2013 Workshop on Genomics, Český Krumlov Faculty
Dr. Beiko’s primary area of focus is in microbial evolutionary genomics and metagenomics. He is particularly interested in what particular traits make an organism suited to a given habitat, and what evolutionary processes can lead to the emergence and spread of these traits.
Dr. Bielawski’s research interests include molecular evolution, phylogenomics, metagenomics, and statistical methods to detect adaptive evolution.
Dr. Catchen is interested in using next-generation sequence data to study non-model and model organisms. He is also interested in how next-generation sequencing can be applied to the study of natural populations. Dr. Catchen will be providing a lecture on the use of next-generation sequencing to study non-model organisms as well as providing a laboratory exercise on how to use Stacks to build loci out of a set of short-read data.
Dr. Chikhi’s research interests are focused on computational theory for de novo assembly of short DNA sequencing reads including algorithms and data structures, graph theory, high-performance computing, parallelism, and DNA sequencing.
The goal of Dr. Cresko’s research group is to understand how changes in allele frequencies affect distributions of developmental processes in natural populations, and, once evolved, how these developmental programs alter subsequent evolutionary change. They use a variety of molecular, developmental, population and quantiative genetic approaches to address these questions. Most of the empirical work focuses on the threespine stickleback, Gasterosteus aculeatus, and members of the closely related family Syngnathidae.
Dr. Garber is interested in how next-generation sequencing can be used to describe an organisms transciptome and how this information can be used to elucidated gene structure. Dr. Garber will be providing an overview lecture on transcriptomics and a laboratory session on how a program he helped develop, Scripture, can be used to analyze RNA-seq data.
Dr. Handley is interested in viral evolution and how microbial ecology can alter disease state in mammals. Dr. Handley along with Naiara Rodriguez-Ezpeleta and Karin Rengefors are the Workshop Co-directors.
Daniel McDonald is a graduate student within the Interdisciplinary
Quantitative Biology program at the BioFrontiers Institute at the
University of Colorado. He is co-advised by Drs. Rob Knight (based at
the BioFrontiers Institute) and Phil Hugenholtz (based at the
Australian Centre for Ecogenomics). Daniel’s primary focus is the
development and improvement of the Greengenes 16S rRNA database and
taxonomy, and is a core developer for the Quantitative Insights into
Microbial Ecology, the BIOM-format and PyCogent packages.
Dr. Paszkiewicz is a bioinformatician with a strong interest in sequencing technology and whole genome analysis for a wide variety of organisms.
Dr. Ponting’s research lies at the intersection between computational genomics, evolution and human disease genetics. His laboratories research seeks to understand the roles of proteins, non-coding genes and other functional elements in the evolution, development and disease-susceptibility of humans. His lab studies how our DNA is conserved, with respect to other species, or how it is different among members of our own species. Computational findings are used to design experiments that elucidate function at different scales, from single bases to whole genomes.
Dr. Rengefors research focus is on understanding the processes underlying speciation and biogeography in aquatic protists. Her approach is to study these processes at the population level by investigating genetic diversity, population genetic structure, dispersal, and local adaptation. Dr. Rengefors along with Scott Handley and Naiara Rodriguez-Ezpeleta are the Workshop Co-directors. She is also the director of the Graduate School in Genomic Ecology (GENECO) at Lund University, Sweden, which is a partner institution of the workshop.
Dr. Rodriguez-Ezpeleta has extensive experience in genome-scale phylogenetics and the study of early eukaryotic evolution. She is co-directing the Workshop along with Karin Rengefors and Scott Handley and will play a critical role in the curriculum design and on-site management of all Workshop activities.
In Dr. Rokas’ group the DNA record is studies to gain insight into the patterns and processes of evolution as well as to understand the evolution of the eukaryotic genome. They do so using both computational and experimental approaches to address questions in two major thematic areas: I. How can we increase the accuracy of methods to reconstruct the tree of life? II. What are the molecular foundations of the fungal lifestyle?
Dr. Zody is the Chief Technologist for the Broad Institute. He has been involved with a large number of whole-genome sequencing and comparative genomics projects.
Faculty from Previous Workshops