Nina Dombrowski
@ndombrowski.bsky.social
Bioinformatician at UvA, interested in microbial communities, phylogenomics, metagenomics/genomes
Reposted by Nina Dombrowski
Reposted by Nina Dombrowski
The detectCores() apocalypse is creeping up on us 👻🐛
As more people are getting access to 128+ CPU cores, code spinning up parallel cluster with detectCores() workers fails - not enough #RStats connections available
Friends, do *not* default to detectCores(), bc www.jottr.org/2022/12/05/a...
As more people are getting access to 128+ CPU cores, code spinning up parallel cluster with detectCores() workers fails - not enough #RStats connections available
Friends, do *not* default to detectCores(), bc www.jottr.org/2022/12/05/a...
Please Avoid detectCores() in your R Packages
The detectCores() function of the parallel package is probably one of the most used functions when it comes to setting the number of parallel workers to use in R. In this blog post, I’ll try to explai...
www.jottr.org
November 5, 2025 at 11:55 PM
The detectCores() apocalypse is creeping up on us 👻🐛
As more people are getting access to 128+ CPU cores, code spinning up parallel cluster with detectCores() workers fails - not enough #RStats connections available
Friends, do *not* default to detectCores(), bc www.jottr.org/2022/12/05/a...
As more people are getting access to 128+ CPU cores, code spinning up parallel cluster with detectCores() workers fails - not enough #RStats connections available
Friends, do *not* default to detectCores(), bc www.jottr.org/2022/12/05/a...
Reposted by Nina Dombrowski
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Index zone by BenLangmead
benlangmead.github.io
October 30, 2025 at 6:11 PM
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Reposted by Nina Dombrowski
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
October 23, 2025 at 8:16 PM
Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it:
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
www.biorxiv.org/content/10.1...
Want to get started? github.com/rickbeeloo/b...
Reposted by Nina Dombrowski
Still fascinated with #webR and its potential for teaching stats
Here students can play (even from their phones) and find out themselves how the p-value depends on sample size
pakillo.github.io/LM-GLM-GLMM-... #rstats
Here students can play (even from their phones) and find out themselves how the p-value depends on sample size
pakillo.github.io/LM-GLM-GLMM-... #rstats
October 22, 2025 at 6:36 AM
Still fascinated with #webR and its potential for teaching stats
Here students can play (even from their phones) and find out themselves how the p-value depends on sample size
pakillo.github.io/LM-GLM-GLMM-... #rstats
Here students can play (even from their phones) and find out themselves how the p-value depends on sample size
pakillo.github.io/LM-GLM-GLMM-... #rstats
Reposted by Nina Dombrowski
To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.
September 29, 2025 at 6:57 AM
To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.
Reposted by Nina Dombrowski
Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply!
Please repost!
Please repost!
September 24, 2025 at 8:46 AM
Job Alert! We're hiring a BIOINFORMATICIAN / NGS SPECIALIST to support our new Molecular Biodiversity Lab in the @terra-cluster.org at @unituebingen.bsky.social. Like the idea to use your skills for understanding biodiversity? To work on diverse questions in a wonderful place? Apply!
Please repost!
Please repost!
Reposted by Nina Dombrowski
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 😄
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
September 23, 2025 at 1:53 AM
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 😄
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 😄
Reposted by Nina Dombrowski
contact me or @csoneson.bsky.social if you want more details
📣The Turco group is seeking a computational biologist to analyze large omics datasets. Work on cutting-edge 3D organoid models of the human placenta and be embedded in our Computational Biology Platform (part of @sib.swiss). Apply here: www.fmi.ch/education-ca...
September 12, 2025 at 7:52 AM
contact me or @csoneson.bsky.social if you want more details
Reposted by Nina Dombrowski
⏳ One week left to register!
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.
🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org
#EuroBioC2025 #RStats
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.
🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org
#EuroBioC2025 #RStats
European Bioconductor Conference 2025 – EuroBioC2025
The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…
eurobioc2025.bioconductor.org
August 21, 2025 at 7:00 AM
⏳ One week left to register!
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.
🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org
#EuroBioC2025 #RStats
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.
🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org
#EuroBioC2025 #RStats
Reposted by Nina Dombrowski
{tinytable} 0.13.0 for #RStats can now draw interactive tables with sorting, filtering & pages!
