Mike Robeson
@drmicrobeson.bsky.social
Microbiome Scientist, UAMS.
#bioinformatics #microbiome #nutrition #cancer #primaryciliarydyskinesia #rotifers #meiofauna #microfauna Posts are my own. Reposts/likes not necessarily endorsement. 😷
#bioinformatics #microbiome #nutrition #cancer #primaryciliarydyskinesia #rotifers #meiofauna #microfauna Posts are my own. Reposts/likes not necessarily endorsement. 😷
Reposted by Mike Robeson
Job Opening **ASSISTANT PROFESSOR MARINE ECOLOGY**, Department of Biological Sciences, University of Rhode Island.
jobs.uri.edu/postings/15960
jobs.uri.edu/postings/15960
November 10, 2025 at 4:03 PM
Job Opening **ASSISTANT PROFESSOR MARINE ECOLOGY**, Department of Biological Sciences, University of Rhode Island.
jobs.uri.edu/postings/15960
jobs.uri.edu/postings/15960
Reposted by Mike Robeson
Amazing new preprint led by my husband, UGA theoretical ecologist Yun Tao (I’m totally not biased here 😅) - this has been his dream project with a coauthor team of NBA super fans. More about Yun’s other work here: research.uga.edu/news/iobs-ta... @ugaresearch.bsky.social
October 31, 2025 at 6:27 PM
Amazing new preprint led by my husband, UGA theoretical ecologist Yun Tao (I’m totally not biased here 😅) - this has been his dream project with a coauthor team of NBA super fans. More about Yun’s other work here: research.uga.edu/news/iobs-ta... @ugaresearch.bsky.social
Reposted by Mike Robeson
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Selection and transmission of the gut microbiome alone can shift mammalian behavior
Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...
rdcu.be
October 28, 2025 at 7:51 AM
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Reposted by Mike Robeson
Yaniv put a ton of work into these resources, and they're absolutely wonderful
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 3:33 PM
Yaniv put a ton of work into these resources, and they're absolutely wonderful
Reposted by Mike Robeson
PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪
October 22, 2025 at 5:55 PM
PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪
Reposted by Mike Robeson
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 Mike Robeson
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques. #Nanopore #Sequencing #Genomics #Bioinformatics #RawSignalAnalysis @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a…
www.biorxiv.org
October 21, 2025 at 9:15 AM
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques. #Nanopore #Sequencing #Genomics #Bioinformatics #RawSignalAnalysis @biorxiv-genomic.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mike Robeson
NEW method! eComp is a new, #evolution-informed #compression method🗜️ for multiple #sequence alignments (#MSAs)...that outperforms gzip!
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
October 21, 2025 at 3:26 PM
NEW method! eComp is a new, #evolution-informed #compression method🗜️ for multiple #sequence alignments (#MSAs)...that outperforms gzip!
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
Unlike gzip's row-based compression, eComp implements a simple #column-based solution for compression, following how biological information is stored in MSAs
Reposted by Mike Robeson
Interested in aligning your long sequences or small genomes against huge reference databases containing millions of prokaryotic genomes ? A new tool has been released that can do this efficiently - LexicMap - www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
October 1, 2025 at 6:48 PM
Interested in aligning your long sequences or small genomes against huge reference databases containing millions of prokaryotic genomes ? A new tool has been released that can do this efficiently - LexicMap - www.nature.com/articles/s41...
Reposted by Mike Robeson
The gut MYCOBIOME is akin to the tiny group of kids in the corner of a huge homecoming dance. Their story is largely unknown. In our latest, @emilyvansyoc.bsky.social dives into the evolutionary associations of gut fungi with @erdavenport.bsky.social & Andres Gomez
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Gut fungal profiles reveal phylosymbiosis and codiversification across humans and nonhuman primates
Fungi in the gut microbiome (the "mycobiome") are a neglected component of the human holobiont. This study of gut fungal profiles across natural populations of humans and non-human primates reveals si...
journals.plos.org
September 24, 2025 at 5:36 PM
The gut MYCOBIOME is akin to the tiny group of kids in the corner of a huge homecoming dance. Their story is largely unknown. In our latest, @emilyvansyoc.bsky.social dives into the evolutionary associations of gut fungi with @erdavenport.bsky.social & Andres Gomez
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Mike Robeson
MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes. #MAGs #Metagenomics #MetagenomeAssembly #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
September 14, 2025 at 7:32 AM
MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes. #MAGs #Metagenomics #MetagenomeAssembly #GenomeBiology
genomebiology.biomedcentral.com/articles/10....
genomebiology.biomedcentral.com/articles/10....
Reposted by Mike Robeson
We welcome today's news of the launch of the Fund for Science and Technology (FFST)!
Funded by the estate of Paul G. Allen, the new private foundation is focused on Allen’s lifelong passions for bioscience, the environment, and the power of AI for good.
www.ff-st.org/news-stories...
Funded by the estate of Paul G. Allen, the new private foundation is focused on Allen’s lifelong passions for bioscience, the environment, and the power of AI for good.
www.ff-st.org/news-stories...
Fund for Science and Technology Announces Inaugural Grants, Planning at Least Half a Billion Dollars in the Next Four Years
$500 million over the next four years to support transformational science and technology for people and the planet
www.ff-st.org
September 1, 2025 at 8:52 PM
Reposted by Mike Robeson
TIR: Legendre, Fortin, Borcard 2015 on why the Mantel test, which is often used to test spatial autocorrelation in measured data, doesn’t actually not actually do that.
