Lab Members

Paul Magwene, Principal Investigator

Alt text My research is aimed at understanding how genetic networks work and how they have evolved. More specifically, my lab combines wet lab experimental techniques and the development of computational and statistical methods in order to characterize the properties of gene regulatory networks. A primary goal is to identify how genetic and environmental variation affects the functioning of regulatory networks, and how this variation relates to relates to intra- and interspecific patterns of phenotypic variation.

Email: paul.magwene@duke.edu

Postdocs

Joshua Granek

Alt text I am using wet lab and computational methods to investigate how genetic diversity effects developmental phenotypes in budding yeast (Saccharomyces cerevisiae). My research is centered on investigations in yeast colony morphology (CM). I am taking genomic scale approaches (chip based QTL mapping, expression microarrays) to dissecting the genetics and dynamics of CM (see figure, left is domesticated morphology, right is wild morphology), and understand the relation of this behavior with other developmental pathways (sporulation and pseudohyphal growth). I will ultimate use this data to construct and parameterize a model of the genetic network underlying CM, with the aim of modeling how genetic diversity produces the wide range of CM phenotypes. I also hope this information will help me understand the ecological significance of CM, and the intercellular communication necessary for this emergent behavior. I expect to expand our understanding of yeast developmental behavior by tying CM into our current model of development.

A few of my other interests include interaction between organisms, especially host-pathogen interactions, emergent behavior, and novel applications of computation to biological problems.

Email: josh@duke.edu

Jeni Reininga

Alt text

Email: jmreinin@duke.edu

Graduate Students

Omur Kayikci

Alt text Currently, I work on identifying causal genetic polymorphisms in sporulation and pseudohyphal developmental pathways in S. cerevisiae in response to an environmental stimulus, lack of nitrogen, using DNA sequencing, expression analysis and gene disruption/ allelic replacement.

I am broadly interested in comparative/functional evolutionary genomics of interactions of regulatory pathways that are involved in sporulation/pseudohyphal developmental responses. I attempt to look at dynamics, functionalities and diversities of the components of the interactions in unusually large IME1 promoter region. IME1 is an important part of a genetic regulatory network that directs sporulation response in S.cerevisiae.

Email: kayikci@duke.edu

David McCandlish

Alt text My primary interest is in the abstract, mathematical structure of the genotype-phenotype map and its consequences for evolutionary dynamics. Because the genotype-phenotype map is itself determined by the properties of particular physical and chemical systems, it seems reasonable to hypothesize that the genotype-phenotype map will often have large-scale, qualitative features that reflect its physical basis. However, detecting these large-scale features has been difficult because both the space of genotypes and the space of phenotypes are typically high-dimensional. My research focuses on the development of new techniques to overcome this problem. More specifically, I have worked to extend a common way of thinking about the genotype-phenotype map based on neutral networks (mutationally contiguous sets of genotypes that share a common phenotype) to encompass multivariate evolution. I have also developed a new method for visualizing fitness landscapes in terms of their effects on evolving populations.

My research combines analytic and simulation-based approaches with the analysis of large datasets. Other interests include the evolution of transcription factor binding sites and the philosophy of biology. I am co-advised by Dan McShea.

Email: david.mccandlish@duke.edu

Research Personnel

Debra Murray (Lab manager / Research scientist)