Matti Ruuskanen
@begia.bsky.social
PhD, University Lecturer at U. of Turku, Adjunct Prof. (docent) at U. of Helsinki |
Research in human microbiomes, health and food, bioinformatics & data science | Musician, partner dancing and outdoors enthusiast
Research in human microbiomes, health and food, bioinformatics & data science | Musician, partner dancing and outdoors enthusiast
Reposted by Matti Ruuskanen
What a title!
Antibiotic Resistomes And Microbial Communities In The 18th-Century Urban Settlement And Slaughterhouse Environment https://www.biorxiv.org/content/10.64898/2026.07.31.742145v1
August 1, 2026 at 4:22 AM
What a title!
Ensimmäinen johtamani tutkimushanke, "Suolistomikrobiston kasviperäisten ruokien metabolian genomipohjainen mallintaminen" on saanut rahoituksen Sakari Alhopuron Säätiöltä! Suuret kiitokset tuesta!
www.sakarialhopuronsaatio.fi/apurahat/myo...
www.sakarialhopuronsaatio.fi/apurahat/myo...
Myönnetyt apurahat
www.sakarialhopuronsaatio.fi
May 26, 2026 at 5:30 AM
Ensimmäinen johtamani tutkimushanke, "Suolistomikrobiston kasviperäisten ruokien metabolian genomipohjainen mallintaminen" on saanut rahoituksen Sakari Alhopuron Säätiöltä! Suuret kiitokset tuesta!
www.sakarialhopuronsaatio.fi/apurahat/myo...
www.sakarialhopuronsaatio.fi/apurahat/myo...
I have been tempted, but luckily haven't really committed yet to trying full-on AI-assisted data analysis. Better safe than sorry! The current best approach might be to only consult LLMs when solving specific issues in your own code.
My advice to biologists tempted to use AI/LLMs to code their analyses: don't.
(I'm continuing with reviewing the analyses for our article, and it's taken me all morning to figure out what the code is trying to do.)
(I'm continuing with reviewing the analyses for our article, and it's taken me all morning to figure out what the code is trying to do.)
Based on this, my advice up to now is: Please don't use an LLM to draft your analyses.
If you don't know what you're doing, it'll lead you badly astray and be unreadable.
If you know what you're doing, you can code the analyses faster and easier yourself.
If you don't know what you're doing, it'll lead you badly astray and be unreadable.
If you know what you're doing, you can code the analyses faster and easier yourself.
March 27, 2026 at 1:55 PM
I have been tempted, but luckily haven't really committed yet to trying full-on AI-assisted data analysis. Better safe than sorry! The current best approach might be to only consult LLMs when solving specific issues in your own code.
Our new paper on allergies and skin microbiomes is now out! Thanks for the informative video, @microbiologysociety.org !
How are allergies linked to our skin microbiome?🍃Researchers at @helsinki.fi investigated this relationship in neighbouring populations divided by lifestyle and the Finnish Russian border🦠
Read the full paper in Microbial Genomics here🔗 doi.org/10.1099/mgen...
Read the full paper in Microbial Genomics here🔗 doi.org/10.1099/mgen...
December 9, 2025 at 9:12 AM
Our new paper on allergies and skin microbiomes is now out! Thanks for the informative video, @microbiologysociety.org !
Our new systematic review is now out! Briefly, temporal multi-omic data and analyses are crucially needed to improve our understanding of microbiomes. Also, often the omics layers are not analyzed in an integrative way, even while such methods exist.
academic.oup.com/bib/article/...
academic.oup.com/bib/article/...
Multi-omics time-series analysis in microbiome research: a systematic review
Abstract. Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and cha
academic.oup.com
October 9, 2025 at 9:42 AM
Our new systematic review is now out! Briefly, temporal multi-omic data and analyses are crucially needed to improve our understanding of microbiomes. Also, often the omics layers are not analyzed in an integrative way, even while such methods exist.
academic.oup.com/bib/article/...
academic.oup.com/bib/article/...
www.nature.com/articles/s41... Our new paper on the risks and socio-demographic dimensions of antibiotic resistance in the human gut is now out in @natcomms.nature.com!
