Aldert Zomer
@aldertzomer.bsky.social
Associate Professor at Utrecht University, Infectious Diseases & Immunology. (meta)genomes, AMR, zoonotic pathogens. Cookie and cake connoisseur.
publications: https://scholar.google.com/citations?hl=nl&user=VHHhpoAAAAAJ&view_op=list_works&sortby=pubdate
publications: https://scholar.google.com/citations?hl=nl&user=VHHhpoAAAAAJ&view_op=list_works&sortby=pubdate
Reposted by Aldert Zomer
I 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.
November 19, 2025 at 4:10 AM
I 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 Zomer
Amazon 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.
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.
November 15, 2025 at 9:30 PM
Amazon 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.
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 Zomer
![4-panel vertical comic. (1) 100 Years Ago [two people standing next to bicycle with small car nearby] PERSON 1: It’s too dangerous riding a bike with these cars around. I should get a car, too. (2) 50 Years Ago [two people between smaller car and bigger car] PERSON 2 with short hair: Small cars are less safe in collisions with larger vehicles, so I should get a bigger one. (3) Today [two people between big car and even bigger car] PERSON 1: Everyone has huge SUVs now. If I don’t get the biggest one, I’m putting my family at risk. (4) Soon [two people next to large armored car with spiked clubs attached] PERSON 2: If I don’t install more whirling spike clubs, I’ll be destroyed by all the other drivers who...](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreiby6can6k76yzfmv2czxs4pu2l7zie7bqbrpswi7h3ifmiadkuqvu@jpeg)
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
🧬 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
November 3, 2025 at 9:00 AM
🎓 #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
🧬 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 Zomer
October 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.
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.
Index zone by BenLangmead
benlangmead.github.io
October 30, 2025 at 6:11 PM
October 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.
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 🗓️
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 🗓️
October 28, 2025 at 1:17 PM
🚨 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 🗓️
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 Zomer
Really 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.
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...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 9:28 PM
Really 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.
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.
Reposted by Aldert Zomer
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...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 8:16 PM
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...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
Reposted by Aldert Zomer
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.
duunitori.fi/tyopaikat/ty...
duunitori.fi/tyopaikat/ty...
Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori
Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!
duunitori.fi
September 30, 2025 at 8:37 AM
Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.
duunitori.fi/tyopaikat/ty...
duunitori.fi/tyopaikat/ty...
Reposted by Aldert Zomer
Come 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 👇
Bursaries are also available!
See details below 👇
Showcase your microbiome research at our 2026 conference! #Microbiome26
Demonstrate how #genomics tools and technologies are contributing to a deeper understanding of the microbiome.
🗓️ 2-4 March
Submit an abstract by 24 November ✍🏼
📎 bit.ly/4kttBOX
#MicrobiomeSky #AcademicSky
Demonstrate how #genomics tools and technologies are contributing to a deeper understanding of the microbiome.
🗓️ 2-4 March
Submit an abstract by 24 November ✍🏼
📎 bit.ly/4kttBOX
#MicrobiomeSky #AcademicSky
September 30, 2025 at 7:22 AM
Come 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 👇
Bursaries are also available!
See details below 👇
Reposted by Aldert Zomer
We 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!
See thread for more information and reach out!
July 22, 2025 at 7:34 PM
We 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!
See thread for more information and reach out!
Reposted by Aldert Zomer
Don'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...
@escmid.bsky.social @esgem-sg.bsky.social
Register today and see you in Porto!
www.escmid.org/congress-eve...
www.escmid.org
July 11, 2025 at 3:57 PM
Don'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...
@escmid.bsky.social @esgem-sg.bsky.social
Register today and see you in Porto!
www.escmid.org/congress-eve...
Reposted by Aldert Zomer
Elon 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.
Again: Elon Musk is directly responsible for 14 million coming deaths. 4.5 million will be children.
Evaluating the impact of two decades of USAID interventions and projecting the effects of defunding on mortality up to 2030: a retrospective impact evaluation and forecasting analysis
USAID funding has significantly contributed to the reduction in adult and child mortality
across low-income and middle-income countries over the past two decades. Our estimates
show that, unless the a...
www.thelancet.com
July 2, 2025 at 8:00 PM
Elon 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.
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
💷 £36,720 to £39,750
🗓️ Apply by 2 July 2025
➡️ buff.ly/7M2mDaa
June 28, 2025 at 2:02 PM
⏰ 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
💷 £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...
💙 🐾 💙
When you've spend hours looking for your little black kitten...
. . . and then...
💙 🐾 💙
June 16, 2025 at 2:55 PM
.
When you've spend hours looking for your little black kitten...
. . . and then...
💙 🐾 💙
When you've spend hours looking for your little black kitten...
. . . and then...
💙 🐾 💙
Reposted by Aldert Zomer
Come join us in beautiful Lausanne! Deadline for applications: August 10th, 2025
wwwfbm.unil.ch/releve/appli...
wwwfbm.unil.ch/releve/appli...
June 10, 2025 at 1:58 PM
Come join us in beautiful Lausanne! Deadline for applications: August 10th, 2025
wwwfbm.unil.ch/releve/appli...
wwwfbm.unil.ch/releve/appli...
Reposted by Aldert Zomer
In 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...
June 13, 2025 at 2:46 PM
In 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 Zomer
New 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
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New 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
github.com/bede/deacon
Reposted by Aldert Zomer
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...
DMF: Tenure Track Assistant Professor towards Associate Professor in Molecular Microbiology - Site des postulations FBM
wwwfbm.unil.ch
June 10, 2025 at 1:53 PM
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 Zomer
Happy 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
Apply by 8th July 25
jobs.quadram.ac.uk/Details.asp?...
@quadraminstitute.bsky.social @earlhaminst.bsky.social
Quadram Institute
jobs.quadram.ac.uk
June 6, 2025 at 1:57 PM
Happy 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
Apply by 8th July 25
jobs.quadram.ac.uk/Details.asp?...
@quadraminstitute.bsky.social @earlhaminst.bsky.social
Reposted by Aldert Zomer
Dorado 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
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
May 21, 2025 at 5:14 PM
Dorado 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
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 Zomer
New 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)
www.biorxiv.org/content/10.1...
(1/6)
Autocycler: long-read consensus assembly for bacterial genomes
Motivation Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using T...
www.biorxiv.org
May 21, 2025 at 3:29 AM
New 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)
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.
Het zoveelste advies waar deze regering niet naar zal luisteren.
IMF waarschuwt Nederland voor op korte termijn gericht kabinetsbeleid
IMF waarschuwt Nederland voor op korte termijn gericht kabinetsbeleid
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.
www.nrc.nl
May 21, 2025 at 6:13 AM
“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.
Het zoveelste advies waar deze regering niet naar zal luisteren.
Reposted by Aldert Zomer
Autocycler: long-read consensus assembly for bacterial genomes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/rrwick/Autoc...
May 17, 2025 at 9:10 AM
Autocycler: long-read consensus assembly for bacterial genomes www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/rrwick/Autoc...