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Reposted by Karel Břinda

Ragnar {Groot Koerkamp} @curiouscoding.nl · 7d

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...

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

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Zamin Iqbal @zaminiqbal.bsky.social · 13d

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

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Michael Baym @baym.lol · Sep 1

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...

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

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Type VI Sophia System @wheezenfeld.bsky.social · Sep 2

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.

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Sina Majidian @sinamajidian.bsky.social · Jul 26

This FTP ftp.ebi.ac.uk/pub/database... from EBI
www.ebi.ac.uk/gwas/docs/di... seems to have the iconic GWAS diagram

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bioRxiv Genomics @biorxiv-genomic.bsky.social · Jul 26

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes https://www.biorxiv.org/content/10.1101/2025.07.22.666184v1

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Tatiana Gurbich @tgurbich.bsky.social · Jul 17

With the addition of the soil genome catalogue, MGnify now hosts over half a million genomes - exciting milestone for the resource.

mgnifydb.bsky.social @mgnifydb.bsky.social · Jul 17

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

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Jonathan Eisen @phylogenomics.bsky.social · Jul 23

This looks phenomenal. Hat tip to
‪@vivekmutalik.bsky.social‬

Eduardo Rocha @epcrocha.bsky.social · Jul 23

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/...

graphical abstract of the article the extended mobility of plasmids

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Eduardo Rocha @epcrocha.bsky.social · Jul 23

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/...

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Jonathan Eisen @phylogenomics.bsky.social · Jul 12

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 ...

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

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CCDD @ccdd-hsph.bsky.social · Jun 25

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

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Michael Baym @baym.lol · Jul 4

GRC insisting on the vote for the next location being in person in the name of democracy

A cartoon titled “sampling bias” showing a slide with 99.8 of survey respondents saying they love responding to surveys, and only 0.2% saying “no, I toss them in the bin”

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Madeleine Kline @mckline98.bsky.social · Jul 3

⚠️ 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...

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

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Tom Ellis @proftomellis.bsky.social · Jun 26

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

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Stephen Turner @stephenturner.us · Jun 20

FastGA: Fast Genome Alignment www.biorxiv.org/content/10.1... 🧬🖥️🧪 www.github.com/thegenemyers...

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Randall Munroe @xkcd.com · Jun 18

Reading a Big Number

xkcd.com/3102/

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.

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Rob Patro @robp.bsky.social · Jun 12

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

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Paul Medvedev @pashadag.bsky.social · Jun 12

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

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Khalimat Murtazalieva @khalimat.bsky.social · Jun 8

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"

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

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Carl T. Bergstrom @carlbergstrom.com · Jun 8

Developing thread that will be a great read.

Harmit Singh Malik @harmitmalik.bsky.social · Jun 8

(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/

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Karel Břinda @brinda.eu · Jun 8

It will become a suffix with the next promotion amzn.eu/d/89NyDxi

Amazon.fr

www.amazon.fr

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Karel Břinda @brinda.eu · Jun 8

Honestly, I expected the minimal number of vim operations. However, as a tolerant person, I respect everyone’s choice to brand themselves as a notepad folk, so I didn’t comment :D.

Karel Břinda @brinda.eu · Jun 6

Fantastic!! Big congratulations, very well deserved!!

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Pierre Peterlongo @pierrepeterlongo.bsky.social · May 27

📜 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

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Rayan Chikhi @rayanchikhi.bsky.social · Jun 3

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

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