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 Moves Locations!

The entrance to the new CGDS lab/work space.

In May 2023, CGDS moved out of Children’s Hospital and to a new location in the 912 Building on the south side of UAB’s Campus. The UAB-Biological Data Science Core (U-BDS) is joining us in the same suite! We are excited about the new location and are planning to host several training sessions, seminars, and events in the new space.

Please feel free to stop by and check out the new space. If you have any questions about the new location, email Kate Daughtry at ked2012@uab.edu.


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 Attends ACMG 2023 in Salt Lake City, UT

Left to right: Dr. Manavalan Gajapathy, Dr. Gurpreet Kaur, Tarun Mamidi, Dr. Liz Worthey

Tarun Mamidi gave a platform presentation on applying his thesis work to identify pathogenic variants causing Neurofibromatosis disease. Mana and Gurpreet also gave poster presentations on their projects. Here are the abstracts submitted to the conference –

  1. Presented by Mana – P464: ROH pipeline enables analysis of regions of homozygosity using next generation sequencing data
  2. Presented by Gurpreet – P492: Identification of molecular modifiers of disease in a group of systematically phenotyped patients with cystic fibrosis
  3. Presented by Tarun – O48: DITTO4NF: In silico classification and prioritization of likely pathogenic variants for NF1 using explainable machine learning

Gurpreet was awarded Office of Postdoctoral Education (OPE) Travel Award for ACMG2023 to present her work on Cystic Fibrosis

Tarun giving his platform presentation at ACMG on DITTO4NF.
Gurpreet presenting her poster on Cystic Fibrosis

CGDS Wins 3 Awards Worth $7.5k at Hack4NF

In late 2022, CGDS, in collaboration with Dr. Deeann Wallis lab, participated in a hackathon organized by the Children’s Tumor Foundation to tackle challenges with Neurofibromatosis disease. Here’s the presentation from the hackathon to learn more about the project.

In response to the ground-breaking work, Hack4NF organizers awarded three prestigious awards to our team.

  1. Winning team for Challenge-II: Devising in silico strategies to prioritize likely pathogenic NF1 germline variants.

2. Awarded Incubation award to work with the foundation to further develop methods for practical use in a clinical setting.

3. Third award for best overall use of the Hack4NF data platform.

CGDS at UAB Cancer Retreat

In October 2022, the O’Neal Comprehensive Cancer Center at the University of Alabama at Birmingham (UAB) held its highly anticipated annual Research Retreat at Regions Field. This event brought together researchers, medical professionals, and trainees to share the latest advancements in cancer research. Among the many projects presented was a groundbreaking study on Pediatric Thyroid Cancer, presented as a poster by Dr. Gurpreet Kaur, a post-doctoral trainee at the Center for Genomic Data Sciences (CGDS).

Dr. Kaur’s research project aimed to shed light on the molecular mechanisms underlying the disease. As a post-doctoral trainee at the CGDS, she utilized cutting-edge genomic technologies and bioinformatics tools to analyze tumor samples from pediatric patients with thyroid cancer. Her poster allowed her to visually convey the key aspects of her research, including the objectives, methodology, findings, and potential implications. Attendees had the opportunity to engage with Dr. Kaur, ask questions, and gain a deeper understanding of her work.

Dr. Gurpreet Kaur presenting her poster on Pediatric Thyroid cancer project

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 (https://sites.uab.edu/cgds/2020/08/04/rico/): 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 https://twitter.com/cctsnetwork/status/1430263483904532488

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 caroline@fpwr.org.

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 https://www.mygenecounsel.com.

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 https://www.fpwr.org.

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.