Karel Břinda
@brinda.eu
‖ Permanent Researcher / INRIA Start. Faculty @ INRIA Rennes 🇫🇷 ‖
BioInfo/CompBio: algorithms, genomics, pathogens & rapid diagnostic of antibiotic resistance《 https://brinda.eu | https://github.com/karel-brinda 》
BioInfo/CompBio: algorithms, genomics, pathogens & rapid diagnostic of antibiotic resistance《 https://brinda.eu | https://github.com/karel-brinda 》
Pinned
Karel Břinda
@brinda.eu
· Apr 11
A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods?
Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/
Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search.
rdcu.be/eg4OA
w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/
Reposted by Karel Břinda
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:55 PM
Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.
Reposted by Karel Břinda
Richard so deserves this - a legend in bioinformatics and computational biology - work genome, human genome, Pfam, 1,000 genomes, Sam/bam format, bwa, vcf, psmc… and so many more
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
November 14, 2025 at 1:37 PM
Richard so deserves this - a legend in bioinformatics and computational biology - work genome, human genome, Pfam, 1,000 genomes, Sam/bam format, bwa, vcf, psmc… and so many more
Reposted by Karel Břinda
cisac.fsi.stanford.edu/content/cisa... In my new role at @stanfordcisac.bsky.social, I'm recruiting for a postdoc to define how benefits of risky research should be evaluated. w Tony Mills of @notredame.bsky.social . #philsci #biosecurity #scipolicy
CISAC Fellowship Program
cisac.fsi.stanford.edu
October 5, 2025 at 11:25 PM
cisac.fsi.stanford.edu/content/cisa... In my new role at @stanfordcisac.bsky.social, I'm recruiting for a postdoc to define how benefits of risky research should be evaluated. w Tony Mills of @notredame.bsky.social . #philsci #biosecurity #scipolicy
Reposted by Karel Břinda
Looking for people to test the latest version of simd-sketch.
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
GitHub - RagnarGrootKoerkamp/simd-sketch: Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.
Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate. - RagnarGrootKoerkamp/simd-sketch
github.com
October 1, 2025 at 2:38 PM
Looking for people to test the latest version of simd-sketch.
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
It's now 2x as fast at sketching, and supports skipping over kmers containing N and other ambiguous bases (which is only ~35% slower).
'cargo install simd-sketch' is right there under your fingertips ;)
github.com/RagnarGrootK...
Reposted by Karel Břinda
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Karel Břinda
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 1, 2025 at 5:49 PM
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Reposted by Karel Břinda
This is one of the findings that really motivates my research: yes, antibiotic resistance genes are ancient, but the age of antibiotics has likely contributed to a big change in their mobility and of the landscape of MGEs we see today! Very happy for Arya and to see this published.
September 2, 2025 at 10:30 PM
This is one of the findings that really motivates my research: yes, antibiotic resistance genes are ancient, but the age of antibiotics has likely contributed to a big change in their mobility and of the landscape of MGEs we see today! Very happy for Arya and to see this published.
Reposted by Karel Břinda
This FTP ftp.ebi.ac.uk/pub/database... from EBI
www.ebi.ac.uk/gwas/docs/di... seems to have the iconic GWAS diagram
www.ebi.ac.uk/gwas/docs/di... seems to have the iconic GWAS diagram
July 26, 2025 at 2:15 PM
This FTP ftp.ebi.ac.uk/pub/database... from EBI
www.ebi.ac.uk/gwas/docs/di... seems to have the iconic GWAS diagram
www.ebi.ac.uk/gwas/docs/di... seems to have the iconic GWAS diagram
Reposted by Karel Břinda
Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes https://www.biorxiv.org/content/10.1101/2025.07.22.666184v1
July 26, 2025 at 8:33 PM
Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes https://www.biorxiv.org/content/10.1101/2025.07.22.666184v1
Reposted by Karel Břinda
With the addition of the soil genome catalogue, MGnify now hosts over half a million genomes - exciting milestone for the resource.
The genome catalogue for the soil microbiome is now live on MGnify! Built from MAGs & isolate genomes across 21 studies (including the recently published SMAG and Microflora Danica catalogues), it features 19,472 species.
MGnify - EBI
www.ebi.ac.uk
July 17, 2025 at 5:37 PM
With the addition of the soil genome catalogue, MGnify now hosts over half a million genomes - exciting milestone for the resource.
Reposted by Karel Břinda
This looks phenomenal. Hat tip to
@vivekmutalik.bsky.social
@vivekmutalik.bsky.social
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
July 23, 2025 at 4:18 PM
This looks phenomenal. Hat tip to
@vivekmutalik.bsky.social
@vivekmutalik.bsky.social
Reposted by Karel Břinda
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
July 23, 2025 at 7:35 AM
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
Reposted by Karel Břinda
Today's reading: Nature should be the model for microbial sciences journals.asm.org/doi/10.1128/... by @brettbakker.bsky.social @emilyraehyde.bsky.social and @pedroleao.bsky.social
Looks ideal for a talk I am working on on model organisms ...
Looks ideal for a talk I am working on on model organisms ...
Nature should be the model for microbial sciences | Journal of Bacteriology
Historically, our understanding of microbes has been based on laboratory cultures.
Much of what we know at a mechanistic level is based on “model organisms” which are
species that readily grow in labo...
journals.asm.org
July 12, 2025 at 2:06 PM
Today's reading: Nature should be the model for microbial sciences journals.asm.org/doi/10.1128/... by @brettbakker.bsky.social @emilyraehyde.bsky.social and @pedroleao.bsky.social
Looks ideal for a talk I am working on on model organisms ...
