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Antti Karkman @anttikarkman.bsky.social · 20h

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...

Nordic AMR Research Centre Conference 2026 | University of Helsinki

4-6 March 2026, Helsinki, Finland

www.helsinki.fi

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Reposted by Antti Karkman

Bioconductor @bioconductor.bsky.social · 8d

🌍 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

Front view of the GBioS building at the University of Abomey-Calavi, Benin, surrounded by palm trees with a sign reading “Genetics, Biotechnology and Seed Science Unit.” Banner text above reads “Apply Now for the Bioconductor Benin 2025 Course!

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Antti Karkman @anttikarkman.bsky.social · 6d

The perfect location for writing an application to the Water4All call.

Harbour view with mountains on the background in Bergen, Norway.

Reposted by Antti Karkman

Ming Tommy Tang @tommytang.bsky.social · 9d

You have 50 files. Same header. You want to merge them. Here’s how to do it without going insane. 🧵 👇

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Reposted by Antti Karkman

Physalia-courses@Online @physaliacourses.bsky.social · Jun 30

🚨 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

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Reposted by Antti Karkman

Tomas Sjöblom @tomassjoblom.bsky.social · 10d

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.

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Reposted by Antti Karkman

Vera Mikkilä @veramikkila.bsky.social · 9d

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.

Tomas Sjöblom @tomassjoblom.bsky.social · 10d

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.

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Reposted by Antti Karkman

Teppo Hiltunen @teppo-h.bsky.social · 9d

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...

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

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Reposted by Antti Karkman

Ryan Wick @rrwick.bsky.social · 11d

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

Autocycler: long-read consensus assembly for bacterial genomes

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

doi.org

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Reposted by Antti Karkman

Zamin Iqbal @zaminiqbal.bsky.social · 14d

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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Reposted by Antti Karkman

Vaughn Cooper @vscooper.micropopbio.org · 13d

nice. you know what would be even more equitable? publishing this in a society journal that actually serves the scientific public.

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Reposted by Antti Karkman

Alex Crits-Christoph @acritschristoph.bsky.social · 13d

Wow! I am very much against this. The deep value of GenBank is in it being a public domain database with 0 limitations on use.

The norm that when we publish, we share the sequencing data supporting its claims *with 0 limitations on use* is so important for open science. I hope it doesn't change!

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Reposted by Antti Karkman

Sami Syrjämäki @samisyrjamaki.bsky.social · 17d

Kiinnostaako suomalainen tutkimus ihan oikeasti. Tässä ketjussa neljä erinomaista palvelua, joiden kautta siihen voi tutustua. 1/

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Reposted by Antti Karkman

Ryan Wick @rrwick.bsky.social · 17d

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

Benchmark update: metaMDBG and Myloasm

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Reposted by Antti Karkman

Prof Sam Illingworth @samillingworth.com · 17d

🥗 Diet shifts cut impacts in Sweden

A new study shows Swedish diets designed for future food scenarios reduce environmental impacts by ~30% while improving health. Cutting food waste boosts gains further.

🔗 www.nature.com/articles/s43...

#SciComm 🧪

Diet changes in food futures improve Swedish environmental and health outcomes - Communications Earth & Environment

In Sweden, dietary changes simulated under four food futures pathways reduced environmental impacts by 30 percent, but waste and fossil fuel emissions reductions are necessary to meet the climate targ...

www.nature.com

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Reposted by Antti Karkman

James Bradley @drbradbrad.bsky.social · 24d

📢 PLEASE RT!
❄️ M2 Masters Internship: Metagenomic analysis of microbial cold adaptation in the cryosphere
🧬 Compile & curate ice nucleation & cold-adaptation protein database
🖥️ Build HMM profiles
🦠 Analyze existing metagenomic data using HMMs

☀️ Marseille, France
Apply by 15 Oct

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Reposted by Antti Karkman

Physalia-courses@Online @physaliacourses.bsky.social · Jul 29

📅 UNIX and Shell Scripting for Bioinformatics
🗓️ 12–16 Jan | 💻 Online
Learn essential UNIX skills to process NGS data and automate bioinformatics tasks. No prior experience needed

www.physalia-courses.org/courses-work...

