As prospects for commercial pure-play bioinformatics opportunities grow ever more doubtful, the academic world may be the last bastion for those with the bioinformatics innovation itch.
A case in point is the head of Baylor University’s new Bioinformatics Research Laboratory, Aleksander Milosavljevic, who was lured away from his position of VP of bioinformatics at Genometrix a year ago by the creative freedom of a funded faculty position.
The selling point for the academic life, said Milosavljevic, was “that I’d be in a position to develop new bioinformatics technologies.”
The risk of remaining in the private sector, he said, is that “a successful genomics company becomes a pharmaceutical company, and then bioinformatics becomes a second-order supporting activity and radical innovation becomes dangerous.” In other words, you’ll have a job, but a boring one.
The BRL’s focus is on comparative genomics. While much of its work is in support of the university’s genome sequencing center, Milosavljevic noted that his lab is a self-sustaining entity with the sole mission of developing creative new tools for their own sake.
“Informatics at the genome center has as its highest priority support for data production, so they have much less freedom to operate in research mode. We’re aiming for new technology development,” he said.
Examples of his lab’s work include Pooled Genomic Indexing, a technology that maps BACs of one species onto the assembled sequence of another species, and Comparative Sequence Assembly, a method to speed assembly by using known sequences from different species.
One of the lab’s newest tools is a web-based Distributed Annotation System client called Genboree. The system is currently being tested at Baylor in the analysis of rat and Drosophila genome sequences. Analysis groups can use Genboree to share preliminary data among themselves, acting as a “whiteboard” for prepublication data, according to Milosavljevic.
But Milosavljevic stressed that his group’s focus on innovation isn’t all just blue-sky research. “I’m keen on developing intellectual property and patenting bioinformatics,” he said. Although some in the academic world see patents as running “counter to science,” he noted that he holds the opposite view — in order for bioinformatics to be considered a “first-class citizen” in the life science world, “it needs to play the game of life sciences, which is emphasis on intellectual property.”
Milosavljevic lamented the lack of IP protection he witnessed in his experiences in the private sector.
“There are no business models now in bioinformatics that can protect the investment in bioinformatics research,” he said. “One of the key reasons behind the fall of bioinformatics as a commercial enterprise is that companies were not seriously considering the intellectual property that they were developing, so they couldn’t capture the value of their research,” he said.
Patenting is important “not only for commercial success” but also for “intellectual content,” he said. While the field now emphasizes software development, Milosavljevic said that the patent system “is about concepts and ideas and emphasizes the intellectual dimension of bioinformatics as opposed to the engineering dimension.”