Kaplow Offers Innovative Approach to Evolutionary Studies

Irene Kaplow excavates historical records from genes.

"My general interest is in understanding how different traits in vertebrates have evolved," said Kaplow, assistant professor in the Department of Biological Sciences. "Part of what's bringing me to Carnegie Mellon is the number of faculty doing cutting edge work into gene regulation."

Kaplow joined the Mellon College of Science as a new faculty member in August 2024, but a few years before, she had worked as a postdoctoral fellow in the lab of Andreas Pfenning, associate professor in the Ray and Stephanie Lane Computational Biology Department.

"Irene was the second postdoc to join the lab, and her work really helped to establish my lab's identity and reputation," Pfenning said. "She led research that leveraged machine learning to more accurately trace the evolutionary history of huge segments of the genome. A large portion of the researchers in my laboratory right now are directly or indirectly building from the foundation that she created."

As a postdoctoral fellow, she investigated how similar traits evolve across different species, which is known as convergent evolution.

"Humans have much longer lives than we'd expect based on our body size, as do naked mole rats, but many other rodents that are genetically much closer to naked mole rats than humans don't live very long," Kaplow said. "I'm interested in understanding how these traits have evolved."

Kaplow noticed that genes that encode protein data are very similar across species, especially highly related species, so it would be difficult to see differences in traits by comparing gene sequences. Instead, she investigated different tissues to see how gene expression influenced the proteins produced, comparing tissues from different species to see how gene expression changed.

So far, Kaplow has found that parts of genomes that are implicated in brain size across species are also implicated in microcephaly, a condition where humans are born with brains that are significantly smaller than expected.

"The direct relevance to a related human disorder was a really nice finding that I didn't expect going in," Kaplow said. "It shows how studying evolution can teach us something about human disease and how the knowledge of human disease can help us better understand how humans evolved."

After her time as a postdoctoral fellow, she worked as a research scientist at Duke University, where she investigated how DNA editing techniques can be used to mitigate heart failure.

"My hope is if I can learn to do these techniques experimentally in my own lab, then if I have a hypothesis about DNA changes between species leading to some difference down the road, I could potentially edit the sequence and see what the effect is," Kaplow said.

As a professor at Carnegie Mellon, Kaplow plans to continue investigating how gene expression has evolved, using some of the DNA editing techniques she used at Duke to see the roles of different regions of the genome in evolution. Pfenning said that students who work in Kaplow's lab will be able to learn a lot from her.

"When Irene was in my laboratory, she did a fantastic job of fostering a friendly, fun and positive working environment," Pfenning said. "If I were a promising young scientist, I would want to join her group!"

Outside of the lab, Kaplow plans to teach classes that blend machine learning and biology. She said she hopes to help students learn how they can apply machine learning models to different areas of research.

"I want to teach students to evaluate a model in a way that allows them to test whether the model is useful for the kind of the biology they want to do," Kaplow said.