2020 Workshop on Genomics, Český Krumlov Faculty


 

dag_ahrenDag Ahrén
Lund University, Sweden
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Arrival: 2 Jan, Departure: 18 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, Rayan Chikhi, Sonya Dyhrman, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

rayan_chikhi

Rayan Chikhi
Institut Pasteur, France
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Arrival: 5 Jan, Departure: 15 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. Dr. Chikhi along with Scott Handley, Dag Ahrén, Sonya Dyhrman, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

Sonya Dyhrman
Columbia University, USA
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Arrival: 5 Jan, Departure: 6 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, Rayan Chikhi, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

Evan Eichler
University of Washington, USA
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Arrival: 10 Jan, Departure: 12 Jan

Prof. Eichler is a Professor of Genome Science at the University of Washington. His research interests are as follows – genomic duplication followed by adaptive mutation is considered one of the primary forces for evolution of new function. Duplicated sequences are also dynamic regions of rapid structural change during the course of chromosome evolution. The long-term goal of his research is to understand the evolution, pathology and mechanism(s) of recent gene duplication and DNA transposition within the human genome.  His team’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.

 

Kirk Gosik
Broad Institute, USA
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Arrival 14 Jan, Departure 17 Jan

Dr. Gosik is a Post Doctorate Associate at the Broad Institute. His research focus on computational biology and statistical genetics/genomics, mainly working with single cell RNA sequence data.

 

Malachi Griffith
Washington University, USA
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Arrival: 8 Jan, Departure: 12 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: 9 Jan, Departure: 14 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.

 

Scott Handley
Washington University, USA
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Arrival: 5 Jan, Departure: 16 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 Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Guy Leonard and Josie Paris are the Workshop Co-directors.

 

Guy Leonard
University of Oxford and University of Exeter, UK
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Arrival: 2 Jan, Departure: 20 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 Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Scott Handley and Josie Paris are the Workshop Co-directors.

 

Antoine Limasset
Université de Lille & CNRS, France
Personal Page

Arrival: 7 Jan, Departure: 16 Jan

Dr. Limasset is a tenured research scientist at CNRS who works on genome assembly, read correction, graphs, and data structure.

 

Camille Marchet
Université de Lille, France
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Arrival: 7 Jan, Departure: 16 Jan

Dr. Marchet is a postdoc researcher working in BONSAI team (Lille, France), with Rayan Chikhi and Mikaël Salson. After a MSc in Ecology and Evolution from Université Claude Bernard Lyon 1 and an engineer degree in Bioinformatics from INSA de Lyon. She worked as an engineer for two years before obtaining PhD funding in GenScale team (Rennes, France). Her postdoc takes part in Transipedia ANR. Transipedia aims at being a transcriptome-encyclopedia, e.g., facilitating indexing, query and exploitation of the numerous publicly available RNA-seq data. She is mostly working on new data structures to index large collections of NGS datasets. Before and during her PhD, she worked on methods for transcriptomics, in particular for de novo variants discovery and RNA long read analysis.

 

Josie Paris
University of Exeter, UK
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Arrival: 2 Jan, Departure: 18 Jan

Dr. Paris 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 Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Sophie Shaw, Scott  Handley and Guy Leonard are the Workshop Co-directors.

 

Christa Schleper
Universitat Wien, Austria
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Arrival: 15 Jan, Departure: 16 Jan

Prof. Schleper works in the Archaea Biology and Ecogenomics Division at the Universitat Wien. Her group are interested in the natural diversity and ecological distribution of archaea as well as in their viruses and virus defense systems. Their specific projects include, genomic and proteomic studies of ammonia oxidizing thaumarchaeota from soils, marine sediments and hot springs; cultivation of novel lineages of archaea and ecogenomics of Lokiarchaeota;  and virus defense and CRISPR-mediated RNA degradation in the hyperthermophilic archaeon Sulfolobus solfataricus.

 

Sophie Shaw
University of Aberdeen, UK
Personal Page

Arrival: 2 Jan, 18 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 Rayan Chikhi, Sonya Dyhrman, Dag Ahrén, Guy Leonard, Scott Handley and Josie Paris are the Workshop Co-directors.

 

Emiliano Trucchi
Marche Polytechnic University, Italy
Personal Page

Arrival: 14 Jan, Departure: 1 Feb

Dr Trucchi enjoys researching the genomic revolution in molecular ecology and evolutionary biology. He is working on many great projects (in phylogeography and population genetics, genotype-phenotype mapping, landscape genetics, speciation genomics of species complexes,…) but his current hot research topic is epigenetics and its evolutionary potential. Dr. Trucchi is also a co-director for the Workshop on Population and Speciation Genomics.

 

chris_wheatChris Wheat
Stockholm University, Sweden
Faculty Page

Arrival: 13 Jan, Departure: 18 Jan

The Wheat lab investigates fundamental questions in evolutionary biology using a range of species and methods. While we primarily work upon butterflies, we also have collaborations with people working on mussels, dragonflies, beetles and fish. Although we extensively integrate OMICS data (whole genome sequencing, RNA-seq, Pool-seq, metabolomics), we also use butterfly nets, respirometers, and CRISPR. We investigate the genetics of diapause, immune performance, wing coloration, life history tradeoffs, plasticity and coevolutionary escalation.

 

Kelly Wrighton
Colorado State University, USA
Personal Page

Arrival: 12 Jan, Departure: 15 Jan

Dr. Wrighton works at the Colorado State University. In her laboratory, computational systems biology approaches result in predictions of metabolic potential in both individual microorganisms and microbial communities. These insights underpin laboratory investigations targeting physical, chemical, and biological controllers on biogeochemical processes. I couple holistic and reductionist approaches to interrogate the interactions between organismal bioenergetics, interconnected community metabolism, and chemical processes.

 

Mike Zody
New York Genome Center, USA
Personal Page

Arrival: 6 Jan, Departure: 11 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
2019

Julian Catchen
Rayan Chikhi
Bill Cresko
Sonya Dyhrman
Malachi Griffith
Brian Haas
Daniel McDonald
Antonis Rokas
Zachary Skidmore
Jacob Steenwyk
Hannah Tavalire
Amy Willis
Mike Zody

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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