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Karel Břinda — Welcome to my website!

I am a Ph.D. student of bioinformatics at the Université Paris-Est in the Laboratoire d'Informatique Gaspard-Monge where I belong to AlgoB group (Algorithmics for Bioinformatics), being supervised by Gregory Kucherov and Valentina Boeva. We are involved in the ABS4NGS project.

In general I am interested in bioinformatics, combinatorics on words, and tactile cartography. My specific research topic concerns efficient algorithms for next-generation sequencing data. I am currently working on the following projects: RNFtools framework, OCOCO online consensus caller, Dynamic Mapping Simulator, and SnakeMake Bioinformatics Library.

My hobby project is Blind Friendly Maps – automatically generated tactile maps for the blind, see (the maximum zoom). Whereas creation of traditional tactile maps was a matter of days or weeks of manual work, now it is possible to create such a map in several minutes (see our poster or paper). I also develop and maintain a Czech chordbook called TP zpěvník.

Prior to my doctoral studies, I studied mathematical computer science at the FNSPE Czech Technical University in Prague where I belonged to TIGR (Theoretical Informatics Group). In 2005—2012 I worked at the Czech Technical University in the TEREZA Centre (nowadays ELSA Centre).

News [Top of the webpage]

2016/11/28 PhD defense Novel computational techniques for mapping and classifying Next-Generation Sequencing data. PhD defense (Paris, France). [Abstract]
2016/11/18 Talk ProPhyle: a memory efficient BWT-based metagenomic classifier using k-mer propagation. Workshop SeqBio 2016 (Nantes, France). [Abstract]
2016/07/07 Talk BWT-based indexing structure for metagenomic classification. Seminar at INRIA/Irisa Rennes (Rennes, France).
2016/06/06 Talk BWT-based indexing structure for metagenomic classification. Student Conference Quantitative Genomics 2016 (London, UK).
2016/05/31 Preprint K. B., V. Boeva, G. Kucherov. Dynamic read mapping and online consensus calling for better variant detection.
[PDF, arXiv, HAL]
2016/03/31 Preprint P. Červenka, K. B., M. Hanousková, P. Hofman, R. Seifert. Blind Friendly Maps: Tactile Maps for the Blind as a Part of the Public Map Portal (
[PDF, arXiv, HAL, Blind Friendly Maps]
2016/03/18 Poster P. Červenka, K. B., R. Seifert, P. Hofman. Blind Friendly Maps. International conference Sensory issues and Disability: Touch to learn, touch to communicate (Paris, France).
2016/02/24 Talk Indexing structures for metagenomic classification. International Workshop Data Structures in Bioinformatics (Bielefeld, Germany).

Contact information [Top of the webpage]
Address: Laboratoire d'Informatique Gaspard-Monge (Cité Descartes, Bât. Copernic)
5 bd Descartes
77454 Marne-la-Vallée
[see on a map, near the RER A station Noisy-Champs]

Links [Top of the webpage]

Student organizations: