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Q&A: Bruce Stillman on Plans to Expand CSHL's Quantitative Biology Center


Bruce0137apart2.jpgNEW YORK (GenomeWeb) – Cold Spring Harbor Laboratory said this week that it has received a $50 million gift from the Jim and Marilyn Simons Foundation and will use the funds to expand and improve its quantitative biology center.

The so-called Simons Center for Quantitative Biology will support research and education programs at CSHL with the help of faculty experts in applied mathematics, computer science, theoretical physics, and engineering. These investigators will be involved in basic research on illnesses such as cancer, autism, bipolar disorder, and depression.

So far, CSHL has tapped Adam Siepel, an associate professor of biological statistics and computational biology and associate director of the Center for Comparative and Population Genomics at Cornell University, to chair the center. He will move to CSHL this summer and start work in September.

In addition, the center has at least eight researchers on staff and plans to recruit more, according to CSHL President and CEO Bruce Stillman. Following [this week's/last week's announcement], BioInform interviewed Stillman about this recruiting effort, CSHL's vision and goals for its quantitative biology center, and how the incoming funds will support those efforts. What follows is an edited version of the conversation.

This is a two-part question. What's CSHL's vision for its quantitative biology center and what are the Simons Foundation funds going to be used for?

We received an initial $10 million gift from the CV Starr Foundation to appoint new faculty in quantitative biology and then the $50 million gift from the Jim and Marilyn Simons Foundation to establish the Simons Center for Quantitative Biology. [Editor's note: the initial $10 million gift was given in 2009]

Even before the human genome [was] completed about a dozen years ago, Cold Spring Harbor set up a genome center to work on functional genomics. That is really focused on using genomic techniques to do biology. We had developed a number of important technologies here including representation difference analysis, a technique that can compare the structure of two related genomes such as a tumor genome and the surrounding normal tissue. Exome sequencing was developed here, [as was?] a technique to re-sequence all the coding regions of a genome, and, later on, the ability to do whole genome sequence analysis on single cells. This obviously generates very large amounts of data and we felt that it was important that we had people who had a background in statistics and other forms of mathematics to be able to help analyze this data. Although they will have research programs that are on their own, we envisioned collaborations between these QB faculty and our biomedical scientists. Although we had many scientists working in the labs who were doing human genetics and genomics, we needed much more in-depth expertise … [in] mathematics and statistics and physics.

That was the genesis of starting the quantitative biology program. And the $50 million gift from Jim and Marilyn really enabled that to happen because they provided [the] essential endowment funds to expand the program considerably. [Prior to this] we would have had to collaborate with a lot of people outside the institution, but there is nothing like having people with this kind of knowledge embedded in the research environment here.

What specifically will you do to expand the center's activities?

We had people here who were doing this quantitative analysis of large data sets, but with the pledge of these funds, we will be able to secure additional people including hiring about eight or nine faculty who work in this area. And then most importantly, we were searching for a chair of the program and we were very lucky to attract Adam Siepel. He will arrive next month and start full time in September. We have already recruited some assistant professors and now that Adam is coming we will recruit additional people. He will lead that effort.

Will you have to purchase any infrastructure for the center?

In 2009 we opened some new research buildings at Cold Spring Harbor, one of which was built specifically for quantitative biology. In the building infrastructure, we included a large computer center with lots of storage and analysis space. This is not only for genomics but also for imaging analysis, we do a lot of high-resolution imaging of activity in the brain and also what's called mapping brain connectivity between the different regions of the brain. We had built that facility in anticipation of starting a program like this.

What are some of CSHL's projects that have benefitted or might benefit from the center's expertise and resources?

A lot of the projects but not all of them involve genomic analysis. One of the biggest projects we've had here is the analysis of the genetics of diseases of cognition, such as autism, schizophrenia, and bipolar disorder. With funding from both private and government sources, CSHL under the leadership of Mike Wigler has been one of the leading centers to understand the genetics of autism. And we are also now following up doing bipolar and schizophrenia. The idea that spontaneous mutations in the genomes are part of the cause for autism really emerged from studies [done] here by Mike Wigler and his collaborator who are members of our quantitative biology program.

We also have a scientist Partha Mitra who is mapping the connectivity of the brain and has generated a large dataset on how different regions of the brain are connected. He has a background in mathematics and physics that has been instrumental in collecting and analyzing this data in a very sophisticated way.

My own laboratory has benefitted from collaboration with one of the quantitative biology faculty Alex Krasnitz who has a background in physics. We did some interesting cancer genetics together.

Will the center only support CSHL's activities or will you open it up to external collaborations?

It's mostly to support the in-house research; however, our faculty in this program will collaborate with lots of people outside the institution and in fact are already doing that. For instance in the autism program, the sequencing of the genomes from a large number of families is happening at three different centers in the US and our quantitative biology people will be collaborating with those scientists to analyze the data. Equally importantly, with the recruitment of Adam Siepel, CSHL already teaches a number of advanced courses in quantitative biology as part of our meetings and courses program and I would like to expand that with Adam's help. This will benefit the entire community because these courses are already very popular and we need to expand [them].

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