Next-gen Approaches to the CEIRS Training Program with Dr. Justin Bahl

Dr. Justin Bahl is an Associate Professor at the University of Texas Health Science Center at Houston, and part of the St. Jude Center of Excellence for Influenza Research and Surveillance (SJCEIRS). He brings expertise in evolutionary biology to understand how influenza viruses emerge and evolve at the population level. Armed with a suite of genomics and bioinformatics approaches, the Bahl lab tackles how environmental and host pressures shape virus diversity and influence disease in human and animal populations. The DPCC Communications team interviewed Dr. Bahl on his innovative approach to the CEIRS Training Program.

The Runstadler-Bahl team collaborating remotely on their research projects. Image of Islam Hussein, Nichola Hill (top row), Truc Pham, and Justin Bahl (bottom row).

The Runstadler-Bahl team collaborating remotely on their research projects. Image of Islam Hussein, Nichola Hill (top row), Truc Pham, and Justin Bahl (bottom row).

A symbiotic structure to the CEIRS Training Program

The CEIRS Training Program is an ongoing NIAID-funded initiative that supports graduate and postdoctoral training experiences in CEIRS laboratories. Students within and outside of the Network can leverage this program to diversify their skills and develop collaborative and interdisciplinary research experience. The standard program places a student in an immersive 2-week rotation in another research setting. After being contacted by trainees Drs. Nichola Hill and Islam Hussein from the Runstadler group at MIT, part of the Center for Influenza Research and Pathogenesis (CRIP), Bahl developed an idea to innovate on the training program’s traditional approach.


Islam Hussein from the Runstadler group (CRIP) and Justin Bahl (right) biking around Houston in between training.

Islam Hussein from the Runstadler group (CRIP) and Justin Bahl (right) biking around Houston in between training.

Akin to his research, Dr. Bahl sought to expand this opportunity from the individual to the group scale. Along with Ms. Truc Pham, a graduate student in his lab, he traveled to MIT and ran a bioinformatics workshop for members of the Runstadler group. The workshop included short lectures that introduced the background theories of evolutionary modeling and comparative genetic analysis in influenza ecology. The fundamentals of these methodologies were emphasized such that trainees could apply the information to their own research. Instead of a “cookie-cutter approach to bioinformatics,” this foundation enables the trainees to further develop approaches to answer research questions. Further solidifying their training experience, members of the Runstadler group later visited Houston to extend their research. The training experience was fruitful, as the introductory lectures led to group brainstorming sessions and collaborative projects resulting in two publications and “a really lovely collaboration,” said Bahl.

Trading benches

In Dr. Bahl’s most recent experience with the training program, he and Dr. Florian Krammer (CRIP) took yet another spin on the program by exchanging students and expertise. Xueting Qiu (SJCEIRS) gained valuable experience at the bench, while Ericka Kirkpatrick (CRIP) refined her systems analysis skills. “Ultimately, this [approach] strengthens the collaboration and enriches the training experience,” said Bahl. The partnership allowed the groups to tackle the challenges of influenza vaccine design from two angles—laboratory approaches to develop and test a vaccine, and computational approaches to optimize vaccine candidates. The program provided a mechanism to combine training such that “students get lab-based skills training and open eyes to how computational methods may be applied to vaccine design.”

Factors for success

Dr. Bahl shared advice on achieving a successful experience in the CEIRS Training Program and developing lasting collaborations. Interested trainees should contact the PI early and facilitate communication between investigators. Take time to develop and structure the project beforehand, and have a goal, timeline, and publication in mind. Dr. Bahl said, “If you have a question you are interested in or a direction you would like to go, you will get more out of your time.” For investigators considering these new approaches, be sure to account for the additional level of coordination and planning up front.

Virtues of a modified approach

The outcomes from the collaborative and shared experience for trainees and investigators are many. By expanding training to a wider audience, and engaging with a follow-up visit, the lessons learned are reinforced. Trainees revisit what they learned during their intensive 2-week rotation and get feedback on their progress. “Often, this time for progress can provide that final push towards publication.” One of the strengths of the Network is the wide array of investigator expertise, and the exchange component strengthens multi-disciplinary research. Investigators learn to translate their methods, communicate the science, and advance the field from multiple angles. By reinforcing the lines of communication, all participants get a better view of cross-Center collaborations and build lasting relationships.

Dr. Bahl’s involvement in the CEIRS Training Program was also beneficial as an investigator. He found a broader need at his own institution for a comparative approach to genetics, ecology, and evolution. The materials prepared for the workshop were eventually developed into a complete graduate course. Reflecting on the experience, Dr. Bahl commented that it further solidified and refined his approach to mentorship and collaboration across the Network.

To read more on the cross-Center work spurred by the training exchange and other ongoing collaborations, check out the publications listed below.

Links to publications:

To apply or learn more about the CEIRS Training Program, please visit this page