Anders Ogechi Hostrup Daugberg
@andersohd.bsky.social
PhD student at Aalborg University 🇩🇰
Using bioinformatics to understand how bacteria produce and secrete biopolymers (the backbone of biofilms!)🦠
Metagenomics/transcriptomics, gene cluster annotation, exopolysaccharides, functional amyloids, eDNA🧬
Using bioinformatics to understand how bacteria produce and secrete biopolymers (the backbone of biofilms!)🦠
Metagenomics/transcriptomics, gene cluster annotation, exopolysaccharides, functional amyloids, eDNA🧬
Reposted by Anders Ogechi Hostrup Daugberg
Opinion: Chaos is coming for scholarly publishing.
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Chaos is coming for scholarly publishing - Research Professional News
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards
www.researchprofessionalnews.com
November 12, 2025 at 10:17 AM
Opinion: Chaos is coming for scholarly publishing.
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social).
www.researchprofessionalnews.com/rr-news-uk-v...
Reposted by Anders Ogechi Hostrup Daugberg
DMS 2025 is a wrap! 🧫
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
November 11, 2025 at 10:59 PM
DMS 2025 is a wrap! 🧫
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
I had a lot of great discussions with people about biofilms and EPS 🦠
Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬
A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥
Reposted by Anders Ogechi Hostrup Daugberg
1/ Working with big data in R?
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
November 11, 2025 at 2:45 PM
1/ Working with big data in R?
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
Your wrangling just got a massive upgrade.
duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵
Reposted by Anders Ogechi Hostrup Daugberg
note, gliding is not comparable to sliding
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
November 4, 2025 at 2:42 PM
note, gliding is not comparable to sliding
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
Reposted by Anders Ogechi Hostrup Daugberg
Cellulose biosynthesis and function in Streptomyces
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
Cellulose biosynthesis and function in Streptomyces
Cellulose, a ubiquitous polysaccharide with critical roles in life, provides structural
integrity to cells in plants and aids biofilm formation in many bacteria. Although
bacterial cellulose biosynthe...
www.cell.com
October 30, 2025 at 12:50 PM
Cellulose biosynthesis and function in Streptomyces
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
@cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen
www.cell.com/trends/micro...
Reposted by Anders Ogechi Hostrup Daugberg
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Anders Ogechi Hostrup Daugberg
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 24, 2025 at 9:15 AM
Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Anders Ogechi Hostrup Daugberg
Diverse biofilm-forming Sphingomonadaceae represent twelve novel species isolated from glaciers on the Tibetan Plateau. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead
October 15, 2025 at 8:01 AM
Diverse biofilm-forming Sphingomonadaceae represent twelve novel species isolated from glaciers on the Tibetan Plateau. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead
Reposted by Anders Ogechi Hostrup Daugberg
PhD opportunity in my lab: exploring how commensals and pathogens build biofilm communities on endotracheal (ventilator) tubes. Microbial ecology, medical microbiology and fancy imaging! Co-supervised with the fabulous Saskia Bakker and Jeremy Webb warwick.ac.uk/fac/cross_fa... #MicroSky
Dr Freya Harrison
Dr Freya Harrison
warwick.ac.uk
October 15, 2025 at 8:09 PM
PhD opportunity in my lab: exploring how commensals and pathogens build biofilm communities on endotracheal (ventilator) tubes. Microbial ecology, medical microbiology and fancy imaging! Co-supervised with the fabulous Saskia Bakker and Jeremy Webb warwick.ac.uk/fac/cross_fa... #MicroSky
Reposted by Anders Ogechi Hostrup Daugberg
Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures
Staphylococcus aureus infections represent a clinical challenge due to their propensity to form biofilms and the increasing prevalence of antibiotic r…
www.sciencedirect.com
September 19, 2025 at 11:23 AM
Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
@biofilmjournal.bsky.social from Agneta Richter-Dahlfors
www.sciencedirect.com/science/arti...
Reposted by Anders Ogechi Hostrup Daugberg
Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.
September 5, 2025 at 3:20 PM
Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.
Reposted by Anders Ogechi Hostrup Daugberg
I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome:
doi.org/10.1093/isme...
doi.org/10.1093/isme...
September 7, 2025 at 2:41 PM
I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome:
doi.org/10.1093/isme...
doi.org/10.1093/isme...
Reposted by Anders Ogechi Hostrup Daugberg
“Writing an essay is hard because it forces you to use your brain in ways you haven't before…Your job is not to turn in completed assignments; it's to learn how to think. Turning in completed assignments can help you learn how to think, but only if you're the one who completed them.”
As always, Ted Chiang is great in this interview.
cdh.princeton.edu/blog/2025/08...
cdh.princeton.edu/blog/2025/08...
August 14, 2025 at 2:21 PM
“Writing an essay is hard because it forces you to use your brain in ways you haven't before…Your job is not to turn in completed assignments; it's to learn how to think. Turning in completed assignments can help you learn how to think, but only if you're the one who completed them.”
Reposted by Anders Ogechi Hostrup Daugberg
Reposted by Anders Ogechi Hostrup Daugberg
Really liked the explanation about human understanding, and what we miss when we use black box models. This has always been my gripe with prediction models for eg AMR - I want to know why that feature is associated with resistance!
This is an excellent long-read on AI and science with lots of useful further reading www.aisnakeoil.com/p/could-ai-s.... Well worth your time to actually read it.
Could AI slow science?
Confronting the production-progress paradox
www.aisnakeoil.com
August 12, 2025 at 4:56 AM
Really liked the explanation about human understanding, and what we miss when we use black box models. This has always been my gripe with prediction models for eg AMR - I want to know why that feature is associated with resistance!
