News – Center for Computational Genomics and Data Science

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 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/.

Mana Gajapathy teaching python to attendees.

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 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.

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 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.

https://www.uab.edu/map/?912-building

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 –

Presented by Mana – P464: ROH pipeline enables analysis of regions of homozygosity using next generation sequencing data
Presented by Gurpreet – P492: Identification of molecular modifiers of disease in a group of systematically phenotyped patients with cystic fibrosis
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.

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.