Variation and prognostic potential of the gut antibiotic resistome in the FINRISK 2002 cohort - Nature Communications
Here, in a representative cohort of 7,095 Finnish adults, the authors reveal that gut antibiotic resistance is shaped not only by antibiotic use but also by the microbiome, diet, lifestyle, household ...
www.nature.com
July 2, 2025 at 5:30 AM
www.nature.com/articles/s41... Our new paper on the risks and socio-demographic dimensions of antibiotic resistance in the human gut is now out in @natcomms.nature.com!
Reposted by Matti Ruuskanen
🚨#infogut2025
The 1st INFOGUT COST Action meeting is taking place at the University of Bologna!
We’re thrilled to come together to discuss the latest advancements in *in vitro colon models* simulating gut microbiota-mediated interactions
#COSTAction #GutMicrobiota #InVitroModels #MicrobiomeResearch
The 1st INFOGUT COST Action meeting is taking place at the University of Bologna!
We’re thrilled to come together to discuss the latest advancements in *in vitro colon models* simulating gut microbiota-mediated interactions
#COSTAction #GutMicrobiota #InVitroModels #MicrobiomeResearch
May 26, 2025 at 1:19 PM
🚨#infogut2025
The 1st INFOGUT COST Action meeting is taking place at the University of Bologna!
We’re thrilled to come together to discuss the latest advancements in *in vitro colon models* simulating gut microbiota-mediated interactions
#COSTAction #GutMicrobiota #InVitroModels #MicrobiomeResearch
The 1st INFOGUT COST Action meeting is taking place at the University of Bologna!
We’re thrilled to come together to discuss the latest advancements in *in vitro colon models* simulating gut microbiota-mediated interactions
#COSTAction #GutMicrobiota #InVitroModels #MicrobiomeResearch
Kaipa se on nyt virallista, kun allekirjotin työsopparinki 😎 Aloitan toukokuun alusta yliopistonlehtorina Bioteknologian laitoksella Turun yliopistossa! Tulevat opetushommat on varmasti antoisia, mutta nyt voin aloittaa myös oman tutkimusryhmän perustamisen, jos rahoituksen tuulet on suotuisia 🤞
January 17, 2025 at 2:15 PM
Kaipa se on nyt virallista, kun allekirjotin työsopparinki 😎 Aloitan toukokuun alusta yliopistonlehtorina Bioteknologian laitoksella Turun yliopistossa! Tulevat opetushommat on varmasti antoisia, mutta nyt voin aloittaa myös oman tutkimusryhmän perustamisen, jos rahoituksen tuulet on suotuisia 🤞
December 20, 2023 at 10:01 AM
Vaikka tagit ei niin hyvin toimi bskyssä, niin: #MinäTutkin ihmisten suolisto- ja ihomikrobistojen vaikutuksia kroonisiin sairauksiin, kuten 2-tyypin diabetekseen ja allergioihin. Lisäksi kehitän ja sovellan mm. koneoppivia mallinnusmenetelmiä mikrobistodatassa.
December 1, 2023 at 4:40 PM
Vaikka tagit ei niin hyvin toimi bskyssä, niin: #MinäTutkin ihmisten suolisto- ja ihomikrobistojen vaikutuksia kroonisiin sairauksiin, kuten 2-tyypin diabetekseen ja allergioihin. Lisäksi kehitän ja sovellan mm. koneoppivia mallinnusmenetelmiä mikrobistodatassa.
Ohoh, seuraajia! Tarkoituksena keskustella lähinnä töistäni eli mikrobiologiasta suomeksi ja englanniksi. X (formerly known as Twitter) alkoi kovasti tökkiä omistajanvaihdoksen jälkeen. En lupaa olla julkaisematta sisältöä mm. pyöräilystä, musiikista, ympäristöstä, ja ehkä jopa politiikasta.
November 29, 2023 at 6:22 PM
Ohoh, seuraajia! Tarkoituksena keskustella lähinnä töistäni eli mikrobiologiasta suomeksi ja englanniksi. X (formerly known as Twitter) alkoi kovasti tökkiä omistajanvaihdoksen jälkeen. En lupaa olla julkaisematta sisältöä mm. pyöräilystä, musiikista, ympäristöstä, ja ehkä jopa politiikasta.