2024 Workshop on Phylogenomics, Český Krumlov Faculty

Anna Karnkowska

University of Warsaw, Poland

My research focuses on the diversity, evolution and ecology of eukaryotic microorganisms (aka protists). I work on eukaryotic cell evolution, including the origin, evolution, and reduction of organelles of endosymbiotic origins, as well as horizontal gene transfer in eukaryotes. I also study the diversity and the role of symbiotic interactions in freshwater environments.

Workshop co-director.


Antonis Rokas

Vanderbilt University, USA

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.



Rosa Fernández

Institute of Evolutionary Biology (CSIC-UPF), Spain

In my lab we are interested in understanding animal genome evolution with particular emphasis on the origin of terrestrial animal biodiversity from marine ancestors, as well as the understanding of the genomic basis of adaptation to life in caves. For that, we follow an integrative approach involving taxonomy, systematics and ‘omics’ methodologies (such as transcriptomics, phylogenomics, comparative genomics and proteomics). We are also interested in species tree phylogenomic reconstruction of the Animal Tree of Life, with particular interest in several invertebrate lineages.

Workshop co-director.


Toni Gabaldón

Center for Genomic Regulation, Spain

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

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.




Oleksyi Kozlov

The Exelixis Lab, Heidelberg Institute for Theoretical Studies, Germany

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.




Jordi Paps Montserrat

University of Bristol, UK

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.




Gergely Szöllősi

Eötvös Loránd University, Hungary

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.


Marina Marcet-Houben

Comparative Genomics Group, Barcelona Supercomputing Centre (BSC-CNS), Spain

My research focuses on the genomic and phylogenomic analysis of fungal species. I am interested in characterizing the genomic diversity of different groups of fungi such as the human pathogen Candida glabrata. I also dedicate efforts in understanding the evolutionary mechanisms that have led to the formation of different species within fungi, focusing on horizontal gene transfer events, gene order conservation and the formation, propagation and conservation of secondary metabolism clusters.



Matthew Christmas

Uppsala University, Sweden

My research focuses on genome evolution in populations and species using both population and comparative genomics in plants, insects, and most recently mammals. I am particularly interested in understanding the evolutionary changes that enable organisms to adapt to their environments. As part of Prof. Kerstin Lindblad-Toh’s group at Uppsala University I have recently been involved in a large-scale comparative genomics project, where we developed a genome alignment for 240 placental mammal species and used it to identify genomic regions under evolutionary constraint and acceleration. We are using this dataset to explore many aspects of mammalian evolution, including lineage-specific trait evolution.


Laura Eme

Universite Paris-Saclay, France

I’m an evolutionary microbiologist and my main research interest revolves around deep evolutionary questions to do with the origin and evolution of eukaryotes (tree of eukaryotes, eukaryotic genome evolution, age of major clades, role of HGT in eukaryotes…). For this I use gemomics, metagenomics and phylogenomics.

In March 2019, I started my group at Paris-Sud University. I previously did a postdoc with Andrew Roger and Ford Doolittle at Dalhousie University (Halifax, Canada) and with Thijs Ettema at Uppsala University (Sweden).


University of Maryland, USA

My research focuses on computational, mathematical, and data science problems in evolutionary genomics, with a focus on algorithms for reconstructing species- and population- level histories, and more recently tumor phylogenies. I am interested in algorithmic properties, like statistical consistency, optimality guarantees, time/storage complexity, parallel efficiency, and accuracy under practical and challenging scenarios, like when there is substantial gene tree heterogeneity due to incomplete lineage sorting and gene tree estimation error.


Aoife McLysaght


Olivier Gascuel


Gytis Dudas

Vilnius University, Lithuania

I’m an evolutionary biologist who works on RNA virus evolution on long and short timescales. My research frequently involves exploiting the quirks of a given study system to learn more about its evolution and/or ecology and will usually incorporate sophisticated but understandable data visualisation techniques. My lab is currently focusing on the long-term evolution of orthomyxoviruses (like influenza and relatives) and genomic epidemiology.



Lisa Pokorny

Real Jardín Botánico, Spain

I am a Ramón y Cajal Researcher based at the Real Jardín Botánico (RJB), a Spanish National Research Council (CSIC) research institute located in Madrid, Spain. I am a botanist and an evolutionary biologist and I seek to understand the mechanisms underlying the origin and maintenance of biodiversity in a changing world, with emphasis on land plants. Beyond focusing on the role abiotic factors (e.g., topology, soil, climate) play, I also explore how biotic factors, both intrinsic (e.g., genome architecture) and extrinsic (e.g., plant associated microbiome), shape biodiversity patterns. For this, I study biogeographic patterns and eco-evolutionary processes across spatiotemporal scales, in land plants. I do so by integrating high-throughput sequencing (HTS) approaches (e.g., target capture sequencing) and phylogenomic workflows on high-performance computing (HPC) architectures.


Hélène Morlon

Ecole Normale Supérieure, France

We combine mathematics, bioinformatics and fieldwork to study questions ranging from macroevolution and macroecology to community assembly, biogeography, and conservation. We are based at the Institute of Biology at the Ecole Normale Supérieure in Paris.