Chris Vulpe
Associate Professor, Department of Nutritional Science and Toxicology, University of California, Berkeley
Associate Professor and Associate Toxicologist in the Agricultural Experiment Station
Office : 317 Morgan Hall
Tel : (510) 642-1834
Fax : (510) 642-0535
Email : vuple(at)berkeley(dot)edu
Ph.D. 1994, Genetics, M.D. 1996, University of California, San Francisco
Postdoctoral Researchers
Hun-Je Jo
Projects involved with: Ecotoxicogenomics
My research has focused on characterization and identification of toxicants in water environment and prediction of their toxicity. Now I am studying on ecotoxicogenomics of water flea Daphnia magna, which plays a key role in the aquatic food chain. Development of daphnia biosensor through establishing database of gene expression profiles of D. magna exposed to a variety of chemicals and computational analyses allow to characterize and/or identify toxicants in field assessment.
Email: hunje.jo(at)berkeley(dot)edu
Ph.D. 2008, Aquatic Toxicology, Korea University, Korea
Stela Masle
Projects involved with: Copper and Iron Metabolism
My main research interest is genetic analysis of complex traits. Currently I am working on a project that studies the association between key genes involved in iron metabolism and the presence of iron deficiency in humans. At the same time I am involved in a project aiming to identify quantitative trait loci (QTL) that have an effect on iron metabolism in inbred mice, by means of in silico QTL mapping and gene expression analysis.
Email : masle(at)berkeley(dot)edu
Ph.D. 2007, Institute for Animal Breeding, Ludwig-Maximilian-University, Germany
Matthew North
Projects involved with: Toxicant Susceptibility
I am using the budding yeast Saccharomyces cerevisiae to identify genes involved in the response to treatment with priority Superfund contaminants, in particular benzene and its metabolites. Using a variety of techniques I am attempting to identify genes that could act as biomarkers of benzene toxicity and exposure in humans, as well as elucidating the mechanisms of toxicity of benzene and its metabolites, all of which are used extensively in industry.
Email : mnorth(at)berkeley(dot)edu
Ph.D. 2007, Molecular Biology, The University of Sheffield, UK
Data Analysis Specialist
Alex Loguinov
Projects involved with: Toxicant Susceptibility, Ecotoxicogenomics
(Microarray Bioinformatics / Data Analysis / Statistical Programming / Biostatistics)
Applying statistical, computational and programming tools to evaluation and validation of algorithms for gene expression data analysis based on microarray experiments (mostly in metal toxicology and plant physiology):
- Developed new robust single-slide and multiple-slide/chip algorithms for exploratory and confirmatory differential gene expression analysis using simultaneous tolerance/prediction intervals, regression smoothers (super smoother, lowess, loess), and outlier identification procedures (quantile-quantile normal plots with simulation envelopes, box plots for residuals etc.).
- Developed, debugged and maintained S-plus and HTML code to present results of single- and multiple-slide gene expression analysis as html-documents.
- Developed robust algorithms for exploratory and confirmatory differential yeast strain sensitivity analysis based on Affymetrix® purpose-built oligonucleotide microarrays for parallel deletion analysis.
- Applied methods for statistical inferences based on qPCR data sets.
- Applied statistical and programming methods to quantify dose-response relationships for toxicants at the whole genome level.
- Acted as a resource on microarray data analysis to staff scientists, research associates, and students with biological background.
- Applying statistical and computational methods to various experimental results based on “experiment vs. control” design.
Graduate Students
Vanessa De La Rosa
Brie Fuqua
Brandon Gaytan
Projects involved with: Toxicant susceptibility
I am a second year graduate student in Molecular Toxicology. My project aims to identify yeast genes involved in the response to various emerging contaminants, such as brominated flame retardants. Although these chemicals are utilized extensively in various consumer and industrial products, their toxicological data is lacking or insufficient. Additionally, I am interested in the idea of toxicity pathways- the cellular signaling pathways that are induced or perturbed in response to a toxicant. I am screening various "model toxicants" to help identify yeast toxicity pathways that may be conserved to higher organisms such as humans.
Email : bgaytan(at)berkeley(dot)edu
M.A. 2008, Biology, Clark University, Worcester MA
B.A. 2007, Molecular Biology and Computer Science, Clark University, Worcester MA
Leona Scanlan
Projects involved with: Ecotoxicogenomics
I am a third year graduate student in Molecular Toxicology and am analyzing Daphnia magna's genomic response to flame-retardants. I hope to 1) determine modes of toxicity and 2) develop a method for detecting flame-retardants in water, using D. magna. I also sequenced the D. magna expressed genome (mRNA) and am looking for novel genes and EST gene fragments..
Email : lds(at)berkeley(dot)edu
BS 2007, Molecular Toxicology, University of California, Berkeley
Research Technicians
Candace Clark
Don Pham
Projects involved with: Ecotoxicogenomics