Karel Břinda

Karel Břinda

Permanent Researcher (INRIA Starting Faculty)

INRIA/IRISA Rennes

Biography

I’m a permanent researcher / INRIA Starting Faculty at INRIA, the French National Research Institute for Computer Science and Automation. I’m based at the Rennes Research Center, where I’m part of the broader GenScale project team.

I work in the area of computational genomics, with a particular focus on pathogens and antibiotic resistance, and the goal of achieving their rapid diagnosis and real-time surveillance. To do so, I develop novel algorithms, data structures, software tools, and genomic databases, which are then provided to the scientific community as building blocks for larger efforts. I’m particularly interested in non-traditional applications of portable genomic technologies, such as nanopore sequencing and CRISPR-based tests, as well as in moving computation from large computational clusters to ordinary laptops and developing comprehensive sequence data search engines.

Download my CV.

Interests
  • Algorithms
  • Computational genomics
  • Rapid diagnostics
  • Pathogens
  • Antibiotic resistance
Education
  • Postdoctoral Fellow, Research Associate, 2017–2021

    Harvard Medical School (Department of Biomedical Informatics) & Harvard TH Chan School of Public Health (Center for Communicable Disease Dynamics)

  • PhD in Computer Science, 2013–2016

    Université Paris-Est (Gaspard Monge Institute), France

  • BSc, MSc in Math. Computer Science, 2018–2013

    Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Czech Republic

Publications

Selected journal articles

[1] K. Břinda, M. Baym, and G. Kucherov, “Simplitigs as an efficient and scalable representation of de Bruijn graphs,” Genome Biology, vol. 22, no. 96, 2021, doi: 10.1186/s13059-021-02297-z.

[2] K. Břinda et al., “Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing,” Nature Microbiology, vol. 5, pp. 455–464, 2020, doi: 10.1038/s41564-019-0656-6.

[3] K. Břinda, V. Boeva, and G. Kucherov, “RNF: A general framework to evaluate NGS read mappers,” Bioinformatics, vol. 32, no. 1, pp. 136–139, 2016, doi: 10.1093/bioinformatics/btv524.

[4] K. Břinda, M. Sykulski, and G. Kucherov, “Spaced seeds improve k-mer-based metagenomic classification,” Bioinformatics, vol. 31, no. 22, pp. 3584–3592, 2015, doi: 10.1093/bioinformatics/btv419.

Other journal articles

[5] Y. Che et al., “High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP-and human/animal-associated bacteria,” Microbiome, vol. 10, no. 1, pp. 1–16, 2022, doi: 10.1186/s40168-021-01192-w.

[6] N. B. Wikle et al., “SARS-CoV-2 epidemic after social and economic reopening in three U.S. States reveals shifts in age structure and clinical characteristics,” Science Advances, vol. 8, no. 4, 2022, doi: 10.1126/sciadv.abf9868.

[7] T. N.-A. Tran et al., “Optimal SARS-CoV-2 vaccine allocation using real-time attack-rate estimates in Rhode Island and Massachusetts,” BMC Medicine, vol. 19, no. 162, 2021, doi: 10.1186/s12916-021-02038-w.

[8] Y. Che et al., “Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes,” Proceedings of the National Academy of Sciences, vol. 118, no. 6, 2021, doi: 10.1073/pnas.2008731118.

[9] D. R. MacFadden et al., “Using genetic distance from archived samples for the prediction of antibiotic resistance in escherichia coli,” Antimicrobial Agents and Chemotherapy, vol. 64, no. 5, pp. 455–464, 2020, doi: 10.1128/aac.02417-19.

[10] B. Grüning et al., “Bioconda: Sustainable and comprehensive software distribution for the life sciences,” Nature Methods, vol. 15, no. 7, pp. 475–476, 2018, doi: 10.1038/s41592-018-0046-7.

[11] K. Břinda, E. Pelantová, and O. Turek, “Balances of m-bonacci words,” Fundamenta Informaticae, vol. 132, no. 1, pp. 33–61, 2014, doi: 10.3233/FI-2014-1031.

[12] Ľ. Balková, K. Břinda, and O. Turek, “Abelian complexity of infinite words associated with quadratic parry numbers,” Theoretical Computer Science, vol. 412, no. 45, pp. 6252–6260, 2011, doi: 10.1016/j.tcs.2011.08.016.

Refereed Full Conference Papers

[13] K. Břinda, “Languages of lossless seeds,” in Proceedings 14th international conference on automata and formal languages (AFL 2014), electronic proceedings in theoretical computer science, vol. 151, 2014, pp. 139–150. doi: 10.4204/EPTCS.151.9.

