2019 Workshop on Phylogenomics, Český Krumlov Faculty

Toni Gabaldón
Center for Genomic Regulation, Spain
Arrival 20 Jan, Departure 2 Feb

Our research interests are focused around the use of comparative genomics and phylogenomics to study the origin, evolution and function of complex biological systems. This includes understanding how specific biochemical pathways, protein complexes or cellular organelles emerged and evolved as well as using this evolutionary information to gain insight into their function. Through collaborations with experimental groups we apply comparative genomics to discover new mechanisms and genes involved in interesting processes, especially those of clinical relevance. On the technical side, our work often involves the development of new bioinformatics tools and algorithms that we make available to the community.

Workshop co-director.


Scott Handley
Washington University, USA
Arrival 5 Jan, Departure: 19 Janhandley_scott

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.

Workshop co-director.


Antonis Rokas
Vanderbilt University, USA
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.

Workshop co-director.


Anna Karnkowska
University of Warsaw, Poland
Arrival 16 Jan, Departure 2 Feb

My research interest is in the diversity, evolution, and ecology of microbial eukaryotes. I am aiming to answer general questions about the eukaryotic cell evolution and energy production in aquatic environments by exploring the diversity of microbial eukaryotes. I use high-throughput sequencing and the bioinformatics analyses of a variety of species and communities from established cultures and from the environment.

Workshop co-director.


South China Agricultural University, China

Arrival 21 Jan, Departure 27 Jan

Xiaofan Zhou currently works at the Integrative Microbiology Research Centre, South China Agricultural University. Xiaofan does research in Bioinformatics, Evolutionary Biology and Comparative Genomics. Their most recent publication is ‘Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets.’


Alexey Kozlov
The Exelixis Lab, Heidelberg Institute for Theoretical Studies, Germany

Arrival 20 Jan, Departure 27 Jan

The Exelixis lab focus is on the evolution of hardware and parallel
computer architectures as well as on the evolution of molecular sequences. We understand Bioinformatics as a discipline that develops algorithms, models, and tools that help Biologists to generate new biological insights and knowledge. We try to bridge the gap between the world of systematics and the world of high performance computing.


Stephen Crotty
Center for Integrative Bioinformatics Vienna, Austria
Arrival 23 Jan, Departure 27 Jan


Celine Scornavacca
ISEM (CNRS-University of Montpellier 2), France
Arrival 23 Jan, Departure 26 Jan

Celine research interests include parameterized complexity, supertree and network methods for phylogenetics, combinatorics, and bioinformatics.


Laura Kubatko
Ohio State University, USA
Arrival 24 Jan, Departure 31 Jan

My research interests are in statistical genetics, particularly in the inference of phylogenetic trees from nucleotide sequence data. My research in this area is focused around the combination of data at the between and within species levels by combining models from phylogenetics and population genetics, particularly the coalescent model. My most recent work involves the application of techniques from algebraic statistics to problems in phylogenetic inference. I have also worked on problems involving linkage and QTL analysis, and the analysis of microarray data.


Mario dos Reis
Queen Mary University of London, UK
Arrival 26 Jan, Departure 29 Jan

Research in the dos Reis Lab is focused on the development and application of statistical methods in phylogenetics. We are particularly interested in using Bayesian statistics to infer times of species divergences (that is, in placing geological times of divergence on the Tree of Life), and on methods to measure the strength of natural selection in molecular sequences.


Tracy Heath
Iowa State University, USA
Arrival 25 Jan, Departure 2 Feb

My research seeks to understand how evolutionary forces have produced the patterns of biodiversity we observe in the Tree of Life. I am intensely motivated by the wide array of evolutionary questions that can be addressed with complex, biologically-realistic models of evolution applied to molecular, morphological, and paleontological data. Because of this, my research program focuses on developing and applying computational methods for understanding evolutionary processes in a phylogenetic context. My primary approach to developing phylogenetic tools is to apply new statistical models as priors using Bayesian inference methods. In particular, I am a developer for RevBayes, a software program for Bayesian inference of evolutionary parameters including (but not limited to) phylogeny, divergence times, rates of character evolution, population dynamics, rates of selection across a genome, and patterns of species diversification.


