CGDS Trainee Presents at 2024 PWS Research Symposium

Brandon Wilk, a doctoral trainee in Genetics, Genomics, and Bioinformatics, gave an oral presentation at the 2024 Prader-Willi Syndrome (PWS) Research Symposium. His talk, “A Patient-Centered WGS-Driven Pilot Study: What Clinically Useful Knowledge Can We Gain from WGS?”, focused on the potential of whole-genome sequencing to provide meaningful insights for improving care in PWS. This work emphasizes the value of leveraging genomics to address patient-specific challenges.

Congratulations to Brandon for representing our lab and contributing to advancing PWS research!

CGDS Scientist Receives GREGoR Consortium Grant Award

The GREGoR Consortium has announced the recipients of the 2024 Deborah Nickerson Memorial Awards, celebrating initiatives to enhance workforce diversity in genomics research. Among the distinguished awardees is Dr. Gurpreet Kaur, a Scientist III at the Center for Genomic Data Science (CGDS), University of Alabama at Birmingham. Dr. Kaur has been honored with an educational award to support her professional development and contribution to the genomics community.

As part of this recognition, Dr. Kaur will participate in the Skills for Health and Research Professionals (SHARP) Training in Quantitative Genomics hosted by Columbia University’s Mailman School of Public Health. This training will bolster her expertise in quantitative genomics and align with GREGoR’s mission to drive inclusivity and innovation in solving unsolved rare genetic diseases. Congratulations to Dr. Kaur and all the awardees for their contributions to advancing genomics research!

Learn more about the awardees and the GREGoR Consortium’s efforts to support workforce diversity in genomics research: 2024 GREGoR Consortium Awardees.

CGDS Publishes Study on Genetic Factors Influencing Vitamin D Status in Cystic Fibrosis

CGDS researchers and collaborators have published new findings on the genetic basis of vitamin D variability in adults with cystic fibrosis (CF). The study analyzed 25-hydroxyvitamin D (25OHD) levels alongside whole genome sequencing data from 80 adults to investigate why some patients remain vitamin D insufficient despite consistent supplementation.

Results showed that 30% of participants had 25OHD concentrations below the 30 ng/mL threshold, despite normal vitamin E levels. Polygenic risk scores (PRS) were significantly correlated with 25OHD status, indicating that common genetic variants contribute to differences in response to vitamin D therapy. These findings align with prior results in children and support a more personalized approach to supplementation in CF care.

Read the full study in Journal of Cystic Fibrosis: Vitamin D status and variable responses to supplements depend in part on genetic factors in adults with cystic fibrosis.

CGDS and U-BDS Host Python-Focused Carpentry Workshop

CGDS and U-BDS recently hosted a Software Carpentry Workshop on March 18-19, 2024, drawing researchers eager to enhance their computational skills for more efficient and effective research practices. Led by a distinguished team of instructors — Manavalan Gajapathy, Bharat Mishra, Samuel Bharti, Austyn Trull, and Angelina Uno-Antonison, with James Scherer assisting — the workshop explored fundamental concepts essential for navigating the challenges of modern research. Participants were taught about bash shell, Python, and version control with git.

Learn more about the workshop at: https://u-bds.github.io/2024-03-18-uab/.

Mana Gajapathy teaching python to attendees.
Angelina Uno-Antonison teaching python to attendees.

CGDS Publishes on Caregiver Perspectives in Prader-Willi Syndrome Pharmacogenomics

Researchers at CGDS, in collaboration with FPWR, have published a study exploring caregiver interest in pharmacogenomic (PGx) testing for children with Prader-Willi syndrome (PWS). The study surveyed caregivers before returning PGx results, aiming to understand their expectations and planned use of this information in clinical care.

Among the 48 caregivers surveyed, 93.8% expressed strong interest in their child’s PGx results. Nearly all respondents (97.9%) intended to share the findings with medical providers, yet fewer than half (47.9%) felt confident that those providers would use the results. The findings highlight the enthusiasm among caregivers and the perceived gap in provider readiness to act on PGx data, signaling a need for increased education and support around clinical implementation.

Read the full study in Pharmacogenomics: Pharmacogenomics for Prader-Willi syndrome: caregiver interest and planned utilization.

CGDS and U-BDS Host R-Focused Carpentry Workshop


UAB’s CGDS and the U-BDS (Biological Data Science Core) held a Software Carpentry Workshop on December 14-15, 2023, to teach researchers computational skills. Instructors Manavalan Gajapathy, Austyn Trull, Bharat Mishra, Shaurita D. Hutchins, and Samuel Bharti, with the help of Santhosh Karthikeyan, Nilesh Kumar, Tarun Mamidi, and Yuwei Song, led sessions on the Unix Shell, version control with Git, and R and RStudio. The workshop included hands-on exercises and covered topics like data frame manipulation with dplyr and creating graphics with ggplot2. The event was designed to enhance participants’ technical skills and encourage using computational methods in research.

Learn more about the workshop at: https://u-bds.github.io/2023-12-14-uab/.

U-BDS member, Bharat Mishra, teaching about R.
U-BDS member, Austyn Trull, waiting to help attendees.
CGDS PhD trainee, Samuel Bharti, teaching about R.
CGDS PhD trainee, Shaurita Hutchins, teaching about R & RStudio.
Current UAB GBS doctoral student, Yuwei Song, observing attendees to ensure they get help.

CGDS Trainee Attends EMBL-EBI Systems Biology Course

In October 2023, Shaurita D. Hutchins, a PhD trainee at the Center for Genomic Data Science (CGDS), was selected as one of 30 researchers to attend the EMBL-EBI Systems Biology Course in Hinxton, England, UK.

The course offered advanced training in systems biology, focusing on network-based modeling, multi-omics integration, and computational approaches critical to understanding complex biological systems. Participants engaged in lectures and hands-on sessions to utilize EMBL-EBI’s bioinformatics resources.

A photo of the course attendees.

This course also allowed network opportunities by bringing together researchers from various backgrounds to share knowledge and explore potential partnerships. Shaurita’s participation reflects CGDS’s commitment to professional growth and innovation in genomics and computational biology.

CGDS is excited to see how the insights and skills gained from this course will enhance ongoing research efforts.

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 using 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!