We are thrilled to celebrate Dr. Tarun Mamidi, who graduated from UAB on Saturday, December 14th.
Dr. Mamidi defended his dissertation, “Improving Molecular Diagnosis Success Rates and Prognosis Prediction for Patients With Rare Diseases,” in June 2024.
He will begin his new role as a Bioinformatics Scientist at Children’s Mercy while continuing as a consultant in our lab.
We wish you continued success in your career, Tarun!
Two researchers from the Center for Computational Genomics and Data Science (CGDS) recently showcased their work at the prestigious Cold Spring Harbor Laboratory (CSHL) Biological Data Science Meeting, held November 13-16, 2024. This meeting, known as #CSHLData24, brings together experts from across the globe to discuss advances in computational biology and genomics.
Dr. Gurpreet Kaur, a Scientist III at CGDS, presented her project titled “Integrative Genomic Characterization of a Rare Pediatric Differentiated Thyroid Cancer.” This project is a collaborative effort to understand the genomic underpinnings of a rare thyroid cancer in pediatric patients.
Shaurita D. Hutchins, a PhD trainee at CGDS, presented a poster titled “Identification of Drug Targets in Pulmonary Arterial Hypertension Using Gene Expression Signature Reversal & Mechanism of Action.” Her attendance was supported by a scholarship from the JXTX Foundation, which “provides support for students to attend conferences in computational biology and data science.”
CGDS is proud to have its researchers contributing to important discussions at leading scientific gatherings. The work presented at #CSHLData24 reflects the lab’s commitment to advancing computational biology.
Learn more about the CSHL Biological Data Science Meeting.
We’re excited to share that our lab’s work was featured in the NIH Research Highlights post on the University of Alabama at Birmingham’s (UAB) Center for Precision Animal Modeling (C-PAM). This recognition underscores our contributions to advancing precision disease modeling, a field at the forefront of personalized medicine.
C-PAM is one of three U54 centers established under the NIH Precision Disease Modeling Initiative, focused on creating advanced animal models for precision therapies targeting complex disorders like ciliopathies and Roberts syndrome. Our tool, Rosalution, plays a key role in these efforts, helping link unique human genomic variants to disease with high-throughput, cost-effective pipelines.
This recognition highlights our lab’s commitment to developing innovative tools that enhance our understanding of disease mechanisms and empower clinicians and researchers.
Read more about the initiative and C-PAM’s work here.
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!
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 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 delved into fundamental concepts crucial 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/.
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/.
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.
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.
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!
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.
