Computational Biology & Bioinformatics

PHD in Computational Biology & Bioinformatics

Program Principles & Goals

CBB students and faculty at the annual retreat

Computational Biology and Bioinformatics (CBB) at Duke University is an integrative, multi-disciplinary Ph.D. program that trains future leaders at the interdisciplinary intersection of quantitative and biomedical sciences.

CBB brings together 55 faculty from 18 departments—including computer science, statistics, mathematics, physics, engineering, biology, chemistry, and medical departments—to conduct cutting-edge research across a wide range of topics in computational biology and to prepare students to engage in innovative solutions to modern problems in the biomedical sciences.

CBB provides high-quality training in both quantitative and biomedical sciences through coursework; research rotations; journal clubs; weekly seminars; and hands-on mentoring from advisors, co-advisors, and dissertation committees. Students are trained to work independently and as part of collaborative teams. They learn to conduct research responsibly, with a commitment to data sharing and reproducible analysis, and they have professional development and teaching opportunities as part of their individual development plans.

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Meet A Faculty Member

  • Daniel Lew
    James B. Duke Professor of Pharmacology and Cancer Biology

    During the cell cycle, the cyclin-dependent kinases (CDKs) at the center of the cell cycle clock trigger a diverse set of events, including remodeling of the cell’s cytoskeleton. A number of internal surveillance pathways called checkpoint controls assess how key events are progressing and, if there is a hitch in some important process, they signal the clock to wait until the defect is corrected. In the past few years we have learned a lot about how the central clock works. However, several central questions remain concerning how the CDKs actually trigger many of the events, and how the checkpoint controls “know” whether things are proceeding according to plan.

    We work with the tractable budding yeast as a model system, allowing us to make rapid progress on complex problems. One focus in the lab concerns a checkpoint pathway called the morphogenesis checkpoint, which monitors cytoskeletal polarization and bud formation, and inhibits G2 CDK activation if environmental stresses affect these processes. We are trying to understand how information about the cytoskeleton and cell shape is sensed and transmitted to the CDKs. A second focus concerns cell polarity, which is switched on by G1 CDKs and switched off by G2 CDKs in yeast. We would like to understand how global CDK activation makes cells develop (or dismantle) an asymmetric cytoskeleton. Because the genes and processes we study are highly conserved, we anticipate that learning the answers to fundamental questions in yeast will be relevant and informative for a wide range of organisms.

    Our research interests encompass questions on cell cycle control, the control of cell polarity, and the specification of distinct cortical domains within cells. We are also trying to understand how cells can monitor their shape and react to environmental influences that affect cytoskeletal behavior.
    One focus is the study of how the Cyclin Dependent Kinases (CDKs) that control cell cycle progression act to promote specific changes in cell polarity. A ras-related G protein, Cdc42p, is key for enacting changes in cell polarity involving reorganization of both actin and septins (a poorly understood filamentous system that specializes specific cortical domains) in response to CDK activity. We are tracing the links between the CDK and Cdc42p to understand how polarity is established, and the links between Cdc42p and the cytoskeleton to determine how polarized behavior is executed.
    A second focus involves investigation of a cell cycle checkpoint control that monitors cell shape. When environmental insults disrupt cytoskeletal organization, this checkpoint delays entry into mitosis through inhibition of CDK/cyclin kinases. A tyrosine kinase, Swe1p, is responsible for the cell cycle block, and we have found that the degradation of Swe1p is regulated both by cell shape and by perturbation of the actin cytoskeleton. Recently, we discovered that the septin cytoskeleton is directly affected by local cell shape, and that proteins controlling Swe1p degradation can monitor this septin change.
    The biological problems we address are universal, and the proteins that we study are widely conserved. We have chosen the experimentally tractable budding yeast as our experimental system and are using genetic, cell biological, and biochemical approaches to study these pathways.
Mengqi Zhang

Mengqi Zhang

5th year CBB Student; Andrew Allen Lab
Apr 1
Apr 8
Xihong Lin
Harvard University

CBB Seminar