Interdisciplinary Education at Rutgers–Camden Center for Computational and Integrative Biology

Rutgers–Camden Center for Computational and Integrative Biology

By Jeanne Leong

The Rutgers–Camden Center for Computational and Integrative Biology is delivering an innovative – and interdisciplinary – approach to solving complex biological questions while also teaching the next generation of leaders in science.

Comprised of five departments (biology, chemistry, computer science, math, and physics), the center offers an interdisciplinary degree at the undergraduate, master’s, and Ph.D. levels by training students to apply quantitative techniques from chemistry, computer science, math, and physics to design and interpret biological experiments.

Computational and integrative biology (CIB) graduate students come from a range of science majors and begin by taking complementary courses. “CIB graduate courses provide a supportive environment for students trained in the life sciences to get more comfortable with math, physics, or programming, and for students from math, computer science, or physics to learn biology and chemistry in a way that’s meaningful to them,” says Grace Brannigan, an assistant professor of physics and the CCIB’s graduate program director.

Most CIB graduate students conduct either experimental or computational research primarily in one CCIB research lab, but have two mentors, representing expertise in both experimental and computational approaches. Both mentors guide the student’s dissertation research.

“A lot of information is coming out of high-throughput experiments, including genome sequences, RNA sequences, and proteomics, which provide information about DNA, RNA, and proteins,” says CCIB Director Nir Yakoby, an associate professor of biology. “These large data sets are complex, and we need computational tools in order to analyze them.”

“Biomedical research is going to require increasingly more quantitative approaches in the future,” says Brannigan. “Even today, it is much harder to do interesting research in biology without using math or programming.”

Through access to the university’s high-performance computing center, including the most powerful supercomputer in New Jersey, researchers can analyze large amounts of data and run simulations.

“Biology is mostly a descriptive science,” says Yakoby. “We say, these are the interactions within networks, these are the molecules, and these are the expected outcomes. However, biology requires quantitative tools to determine how many cells are involved, how many molecules, what are the thresholds of reactions, when do they interact and for how long? Our students study multiple dimensions in integrative biology.”

The CCIB also offers an undergraduate program in computational biology that requires students to initially take basic courses in chemistry, biology, computer science, math, and physics. Later, students specialize in one of three tracks. The molecular option focuses mainly on chemistry and biology. The systems option provides a greater emphasis on mathematics and computer science. The physical option focuses on biophysics. CCIB also offers a five-year BS/MS track to accelerate progress toward the master’s degree.

Rutgers–Camden Center for Computational and Integrative BiologyRutgers University–Camden offers state-of-the-art equipment for teaching basic and advanced procedures in cytological, physiological, molecular, ecological, and environmental analyses. Through the CCIB, Rutgers–Camden faculty and student researchers can access resources that are comparable to (or exceed) those available at many larger universities. “We have a large amount of equipment and fewer people using it, so it just means that everyone has better access,” says Brannigan.

The CCIB is home to instrumentation that includes electrophoretic and DNA sequencing equipment, liquid chromatographic and TLC apparatuses, and a gas chromatograph. Researchers also have access to a scanning electron microscope equipped with energy dispersive X-ray for elemental analysis. The apparatus operates under low vacuum, allowing samples to be examined without traditional time-consuming and costly preparative methodologies.

In addition, the CCIB offers a large variety of imaging tools to students and researchers, including a Neoscope, transmitting electron microscope, confocal microscope facilities, and force atomic microscopy.

In the Yakoby lab, students study the process of cell differentiation, which is the process of cells’ specialization. “We all begin from one cell that divides to generate billions of cells, but these cells are not the same,” says Yakoby. “Some cells form the heart and others form the eye tissue. We try to understand how cells perceive the information about what to become, and what are the responses to obtain different types of cells. We focus on cell signaling pathways that are highly conserved across animals. Malfunction in these pathways is associated with tissues’ pathologies and different types of cancers.”

Yakoby has been collaborating with Benedetto Piccoli, the Lopez Chair of Mathematics and the associate provost for research at Rutgers University–Camden, to try to understand how the distribution of information in a developing tissue is happening. They use computational modeling to predict the mechanisms underlying the formation of diverse signaling patterns among species that evolved for over 65 million years. Yakoby also collaborated with Desmond Lun, a professor in computer science, and currently collaborates with Andrey Grigoriev, a professor in biology, who is also a bioinformatician.

Brannigan’s research involves using large-scale, physics-based molecular simulations to investigate molecular processes occurring in the brain that experiments can’t access. The physicist collaborates with Joseph Martin, a professor of biology and associate dean for STEM, and Eric Klein, an assistant professor of biology, to learn how hormones and cholesterol cause their effects on neuronal receptors. She also collaborates with faculty in the Perelman Medical School of the University of Pennsylvania to understand what allows anesthetics to affect these same receptors, which is crucial to improving and developing new anesthetics.

“The fact that we have a broad range of expertise in many different areas is definitely useful,” says Lun. “It’s very useful to have people with expertise to consult, and are nearby.”

“Many students graduate from the program with advanced programming or computational abilities, and even those focusing on experiments will be able work with computational researchers,” says Brannigan. “Incorporating computation into scientific research usually leads to a much more efficient and powerful process, so it is a skill highly valued by many employers.”

Master’s and Ph.D. students who have graduated from the CCIB program are now working at biotechnology companies, federal agencies such as the Food and Drug Administration, and post-doctoral positions in the Fox Chase Cancer Center and such prestigious universities as Princeton, Purdue, and Boston University.

Posted in: Research Highlights

Comments are closed.