring every member of the UAB community is treated with dignity and worth without any bias. This person will have made an active effort “to build an inclusive UAB.”

Shaurita also won the Campus Impact Award along with the Informatics Club for helping plan Hackin’ Omics 2022, which CGDS helped to plan along with CGDS trainee, Tarun Mamidi, as the hackathon’s co-chair.

CGDS at ISMB 2022 Madison, WI

Dr. Manavalan Gajapathy, Dr. Liz Worthey, and Tarun Mamidi attended the Intelligent Systems for Molecular Biology (ISMB) conference in July 2022.

Manavalan Gajapathy, Elizabeth Worthey and Tarun Mamidi at ISMB 2022 (left to right)

Mana and Tarun both presented posters on their current projects.

Additionally, members of CDGS were able to network with others at the conference as well as spend time with collaborators in Dr. Brittany Lasseigne’s lab.

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.

ACMG Research Presentations 2021

ME/CFS: Whole Genome Sequencing Uncovers a Misclassified Case of Glycogen Storage Disease Type 13 (GSD13) Previously Diagnosed as ME/CFS – Donna Brown

Identification of Genetic Modifiers Altering the Prognosis of Cystic Fibrosis in a Cohort of Young CF Patients – Donna Brown

Diagnosing Rare Diseases in HD (HAZEL and DITTO) – Tarun Karthik Kumar Mamidi

Computational Biologist Position

Apply Here:

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) as part of 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 datamigration.

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 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.DisclaimerPlease 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.


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