You probably want dbMEM analysis instead!
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12425
You probably want dbMEM analysis instead!
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12425
August 27, 2025 at 2:08 PM
TIR: Legendre, Fortin, Borcard 2015 on why the Mantel test, which is often used to test spatial autocorrelation in measured data, doesn’t actually not actually do that.
You probably want dbMEM analysis instead!
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12425
You probably want dbMEM analysis instead!
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12425
Reposted by Mike Robeson
Grad student Iyanu Oduwole, Tatiana Vishnevetskaya and I have a new preprint out with a curious observation: permafrost microbes that are predicted to grow slowly are also predicted to have higher temperatures than microbes that grow faster. This is counterintuitive!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Thermophilic traits correlate with slow growth in permafrost soils
Permafrost soil is characterized by prolonged freezing conditions. Thermophilic microbes have been discovered in various permanently cold environments, including permafrost, where they can persist for...
www.biorxiv.org
July 27, 2025 at 7:22 PM
Grad student Iyanu Oduwole, Tatiana Vishnevetskaya and I have a new preprint out with a curious observation: permafrost microbes that are predicted to grow slowly are also predicted to have higher temperatures than microbes that grow faster. This is counterintuitive!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Mike Robeson
PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2 academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/picrust/picr...
June 19, 2025 at 6:30 PM
PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2 academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/picrust/picr...
Reposted by Mike Robeson
Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...
Emergence and disruption of cooperativity in a denitrifying microbial community
Abstract. Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the em
academic.oup.com
June 13, 2025 at 9:09 PM
Interesting new study on emergence and disruption of cooperativity in a denitrifying microbial community, by postdoc in the lab Alex Carr (from his PhD work with Nitin Baliga). academic.oup.com/ismej/articl...
Reposted by Mike Robeson
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search.
github.com/bede/deacon
github.com/bede/deacon
Reposted by Mike Robeson
This paper was much needed to highlight again the fact that protists make (almost) all main branches of the eukaryote tree of life, yet they continue to be dramatically understudied. Genomics is one example of this. Cite it!!! #protistsonsky
Happy to have contributed to this great article: #Protist genomics: key to understanding eukaryotic evolution. Congrats Alexandra Schoenle et al. #ProtistsOnSky
authors.elsevier.com/sd/article/S...
authors.elsevier.com/sd/article/S...
June 13, 2025 at 7:24 AM
This paper was much needed to highlight again the fact that protists make (almost) all main branches of the eukaryote tree of life, yet they continue to be dramatically understudied. Genomics is one example of this. Cite it!!! #protistsonsky
Reposted by Mike Robeson
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
Reposted by Mike Robeson
🦠🧬🖥️ #AcademicSky
Happy to announce that we have an open PDRA position in my lab, that will be about a) soil metagenomics b) green house gases c) Archaea d) combine metaGenomics with metaTranscriptomics.
Apply by 8th July 25
jobs.quadram.ac.uk/Details.asp?...
@quadraminstitute.bsky.social @earlhaminst.bsky.social
Apply by 8th July 25
jobs.quadram.ac.uk/Details.asp?...
@quadraminstitute.bsky.social @earlhaminst.bsky.social
Quadram Institute
jobs.quadram.ac.uk
June 6, 2025 at 7:57 PM
🦠🧬🖥️ #AcademicSky
Reposted by Mike Robeson
AutoMLST2: a web server for phylogeny and microbial taxonomy. #MicrobialTaxonomy #Phylogeny @narjournal.bsky.social 🧬 🖥️
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
academic.oup.com
June 1, 2025 at 3:01 PM
AutoMLST2: a web server for phylogeny and microbial taxonomy. #MicrobialTaxonomy #Phylogeny @narjournal.bsky.social 🧬 🖥️
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Mike Robeson
Should microbes be targets of conservation efforts? They are certainly key to conservation of macrobes.
These were some of the questions tackled by a bunch of fellow nerds at a recent meeting in San Diego led by @gilbertjacka.bsky.social.
Fun to see a few old friends and make some new ones.
These were some of the questions tackled by a bunch of fellow nerds at a recent meeting in San Diego led by @gilbertjacka.bsky.social.
Fun to see a few old friends and make some new ones.
May 30, 2025 at 4:42 PM
Should microbes be targets of conservation efforts? They are certainly key to conservation of macrobes.
These were some of the questions tackled by a bunch of fellow nerds at a recent meeting in San Diego led by @gilbertjacka.bsky.social.
Fun to see a few old friends and make some new ones.
These were some of the questions tackled by a bunch of fellow nerds at a recent meeting in San Diego led by @gilbertjacka.bsky.social.
Fun to see a few old friends and make some new ones.
Reposted by Mike Robeson
New study out - we developed a pipeline for targeted assembly of genomes from (complex) soil metagenomes to examine the strain-level diversity and ecology of a dominant soil bacterial genus (Bradyrhizobium). Feedback appreciated. www.biorxiv.org/content/10.1...
Continent-wide assessment of the strain-level diversity of Bradyrhizobium, a dominant soil bacterial genus
Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa ar...
www.biorxiv.org
May 30, 2025 at 5:59 PM
New study out - we developed a pipeline for targeted assembly of genomes from (complex) soil metagenomes to examine the strain-level diversity and ecology of a dominant soil bacterial genus (Bradyrhizobium). Feedback appreciated. www.biorxiv.org/content/10.1...