PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41... #jcampubs
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks - Nature Communications
Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors p...
www.nature.com
November 10, 2025 at 3:45 PM
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41... #jcampubs
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41...
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks - Nature Communications
Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors p...
www.nature.com
November 10, 2025 at 11:37 PM
PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41...
In 2026 I'm taking a sabbatical in @peterfineran.bsky.social lab @universityofotago.bsky.social. I'm looking forward to learning a lot from Peter's lab and excited to get back to my prokaryotic/viral roots! Also planning to some trips to the rest of the Pacific and Asia. So much to look forward to!
November 5, 2025 at 3:36 PM
In 2026 I'm taking a sabbatical in @peterfineran.bsky.social lab @universityofotago.bsky.social. I'm looking forward to learning a lot from Peter's lab and excited to get back to my prokaryotic/viral roots! Also planning to some trips to the rest of the Pacific and Asia. So much to look forward to!
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by Dimitrios - Georgios Kontopoulos, Ilias Patmanidis, Timothy G Barraclough, and Samraat Pawar
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by Dimitrios - Georgios Kontopoulos, Ilias Patmanidis, Timothy G Barraclough, and Samraat Pawar
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
Abstract. Understanding the structural changes that enable enzymes to remain active in extreme thermal conditions is of broad scientific interest for both
doi.org
November 3, 2025 at 3:30 PM
Changes in flexibility but not in compactness underlie the thermal adaptation of prokaryotic adenylate kinases
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by Dimitrios - Georgios Kontopoulos, Ilias Patmanidis, Timothy G Barraclough, and Samraat Pawar
doi.org/10.1093/evle...
Now in @evolletters.bsky.social by Dimitrios - Georgios Kontopoulos, Ilias Patmanidis, Timothy G Barraclough, and Samraat Pawar
Intriguing structures of Asgard hypernucleosomes in open and closed conformations provide a glimpse into the evolution of chromatin from our closest prokaryotic relatives. Bold and eye-opening work by the @dodonova-sveta.bsky.social lab! Also great visualization 🧪👩🔬🎨 #CryoEM #ArchaeaSky
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
October 29, 2025 at 4:12 AM
Intriguing structures of Asgard hypernucleosomes in open and closed conformations provide a glimpse into the evolution of chromatin from our closest prokaryotic relatives. Bold and eye-opening work by the @dodonova-sveta.bsky.social lab! Also great visualization 🧪👩🔬🎨 #CryoEM #ArchaeaSky
Interesting paper on bacteriophage genomics and bioinformatics
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world
Abstract. The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detectio
academic.oup.com
October 21, 2025 at 1:45 PM
Interesting paper on bacteriophage genomics and bioinformatics
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
'Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world' by @sebwielgoss.bsky.social and colleagues
academic.oup.com/bib/article/...
Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean www.biorxiv.org/content/10.1... #jcampubs 🌊
October 21, 2025 at 4:22 AM
Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean www.biorxiv.org/content/10.1... #jcampubs 🌊
Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean https://www.biorxiv.org/content/10.1101/2025.10.20.683375v1
October 20, 2025 at 8:17 PM
Comparison of picolyl azide-based BONCAT and microautoradiography for assessing the heterotrophic prokaryotic activity in the deep ocean https://www.biorxiv.org/content/10.1101/2025.10.20.683375v1
Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem
#microbiology #bacteria
www.nature.com/articles/s41...
#microbiology #bacteria
www.nature.com/articles/s41...
Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem
www.nature.com
October 19, 2025 at 1:14 PM
Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem
#microbiology #bacteria
www.nature.com/articles/s41...
#microbiology #bacteria
www.nature.com/articles/s41...
🌿 REVIEW 🌿
PPO, an enzyme vital for heme & chlorophyll synthesis, is the target of photodynamically active herbicides. The slow emergence of resistance to PPO herbicides enables more sustainable weed control strategies - Ali et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
PPO, an enzyme vital for heme & chlorophyll synthesis, is the target of photodynamically active herbicides. The slow emergence of resistance to PPO herbicides enables more sustainable weed control strategies - Ali et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
October 18, 2025 at 11:46 AM
🌿 REVIEW 🌿
PPO, an enzyme vital for heme & chlorophyll synthesis, is the target of photodynamically active herbicides. The slow emergence of resistance to PPO herbicides enables more sustainable weed control strategies - Ali et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
PPO, an enzyme vital for heme & chlorophyll synthesis, is the target of photodynamically active herbicides. The slow emergence of resistance to PPO herbicides enables more sustainable weed control strategies - Ali et al.
🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪
We’re excited to announce the incredible speaker line-up for the Prokaryotic Cell Biology Conference! Join the leading researchers as they explore the latest advances in Nanoimaging, Cell Growth and Cellular Structures.
Join our speakers & register today! ➡️https://bit.ly/47rtkbw
#ProkaryoticCellBio
Join our speakers & register today! ➡️https://bit.ly/47rtkbw
#ProkaryoticCellBio
October 16, 2025 at 2:27 PM
We’re excited to announce the incredible speaker line-up for the Prokaryotic Cell Biology Conference! Join the leading researchers as they explore the latest advances in Nanoimaging, Cell Growth and Cellular Structures.
Join our speakers & register today! ➡️https://bit.ly/47rtkbw
#ProkaryoticCellBio
Join our speakers & register today! ➡️https://bit.ly/47rtkbw
#ProkaryoticCellBio
Got excited too fast!!!! 😭 "We’re not currently able to accept tissue samples or plant, fungal, or prokaryotic cells - only cultured animal cells for now. " I will be waiting!!!
October 16, 2025 at 3:05 PM
Got excited too fast!!!! 😭 "We’re not currently able to accept tissue samples or plant, fungal, or prokaryotic cells - only cultured animal cells for now. " I will be waiting!!!
I'm preparing a lecture on prokaryotic chromosomes, which will include some discussion on ploidy. I was curious to know if some of the ASGARD archaea are polyploid so I googled it. This is Gemini's results 😅😅😑
October 14, 2025 at 8:35 AM
I'm preparing a lecture on prokaryotic chromosomes, which will include some discussion on ploidy. I was curious to know if some of the ASGARD archaea are polyploid so I googled it. This is Gemini's results 😅😅😑
Become my colleague @oxfordbiochemistry.bsky.social !
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism
my.corehr.com/pls/uoxrecru...
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism
my.corehr.com/pls/uoxrecru...
Job Details
my.corehr.com
September 29, 2025 at 9:25 AM
Become my colleague @oxfordbiochemistry.bsky.social !
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism
my.corehr.com/pls/uoxrecru...
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism
my.corehr.com/pls/uoxrecru...
📣Congress📣
The One Health Pangenome
2–5 December 2025, Valencia 🇪🇸
This 2nd edition is focused on the prokaryotic pangenome in the One-Health context.
alocongress.com/pangenome2025
🧬 🖥️ 🦠🔬🧪
#OneHealthPangenome2025 #Valencia #OneHealth #Microbial #Genomics #Bioinformatics #Pangenome
The One Health Pangenome
2–5 December 2025, Valencia 🇪🇸
This 2nd edition is focused on the prokaryotic pangenome in the One-Health context.
alocongress.com/pangenome2025
🧬 🖥️ 🦠🔬🧪
#OneHealthPangenome2025 #Valencia #OneHealth #Microbial #Genomics #Bioinformatics #Pangenome
PANGENOME2025
The biology of prokaryotic cells is directly dependent on the differential gene pools that characterize each cell or strain. This has been a fundamental aspect of epidemiology for delimiting outbreaks...
alocongress.com
September 24, 2025 at 6:23 PM
📣Congress📣
The One Health Pangenome
2–5 December 2025, Valencia 🇪🇸
This 2nd edition is focused on the prokaryotic pangenome in the One-Health context.
alocongress.com/pangenome2025
🧬 🖥️ 🦠🔬🧪
#OneHealthPangenome2025 #Valencia #OneHealth #Microbial #Genomics #Bioinformatics #Pangenome
The One Health Pangenome
2–5 December 2025, Valencia 🇪🇸
This 2nd edition is focused on the prokaryotic pangenome in the One-Health context.
alocongress.com/pangenome2025
🧬 🖥️ 🦠🔬🧪
#OneHealthPangenome2025 #Valencia #OneHealth #Microbial #Genomics #Bioinformatics #Pangenome
That’s a wrap for The Biology and Physics of Prokaryotic Chromosomes VII 2025. A big thank you to all those who attended 🧪 #BioPhyChrom2025 #BiochemEvents
September 19, 2025 at 8:50 AM
That’s a wrap for The Biology and Physics of Prokaryotic Chromosomes VII 2025. A big thank you to all those who attended 🧪 #BioPhyChrom2025 #BiochemEvents
#Biophychrom2025 is over, but we spent four exciting days discussing the biology and physics of prokaryotic chromosomes. Congratulations to all the attendees for making this conference a success.
