Antti Karkman
@anttikarkman.bsky.social
University lecturer in microbial bionformatics at University of Helsinki
(@helsinki.fi)
Co-founder of Aluke (www.aluke.fi)
(he/him)
(@helsinki.fi)
Co-founder of Aluke (www.aluke.fi)
(he/him)
Reposted by Antti Karkman
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
Metagenomic classification survey
Background: We're seeking the views of researchers on the possibility of a repository for metagenomic classification data, which we're hoping to build. The rationale is that people are familiar with t...
docs.google.com
November 10, 2025 at 6:24 PM
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
Reposted by Antti Karkman
Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Orchestrating Microbiome Analysis with Bioconductor
The expansion of microbiome research has led to the accumulation of interlinked datasets encompassing versatile taxonomic and functional assays. The analysis of increasingly large and heterogeneous…
www.biorxiv.org
November 9, 2025 at 11:31 AM
Orchestrating Microbiome Analysis with Bioconductor. #Microbiome #DataAnalysis #Bioconductor @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Antti Karkman
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 6, 2025 at 11:25 PM
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
The abstract deadline for Nordic AMR Conference 2026 has been extended. Also see the list of keynote speakers.
More information at www.helsinki.fi/en/conferenc...
More information at www.helsinki.fi/en/conferenc...
November 7, 2025 at 8:37 AM
The abstract deadline for Nordic AMR Conference 2026 has been extended. Also see the list of keynote speakers.
More information at www.helsinki.fi/en/conferenc...
More information at www.helsinki.fi/en/conferenc...
Reposted by Antti Karkman
Newly released Stockholm Declaration recommends the following reforms to publishing:
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
Reformation of science publishing: the Stockholm Declaration | Royal Society Open Science
Science relies on integrity and trustworthiness. But scientists under career pressure
are lured to purchase fake publications from ‘paper mills’ that use AI-generated data,
text and image fabrication....
royalsocietypublishing.org
November 5, 2025 at 7:07 PM
Newly released Stockholm Declaration recommends the following reforms to publishing:
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
1. Academia resumes control of publishing
2. Incentive systems to merit quality, not quantity
3. Independent fraud detection and prevention
4. Legislation and policies to protect science quality and integrity
This year the sequencing was not perfect, but we got one circular (hopefully complete) genome.
On Wednesday we continue with more in depth annotations and will learn more.
On Wednesday we continue with more in depth annotations and will learn more.
November 3, 2025 at 1:13 PM
This year the sequencing was not perfect, but we got one circular (hopefully complete) genome.
On Wednesday we continue with more in depth annotations and will learn more.
On Wednesday we continue with more in depth annotations and will learn more.
Reposted by Antti Karkman
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Antti Karkman
📣 Open position:
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
October 31, 2025 at 5:41 PM
📣 Open position:
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
Reposted by Antti Karkman
Kun pidät tieteellisen seminaarin jossa tarjolla ”pientä purtavaa”, pidä se ravitsemustieteilijöiden kanssa. Koska TOTTA KAI niiden väitöskirjatutkija on artesaanileipuri! Niissä piireissä tiedetään, että ruoalla on paitsi terveys-, myös mielenterveysvaikutuksia.
October 30, 2025 at 5:36 AM
Kun pidät tieteellisen seminaarin jossa tarjolla ”pientä purtavaa”, pidä se ravitsemustieteilijöiden kanssa. Koska TOTTA KAI niiden väitöskirjatutkija on artesaanileipuri! Niissä piireissä tiedetään, että ruoalla on paitsi terveys-, myös mielenterveysvaikutuksia.
And it is (finally) accepted to be published in Microbiology Spectrum.
Our work on the sulfonamide resistance gene, sul4, is (finally) available as preprint. Thanks to an excellent PhD student Melina Markkanen. Hopefully soon it will be also peer-reviewed and published. After the first desk rejection, we are looking for another journal.
doi.org/10.1101/2025...
doi.org/10.1101/2025...
Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts including clinically relevant species
The introduction of the first broad-spectrum antibiotics, sulfonamide drugs fundamentally revolutionized medicine in the 1930s. Shortly after and ever since sulfonamide resistance genes (sul genes) ha...
doi.org
October 25, 2025 at 2:54 PM
And it is (finally) accepted to be published in Microbiology Spectrum.
