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Karel Břinda – Welcome to my website!

Contact information [Top of the webpage]

E-mail:kbrinda@hsph.harvard.edu
karel.brinda@hms.harvard.edu
 
Address: Kresge Building, Office 506
Center for Communicable Disease Dynamics
Harvard TH Chan School of Public Health
677 Huntington Avenue
Boston, MA 02115
USA
 
Links: Github, Google Scholar, Twitter, Bioinformatics StackExchange, ResearchGate, LinkedIn, Hanage Lab Blog

About [Top of the webpage]

I am a postdoctoral research fellow at Harvard University working with Dr. Bill Hanage at the Harvard T.H. Chan School of Public Health in the Center for Communicable Disease Dynamics and Dr. Michael Baym at Harvard Medical School in the Department of Biomedical Informatics. My research focuses on methods for rapid antibiotic resistance detection from point-of-care sequencing data obtained by mobile sequencing technologies.

Prior to coming to Harvard, I received my Ph.D. in computer science at Université Paris-Est in the Laboratoire d'Informatique Gaspard-Monge in 2016, under the supervision of Dr. Gregory Kucherov and Dr. Valentina Boeva. I studied algorithms and data structures for Next-Generation Sequencing data and our work resulted in the following projects: ProPhyle (phylogeny-based metagenomic classification using Burrows-Wheeler Transform), RNFtools framework (read simulation and NGS mapper evaluation framework), OCOCO (the first online consensus caller), and Dynamic Mapping Simulator.

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. I focused on combinatorics on words, in particular Abelian complexity of infinite words and algorithms for text filtration. In 2005–2012 I worked at the Czech Technical University in the TEREZA Centre (nowadays ELSA Centre).

My hobby project is Blind Friendly Maps – automatically generated tactile maps for the blind, see http://hapticke.mapy.cz (the maximum zoom). Whereas creation of traditional tactile maps used to be 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).

News [Top of the webpage]

2017/04/26 Poster K. B., K. Salikhov, S. Pignotti, G. Kucherov. ProPhyle: a phylogeny-based metagenomic classifier using Burrows-Wheeler Transform. Harvard Chan Poster Day, Harvard TH Chan School of Public Health (Boston, USA). [Download]
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). [Download]
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).
[Abstract]
2016/06/06 Talk BWT-based indexing structure for metagenomic classification. Student Conference Quantitative Genomics 2016 (London, UK).
[Abstract]
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 (Mapy.cz).
[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).
[PDF, HAL]
2016/02/24 Talk Indexing structures for metagenomic classification. International Workshop Data Structures in Bioinformatics (Bielefeld, Germany).
[Abstract]