We're recruiting! We always enjoy working with curious researchers with a passion for computer science and biology! If you're interested in joining us as a student (at any level) or a postdoc – to work on a project related to ①sequence data search engines, ②rapid diagnostics of antibiotic resistance, or ③computational metagenomics – please reach out!

	Loren Dejoies, Ph.D. Inria Postdoctoral Researcher
	Gaëtan Benoit, Ph.D. Inria Research Engineer
	Arya Kaul Visiting PhD. student from the Baym lab at Harvard Medical School (Chateaubriand fellow)
	Veronika Hendrychová Visiting M1 student from the Czech Technical University in Prague (Erasmus)
	Ondřej Sladký BSc. student at Charles University, co-supervised with Pavel Veselý

Alumni

• Léo Laffeach, M1 student, École normale supérieure de Rennes
• Katya Milyutina, BSc. student, Charles University in Prague

1. K. Břinda, L. Lima, S. Pignotti, N. Quinones-Olvera, K. Salikhov, R. Chikhi, G. Kucherov, Z. Iqbal, and M. Baym.

   Efficient and robust search of microbial genomes via phylogenetic compression,

   bioRxiv 2023.04.15.536996, 2023. [preprint] [software] [supplement]

2. O. Sladký, P. Veselý, and K. Břinda.

   Masked superstrings as a unified framework for textual k-mer set representations,

   RECOMB-Seq, 2023. [preprint] [software] [supplement]

3. K. Břinda, M. Baym, and G. Kucherov.

   Simplitigs as an efficient and scalable representation of de Bruijn graphs,

   Genome Biology 22(96), 2021. [preprint] [journal] [software] [supplement]

4. K. Břinda, A. Callendrello, K. C. Ma, D. R. MacFadden, T. Charalampous, R. S. Lee, L. Cowley, C. B. Wadsworth, Y. H. Grad, G. Kucherov, J. O’Grady, M. Baym, and W. P. Hanage.

   Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing,

   Nature Microbiology 5, pp. 455–464, 2020. [preprint] [journal] [software] [supplement]

5. K. Břinda, M. Sykulski, and G. Kucherov.

   Spaced seeds improve k-mer-based metagenomic classification,

   Bioinformatics 31(22), pp. 3584–3592, 2015. [preprint] [journal] [supplement]

For a full publication list, see Google Scholar.

A. Phylogenetic compression

Framework implementing phylogenetic compression, a technique using evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. This improves the compression ratios of assemblies, de Bruijn graphs, and k-mer indexes by one to two orders of magnitude.

Associated tools:

• MOF-Search – BLAST-like search across all pre-2019 bacteria on standard desktops and laptop computers.
• MOF-Compress – Phylogenetic compression of individual genome batches.

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B. Metagenomic classification

• ProPhyle - Accurate, resource-frugal, and deterministic metagenomic classification, based on k-mer propagation, simplitigs, and k-mer indexing using the Burrows-Wheeler Transform.
  

• ProphAsm - rapid and memory-efficient computation of simplitigs (spectrum-preserving string sets) and set operations with k-mer sets.
  

• ProPhex An efficient k-mer index based on the Burrows-Wheeler Transform.
  

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C. Genomic Neighbor Typing

A proof-of-concept framework for Genomic Neighbor Typing for within-minutes predictions of antibiotic resistance during nanopore sequencing. Pipeline, library, two species databases (S. pneumoniae and N. gonorrhoeae), and demonstrations of within-minutes diagnostic from isolates and metagenomes.

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D. Read mapping and variant calling

• Ococo – Online variant and consensus caller, based on streaming and maintaining variant statistics in small counters per individual genomic positions, which enables real-time analyzes of unsorted SAM/BAM data.
  

• RNFtools – A generic format for naming simulated sequencing reads using arbitrary tools and the associated toolkit and pipeline for read simulation and read mapper evaluation.
  

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E. Auxiliary tools

• SAMsift – Advanced filtering and tagging of SAM/BAM alignments using Python expressions.
  

• Disty McMatrixFace – Tool for computing a distance matrix from a core genome alignment.
  

• NanoSim-H – An easy-to-use simulator of nanopore reads, a fork of NanoSim.
  

For a full software list, see the Github page.

École normale supérieure de Rennes

• Experimental Bioinformatics; BOX (Fall 2023, Lecturer)

  Masters' level course (M1), focused on computational methods for genomics. Taught joinly with Riccardo Vicedomini.

Harvard Medical School

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

  PhD level course, focused on quantitative aspects of genetics and genomics, including computational and statistical methods of genomic analysis. Close collaboration with Profs. Shamil R. Sunyaev, Michael Baym, Cheng-Zhong Zhang, and Heng Li.

Czech Technical University in Prague

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

  Masters' level course.

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

  Masters' level course.

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 media coverage

• Rapid DNA sequencing of unknown bacteria helps doctors choose which antibiotics to treat it with

• Seven significant bacterial genomics papers from the 2010s