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Paradigm Genetics Pulls Itself Together With New Computational Systems Biology Group


Considering that systems biology pioneer Lee Hood is on Paradigm Genetics’ board of directors, it shouldn’t come as a surprise that the company has launched a new computational systems biology research group within its human health unit.

But according to Thomas Colatsky, VP of healthcare research, the new group doesn’t signify a new direction for Paradigm, but rather a coordination of independent computational and experimental efforts that are already underway at the company. “We’ve really moved beyond the concept of data integration,” said Colatsky. “It’s not just enough to collect information and look at it; you have to start looking for relationships among different kinds of data.” Computational systems biology, according to Colatsky, “is the ability to look at a lot of different things at the same time, and to have the information that derives from that actually impact the way you do your next set of experiments or develop your next drug.”

As the latest step in a year-long restructuring effort at Paradigm that entailed significant layoffs, an overhaul of its executive management team, and the creation of two separate agricultural and human health business units, the new group will serve as a keystone of sorts for research activity in the healthcare side of the business, Colatsky said. Brian Bullard, an industry veteran who has held informatics management positions at Morphochem, AxCell Biosciences, PE Informatics, and Gene Logic, will lead the new group, which is expected to employ around 10 people when fully staffed. The new unit will join three major research groups within the healthcare business: a core informatics group, which handles databases, LIMS, and software development; an experimental biology group; and an analytical biochemistry group.

Bullard’s team will be charged with synthesizing genomic, proteomic, and metabolomic data from all of these teams within the context of biological pathways. The team will build upon work already underway at the company on two projects — an $11.7 million ATP-funded project in which the company is collaborating with Lion Bioscience to create tools to study multiple data streams in a single analytical space and a $32.2 million contract with NIEHS to build a toxicogenomics database. The computational systems biology group will continue to develop this technology and will also create several new data mining and visualization methods for the analysis of pathway information.

Bullard said the team will draw heavily from public data sources, such as the KEGG pathway database, but these sources provide only “a slice of the information” that requires additional data, annotation, and curation to answer healthcare-related questions. On the computational side, he said he envisions “being able to apply traditional multivariate analysis techniques to these disparate data sets so that the weighting is equal, and you get more of a systems view of what’s going on.”

The computational systems biology group will support a three-pronged strategy at the company, comprising predictive toxicology, biomarker discovery, and pharmacogenomics-based diagnostics, Colatsky said. Paradigm has already established partnerships with several academic and clinical centers that are providing tissue samples that the company can assay and analyze for relationships between genes, serum, and tissue markers. “We’re looking to extend that in collaborations with pharmaceutical and biotechnology partners,” Colatsky said.

While Paradigm’s agricultural bioscience business has partnerships with Bayer Crop Science and Monsanto, the nascent healthcare group has yet to find industry sponsorship. But it seems that the pieces are finally falling into place for the company after a year of upheaval and uncertainty. In addition to the new computational systems biology group, Paradigm also launched a microarray analysis services business last month with the goal of bringing in short-term revenues. Its microarray database contract with the NIEHS was expanded last week from $23.8 million to $32.2 million, and most importantly, the company narrowly avoided a Nasdaq delisting earlier this month, when it was granted an extension until July 3 to bring its stock price up to the $1.00 minimum.

Indeed, even as Colatsky stressed that the group’s efforts wouldn’t be entirely new, the formal launch of the research effort is not without a high degree of optimism for the company. “I think what Brian’s appointment and the formation of this group really signals for us, and I hope for this sector, is that it’s not just about tool development, it’s not just about content, it’s also about being able to generate new data and then to use all of that together to develop something that would be useful medically and pharmaceutically.”

— BT

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