And the 📦 is still an ultra-simple, powerful, and 0-dep way to create beautiful tables in basically any format: tex, typ, docx, pdf, png, md, etc
Gallery & Docs: vincentarelbundock.github.io/tinytable/
And the 📦 is still an ultra-simple, powerful, and 0-dep way to create beautiful tables in basically any format: tex, typ, docx, pdf, png, md, etc
Gallery & Docs: vincentarelbundock.github.io/tinytable/
August 19, 2025 at 9:24 PM
{tinytable} 0.13.0 for #RStats can now draw interactive tables with sorting, filtering & pages!
And the 📦 is still an ultra-simple, powerful, and 0-dep way to create beautiful tables in basically any format: tex, typ, docx, pdf, png, md, etc
Gallery & Docs: vincentarelbundock.github.io/tinytable/
And the 📦 is still an ultra-simple, powerful, and 0-dep way to create beautiful tables in basically any format: tex, typ, docx, pdf, png, md, etc
Gallery & Docs: vincentarelbundock.github.io/tinytable/
Reposted by Nina Dombrowski
We’re hiring a Postdoc in Gut Microbiome Metabolomics!
Help us decode microbial metabolism and its impact on human health @leibniz-hki.de , Jena 🇩🇪
🔗 jobs.hki-jena.de/jobs/Postdoc...
Help us decode microbial metabolism and its impact on human health @leibniz-hki.de , Jena 🇩🇪
🔗 jobs.hki-jena.de/jobs/Postdoc...
Job opportunity Postdoctoral Researcher (m/f/div) in Gut Microbiome Metabolomics at Leibniz HKI Jobportal
Wissenschaft/Forschung in Jena
jobs.hki-jena.de
August 12, 2025 at 8:55 AM
We’re hiring a Postdoc in Gut Microbiome Metabolomics!
Help us decode microbial metabolism and its impact on human health @leibniz-hki.de , Jena 🇩🇪
🔗 jobs.hki-jena.de/jobs/Postdoc...
Help us decode microbial metabolism and its impact on human health @leibniz-hki.de , Jena 🇩🇪
🔗 jobs.hki-jena.de/jobs/Postdoc...
Reposted by Nina Dombrowski
"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein structure alignment significance is often exaggerated
Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...
www.biorxiv.org
August 17, 2025 at 10:53 PM
"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nina Dombrowski
IT'S HERE!!!!!!!!! I had the opportunity to work with @gostudyhall.bsky.social to film a video on How to Become a Marine Biologist a few months ago and now it's live! www.youtube.com/watch?v=ezaE...
How to Become: a Marine Biologist
YouTube video by Study Hall
www.youtube.com
August 14, 2025 at 4:50 PM
IT'S HERE!!!!!!!!! I had the opportunity to work with @gostudyhall.bsky.social to film a video on How to Become a Marine Biologist a few months ago and now it's live! www.youtube.com/watch?v=ezaE...
Reposted by Nina Dombrowski
www.pnas.org/doi/10.1073/... Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis #protistsonsky
Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis | PNAS
Endosymbiotic gene transfer (EGT) and import of host-encoded proteins have been considered
hallmarks of organelles necessary for stable integration...
www.pnas.org
August 14, 2025 at 3:55 AM
www.pnas.org/doi/10.1073/... Genomes of nitrogen-fixing eukaryotes reveal an alternate path for organellogenesis #protistsonsky
Reposted by Nina Dombrowski
The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment:
www.uu.se/en/about-uu/...
www.uu.se/en/about-uu/...
Bioinformatician - Uppsala University
Bioinformatician, Department of Organismal Biology, Uppsala University
www.uu.se
August 12, 2025 at 7:10 AM
The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment:
www.uu.se/en/about-uu/...
www.uu.se/en/about-uu/...
Reposted by Nina Dombrowski
DPANN Archaea and CPR Bacteria: insights into early cellular evolution? royalsocietypublishing.org/doi/full/10.... #jcampubs
DPANN Archaea and CPR Bacteria: insights into early cellular evolution? | Philosophical Transactions of the Royal Society B: Biological Sciences
Cultivation-independent techniques have facilitated the discovery of a diversity of
thus far uncultivated organisms and led to the identification of new branches within
the tree of life. This has resh...
royalsocietypublishing.org
August 11, 2025 at 4:16 PM
DPANN Archaea and CPR Bacteria: insights into early cellular evolution? royalsocietypublishing.org/doi/full/10.... #jcampubs
Reposted by Nina Dombrowski
My latest post on @carpentries.carpentries.org blog is a call to action for the community to engage in curriculum development for workshops about genAI. How can we help our target audience make more informed choices about when and how to use it?
carpentries.org/blog/2025/08...
carpentries.org/blog/2025/08...
