Steven Robbins
@stevenjrobbins.bsky.social
Do my science @ace_uq studying coral reef microbiomes. Data wrangler, meta-omics and long-read wonk, clean energy enthusiast, Saganist zealot, collector of weird zoology facts, other nonsense.
Pinned
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
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...
Reposted by Steven Robbins
Symbiont-coral partnerships
Hologenome of B. pseudoalternata reveals a division of labor between deep-sea coral & symbionts. Host provides habitat & manages immunity, while symbionts recycle waste, supply nutrients, resist viruses & produce antioxidants
www.cell.com/cell-host-mi...
Hologenome of B. pseudoalternata reveals a division of labor between deep-sea coral & symbionts. Host provides habitat & manages immunity, while symbionts recycle waste, supply nutrients, resist viruses & produce antioxidants
www.cell.com/cell-host-mi...
Hologenomic insights into the molecular adaptation of deep-sea coral Bathypathes pseudoalternata
Wei et al. reveal how deep-sea corals partner with symbionts in the extreme environment
using the hologenome of Bathypathes pseudoalternata. A division of labor shows that
the host provides a protecte...
www.cell.com
November 20, 2025 at 8:03 PM
Symbiont-coral partnerships
Hologenome of B. pseudoalternata reveals a division of labor between deep-sea coral & symbionts. Host provides habitat & manages immunity, while symbionts recycle waste, supply nutrients, resist viruses & produce antioxidants
www.cell.com/cell-host-mi...
Hologenome of B. pseudoalternata reveals a division of labor between deep-sea coral & symbionts. Host provides habitat & manages immunity, while symbionts recycle waste, supply nutrients, resist viruses & produce antioxidants
www.cell.com/cell-host-mi...
Reposted by Steven Robbins
Enormous milestone. All thanks to vaccinations!!!
November 27, 2025 at 3:02 AM
Enormous milestone. All thanks to vaccinations!!!
Reposted by Steven Robbins
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Hey Team! What do you think are the best free digital notebooks these days.
I've used:
Evernote--great, but now it's paid
TiddlyWiki wasn't bad, but got rid of scrollable code blocks
Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki.
Suggestions?
I've used:
Evernote--great, but now it's paid
TiddlyWiki wasn't bad, but got rid of scrollable code blocks
Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki.
Suggestions?
November 26, 2025 at 9:49 PM
Hey Team! What do you think are the best free digital notebooks these days.
I've used:
Evernote--great, but now it's paid
TiddlyWiki wasn't bad, but got rid of scrollable code blocks
Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki.
Suggestions?
I've used:
Evernote--great, but now it's paid
TiddlyWiki wasn't bad, but got rid of scrollable code blocks
Obsidian--basic, and I don't like not being able to scroll my code blocks like OG Tiddlywiki.
Suggestions?
Reposted by Steven Robbins
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 2:02 PM
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
Reposted by Steven Robbins
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
Reposted by Steven Robbins
Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
ECR connection: Meet Meren when you need to
A means for ECRs to get advice from a senior scientist outside of their support network
merenlab.org
November 16, 2025 at 4:56 PM
Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Reposted by Steven Robbins
“My magic beans can work miracles, they’re different from all of the fake magic beans out there” has been the sales pitch of charlatans since time immemorial.
Anthropic CEO Dario Amodei thinks AI could help find cures for most cancers, prevent Alzheimer’s, and even double the human lifespan. cbsn.ws/4oRZ8Nm
November 17, 2025 at 1:46 AM
“My magic beans can work miracles, they’re different from all of the fake magic beans out there” has been the sales pitch of charlatans since time immemorial.
Reposted by Steven Robbins
I just published my weekly newsletter to >10K subscribers: The truth about AI coding for bioinformatics divingintogeneticsandgenomics.kit.com/posts/ai-po...
AI ported 6,000+ lines of Python in 8 hours. Here’s the catch
divingintogeneticsandgenomics.kit.com
November 15, 2025 at 3:41 PM
I just published my weekly newsletter to >10K subscribers: The truth about AI coding for bioinformatics divingintogeneticsandgenomics.kit.com/posts/ai-po...
Reposted by Steven Robbins
The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity academic.oup.com/gbe/article/... 🧬🖥️🧪
November 15, 2025 at 5:00 PM
The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity academic.oup.com/gbe/article/... 🧬🖥️🧪
Reposted by Steven Robbins
Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges www.nature.com/articles/s41... #jcampubs
Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges - Nature Chemical Biology
Marine sponges host bacteria that produce diverse bioactive compounds. Here, the authors conduct a large-scale metagenomic, single-bacterial and biochemical study to reveal the untapped biosynthetic p...
www.nature.com
November 13, 2025 at 7:49 PM
Chemical richness and diversity of uncultivated ‘Entotheonella’ symbionts in marine sponges www.nature.com/articles/s41... #jcampubs
Thought i'd show a bit of personality outside of metagenomics talk here.
Caught a bit of the aurora in Ohio yesterday. Was my first time seeing one, and also trying to photograph it. I love how these turned out.
Anybody else see it?
Caught a bit of the aurora in Ohio yesterday. Was my first time seeing one, and also trying to photograph it. I love how these turned out.
Anybody else see it?
November 14, 2025 at 1:44 AM
Thought i'd show a bit of personality outside of metagenomics talk here.
Caught a bit of the aurora in Ohio yesterday. Was my first time seeing one, and also trying to photograph it. I love how these turned out.