On Wednesday the student got to whole genome sequence their isolates on the exploratory laboratory course (studies.helsinki.fi/courses/cour...).
Next weeks we will analyse the data and try to assemble as many complete genomes as possible. Thanks @nanoporetech.com for the support.
Next weeks we will analyse the data and try to assemble as many complete genomes as possible. Thanks @nanoporetech.com for the support.
October 24, 2025 at 7:16 AM
On Wednesday the student got to whole genome sequence their isolates on the exploratory laboratory course (studies.helsinki.fi/courses/cour...).
Next weeks we will analyse the data and try to assemble as many complete genomes as possible. Thanks @nanoporetech.com for the support.
Next weeks we will analyse the data and try to assemble as many complete genomes as possible. Thanks @nanoporetech.com for the support.
Reposted by Antti Karkman
Turun kaupunki juhlii vuosisataista historiaansa vuonna 2029. Turun yliopiston arkeologit ja historioitsijat julkaisevat tässä blogissa lyhyitä kirjoituksia Turun menneisyydestä, ihmiskohtaloista ja tarinoista, niin arjen kuin juhlankin hetkistä.
blogit.utu.fi/turku800/
blogit.utu.fi/turku800/
800 tarinaa Turun historiasta | Ihmisiä, hetkiä, tarinoita
blogit.utu.fi
October 18, 2025 at 9:41 AM
Turun kaupunki juhlii vuosisataista historiaansa vuonna 2029. Turun yliopiston arkeologit ja historioitsijat julkaisevat tässä blogissa lyhyitä kirjoituksia Turun menneisyydestä, ihmiskohtaloista ja tarinoista, niin arjen kuin juhlankin hetkistä.
blogit.utu.fi/turku800/
blogit.utu.fi/turku800/
Reposted by Antti Karkman
Another great edition of Environmental #Metagenomics is wrapping up!
Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌
We wish you all the best with your research projects!
Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌
We wish you all the best with your research projects!
October 17, 2025 at 7:33 AM
Another great edition of Environmental #Metagenomics is wrapping up!
Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌
We wish you all the best with your research projects!
Huge thanks to @oskolkov.bsky.social , @aroneys.bsky.social and all the amazing participants who joined us this week. 🙌
We wish you all the best with your research projects!
Reposted by Antti Karkman
Well done Shafaq Aftab. When a reviewer stole her work and published it under his own name, she fought for a YEAR to get the journal to retract the paper. Just wondering why it took Wiley a YEAR to do this. 🧪 #academicsky
retractionwatch.com/2025/10/03/w...
retractionwatch.com/2025/10/03/w...
Wiley retracts study stolen by reviewer, following Retraction Watch coverage
A Wiley journal has retracted a paper more than a year after a researcher reported the work was hers and had been stolen by a reviewer for another journal. As we reported in July, Shafaq Aftab, now…
retractionwatch.com
October 12, 2025 at 4:57 AM
Well done Shafaq Aftab. When a reviewer stole her work and published it under his own name, she fought for a YEAR to get the journal to retract the paper. Just wondering why it took Wiley a YEAR to do this. 🧪 #academicsky
retractionwatch.com/2025/10/03/w...
retractionwatch.com/2025/10/03/w...
Reposted by Antti Karkman
Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.
Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
Evolution induced state shifts in a long-term microbial community experiment
Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...
www.biorxiv.org
October 11, 2025 at 5:00 AM
Massive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.
Reposted by Antti Karkman
Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
Evolution induced state shifts in a long-term microbial community experiment
Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...
www.biorxiv.org
October 11, 2025 at 4:48 AM
Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
Why not visit Helsinki next winter? There might be snow.
Abstract submission is open for the Nordic AMR Research Centre Conference 2026.
www.helsinki.fi/en/conferenc...
Abstract submission is open for the Nordic AMR Research Centre Conference 2026.
www.helsinki.fi/en/conferenc...
Nordic AMR Research Centre Conference 2026 | University of Helsinki
4-6 March 2026, Helsinki, Finland
www.helsinki.fi
October 9, 2025 at 11:54 AM
Why not visit Helsinki next winter? There might be snow.
Abstract submission is open for the Nordic AMR Research Centre Conference 2026.
www.helsinki.fi/en/conferenc...
