Aldert Zomer
Associate Professor at Utrecht University, Infectious Diseases & Immunology. (meta)genomes, AMR, zoonotic pathogens. Cookie and cake connoisseur.
publications: scholar.google.com/citations?hl=nl&use…
- Reposted by Aldert ZomerAnnouncing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...
- Reposted by Aldert ZomerWe’re looking for a Summer Intern to generate microscopy videos of bacteria bursting in response to administering antibiotics as part of a public education video on the uses of antibiotics and risks of misuse 🔬 🗓️ Apply by 5 January ➡️ buff.ly/YlUQUho
- Reposted by Aldert Zomer💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...
- Reposted by Aldert ZomerIf you ever need to fuzzy search some DNA, sassy is your tool. Please spread the word; I think many people just outside my own circle could benefit from this :) cc @rickbitloo.bsky.social github.com/RagnarGrootK...
- MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...
- 1/ Our preprint on MetaPointFinder is online: www.biorxiv.org/content/10.6... Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.
- 2/ In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.
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View full thread8/ Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social). Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg... Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.
- Reposted by Aldert Zomer💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics github.com/tseemann/abr...
- Reposted by Aldert ZomerIt's the last few days to apply for this #PhDposition starting in Oct 2026 with us @quadraminstitute.bsky.social. Do you like bacteria, genomics & puzzles?🦠🧬🧩 Do you wanna work in a cutting edge of science, with some awesome people? 😜 Please apply or share by 2 Dec 🗓️ Find out more ⬇
- Reposted by Aldert ZomerI am increasingly of the opinion that people who change menus and look and feel of computer software just so that you know it's a new version should be personally forced to play tech support to my mother for five months.
- Reposted by Aldert ZomerAmazon announced 14,000 layoffs. Its CEO made over $40M last year. UPS announced 48,000 layoffs. Its CEO made over $24M last year. Intel announced 20,000 layoffs. Its new CEO's pay package is valued at nearly $69M. This is what I mean when I say the system is rigged.
- Reposted by Aldert ZomerCar Size xkcd.com/3167/
- Reposted by Aldert Zomer🎓 #PhDPosition ! 🧬 Out of order: investigating genetic and environmental drivers of genome rearrangement with Dr Gemma Langridge @langridgelab.bsky.social 📅Apply by 2 December ➡️https://buff.ly/k31MNuV
- Reposted by Aldert ZomerOctober 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2 Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
- Reposted by Aldert Zomer🚨 Another funded PhD alert🚨 We are recruiting again! For a PhD student to start with us in the @langridgelab.bsky.social October 2026 - please share 👀 If you are interested in foodborne pathogens, public health and phage, look no further 🦠🏥🧬 ➡️ tinyurl.com/3zvavp2t ⬅️ Apply by 6 Jan 2026 🗓️
- Reposted by Aldert ZomerReally exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.
- Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...
- Reposted by Aldert ZomerAround 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...
- Reposted by Aldert ZomerProfessor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share. duunitori.fi/tyopaikat/ty...
- Reposted by Aldert ZomerCome join us 2-4th March 2026 for a cracking #microbiome conference in Hinxton UK! Speaker line up is AMAZING and lots of opportunities for ECRs for selected talks, flash talks and posters. Bursaries are also available! See details below 👇
- Reposted by Aldert Zomer
- Reposted by Aldert ZomerWe are on the lookout for postdocs for two different projects at the intersection of ecology, evolution, and the human microbiome. See thread for more information and reach out!
- Reposted by Aldert ZomerDon't miss the chance to be a part of this exciting conference on microbial typing & genomics #IMMEMXIV. The theme this year is Microbial typing: from fundamental to daily microbiology. @escmid.bsky.social @esgem-sg.bsky.social Register today and see you in Porto! www.escmid.org/congress-eve...
- Reposted by Aldert ZomerElon Musk casually, and illegally, dismantled USAID. According to a new study in the Lancet, that action will lead to *14 million* premature deaths between 2025 and 2030. Again: Elon Musk is directly responsible for 14 million coming deaths. 4.5 million will be children.
- Reposted by Aldert Zomer⏰ Closing soon! We’re looking for a Research Scientist to join Dr Evelien Adriaenssens's group to study bacteriophages, drug resistance and genetic evolution of Salmonella 🦠 💷 £36,720 to £39,750 🗓️ Apply by 2 July 2025 ➡️ buff.ly/7M2mDaa
- Reposted by Aldert Zomer. When you've spend hours looking for your little black kitten... . . . and then... 💙 🐾 💙
- Reposted by Aldert ZomerCome join us in beautiful Lausanne! Deadline for applications: August 10th, 2025 wwwfbm.unil.ch/releve/appli...
- New tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...
- Reposted by Aldert ZomerIn his #ParentCarerScientist case study, Professor Ben Sheldon FRS talks about navigating crises at home and at work, and why it's important for leaders to set an example when it comes to balancing work with caring responsibilities: #CarersWeek #AndAScientist royalsociety.org/about-us/who...
- Reposted by Aldert ZomerNew preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon
- Deacon: fast sequence filtering and contaminant depletion biorxiv.org/content/10.1101/202…
- Reposted by Aldert ZomerNew tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...
