Robots don’t just stand in for humans on assembly lines. They now help doctors perform surgeries remotely. They explore Mars. And they bring a lifelike sense of touch to artificial limbs....
Gary and the bioinformatics team at the Bader Lab map the millions of molecules and systems inside a human cell – from simple water and sugar molecules to complicated proteins and systems like the cell nucleus. Bioinformatics mashes up biology, computers and engineering.
“We’re building a Facebook for the proteins in human cells.”
Most children with severe autism are isolated in their own private worlds and can’t communicate with other people. Gary and his research team worked with leading researchers at the Hospital for Sick Children in Toronto to unravel the genetic causes of this frightening disease. The challenge was this: kids display hundreds of genetic mutations that seem related to their autism. But few kids have the same mutations. The mutations are all over the map! Gary’s research team put the mutant proteins into their protein Facebook. They discovered the mutants are all “friends” in a group of proteins that controls the development of the human brain.
“This explains a huge challenge,” says Gary. “Autism is much more complex than we realize, and there are lots of ways to get it.” Next step: map these causes and figure out what to do about them.
Gary and the bioinformatics team at the Bader Lab map the millions of molecules and systems inside a human cell –from simple water and sugar molecules to complicated proteins and systems like the cell nucleus. Building on research from around the world, they answer questions like: What goes into this parts catalogue? What are the parts made of? What do they do? How do they interact with one another and the world outside the cell?
Bioinformatics mashes up biology, computers and engineering. Computer gurus catalogue the millions of parts in a cell and to 3D-visualize what the parts do. Engineers figure out the workings of these many parts, and design robots for complex, high speed lab experiments.
The tens of thousands of proteins swimming around in every cell are a lot like people. Each has a personality and things it “likes” to do. Proteins cooperate (“friend”) with other proteins. They use energy resources and building blocks like fat and sugar molecules to get stuff done. A broken protein can do bad things that make you sick.
We humans know very little about how our proteins work, what they do, or how they “socialize” with one another. Gary’s Facebook for proteins is a computer-based network map that shows which proteins do stuff together. Starting with protein “friend” links, he builds up their “social networks” and what they “like.” The result is insight into how life works, and what happens when it doesn’t.
This isn’t easy. Gary doesn’t always know which proteins “friend” each other. In bio-speak, he doesn’t know the protein interactions in advance. In fact, a big part of Gary’s job is to find these interactions.
“To figure out if two people are Facebook friends, you would look at their profiles,” says Gary. “Do they like the same music or go to the same school? Do they have friends in common or are they members of the same clique? Similarly with proteins, we ask where they hang out inside the cell, what attributes they have, what do they do? For example, are they both involved in cellular garbage collection?”
Gary and his 20-person team of biologists, computer scientists, engineers and graduate students don’t use microscopes, Petri dishes, or test tubes. They do everything on computers. He spends about 80% of a typical day thinking about and doing research, 10% teaching, and the rest on administration.
Gary did a double undergrad degree at McGill University in biochemistry and computer science. He discovered the emerging field of bioinformatics, “but no one at McGill had heard of it, and people thought I couldn’t get into it.” As a graduate student at the University of Toronto, “I met Christopher Hogue, who was starting the first bioinformatics lab in Toronto. I did a PhD thesis project on a bioinformatics database that became a project at Chris’s lab. Called Blueprint, it was the first Facebook of proteins.” After post-doctoral work at the Memorial Sloan-Kettering Cancer Center in New York, Gary won an appointment at the University of Toronto where he founded the Bader lab.