Looks ideal for a talk I am working on on model organisms ...
Reposted by Karel Břinda
New tool for pangenome analysis! CLARC refines bacterial gene clusters using functional annotation + linkage—not just sequence. New publication by @indragon.bsky.social & collaborators, advised by @mlipsitch.bsky.social & @billhanage.bsky.social. Read more at bit.ly/4ek0Y51
Linkage-based ortholog refinement in bacterial pangenomes with CLARC
Abstract. Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying g
bit.ly
June 25, 2025 at 4:06 PM
New tool for pangenome analysis! CLARC refines bacterial gene clusters using functional annotation + linkage—not just sequence. New publication by @indragon.bsky.social & collaborators, advised by @mlipsitch.bsky.social & @billhanage.bsky.social. Read more at bit.ly/4ek0Y51
Reposted by Karel Břinda
GRC insisting on the vote for the next location being in person in the name of democracy
July 4, 2025 at 10:03 AM
GRC insisting on the vote for the next location being in person in the name of democracy
Reposted by Karel Břinda
⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10]
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Comparing Strategies to Introduce Two New Antibiotics for Gonorrhea: A Modeling Study
Introduction Drug resistance in Neisseria gonorrhoeae is an urgent public health threat. The anticipated approval of two new antimicrobials for gonorrhea prompts the need for evidence-based rollout st...
www.medrxiv.org
July 3, 2025 at 3:29 PM
⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10]
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Karel Břinda
It's 25 yrs to the day since the Human Genome Project & Craig Venter declared joint victory in sequencing the human genome - an ideal time for @wellcometrust.bsky.social to annouce their new project, involving our lab, to begin work towards synthesising human genomes. wellcome.org/news/researc...
Researchers take first steps to creating synthetic human genomes | Wellcome
Scientists are developing technology to create the first synthetic human chromosome. The ability to write large genomes could transform our understanding of health.
wellcome.org
June 26, 2025 at 12:29 PM
It's 25 yrs to the day since the Human Genome Project & Craig Venter declared joint victory in sequencing the human genome - an ideal time for @wellcometrust.bsky.social to annouce their new project, involving our lab, to begin work towards synthesising human genomes. wellcome.org/news/researc...
Reposted by Karel Břinda
FastGA: Fast Genome Alignment www.biorxiv.org/content/10.1... 🧬🖥️🧪 www.github.com/thegenemyers...
June 20, 2025 at 9:39 AM
FastGA: Fast Genome Alignment www.biorxiv.org/content/10.1... 🧬🖥️🧪 www.github.com/thegenemyers...
Reposted by Karel Břinda
![Comic. Thought Process While Reading A Big Number: 54,000,000,000,000,000,000,0000,0000,054,000"000,00c2ef46
[comments progress along the line, approximately every 3 digits] (1) 54! Great! I know that number. Solid start. (2) Oh, a comma and some zeros. Cool. Must be at least 54 thousand. (3) A second comma! I wonder if we’re talking population or money. (4) Yikes! If this is money, it’s a *lot* of money. (5) Why am I reading this? Whatever this number is, I’m not going to be able to visualize it. (6) All right, either someone made a unit conversion error or this is one of those incomprehensible astronomy numbers. (7) [4 zeroes between commas instead of 3]] Oh no. Is this a misplaced comma or an extra zero? I guess we’ll see if the next group has two zeros or three. If it’s two, we can at least hope the digits are right. (8) [4 zeroes between commas] Oh *no*. (9) [repeat of the digits 54] What is happening. (10) [a quotation mark in place of comma] Someone messed up real bad. (11) [final digits are c2ef46, cut off] Someone messed up real bad and I hope it wasn’t me.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreih3hirktm65hdw44t573arldaizpyect42tpkiochyewbagbj5gh4@jpeg)
June 18, 2025 at 8:36 PM
Reposted by Karel Břinda
This seems like an awesome course! jshun.csail.mit.edu/6506-s24/! If there were more hours in the day, I'd want to put something like this together at UMD.
6.506 Algorithm Engineering Spring 2024
jshun.csail.mit.edu
June 12, 2025 at 1:44 PM
This seems like an awesome course! jshun.csail.mit.edu/6506-s24/! If there were more hours in the day, I'd want to put something like this together at UMD.
Reposted by Karel Břinda
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Dropbox
tinyurl.com
June 12, 2025 at 11:26 AM
1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from the community.
Reposted by Karel Břinda
Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at EMBL-EBI (@ebi.embl.org)
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
Elucidating the mechanisms of action and evolutionary history of phage anti-defence proteins
Phages and bacteria are locked in a molecular arms race, with phage anti-defence proteins (ADPs) enabling them to evade bacterial immune systems. To streamline access to information on ADPs, we develo...
www.biorxiv.org
June 8, 2025 at 11:08 AM
Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at EMBL-EBI (@ebi.embl.org)
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
and the University of Cambridge (@cam.ac.uk)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"
Reposted by Karel Břinda
Developing thread that will be a great read.
(Longish thread. Apologies)
I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
I have met many inspiring colleagues over the past few months, many of whom are in academic institutions targeted by the current administration, and many others who are about to be (the analogy to the ‘eye of Sauron’ has been invoked many times; gallows humor). 1/
June 8, 2025 at 6:58 PM
Developing thread that will be a great read.
Reposted by Karel Břinda
📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8
May 27, 2025 at 12:06 PM
📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8
Reposted by Karel Břinda
Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...
June 3, 2025 at 9:25 AM
Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...