- Reposted by Aldert ZomerHappy to announce that we have an open PDRA position in my lab, that will be about a) soil metagenomics b) green house gases c) Archaea d) combine metaGenomics with metaTranscriptomics. Apply by 8th July 25 jobs.quadram.ac.uk/Details.asp?... @quadraminstitute.bsky.social @earlhaminst.bsky.social
- Reposted by Aldert ZomerDorado is 1.0! 🎉 LC25 release adds v5.2 DNA/RNA models with a new suite of mod models that are higher accuracy, lower FP rates, and significantly faster. - Introducing dorado variant 👀 - HAC error rate is down over 25%. - New 2’Ome mod models - Hopper & Blackwell SUP speed ups #Nanoporeconf
- Reposted by Aldert ZomerNew preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)
- Reposted by Aldert Zomer“Volgens het Internationaal Monetair Fonds gaat er veel geld naar koopkrachtondersteuning, maar zou het voor de Nederlandse economie beter zijn te investeren in infrastructuur, onderwijs en onderzoek.” Het zoveelste advies waar deze regering niet naar zal luisteren.
- Reposted by Aldert ZomerAutocycler: long-read consensus assembly for bacterial genomes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/rrwick/Autoc...
- Reposted by Aldert ZomerInterested in phages ? Want to work as team that will isolate, genome sequence and charachterise 1000s of phage to build a biobank . Come work with me and Martha Clokie at Leicester jobs.le.ac.uk/vacancies/va...
- Reposted by Aldert Zomer📣 🥳 🧑💻 Our department is hiring: Tenure-Track Assistant Professor / Associate Professor in Bioinformatics at Aarhus University, Denmark Deadline June 1st Thanks for sharing! mbg.au.dk/en/news-and-...
- Reposted by Aldert Zomer🆕 Vacancy! We are looking for a Group Leader in Functional Microbiome Research to join the laboratory of Professor @dfigeys.bsky.social 💷 Competitive 🗓️ Apply by 28 May 2025 ➡️ buff.ly/Kef1N76
- Reposted by Aldert ZomerNew vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky
- Reposted by Aldert ZomerEvery now again it’s useful to repeat advice about accessing papers that are behind a paywall that excludes you. Email the author. My estimate is that 90% of academics are so thrilled that a living, breathing, possibly even reading, person shows interest that they will swiftly send you a copy.
- Reposted by Aldert ZomerA small group of profoundly stupid people are putting us all at risk. www.theguardian.com/us-news/2025...
- Reposted by Aldert ZomerJoin the Blokesch lab (@EPFL) as a postdoc in Molecular Microbiology 🤩 Study Vibrio cholerae defense systems (phage/plasmid) in a dynamic, collaborative environment in Lausanne close to Lake Geneva in 🇨🇭! Please visit my lab's webpage for details about the position and how to formally apply.
- Reposted by Aldert ZomerTrue facts are true
- Reposted by Aldert ZomerESCMID meant I found a bunch more AMR people to add to the Starter Packs! If you've recently joined Bluesky and looking for AMR people to follow, check out the packs here, as well as the AMR feed. If I've missed you and want to be added, reply to this post
- Volume 2 of the #AMR Starter Pack is here! go.bsky.app/EUY2FUJ Follow these amazing people along with those in Vol. 1 go.bsky.app/KkZfvrh And don't forget to pin the Antimicrobial Resistance feed to get all the AMR posts in one place bsky.app/profile/did:...at://did:plc:swgxhx3zgg47bscokhlo2j24/app.bsky.graph.starterpack/3lccjrm3prm2o
- Reposted by Aldert ZomerThe problem with most machine-based random number generators is that they’re not TRULY random, so if you need genuine randomness it is sometimes necessary to link your code to an external random process like a physical noise source or the current rate of US tariffs on a given country.
- Reposted by Aldert ZomerHello binfies 👋! There is an open position for a senior bioinformatician to join our fab **core bioinformatics** team at @quadraminstitute.bsky.social. jobs.quadram.ac.uk/Details.asp?...
- Reposted by Aldert ZomerKicking off our #KNVM Spring Meeting 2025 #SSM25 with a sparkling keynote talk by @kaltenpoth-lab.bsky.social on insect microbe symbiosis
- Reposted by Aldert ZomerSo glad to be here at #microbio25 ! Very important opening words: “publishing 1 paper with us allows 4 students to attend this AC for free” #publishforthecommunity
- Reposted by Aldert ZomerIf you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!
- Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis biorxiv.org/content/10.1101/202…
- Reposted by Aldert ZomerHey, I just met you And this crazy But here’s my war plans Signal me maybe?
- Reposted by Aldert ZomerToday for the first time in decades, a new oral antibiotic to treat urinary tract infections was approved by the FDA Gepotidacin is a triazaacenaphthylene that inhibits bacterial DNA replication by targeting DNA gyrase and topoisomerase IV Trade name? BLUJEPA® !!! www.gsk.com/en-gb/media/...
- Reposted by Aldert Zomer🎓 #PhDPosition ! 🤰 Understanding the relationship between the maternal microbiome and fetal growth restriction with Professor Mark Webber @webberma.bsky.social and Professor Alison Mather @alisonmather.bsky.social 📅Apply by Monday 14 April ➡️ buff.ly/QL3JFtg
- Reposted by Aldert ZomerExciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...
- Reposted by Aldert ZomerMicrobiome is important not only to human but also plant health. Looking forwards to seeing you at my talk at Utrecht Microbiome Research Day this Thursday 6 March. www.uu.nl/en/events/ut... @utrechtpmi.bsky.social