Reposted by Anders Ogechi Hostrup Daugberg
I frequently meet ppl who tell me about medieval German, or fen art, or alchemy, muons, human language processing, or extremely specific sorts of religious scholarship. Occasionally inventors of extraordinary things. I love how all these diverse specialties can be in one place (a university canteen)
a university is not for generating profit, it provides cultural enrichment via weird little gremlin people who love visigoths or haikus, and very occasionally a scientist who figures out faster than light travel
August 12, 2025 at 12:35 PM
I frequently meet ppl who tell me about medieval German, or fen art, or alchemy, muons, human language processing, or extremely specific sorts of religious scholarship. Occasionally inventors of extraordinary things. I love how all these diverse specialties can be in one place (a university canteen)
Reposted by Anders Ogechi Hostrup Daugberg
Reposted by Anders Ogechi Hostrup Daugberg
#ResearchBriefing
Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity
#MicroSky
www.nature.com/articles/s41...
Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity
#MicroSky
www.nature.com/articles/s41...
Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity - Nature Microbiology
Deep, long-read metagenome sequencing of 154 soil and sediment samples from diverse habitats in Denmark enabled recovery of 4,894 high-quality and highly contiguous microbial genomes. The vast untappe...
www.nature.com
August 1, 2025 at 2:16 PM
#ResearchBriefing
Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity
#MicroSky
www.nature.com/articles/s41...
Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity
#MicroSky
www.nature.com/articles/s41...
Reposted by Anders Ogechi Hostrup Daugberg
Gaza has recorded the most health-care worker deaths (over 1400 deaths), UN deaths (295) & journalist deaths (212) than in any recent conflict zone.
Life expectancy at birth dropped 35 yrs in 2024. From Oct '23-May '25, there were 720 attacks on healthcare targets www.thelancet.com/journals/lan...
Life expectancy at birth dropped 35 yrs in 2024. From Oct '23-May '25, there were 720 attacks on healthcare targets www.thelancet.com/journals/lan...
Break the selective silence on the genocide in Gaza
Substantial and well-documented evidence indicates a catastrophic public health emergency
in Gaza (appendix pp 1–5), marked by severe food insecurity and alarming levels of
malnutrition-related deaths...
www.thelancet.com
August 1, 2025 at 3:22 AM
Gaza has recorded the most health-care worker deaths (over 1400 deaths), UN deaths (295) & journalist deaths (212) than in any recent conflict zone.
Life expectancy at birth dropped 35 yrs in 2024. From Oct '23-May '25, there were 720 attacks on healthcare targets www.thelancet.com/journals/lan...
Life expectancy at birth dropped 35 yrs in 2024. From Oct '23-May '25, there were 720 attacks on healthcare targets www.thelancet.com/journals/lan...
Reposted by Anders Ogechi Hostrup Daugberg
What is the role of extracellular polymeric substances (EPS) in carbon exchange among microbial species? @sammy-pontrelli.bsky.social &co show that #EPS, formed via #chitin degradation, drives #MicrobialDiversity by acting as a sequentially degraded #CarbonSource @plosbiology.org 🧪 plos.io/3J9kbuu
July 31, 2025 at 1:54 PM
What is the role of extracellular polymeric substances (EPS) in carbon exchange among microbial species? @sammy-pontrelli.bsky.social &co show that #EPS, formed via #chitin degradation, drives #MicrobialDiversity by acting as a sequentially degraded #CarbonSource @plosbiology.org 🧪 plos.io/3J9kbuu
Reposted by Anders Ogechi Hostrup Daugberg
Someone on here compared AI produced material as "digital asbestos " which in a few decades' time we will have to work out how to eradicate from the fabric of research.
From my own academic research, even pre LLMs there was a huge danger of zombie factoids that begin in a respectable publication by mistake and then get reprinted for decades because no one is backtracing to the original source. Once bad info gets into the system it can take years to clear it out.
I've seen numerous examples of this in recent days - we're at a point where some reporters are using LLMs as a source and not even remotely properly factchecking, but also where LLM generated material is making its way into other material and being unknowingly reproduced by others.
July 30, 2025 at 8:39 AM
Someone on here compared AI produced material as "digital asbestos " which in a few decades' time we will have to work out how to eradicate from the fabric of research.
Reposted by Anders Ogechi Hostrup Daugberg
Was talking to a student who wasn't sure about why one would get a PhD. So I wrote up a list of reasons!
www.eugenevinitsky.com/posts/reason...
www.eugenevinitsky.com/posts/reason...
Eugene Vinitsky
www.eugenevinitsky.com
July 27, 2025 at 7:30 PM
Was talking to a student who wasn't sure about why one would get a PhD. So I wrote up a list of reasons!
www.eugenevinitsky.com/posts/reason...
www.eugenevinitsky.com/posts/reason...
Reposted by Anders Ogechi Hostrup Daugberg
knowablemagazine.org/content/arti... My favorite advice piece.
I compile this and other useful advice articles on my lab website: lowepowerlab.ucdavis.edu/resources
I compile this and other useful advice articles on my lab website: lowepowerlab.ucdavis.edu/resources
Why scientists need to be better at data visualization
The scientific literature is riddled with bad charts and graphs, leading to misunderstanding and worse. Avoiding design missteps can improve understanding of research.
knowablemagazine.org
July 25, 2025 at 4:01 PM
knowablemagazine.org/content/arti... My favorite advice piece.
I compile this and other useful advice articles on my lab website: lowepowerlab.ucdavis.edu/resources
I compile this and other useful advice articles on my lab website: lowepowerlab.ucdavis.edu/resources
Reposted by Anders Ogechi Hostrup Daugberg
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
FAMSA2 enables accurate multiple sequence alignment at protein-universe scale
We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...
www.biorxiv.org
July 19, 2025 at 9:28 PM
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...