[14] P. Červenka, K. Břinda, M. Hanousková, P. Hofman, and R. Seifert, “Blind Friendly Maps: Tactile Maps for the Blind as a Part of the Public Map Portal (Mapy.cz),” in Computers helping people with special needs, ICCHP 2016, 2016, proceedings, part II, 2016, pp. 131–138. doi: 10.1007/978-3-319-41267-2_18.

Patents

[15] W. P. Hanage, K. Břinda, and M. Baym, “Rapid identification of strains from sequence data,” United States Patent Application, no. 17/251343, 2021.

Technical Reports

[16] K. Břinda, V. Boeva, and G. Kucherov, “Ococo: An online consensus caller,” arXiv:1712.01146, 2018.

[17] K. Břinda, V. Boeva, and G. Kucherov, “Dynamic read mapping and online consensus calling for better variant detection,” arXiv:1605.09070, 2016.

Theses

[18] K. Břinda, “Novel computational techniques for mapping and classification of Next-Generation sequencing data.” PhD thesis, Université Paris-Est, 2016.

[19] K. Břinda, “Lossless seeds for approximate string matching.” MS thesis, Czech Technical University, 2013.

[20] K. Břinda, “Abelian complexity of infinite words.” BS thesis, Czech Technical University, 2011.

Software

ProPhyle

A metagenomic classifier. Written in Python. See http://prophyle.github.io.

RASE

Rapid prediction of antibiotic resistance. Tool, pipeline, library and databases (S. pneumoniae and N. gonorrhoeae) for rapid inference of antibiotic resistance and susceptibility by genomic neighbor typing using nanopore sequencing. Written in Python/Snakemake/Make. See https://github.com/c2-d2/rase.

ProphAsm

Tool for rapid and memory-efficient computation of simplitigs. Written in C++. See http://github.com/prophyle/prophasm..

Ococo

An online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream. Written in C++. See http://github.com/karel-brinda/ococo.

ProPhex

An exact k-mer index based on the Burrows-Wheeler Transform. Co-developed with Kamil Salikhov. Written in C. See http://github.com/prophyle/prophex.

RNFtools

A format for simulating sequencing reads evaluating read mappers and an associated framework. Written in Snakemake/Python. See http://rnftools.github.io.

DyMaS

A simulator of dynamic read mapping. Written in Python/Snakemake. See http://github.com/karel-brinda/dymas.

SAMsift

Advanced filtering and tagging of SAM/BAM alignments using Python expressions. See http://github.com/karel-brinda/samsift.

Disty McMatrixFace

Tool for computing a distance matrix from a core genome alignment. Written in C++. See http://github.com/c2-d2/disty.

NanoSim-H

Simulator of nanopore reads (a fork of the NanoSim package). See http://github.com/karel-brinda/nanosim-h.

SMBL

Snakemake bioinformatics library (retired). See http://github.com/karel-brinda/smbl.

Teaching

Prospective students and postdocs

I’m hiring! If you are interested in working with me as a student (M1, M2, or PhD) or a postdoc on a topic related to rapid diagnostics of antibiotic resistance resistance, sequence data search engines, or computational metagenomics, please contact me at karel.brinda@inria.fr.

Harvard Medical School

  • Concepts in Genome Analysis (BMIF 201) (Fall 2019; TA)

    Instructors: Profs. Shamil R. Sunyaev, Michael Baym, Cheng-Zhong Zhang, and Heng Li

    The course focused on quantitative aspects of genetics and genomics, including computational and statistical methods of genomic analysis.

Czech Technical University in Prague

  • Assistive Technology (01ASTE) (Falls 2010–2012 ; Instructor)

  • Software Project (01SWP1, 01SWP2) (Falls and springs 2010–2012 ; Supervisor)

Media

Interviews

  • BBC World Service – Science in Action – 13 Feb 2020

    Our paper about rapid diagnostics of antibiotic resistance was covered by BBC World Service in the show Science in Action (13 Feb 2020; starts at 8.10 minutes). 2020-BBC-ScienceInAction-GNT.mp3

  • The Bioinformatics Chat – Spectrum-preserving string sets and simplitigs – 28 Feb 2020

    Our paper about simplitigs for an efficient and scalable representation of de Bruijn graph was covered by the The Bioinformatics Chat podcast series (#42, 28 Feb 2020). 2020-TheBioinformaticsChat-Simplitigs.mp3

Other coverage

Contact