@biochemsoc.bsky.social
@danielabarilla.bsky.social
@graingerlab.bsky.social
@damelab.bsky.social
@biochemsoc.bsky.social
@danielabarilla.bsky.social
@graingerlab.bsky.social
@damelab.bsky.social
September 19, 2025 at 5:57 PM
#Biophychrom2025 is over, but we spent four exciting days discussing the biology and physics of prokaryotic chromosomes. Congratulations to all the attendees for making this conference a success.
@biochemsoc.bsky.social
@danielabarilla.bsky.social
@graingerlab.bsky.social
@damelab.bsky.social
@biochemsoc.bsky.social
@danielabarilla.bsky.social
@graingerlab.bsky.social
@damelab.bsky.social
Congratulations to Cees Dekker @ceesdekker.bsky.social who showcased his work on single-molecule biophysics studies of DNA loop extrusion in his 2026 #BiochemAward Lecture for Significant Breakthrough or Achievement! We hope everyone enjoyed Prokaryotic Chromosomes VII!
September 19, 2025 at 11:30 AM
Congratulations to Cees Dekker @ceesdekker.bsky.social who showcased his work on single-molecule biophysics studies of DNA loop extrusion in his 2026 #BiochemAward Lecture for Significant Breakthrough or Achievement! We hope everyone enjoyed Prokaryotic Chromosomes VII!
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
@ruoshiz.bsky.social @milot.bsky.social
www.nature.com/articles/s41...
De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods
This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.
www.nature.com
September 16, 2025 at 8:26 PM
Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵
YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1
September 16, 2025 at 6:17 AM
YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1
A big welcome to the attendees of The Biology and Physics of Prokaryotic Chromosomes VII. We’re looking forward to bringing together the community in York #BiochemEvent #BioPhyChrom2025
September 16, 2025 at 1:55 PM
A big welcome to the attendees of The Biology and Physics of Prokaryotic Chromosomes VII. We’re looking forward to bringing together the community in York #BiochemEvent #BioPhyChrom2025
Check out our new paper: a review of translational coupling, the phenomenon where translation of one prokaryotic gene can promote translation of the gene downstream. We cover the history, and delve into the mechanism, which is still not fully understood. journals.asm.org/doi/10.1128/...
Translational coupling of neighboring genes in prokaryotes | Journal of Bacteriology
Prokaryotic genes are arranged in operons, with functionally related genes often located
adjacent to one another (1). There are several ways in which the operonic organization of genes facilitates
the...
journals.asm.org
September 11, 2025 at 4:45 PM
Check out our new paper: a review of translational coupling, the phenomenon where translation of one prokaryotic gene can promote translation of the gene downstream. We cover the history, and delve into the mechanism, which is still not fully understood. journals.asm.org/doi/10.1128/...
"Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity" by @omaistrenko.bsky.social (2020) investigated which factors contribute to pangenome size – e.g. it's higher in soil and lower in host-associated habitats
academic.oup.com/ism...
academic.oup.com/ism...
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
AbstractMicrobial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an under
academic.oup.com
December 6, 2024 at 2:00 PM
"Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity" by @omaistrenko.bsky.social (2020) investigated which factors contribute to pangenome size – e.g. it's higher in soil and lower in host-associated habitats
academic.oup.com/ism...
academic.oup.com/ism...
Consistent prokaryotic successional dynamics across contrasting phytoplankton blooms aslopubs.onlinelibrary.wiley.com/doi/10.1002/... #jcampubs 🌊
December 27, 2024 at 7:35 PM
Consistent prokaryotic successional dynamics across contrasting phytoplankton blooms aslopubs.onlinelibrary.wiley.com/doi/10.1002/... #jcampubs 🌊
“machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes.”👇🏼
Computational exploration of the global microbiome for antibiotic discovery https://www.biorxiv.org/content/10.1101/2023.08.31.555663v1
Computational exploration of the global microbiome for antibiotic discovery https://www.biorxiv.org/content/10.1101/2023.08.31.555663v1
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machi
www.biorxiv.org
September 1, 2023 at 4:30 AM
“machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes.”👇🏼