Laszlo Garamszegi
Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Spain
Arrival 28 Jan, Departure 1 Feb

My principal interest focuses on the evolutionary ecology of birds. The topics that are central in my researches include questions about the evolution of bird song, the adaptive role of behavioral consistency and plasticity and host-parasite interactions. A large part of my studies relies on the field study of the collared flycatcher, but I frequently apply phylogenetic comparative approaches to investigate interspecific patterns.


Jason Stajich
University of California, Riverside, USA
Arrival 28 Jan, Departure 2 Feb

Research in the Stajich lab focuses on evolution of fungi through use of genetic and genomic approaches incorporating experimental and computational tools. We are focused on evolutionary relationships of fungi in particular zygomycete and chytrid fungi. To better understand the evolution of the whole kingdom we have embarked on a project to sequence 1000 fungal genomes. The lab is also curious about the evolution of pathogenic lifestyles in fungi and the evolutionary processes that promote these changes. To address these questions we study genomes and expressed transcriptome of individuals or populations of a species.  We also develop bioinformatic approaches to visualizing and studying genome evolution. This work also include a focus on transposable elements in fungi, rice, and mosquitoes. Recent projects have also taken us to look more at extremophile fungi that live in cold or hot deserts or high saline environments and the adaptations or cooperative lifestyles these fungi utilize to thrive under these conditions.


Jordi Paps Montserrat
University of Bristol, UK
Arrival 30 Jan, Departure 2 Feb

I am an evolutionary biologist fascinated by the causes that underlie the origins and diversity of the organisms. I am interested in the evolution of animals and plants, their systematics, body plans and their genomes. My primary focuses are molecular phylogenetics and comparative genomics, mixing classical biology (especially invertebrates) with genetics, molecular biology, developmental biology, phylogeography and biodiversity.


Martin Kolisko
Institute of Parasitology Biology Centre, Czech Republic
Arrival 29 Jan, Departure 1 Feb

Our laboratory is predominantly using methods of next-generation sequencing, comparative genomics and phylogenomics, differential expression, and bioinformatics. Our main research themes are: (1) Evolution of parasitic genomes in comparison to free-living relatives and commensals: Are there genes specific to parasitic species versus commensalic species? (2) Evolution of secondarily free-living protists: How do they adapt “back” to a free-living lifestyle and what are the major evolutionary mechanisms behind such changes? (3) Interactions between gut parasites and commensals and the gut microbiome: How do parasites and commensalic protists impact the gut microbiome of mammals? We are using differential expression analyses to track changes in the gut microbiome pre- and post-infection with parasitic protists.


Gergely Szöllősi
Eötvös Loránd University, Hungary
Arrival 29 Jan, Departure 1 Feb

My research is best described as “model-based evolutionary genomics” and is based on the recognition that our understanding of biological systems is often limited not by the lack of data, but by our ability to extract information from already available large scale datasets. My aim is to develop a coherent treatment of evolutionary process at different time scales, from the diversification of species over hundreds of millions of years to the decade long development of tumors. Our research focuses on two topics that are currently the subject of intense international interest, each aiming to extract quantitative information on the underlying biological processes from large genomic datasets: 1. reconstructing a dated tree of life from complete genomes using phylogenetic discord as molecular fossils and 2. understanding cancer evolution in hierarchically differentiating tissue using tumor genomes.





Joe Bielawski
Dalhousie University, Canada


Toni Gabaldón
Center for Genomic Regulation, Spain

Matthew Hahn
Indiana University Bloomington, EEUU


Scott Handley
Washington University in Saint Louis, EEUU



Tracy Heath
Iowa State University, EEUU

Tracy heath

Laura Kubatko
Ohio State University, EEUU

Guy Leonard
University of Exeter, UK


Jordi Paps
University of Essex, UK



Antonis Rokas
Vanderbilt University, EEUU

Céline Scornavacca
ISEM (CNRS-University of Montpellier 2), France


David Swofford
Duke University, EEUU

Xiaofan Zhou
Vanderbilt University, EEUU