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Karel Břinda — Welcome to my website!

Contact information [Top of the webpage]
Address: Kresge Building, Office 506
Harvard School of Public Health
677 Huntington Avenue
Boston MA 02115

Background [Top of the webpage]

I am a postdoctoral researcher at the Harvard T.H. Chan School of Public Health, Center for Communicable Disease Dynamics, working with Dr. Bill Hanage. Prior to joining HSPH, I did my Ph.D. in bioinformatics at the Université Paris-Est in the Laboratoire d'Informatique Gaspard-Monge, being supervised by Dr. Gregory Kucherov and Dr. Valentina Boeva.

Prior to my doctoral studies, I studied mathematical computer science at the Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague where I belonged to TIGR (Theoretical Informatics Group) and was supervised by Dr. Edita Pelantová and Dr. Karel Klouda. In 2005—2012 I worked at the Czech Technical University in the TEREZA Centre (nowadays ELSA Centre).

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 have been working on the following projects: ProPhyle (a metagenomic classification tool), RNFtools framework (a read simulation and NGS mapper evaluation framework), OCOCO (the first online consensus caller), or Dynamic Mapping Simulator.

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.

News [Top of the webpage]

2017/02/28 PhD thesis online Novel computational techniques for mapping and classifying Next-Generation Sequencing data. [Download]
2017/02/16-17 Poster K. B., K. Salikhov, S. Pignotti, G. Kucherov. ProPhyle: a phylogeny-based metagenomic classifier using Burrows-Wheeler Transform. Second Workshop on Challenges in Microbiome Data Analysis, Broad Institute - MIT/Harvard (Cambridge, USA).
2017/01/26 Talk Efficient phylogeny-based metagenomic classification. Workshop Permafrost 2017 (Bormio, Italy).
2016/11/28 PhD defense Novel computational techniques for mapping and classifying Next-Generation Sequencing data. PhD defense (Paris, France). [Abstract, Thesis]
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).