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Reposted by Antti Karkman

EvolDir @evoldir.bsky.social · Sep 4

Join the Physalia online course on Metabolomics with R/Bioconductor from Nov 11-14, 9:30 AM - 1:30 PM Berlin time. Learn data analysis workflows and statistical methods. More info: https://www.physalia-courses.org/courses-workshops/course55/ #course

Metabolomics with R/Bioconductor

Dates 11-14 November 2025 To foster international participation, this course will be held online

www.physalia-courses.org

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Reposted by Antti Karkman

Anna-Liisa Laine @annaliisalaine.bsky.social · Sep 3

🚨 Postdoc opportunities! 🚨
We’re looking for postdocs in 🌿 biodiversity science, 🧬 genetic indicator assessment, and 📊 ecological statistics.

Join us in unraveling the drivers & consequences of global change on biodiversity — and be part of a supportive & collaborative environment!
DL 24 September

Research Centre For Ecological Change @rececochange.bsky.social · Sep 3

📢 Post doc! Want to join our team?

We are looking for 3 post docs in biodiversity science, genetic indicator assessment, and ecological statistics for a fixed term of 2 years!

Come unravel the drivers and consequences of global change on biodiversity with us!

DL 24.9.
#universityofhelsinki

3 Post doc positions in biodiversity science, genetic indicator assessment and ecological statistics

jobs.helsinki.fi

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Reposted by Antti Karkman

Vera Mikkilä @veramikkila.bsky.social · Aug 28

Kaikki liittovaltion tiederahoitus alistetaan poliittiseen ohjaukseen. Valkoinen talo määrää, että jatkossa varta vasten nimetyt viranomaiset suuntaavat rahoituksen ”hyödylliseen” tutkimukseen.

Kuulostaako tutulta?

Me Akatemiassa tiedämme, että suurin hyöty syntyy tieteen vapaudesta.

Improving Oversight of Federal Grantmaking

By the authority vested in me as President by the Constitution and the laws of the United States of America, and to improve the process of Federal

www.whitehouse.gov

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Antti Karkman @anttikarkman.bsky.social · Jun 22

The latest update of VS Code broke the SSH connection to our HPC cluster, so looking for a good alternative. I might give Warp a try. If you would also like try it, click the link (not a paid ad, but I might get stickers if you do).
app.warp.dev/referral/R49LWY

Other suggestions are also welcome.

Reposted by Antti Karkman

Leo Lahti @antagomir.bsky.social · May 22

Antimicrobial resistance #AMR is a major #globalhealth threat. How does it vary between genders? We analyzed 14,641 open human gut #metagenomes from 32 countries to investigate gender differences in #antibioticResistance genes (ARGs). www.nature.com/articles/s41...

Gender differences in global antimicrobial resistance - npj Biofilms and Microbiomes

npj Biofilms and Microbiomes - Gender differences in global antimicrobial resistance

www.nature.com

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Reposted by Antti Karkman

Leo Lahti @antagomir.bsky.social · May 22

Did you know that the female #microbiome is unique in many ways, and antibiotic resistance in the gut microbiome varies between genders? See npj Biofilms and Microbiomes special issue, Women and their microbes, to learn more! www.nature.com/collections/...

Women and their microbes

This collection invites research on all aspects of women’s health involving the microbiome from different body sites and its interplay with fertility, ...

www.nature.com

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Reposted by Antti Karkman

Tieteentekijät @tieteentekijat.bsky.social · May 23

Tieteen vapaus on yksi demokraattisen yhteiskunnan kulmakivistä. Viime vuosien kehitys, jossa tutkimuksen vapautta ja tutkitun tiedon tärkeyttä on vähätelty, herättää aiheellista huolta tiedeyhteisössä, toteaa Tieteentekijöiden liittokokous julkilausumassaan.

#TieteenVapaus

buff.ly/1JjWkEC

Julkilausuma: Tieteen vapaus on demokratian perusta

Tieteen vapaus on yksi demokraattisen yhteiskunnan kulmakivistä. Viime vuosien kehitys, jossa tutkimuksen vapautta ja tutkitun tiedon tärkeyttä on vähätelty, herättää aiheellista huolta…

tieteentekijat.fi

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Antti Karkman @anttikarkman.bsky.social · May 20

I guess I won’t be doing reviews for SpringerNature anymore. Not the first time they send an email days before the review deadline that my report is no longer needed. This time 10 days before the DL. What if I already started? (Of course I didn’t, because the deadline was end of the month).