My research interest is to develop methods and software that help to understand current questions in biology and evolution. A particular focus are tools to analyze and visualize large scale datasets from different sources, such as high throughput sequencing data, phylogenetic information, and environmental factors. By combining these data, patterns and interactions between them can be found and interpreted in a biological context. My methods draw inspiration from and make use of concepts from diverse fields, such as graph theory, statistical data analysis, and machine learning.

One of the main applications of my research is the so-called phylogenetic placement of metagenomic sequences from environmental samples. The methods allow to understand the connections and patterns in the samples in the context of a phylogenetic reference tree, while taking respective meta-data into account. See below for the publications on these methods.

Over the years, I have also contributed to several empirical studies, in particular large scale metagenomic studies. This helped me to gain an understanding of the apporaches and needs of biologists, and inspired a lot of my research.

Due to the current and future growth of biological datasets, an important consideration is the scalability of the software. To this end, I mostly develop in modern C++11, which allows for highly efficient implementations. Still, my software design strives to be easy to understand and to adapt for other researchers. See my main library genesis for an example. Furthermore, for end users who simply want to use the methods, I offer the command line tool gappa. Both are also described in the software section.


Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data Lucas Czech, Pierre Barbera, Alexandros Stamatakis. bioRxiv. 2019.
Long Metabarcoding of the Eukaryotic rDNA Operon to Phylogenetically and Taxonomically Resolve Environmental Diversity Mahwash Jamy, Rachel Foster, Pierre Barbera, Lucas Czech, Alexey Kozlov, Alexandros Stamatakis, David Bass, Fabien Burki. bioRxiv. 2019.
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences Pierre Barbera, Alexey Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis. Systematic Biology. 2018.
Clarifying the Relationships between Microsporidia and Cryptomycota David Bass, Lucas Czech, Bryony Williams, Cédric Berney, Micah Dunthorn, Frederic Mahe, Guifré Torruella, Grant Stentiford, Tom Williams. Journal of Eukaryotic Microbiology. 2018.
Methods for Automatic Reference Trees and Multilevel Phylogenetic Placement Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Bioinformatics. 2018.
UniEuk: Time to Speak a Common Language in Protistology! Cédric Berney, Andreea Ciuprina, Sara Bender, Juliet Brodie, Virginia Edgcomb, Eunsoo Kim, Jeena Rajan, Laura Wegener Parfrey, Sina Adl, Stéphane Audic, David Bass, David Caron, Guy Cochrane, Lucas Czech, Micah Dunthorn, Stefan Geisen, Frank Oliver Glöckner, Frédéric Mahé, Christian Quast, Jonathan Kaye, Alastair Simpson, Alexandros Stamatakis, Javier del Campo, Pelin Yilmaz, Colomban de Vargas. Journal of Eukaryotic Microbiology. 2017.
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits Lucas Czech, Jaime Huerta-Cepas, Alexandros Stamatakis. Molecular Biology and Evolution. 2017.
An Efficient Approach to Merging Paired-End Reads and Incorporation of Uncertainties Tomáš Flouri, Jiajie Zhang, Lucas Czech, Kassian Kobert, Alexandros Stamatakis. Book Chapter. Algorithms for Next-Generation Sequencing Data. 2017.
Parasites Dominate Hyperdiverse Soil Protist Communities in Neotropical Rainforests Frédéric Mahé, Colomban de Vargas, David Bass, Lucas Czech, Alexandros Stamatakis, Enrique Lara, David Singer, Jordan Mayor, John Bunge, Sarah Sernaker, Tobias Siemensmeyer, Isabelle Trautmann, Sarah Romac, Cédric Berney, Alexey Kozlov, Edward Mitchell, Christophe Seppey, Elianne Egge, Guillaume Lentendu, Rainer Wirth, Gabriel Trueba, Micah Dunthorn. Nature Ecology & Evolution. 2017.
Quartet-Based Computations of Internode Certainty Provide Accurate and Robust Measures of Phylogenetic Incongruence Xiaofan Zhou, Sarah Lutteropp, Lucas Czech, Alexandros Stamatakis, Moritz von Looz, Antonis Rokas. bioRxiv. 2017.
A System for Recognizing Natural Spelling of English Words Lucas Czech. Diploma Thesis. Karlsruhe Institute of Technology and Carnegie Mellon University. 2014.
A Study of Distance Measures for Clustering Generalized Polyphones Lucas Czech. Student Research Paper. Karlsruhe Institute of Technology. 2012.