Abstract submission is open for the Nordic AMR Research Centre Conference 2026.
www.helsinki.fi/en/conferenc...
Reposted by Antti Karkman
🌍 Applications now open for our first Bioconductor course in West Africa!
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
October 1, 2025 at 2:32 PM
🌍 Applications now open for our first Bioconductor course in West Africa!
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
📅 17–21 Nov 2025 | 📍 Abomey-Calavi, Benin
Free, in-person training on R, RStudio & RNA-seq workflows.
Apply by 15 Oct 👉 forms.gle/d32F6xJJbsFa...
More info 🔗 training.bioconductor.org/workshops/20...
#Bioconductor #RStats
The perfect location for writing an application to the Water4All call.
October 3, 2025 at 10:53 AM
The perfect location for writing an application to the Water4All call.
Reposted by Antti Karkman
You have 50 files. Same header. You want to merge them. Here’s how to do it without going insane. 🧵 👇
September 30, 2025 at 2:15 PM
You have 50 files. Same header. You want to merge them. Here’s how to do it without going insane. 🧵 👇
Reposted by Antti Karkman
🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social !
🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.
shorturl.at/HOm6X
🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.
shorturl.at/HOm6X
June 30, 2025 at 1:21 PM
🚨 Join us for the Environmental Metagenomics course (Oct 13–17, online) with @oskolkov.bsky.social & @aroneys.bsky.social !
🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.
shorturl.at/HOm6X
🔬 Hands-on training on read-based & assembly-based methods, MAGs, and integrating short & long-read @nanoporetech.com data.
shorturl.at/HOm6X
Reposted by Antti Karkman
Tämä ei ole hyvän mielen postaus, mutta ehkä syksyn tärkein postaukseni. Suosittelen kaikille tutkijoille ja tutkimusryhmille: käsitelkää törkyriskejä ja suunnitelkaa toimenpiteitä etukäteen yhdessä.
Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.
Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.
September 30, 2025 at 6:59 AM
Tämä ei ole hyvän mielen postaus, mutta ehkä syksyn tärkein postaukseni. Suosittelen kaikille tutkijoille ja tutkimusryhmille: käsitelkää törkyriskejä ja suunnitelkaa toimenpiteitä etukäteen yhdessä.
Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.
Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.
Reposted by Antti Karkman
Tärkeä ketju tutkijoille, heidän esihenkilöilleen ja tutkimusorganisaatioiden johdolle!
Lisäisin vielä yhden toiveen: Älä ryhdy vaihtamaan tai peittelemään tutkimuksesi aihetta häirinnän pelossa. Esihenkilö, sinun tehtäväsi on huolehtia tutkimuksen vapauden toteutumisesta omassa yksikössäsi.
Lisäisin vielä yhden toiveen: Älä ryhdy vaihtamaan tai peittelemään tutkimuksesi aihetta häirinnän pelossa. Esihenkilö, sinun tehtäväsi on huolehtia tutkimuksen vapauden toteutumisesta omassa yksikössäsi.
Tämä ei ole hyvän mielen postaus, mutta ehkä syksyn tärkein postaukseni. Suosittelen kaikille tutkijoille ja tutkimusryhmille: käsitelkää törkyriskejä ja suunnitelkaa toimenpiteitä etukäteen yhdessä.
Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.
Lähiaikoina on tiettävästi odotettavissa törkyä tiedeyhteisöä kohtaan. Ketjusta muutama pikavinkki.
September 30, 2025 at 8:41 AM
Tärkeä ketju tutkijoille, heidän esihenkilöilleen ja tutkimusorganisaatioiden johdolle!
Lisäisin vielä yhden toiveen: Älä ryhdy vaihtamaan tai peittelemään tutkimuksesi aihetta häirinnän pelossa. Esihenkilö, sinun tehtäväsi on huolehtia tutkimuksen vapauden toteutumisesta omassa yksikössäsi.
Lisäisin vielä yhden toiveen: Älä ryhdy vaihtamaan tai peittelemään tutkimuksesi aihetta häirinnän pelossa. Esihenkilö, sinun tehtäväsi on huolehtia tutkimuksen vapauden toteutumisesta omassa yksikössäsi.
Reposted by Antti Karkman
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...
