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GeneGo Maps Pathways With Trial and Error

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When Tatiana Nikolskaya says her company “is not doing what everyone else is doing,” she means it. GeneGo, incorporated in December 2000, is a genomics company that says the genome isn’t all it’s cracked up to be.

Nikolskaya, a former wetlab biologist originally from Russia, focuses on what she calls functional reconstruction. “We don’t care about actual sequence or structure,” says the president and CEO. “The only thing that is really important is function.” Basically, using biology and mathematical algorithms, GeneGo proposes pathways and then uses trial and error to test the theory. “If all the little parts fit together, it must be right,” Nikolskaya says.

According to GeneGo logic, trying to establish pathways and find drug targets by examining sequence and structure is useless at this point — “the human genome isn’t at that level yet,” she says. “The human genome sequence as it is would give us a skeleton. Not even a skeleton, maybe a tail and an ear.”

Sound a little too simple? It’s not, says Nikolskaya. “Building a [pathway] map is a very painful process.” If a proposed pathway is wrong — as is often the case — it will show itself, eventually. “At some point we’ll have a problem. And in chasing down the problem, we’ll find out what was wrong,” she explains.

Nikolskaya and her associates start with a model of the disease and rely heavily on ESTs to come up with potential pathways. She has worked on this problem for nearly three years. She recruited people for metabolic networking, computer support, and annotation; the company has so far identified more than 1,800 human-specific pathways.

Much of that comes from the mathematical expertise of Alexander Markov, one of GeneGo’s 13 employees. Markov is a Russian paleontologist who designed the architecture for the company’s highly flexible database. Roughly half the staff work in Moscow, focusing more on the math side, and half are scattered throughout the US, mainly working on the biological angle. “We’re a virtual company,” Nikolskaya says.

But she has found a place for the company to call home. Though the plans were to set up shop in Illinois, Michigan’s life sciences funding incentives proved too tempting, and Nikolskaya is looking at space in New Buffalo, a resort town on Lake Michigan. If functional reconstruction really does work so much better than sequence- and structure-based studies, perhaps she’s just preparing for an early retirement.

— Meredith Salisbury

 

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