AI Carpentry? Helping learners make better choices with genAI.
In two recent community discussion sessions, we explored what mental model of machine learning/deep learning we could teach to learners already familiar with the basics of programming, to help them sa...
carpentries.org
August 5, 2025 at 9:24 AM
My latest post on @carpentries.carpentries.org blog is a call to action for the community to engage in curriculum development for workshops about genAI. How can we help our target audience make more informed choices about when and how to use it?
carpentries.org/blog/2025/08...
carpentries.org/blog/2025/08...
Reposted by Nina Dombrowski
Oatk: a de novo assembly tool for complex plant organelle genomes. #DeNovoAssembly #OrganelleGenomes #Bioinformatics #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
August 11, 2025 at 10:30 AM
Oatk: a de novo assembly tool for complex plant organelle genomes. #DeNovoAssembly #OrganelleGenomes #Bioinformatics #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Nina Dombrowski
I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
shorturl.at
August 8, 2025 at 10:09 AM
I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
Reposted by Nina Dombrowski
New preprint up now!
Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota
www.biorxiv.org/content/10.1...
Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota
www.biorxiv.org/content/10.1...
Caliditerrarchaeota, a new sister to Nanohaloarchaeota, provides insights into the evolution of DPANN halophily
The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However,...
www.biorxiv.org
August 8, 2025 at 6:49 AM
New preprint up now!
Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota
www.biorxiv.org/content/10.1...
Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota
www.biorxiv.org/content/10.1...
Reposted by Nina Dombrowski
This video by Melissa Van Bussel helped me set up my very first GitHub Action to publish my site. It took exactly 10 minutes!
👉 tiny.cc/gh-actions
Here’s the site I published using that workflow:
🔗 jformoso.github.io
And her website, she has great resources!
🌐 www.melissavanbussel.com
#RLadies
👉 tiny.cc/gh-actions
Here’s the site I published using that workflow:
🔗 jformoso.github.io
And her website, she has great resources!
🌐 www.melissavanbussel.com
#RLadies
Publish a Quarto project using GitHub Pages+GitHub Actions in 6 minutes (no need to render locally!)
Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.
tiny.cc
July 16, 2025 at 1:13 PM
This video by Melissa Van Bussel helped me set up my very first GitHub Action to publish my site. It took exactly 10 minutes!
👉 tiny.cc/gh-actions
Here’s the site I published using that workflow:
🔗 jformoso.github.io
And her website, she has great resources!
🌐 www.melissavanbussel.com
#RLadies
👉 tiny.cc/gh-actions
Here’s the site I published using that workflow:
🔗 jformoso.github.io
And her website, she has great resources!
🌐 www.melissavanbussel.com
#RLadies
Reposted by Nina Dombrowski
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
July 20, 2025 at 4:58 PM
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
Reposted by Nina Dombrowski
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reply to: Reply to: False positives in the study of memory-related gene expression
In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…
liorpachter.wordpress.com
June 16, 2025 at 9:31 PM
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reposted by Nina Dombrowski
I’ve written threads about the GBR-MGDs pMAGs, but it also contains viruses (vMAGs), including a monophyletic clade of marine Crassvirales, chromosome-level eukaryote eMAGs, and putative plasmids. We wanted a holistic DB.
One problem: some key software appear to break with long reads. A 🦠 🧵.
One problem: some key software appear to break with long reads. A 🦠 🧵.
Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The planktonic microbiome of the Great Barrier Reef
Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...
www.biorxiv.org
June 10, 2025 at 9:03 AM
I’ve written threads about the GBR-MGDs pMAGs, but it also contains viruses (vMAGs), including a monophyletic clade of marine Crassvirales, chromosome-level eukaryote eMAGs, and putative plasmids. We wanted a holistic DB.
One problem: some key software appear to break with long reads. A 🦠 🧵.
One problem: some key software appear to break with long reads. A 🦠 🧵.