2017 Workshop on Genomics, Český Krumlov Faculty


dag_ahrenDag Ahrén
Lund University, Sweden
Personal Page

Arrival: 4 Jan, Departure: 23 Jan

Dr. Ahrén’s primary interest is understanding genetic and genomic mechanisms related to fungal host interactions (parasitic as well as symbiotic). Typically he applies genomics and transcriptomics approaches coupled with bioinformatics analyses to provide novel insights into fungal host interactions. Dr. Ahrén along with Konrad Paszkiewicz, Scott Handley, and Karin Rengefors are the Workshop Co-directors..


Julian M. Catchenjcatchen
University of Illinois, USA
Personal Page

Arrival: 8 Jan, Departure: 18 Jan

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.



Rayan Chikhi
CNRS Lille, France
Personal Page

Arrival: 10 Jan, Departure: 21 Jan

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.


Bill Cresko
University of Oregon, USA
Personal Page

Arrival: 12 Jan, Departure: 20 Jan

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.


Sonya Dyhrman
Columbia University, USA
Personal Page

Arrival: 11 Jan, Departure: 22 Jan

Members of the Dyhrman group are broadly interested in how marine microbes interact with each other and their geochemical environment, looking at the interface of microbial physiology and the biogeochemical cycles of carbon, nitrogen and phosphorus. Much of their current work leverages ‘omics’ approaches to examine the physiological ecology of microbes that play a keystone role in marine ecosystems.


Evan Eichler220px-Evan_Eichler
University of Washington, USA
Personal Page

Arrival: 7 Jan, Departure: 9 Jan

The long-term goal of Dr. Eichler’s research is to understand the evolution, pathology and mechanism(s) of recent gene duplication and DNA transposition within the human genome.  The lab’s work involves the systematic discovery of these regions, the development of methods to assess their variation, the detection of signatures of rapid gene evolution and ultimately the correlation of this genetic variation with phenotypic differences within and between species.


Brian Haas
Broad Institute, USA
Personal Page

Arrival: 15 Jan, Departure: 20 Jan

Brian Haas is a senior computational biologist at the Broad Institute. He is one of the authors of the well-known transcriptome assembler Trinity.


Jennifer Gardy
University of British Columbia, CanadaJennifer Gardy
Personal Page

Arrival: 19 Jan, Departure: 21 Jan

Dr. Gardy is a Senior Scientist at the British Columbia Centre for Disease Control, responsible for the genomics/molecular epidemiology portfolio in Communicable Disease Prevention and Control Services.


Scott Handley
Washington University, USA
Personal Page

Arrival: 8 Jan, Departure: 24 Jan

Dr. Handley is interested in how viral and bacterial communities impact health and disease in humans. His research program is split between investigating the gut virome and bacterial microbiome in either AIDS or IBD. Dr. Handley along with Konrad Paszkiewicz , Dag Ahrén, and Karin Rengefors are the Workshop Co-directors.


mcdonald_danielDaniel McDonald
University of California San Diego, USA
Personal Page

Arrival: 14 Jan, Departure: 22 Jan

Dr. McDonald is a bioinformatics scientist in the Knight lab at the University of California San Diego, and his primary interest is in the study of the human microbiome in relation to health. Daniel’s graduate work was done under the mentorship of Dr. Rob Knight and focused on the development of the American Gut Project, Quantitative Insights into Microbial Ecology (QIIME), Greengenes 16S rRNA database, and the BIOM-format.



Paul McMurdie
Whole Biome, USA
Personal Page

Arrival: 14 Jan, Departure: 19 Jan

Dr. McMurdie is a Biostatistician at Whole Biom, helping to develop microbiome-oriented therapeutics for the treatment of specific human diseases. His interests include development of new analytical and computational tools required of this growing area of medical science, especially the analysis of complex multivariate datasets and machine learning, with an emphasis on open-source tools and the R language in particular. Paul is also responsible for phyloseq, an R package for reproducible analysis and graphics of microbiome data.



Konrad Paszkiewicz
University of Exeter, UK
Faculty Page

Arrival: 4 Jan, Departure: 23 Jan

Dr. Paszkiewicz is a bioinformatician with a strong interest in sequencing technology and whole genome analysis for a wide variety of organisms. Dr. Paszkiewicz along with Scott Handley, Dag Ahrén, and Karin Rengefors are the Workshop Co-directors.


Karin Rengeforsrengefors_portrait
Lund University, Sweden
Faculty Page

Arrival: 4 Jan, Departure: 23 Jan

Dr. Rengefors’ research focus is on understanding the processes underlying speciation and biogeography in phytoplankton. Her approach is to study these processes at the population level by investigating genetic diversity, population genetic and genomic structure, dispersal, and local adaptation. Dr. Rengefors along with Konrad Paszkiewicz, Scott Handley, and Dag Ahrén are the Workshop Co-directors.


Ramunas Stepanauskas
Bigelow Laboratory for Ocean Sciences
Faculty Pagerstepanauskas

Arrival: 17 Jan, Departure: 21 Jan

Dr. Stepanauskas research group studies biogeochemical roles, trophic interactions, evolutionary histories and biotechnological potential of microorganisms inhabiting oceans, deep subsurface, and other environments. His group has developed robust methods and high-throughput infrastructure for microbial single cell genomics, which uncovers hereditary information at the most basic level of biological organization and provides genomic blueprints of the vast “microbial dark matter”.


Tobias Uller
Lund University, Sweden
Faculty Pageuller

Arrival: 18 Jan, Departure: 21 Jan

Dr. Uller is interested in the relationships between development, heredity and evolution. His study systems include lizards, frogs, birds and, more recently, water fleas (Daphnia), which are good models to study how development can contribute to evolution in laboratory settings. His group uses a range of tools from genomics to comparative and meta-analytical methods.


chris_wheatChris Wheat
Stockholm University, Sweden
Faculty Page

Arrival: 16 Jan, Departure: 25 Jan

Dr. Wheat’s research is focused on finding and studying the genetic variation causing performance and fitness variation in natural populations of the butterfly Pieris napi, as well as putting this into an evolutionary context. They use whatever tools we can to address a given question, from butterfly nets to genomes.


Mike Zody
New York Genome Center, USA
Personal Page

Arrival: 8 Jan, Departure: 13 Jan

Dr. Zody is the Research Director of Computational Biology at the New York Genome Center, formerly 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

Julian Catchen
Rayan Chiki
Bill Cresko
Sonya Dyhrman
Evan Eichler
Toni Galbaldón
Brian Haas
Daniel McDonald
Paul McMurdie
Antonis Rokas
Gosia Trynka
Chris Wheat
Mike Zody

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  1. Pingback: Faculty Highlight: Dr. Rob Knight | Evolution and Genomics

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