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Brown University's David Rand on Goals, Priorities for New Computational Biology Center of Excellence


NEW YORK (GenomeWeb) – Brown University recently unveiled plans to launch a Center for Biomedical Research Excellence (COBRE) in Computational Biology of Human Disease supported by a five-year $11.5 million grant from the National Institutes of Health.

The new center is expected to support ongoing collaborative projects involving junior and senior researchers from several of the university's departments including its computer science, applied mathematics, biology, medicine, and public health departments. The institution will also focus on building a bioinformatics core within the center where expert staff will develop algorithms and programs that will support its research projects, according to Brown.

This first round of funding will support five teams of scientists, in which younger faculty members will pursue projects under the mentorship more senior professors. One of these projects will focus on using bioinformatics tools to identify the genomic and cellular mechanisms that enable viral and bacterial co-infection in the lung, while another project will use bioinformatics tools to screen genomic data from fruit flies to identify new drug targets.

A third project will develop computational and analytical methods for identifying risk genes for leukemia that differ in incidence across ethnic groups and genders. The fourth project will assess potential variants associated with preeclampsia, and the fifth will study spatial variation in the gut microbiome in response to antimicrobials and immunity pathways.

Recently, GenomeWeb spoke with David Rand, chair of Brown's department of ecology and evolutionary biology and director of the new center, to discuss the goals and priorities of the center in more depth. The following is an edited version of the conversation.

Brown University already has a computational biology center, so what's the purpose and benefit of establishing a second one?

Most of the centers at Brown, including the existing Center for Computational Molecular Biology, are research-oriented centers where the faculty work or collaborate on a central idea. The goal of this new COBRE is really to provide a service center for computational biology to aid junior faculty. Most of the research centers don't have dedicated staff to help people do things. These are intellectual centers more than 'repair shops' for data questions. The COBRE center is a core of data scientists who will aid junior faculty in accomplishing their research, and that's really the main distinction from the other existing centers that are really research-based. This is service-oriented. [And], we are hiring data scientists to provide a foundation of computational services for junior faculty. 

So you've already selected five inaugural projects for the center. What was the rationale for selecting these particular projects?

We wanted a mixture of wet bench and dry lab scientists. So, people generating new genetic sequences for their research and others who are more computational and analytical who would use existing databases. We also wanted it to encompass more than one disease. The common theme in each of these [projects], whether they are generating new data or analyzing existing data like the 1000 Genomes Project data, are the pipelines for data analysis. [These] are actually quite similar.

The rationale was to increase the breadth of exposure and therefore build a service that would be able to accommodate a variety of data science pipelines that would be useful for the community in the future.

You have been awarded an $11.5 million grant from the NIH for the center. Have you begun allocating funds for the projects yet?

We are just starting. The majority of the money goes to the individual junior investigators for research in their labs. The next big chunk of support covers the salaries for the data scientists who will work in the COBRE center. The main goal of these COBRE awards is really to foster research [that will] promote junior faculty and get them to the next stage of independent NIH funding. That's the primary goal. Often, if a faculty member has to perform computational analyses on genomic data on their own grant, they usually don't have funds to hire a separate, dedicated computational person in their labs.

We will hire four data scientists who can work together in a core facility, and consolidate redundancies that five independent labs would have if they were working alone.

About how much will each project get?

Each junior investigator gets about $175,000 a year in direct costs for their own lab. Most of the remaining funds go towards hiring the core facility staff that will support the research of the junior faculty, and additional mentoring programs that will help junior faculty become more competitive for new external grant funding.

What sort of infrastructure do you have to put in place to support the center?

There are existing computational scientists at Brown who do computational science as a discipline and run the supercomputer here. Some of these people will work [with the junior faculty].

The way this COBRE program is intended is that each of the data scientists will affiliate with one or two of the junior faculty members … and get actively involved in their research programs. The model is to hire people who are embedded in the research as data scientists. They may not be biologists but they understand enough biology to participate in the lab group. Human infrastructure is really what we are putting in place.

What is your role as director of the center?

My role is to oversee the whole project and make sure that the goals of the project are being met at a regular schedule. My primary goal is to graduate the junior faculty members. [As] they get external funding, they move out of the COBRE support and onto other NIH support. Then my role is to work with the executive committee to identify new junior faculty who are compatible with our goals and bring them into the support system and [get] them through the pipeline, so to speak.

Our goal is human infrastructure and efficient workflow among personnel. We want to identify new junior faculty who fit the model that we are trying to advance and get them involved in the program as the program matures. So that's my role.

Do you see opportunities for collaboration with COBREs at other institutions?

That's an important goal of the COBRE mechanism — it's to be in touch with other investigators who are supported by COBRE awards and connect with them [and] identify areas for collaboration. We certainly will reach out to these other COBRE centers that are nearby. Next week, I'll go to a COBRE PI meeting in Washington to learn from others who have run COBRE's and hear about best practices. And there are several COBRE programs here in Rhode Island that are doing different things, and we will certainly interact with them and learn from their experiences.

What tangible contributions do you hope the center will make to life science research?

The primary goal is to ensure the success of the junior faculty. The tangible results from that will be research findings from their groups. One is working on ethnic diversity in cancer risk, two others are working on the host's impact on microbiome and the roles in human co-infection and disease, and one is working on gene expression effects in aging and trying to match those to similar gene expression profiles for drugs. And one is working on preeclampsia and one tangible outcome of that would be the identification of risk factors for preeclampsia that would identify the mechanisms underlying the causes of this disease that will open the door for new treatments.

Those are the tangible outcomes we expect out of these research programs. Another one would be a body of algorithms or data analysis pipelines that could be used by multiple labs at Brown and elsewhere. That is a longer term goal … to have this center blend into the Brown infrastructure in the years ahead so that our computational biology [and] data science core facility would be built and be able to serve the broader research community at Brown and the affiliated hospitals in the future  

How do you plan to sustain the center in the long-term, especially in the current climate when research funding is harder to come by?

The COBREs typically have three phases. Phase one is the first five years where we implement and establish this core facility and graduate junior faculty onto independent funding. The next phase is a competitive renewal, and we need to demonstrate that we have done what we proposed to do in phase one. We've already started planning for that right now. We make sure we hire the right data scientists, we set them up in a network where the working environment is attractive so that they will stay. Some of the support actually goes to a small fraction of salary time for senior faculty who serve as mentors for the junior faculty, and we want to ensure that this mentoring program is effective.

If we can show in the next five years that we've moved the junior faculty on to funding, and that we've brought in new people into the system, and the core is running effectively, and the methods are working, we should be able to make a case that we are competitive for the second phase. [That] would be where we blend the core more into other support mechanisms. So, other researchers at Brown would be able to buy the time of the data science group and provide other means of support for them to grow into a larger facility. If we can demonstrate that, I think we'll be competitive for the next phase.