Anybody else see it?
Caught a bit of the aurora in Ohio yesterday. Was my first time seeing one, and also trying to photograph it. I love how these turned out.
Anybody else see it?
Reposted by Steven Robbins
A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT.
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
Plastic degradation by enzymes from uncultured deep sea microorganisms
Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are
academic.oup.com
November 10, 2025 at 6:04 PM
A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT.
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
Reposted by Steven Robbins
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
November 13, 2025 at 10:09 AM
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Reposted by Steven Robbins
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
November 11, 2025 at 8:21 PM
Metagenomics colleagues!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data.
Please help and share!
Reposted by Steven Robbins
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 Steven Robbins
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
Reposted by Steven Robbins
Our new paper in @currentbiology.bsky.social, led by @renatoamorais.bsky.social, examined the history and veracity of the alleged paradox and its patron Charles Darwin.
www.cell.com/current-biol...
@oclaripv.bsky.social
@paulinenarvaez.bsky.social
@utaustin.bsky.social
@psl-univ.bsky.social
www.cell.com/current-biol...
@oclaripv.bsky.social
@paulinenarvaez.bsky.social
@utaustin.bsky.social
@psl-univ.bsky.social
Rethinking Darwin’s coral reef paradox and the ubiquity of “marine oases”
Morais et al. evaluate the history of Darwin’s paradox and the prevalence of oligotrophic
conditions among coral reefs. They find no link between Darwin and the marine oasis
concept. Most coral reefs ...
www.cell.com
June 6, 2025 at 1:32 PM
Our new paper in @currentbiology.bsky.social, led by @renatoamorais.bsky.social, examined the history and veracity of the alleged paradox and its patron Charles Darwin.
www.cell.com/current-biol...
@oclaripv.bsky.social
@paulinenarvaez.bsky.social
@utaustin.bsky.social
@psl-univ.bsky.social
www.cell.com/current-biol...
@oclaripv.bsky.social
@paulinenarvaez.bsky.social
@utaustin.bsky.social
@psl-univ.bsky.social
Reposted by Steven Robbins
Heard of "Darwin's paradox"? It refers to Charles Darwin's observation that coral reefs are wildly productive despite occurring in nutrient-poor tropical oceans. Reefs are, so the story goes, oases in marine deserts 🏝️...
Turns out that 2/3 of these assertions are very wrong...
🌐
🦑🧪
🧵⬇️
Turns out that 2/3 of these assertions are very wrong...
🌐
🦑🧪
🧵⬇️
June 6, 2025 at 1:32 PM
Heard of "Darwin's paradox"? It refers to Charles Darwin's observation that coral reefs are wildly productive despite occurring in nutrient-poor tropical oceans. Reefs are, so the story goes, oases in marine deserts 🏝️...
Turns out that 2/3 of these assertions are very wrong...
🌐
🦑🧪
🧵⬇️
Turns out that 2/3 of these assertions are very wrong...
🌐
🦑🧪
🧵⬇️
Reposted by Steven Robbins
#NewResearch
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
@rstepanauskas.bsky.social & co
#microsky
www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
@rstepanauskas.bsky.social & co
#microsky
www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes - Nature Microbiology
Environmental micro-compartment genomics provides efficient and high-throughput single-particle DNA sequencing that captures overlooked members of microbial communities.
www.nature.com
November 7, 2025 at 11:19 AM
#NewResearch
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
@rstepanauskas.bsky.social & co
#microsky
www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
@rstepanauskas.bsky.social & co
#microsky
www.nature.com/articles/s41...
Reposted by Steven Robbins
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 6, 2025 at 11:25 PM
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
Reposted by Steven Robbins
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Steven Robbins
This is a very informative read: Seven data-driven lessons from the 2025 elections
open.substack.com/pub/gelliott...
open.substack.com/pub/gelliott...
Seven data-driven lessons from the 2025 elections
Democrats outran their polls and swept statewide races from Georgia to New Jersey, on an agenda of affordability and a broad anti-Trump backlash
open.substack.com
November 5, 2025 at 12:25 PM
This is a very informative read: Seven data-driven lessons from the 2025 elections
open.substack.com/pub/gelliott...
open.substack.com/pub/gelliott...
Reposted by Steven Robbins
Omg I’m dying 😂😂😂…so…So Emily Austin, a right wing 'influencer' who works for Bibi and the GOP, launched 'Hot Girls for Cuomo'.
Guess who didn't bother to register the URL when she did that? What do you think Hot Girls for Cuomo dot com leads to now?... 😄 Enjoy.
[ HotGirlsforCuomo.com ]
Guess who didn't bother to register the URL when she did that? What do you think Hot Girls for Cuomo dot com leads to now?... 😄 Enjoy.
[ HotGirlsforCuomo.com ]
November 5, 2025 at 1:48 AM
Omg I’m dying 😂😂😂…so…So Emily Austin, a right wing 'influencer' who works for Bibi and the GOP, launched 'Hot Girls for Cuomo'.
Guess who didn't bother to register the URL when she did that? What do you think Hot Girls for Cuomo dot com leads to now?... 😄 Enjoy.
[ HotGirlsforCuomo.com ]
Guess who didn't bother to register the URL when she did that? What do you think Hot Girls for Cuomo dot com leads to now?... 😄 Enjoy.
[ HotGirlsforCuomo.com ]