2019 Workshop on Genomics, Český Krumlov Faculty


 

dag_ahrenDag Ahrén
Lund University, Sweden
Personal Page

Arrival: 3 Jan, Departure: 19 Jan

Dr. Ahrén’s primary interest is understanding genetic and genomic mechanisms related to fungal host interactions (parasitic as well as symbiotic). He works as a lecturer at Lund University and is a senior bioinformatician and NGS coordinator of the National Bioinformatics Infrastructure Sweden (NBIS). He also has a keen interest in targeted metagenomics using custom made probes for targeting important ecological processes such as carbon turnover and methane synthesis and degradation. Dr. Ahrén along with Scott Handley, Brian Haas, Sonya Dyhrman, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

 

Julian M. Catchenjcatchen
University of Illinois, USA
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Arrival: 13 Jan, Departure: 20 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

Rayan Chikhi
Institut Pasteur, France
Personal Page

Arrival: 8 Jan, Departure: 19 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: 7 Jan, Departure: 14 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: 6 Jan, Departure: 17 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. Dr. Dyhrman along with Scott Handley, Brian Haas, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

Malachi Griffith
Washington University, USA
Personal Page

Arrival: 8 Jan, Departure: 16 Jan

Dr. Griffith is the assistant director of the McDonnell Genome Institute (MGI) at the University of Washington. His research is focused on the development of personalized medicine strategies for cancer using genomic technologies. Over the last 15 years, he has worked on developing methods in data mining, genomics, and bioinformatics for application to cancer precision medicine.

 

Brian Haas
Broad Institute, USA
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Arrival: 8 Jan, Departure: 16 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. Dr. Haas along with Scott Handley, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

Scott Handley
Washington University, USA
Personal Page

Arrival: 5 Jan, Departure: 19 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 Brian Haas, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

Guy Leonard
University of Exeter, UK
Personal Page

Arrival: 3 Jan, Departure: 19 Jan

Dr Leonard works with comparative genomics, phylogenomics and genome assembly with an interest in the evolutionary relationships of eukaryotes and the cellular & genomic innovations of the diversity of eukaryotic cells. This led him to specifically look at the prevalence of gene fusion & fission events. More recently he has been trying to understand the adaptations and evolutionary history of a oomycete-relative, Hyphochytrium catenoides and the fungal-eye complex of the chytrid fungus Blastocladiella emersonii. Dr. Leonard along with Brian Haas, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Scott Handley and Josie Paris are the Workshop Co-directors.

 

mcdonald_danielDaniel McDonald
University of California San Diego, USA
Personal Page

Arrival: 7 Jan, Departure: 19 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.


Josie Paris
University of Exeter, UK
Personal Page

Arrival: 3 Jan, Departure: 19 Jan

Josie is an evolutionary biologist with interests in using population genomics in understanding how species adapt, particularly in a conservation and management context. She is especially interested in the use of genome-wide signals generated by massive parallel sequencing applications: whole-genome sequencing, RADseq and RNAseq. Josie is a postdoctoral research associate in the Fraser Lab working on a NERC-NSF funded project investigating the ecological genomics of adaptive polymorphism in the Trinidadian guppy (Poecilia reticulata). Dr. Paris along with Brian Haas, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Scott  Handley and Guy Leonard are the Workshop Co-directors.

 

Antonis Rokas
Vanderbilt University, USA
Personal Page

Arrival: 16 Jan, Departure 27 Jan

The Rokas lab study the DNA record to gain insight into the patterns and processes of evolution within several eukaryotic lineages, but mainly with mammals and fungi. They employ many novel computational and experimental approaches and investigate their utility for studying the function and evolution of the genomes of non-model organisms.

 

Sophie Shaw
University of Aberdeen, UK
Personal Page

Arrival: 3 Jan, 19 Jan

Dr. Shaw works as a Bioinformatician at the Centre for Genome Enabled Biology and Medicine. She provides analysis of numerous different data sets including differential expression analysis, transcriptomics, whole genome assembly and single cell genomics. Alongside this gives support to researchers analysing their own data. She is involved in the running of numerous international workshops focused on genomics analysis as well as teaching within her institute. Dr. Shaw along with Brian Haas, Sonya Dyhrman, Dag Ahrén, Guy Leonard, Scott Handley and Josie Paris are the Workshop Co-directors.

 

Zachary Skidmore
Washington University, USA
Personal Page

Arrival 9 Jan, Departure 16 Jan

Zach works as part of the Griffith lab at the McDonnell Genome Institute, with research focusing on the analysis and interpretation of next generation sequencing data as it relates to cancer biology. Specifically, he develops and employs methods in the areas of neoantigen discovery, cancer immunotherapy, precision medicine, and the analysis of large cohort data.

 

Hannah Tavalire
University of Oregon, USA
Personal Page

Arrival: 4 Jan, Departure 13 Jan

Dr. Tavalire is a postdoctoral scholar at the University of Oregon. Her research focuses on identifying genetic and environmental drivers of variation in the microbiome of humans and model organisms. She is particularly interested in the roles of early life trauma/stress and immune function in shaping the microbiome throughout life.

 

Amy Willis
University of Washington, USA
Personal Page

Arrival: 13 Jan, Departure: 16 Jan

Dr Willis works as an Assistant Professor in the Department of Biostatistics at the University of Washington, Seattle. Her work aims to develop statistical methods for the analysis of ecological data obtained from high throughput sequencing, with a particular emphasis on microbiome data.

 

chris_wheatChris Wheat
Stockholm University, Sweden
Faculty Page

Arrival: 10 Jan, Departure: 19 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: 6 Jan, Departure: 12 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
2018

Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Evan Eichler
Brian Haas
Sarah Hird
Eline Lorenzen
Daniel McDonald
Antonis Rokas
Karthik Shekhar
Mike Zody

2017

Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Evan Eichler
Jennifer Gardy
Brian Haas
Daniel McDonald
Paul McMurdie
Ramunas Stepanauskas
Tobias Uller
Chris Wheat
Mike Zody

2016

Julian Catchen
Rayan Chikhi
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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