Allen Rodrigo, Principal Investigator. Director of NESCent and Professor of Biology at Duke. I did my undergraduate degree and PhD at the University of Canterbury in New Zealand. I had postdoc appointments at the University of Auckland and Stanford, and later, I became an Acting Assistant Professor at the University of Washington. I moved back to the University of Auckland in 1999. I was a Professor of Computational Biology and Bioinformatics and Director of the Bioinformatics Institute. I joined Duke in February 2010.
Steven Wu, Postdoctoral Fellow. I completed my PhD at the University of Auckland, New Zealand, in 2010. For my PhD dissertation, I developed novel statistical methods to analyze proteomic and clinical data associated with pregnancy-related diseases. My primary research interests are developing novel statistical and computational methods to address biological problems and understand the underlying biological processes. I have used various statistical techniques over the years, including Bayesian inference, multidimensional analysis, and hierarchical modeling. In addition, I use simulation techniques to gain insight into the behavior of biological processes and this is then used to construct more realistic statistical models. Currently I am developing a novel algorithm to estimate evolutionary parameters (e.g. effective population size) from next generation sequencing data for individuals sampled from a single species. Another project I am currently working on involves the construction of a pipeline to analyze metagenomic data from lemurs and understanding the genetic functions of their microbiomes. A third project involves estimating the divergence time of a group of fungi using genomic data. (Steven’s software resources, including programs for the statistical analysis of 2D-PAGE data are available here).
Fabricia Nascimento, Adjunct Postdoctoral Fellow. I am currently doing a postdoc at NESCent on the evolutionary dynamics of endogenous retroviruses. I have also a strong interest on mammalian phylogenetics and biogeography. I did both my undergraduate and Masters degree in Brazil at the Universidade Federal do Rio de Janeiro and Oswaldo Cruz Foundation, respectively. At that time I was working on population genetics of howler monkey populations from Brazil. I did my PhD at the University of Sydney, Australia on the evolution of pigs and their endogenous retroviruses. I returned to Brazil for three years and I worked on phylogeography of small mammals of Brazil. This year I started a postdoc position at NESCent. (Check out Fabricia’s blog).
Yuantong Ding, Graduate Student. I received my bachelor’s degree from Fudan University in Shanghai (2012) and I’m currently a PhD student at Duke University in the Department of Biology. During my undergraduate studies, I tried different “wet lab” projects including a phytogeography study of Hippophaec tibetana schlechtend (a plant in Tibet), identification of a new extremophile from acid mine drainage and synthetic of a E. coli nitrate detection system. But finally I developed an interest in computational biology. Here at Duke, I just finished a comparison study of programs for assembling Next Generation Sequencing (NGS) data. And recently I’m interested in a new project, which aims to understand cancer evolution and applies population genetic/phylogenetic analyses on cancer cell samples to predict likely clinical outcomes.
Erin McKenney, Graduate Student. I study gut microbiota in lemurs, and am co-advised by Allen Rodrigo and Anne Yoder. I am interested in microbial community ecology, given that microbes use lateral gene transfer to share genetic material across vast phylogenetic distances. I am using a combination of 16S and metagenomic sequencing to monitor succession processes and general dynamics, across life stages, health, and disease, between four lemur species. I earned my Bachelor’s degree in Biology at UNC-Chapel Hill, and my Master’s in Animal Science at NC State University. I have also completed three internships focusing on exotic animal husbandry, nutrition, and rehabilitation. 2013 Marks my third year both at Duke and teaching Natural Science at the NC Governor’s School.
Qinglong Zeng, Graduate Student. I’m a graduate student in the Rodrigo lab. I joined in Dec 2012 and I’m interested in modelling the ecological and evolutionary dynamics of microbiomes. Microbiomes play an important role in maintaining the health of their hosts: microbial communities assist with digestion of nutrients and protect hosts from pathogen invasion. There are many sequencing projects that generate massive amounts of genetic data to characterize the microbial community associated with human health and disease; however, many current biological perspectives of microbiome evolution are based on limited observations of microbial communities. I would like to develop computational models that provide a basic framework for understanding the evolution of the microbiome and incorporate broad ecological views of the variation of microbial community over time and amongst hosts.