Program: Ph.D. in informatics, bioinformatics track, 2017
Hometown: West Lafayette, IN
What he loves about bioinformatics: Working with a vareity of subjects
Nobody could confuse a dolphin and a bat.
One is a large, highly-intelligent aquatic mammal that is playful and glides through the ocean with ease. The other is a smaller, winged rodent that isn’t a big fan of the daylight and shows up more in nightmares than happy memories.
So why do they have something as critical as echolocation in common?
That’s what Gregg Thomas wants to know.
Thomas, a Ph.D. student in the School of Informatics and Computing, is using a computer to break down the genetic sequence of both dolphins and bats to try to come up with an answer.
“They both evolved the ability to echolocate despite being distantly related,” Thomas says. “We can now look at all the genes in the dolphin genome and these echolocating bat genomes, and we can see where the specific changes are that are the same between them and no one else. There are some pretty interesting examples, especially in a hearing gene called ‘prestin.’ There are specific changes in bats and dolphins, but not in anyone else.”
Thomas has always been interested in biology, and he attended Purdue for his undergraduate work in biology, and he came to IU to pursue his master’s in bioinformatics. He didn’t plan on staying for his Ph.D., but his plans changed once he met Professor of Informatics Matt Hahn.
“He works as a cross-listed professor in informatics and biology,” Thomas says. “He works with evolution, and evolution has always been interesting to me because it’s a hot-button topic, and I thought it would be cool to become an expert.”
Hahn’s focus is on genomics and evolution, and Thomas followed him down that same path.
“I do a lot of what we would call comparative genomics,” Thomas says. “We have so many genomes that are being sequenced that we can finally take the full genomes of different species and compare them to each other to see what makes them different or possibly the same. I’m specifically interested in a few things. Gene family evolution—a species can have different copies of the same gene, different numbers of copies, and if there are differences that could lend some insight to the function. I’m also interested in convergent evolution, which is the development of similar characteristics in different species.”
The fact that Thomas doesn’t work in a wet lab with actual organisms has been a huge positive. He doesn’t take samples from animals. Instead, he works on a computer to study different genomes, a fact that keeps his research fresh.
“I like to tell people that in my few years being here, I’ve worked on humans, dolphins, bats, flies, yeast, all these different organisms,” Thomas says. “I love working on such a diverse set of species. If I worked in a wet lab, I probably wouldn’t get that opportunity.”
The community of SoIC and the flexibility has helped Thomas take strides in his work.
“I can get advice from people at SoIC about machine learning problems, and I can go to the biology department if I have a question about phylogenetics,” Thomas says.
Thomas admits his computer skills have come a long way since he arrived at IU thanks to his work and the help of others, and he encourages others to forget any apprehension they might have over their programming knowledge.
“I’ve learned so much in my time at SoIC,” Thomas says. “I look at my code from three or four years ago, and I wonder how I ever wrote code like that. Being in the classes or talking to professors, especially my colleagues in the lab, they’ve really helped me become a better programmer.”
Thomas also is excited about the future of the field.
“It’s all brand new,” Thomas says. “Since we have all this data now, it’s all stuff that has never been considered before for these specific questions. It’s exciting.”