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
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 ]
Reposted by Steven Robbins
Australia has so much clean energy they're literally giving it away. Meanwhile, GOP is in all-out war to stamp out solar
www.abc.net.au/news/2025-11...
www.abc.net.au/news/2025-11...
Australian households to get free electricity three hours a day
Saying there is enough solar power for everyone in the daytime, the federal government will direct retailers to provide three hours of free power every day to consumers.
www.abc.net.au
November 4, 2025 at 1:23 AM
Australia has so much clean energy they're literally giving it away. Meanwhile, GOP is in all-out war to stamp out solar
www.abc.net.au/news/2025-11...
www.abc.net.au/news/2025-11...
Reposted by Steven Robbins
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 3, 2025 at 1:55 PM
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
Reposted by Steven Robbins
GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...
gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research
Abstract. The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportuniti
academic.oup.com
November 3, 2025 at 9:01 AM
GcMeta - a new global resource of metagenome-assembled genomes and their encoded functions with an easy to use, interactive and searchable website academic.oup.com/nar/advance-...
Reposted by Steven Robbins
Don’t forget to register and join us for our ASM-QLD and BrisJAMS careers beyond academia session this Thursday 😎
🚀 Thinking about life beyond academia?
Join BrisJAMS and Australian Society of Microbiology Qld Branch, this November for an inspiring evening of stories, insights, and real-world advice from scientists who’ve successfully built careers outside the academic path!🌟
6 November 2025, 6:00 PM – 8:00 PM
Join BrisJAMS and Australian Society of Microbiology Qld Branch, this November for an inspiring evening of stories, insights, and real-world advice from scientists who’ve successfully built careers outside the academic path!🌟
6 November 2025, 6:00 PM – 8:00 PM
November 3, 2025 at 1:06 AM
Don’t forget to register and join us for our ASM-QLD and BrisJAMS careers beyond academia session this Thursday 😎
Interesting. Glad they also mention the small METR study showing that AI agents slowed down experienced coders, despite reporting productivity increase.
I’d guess agents will be like the internet and research—useful for diligent experts and detrimental to those to dabble and don’t recognize slop.
I’d guess agents will be like the internet and research—useful for diligent experts and detrimental to those to dabble and don’t recognize slop.
2nd edition of our The AI Shift newsletter is out. The question today: could AI be making us LESS productive? @jburnmurdoch.ft.com www.ft.com/content/2480... At the individual level, it's clear we're not reliable witnesses on this Q. At an organisational level, it gets even more interesting...
October 30, 2025 at 2:31 PM
Interesting. Glad they also mention the small METR study showing that AI agents slowed down experienced coders, despite reporting productivity increase.
I’d guess agents will be like the internet and research—useful for diligent experts and detrimental to those to dabble and don’t recognize slop.
I’d guess agents will be like the internet and research—useful for diligent experts and detrimental to those to dabble and don’t recognize slop.
Reposted by Steven Robbins
Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...
Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients - Cell Death Discovery
Cell Death Discovery - Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients
www.nature.com
October 28, 2025 at 6:22 PM
Happy to have been involved in this paper. @nanoporetech.com www.nature.com/articles/s41...
Reposted by Steven Robbins
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 Steven Robbins
not to brag but i can generate slop with natural intelligence
October 28, 2025 at 4:15 PM
not to brag but i can generate slop with natural intelligence
Reposted by Steven Robbins
Indeed does happen, but more often they are duplex reads that are not detected as such by Dorado. Then the sequences on either side of the mid strand adapter are reverse complement (example pic)
October 25, 2025 at 2:12 PM
Indeed does happen, but more often they are duplex reads that are not detected as such by Dorado. Then the sequences on either side of the mid strand adapter are reverse complement (example pic)
Our pipeline for years has used PoreChop for adapter clipping because dorado doesn’t remove all barcodes.
Mainly troubling if the Dorado demultiplexing/trimming leads to an appreciable % of reads demtiplexed into the wrong sample before PoreChop, but doesn’t look like that happens at a high rate.
Mainly troubling if the Dorado demultiplexing/trimming leads to an appreciable % of reads demtiplexed into the wrong sample before PoreChop, but doesn’t look like that happens at a high rate.
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 24, 2025 at 1:58 PM
Our pipeline for years has used PoreChop for adapter clipping because dorado doesn’t remove all barcodes.
Mainly troubling if the Dorado demultiplexing/trimming leads to an appreciable % of reads demtiplexed into the wrong sample before PoreChop, but doesn’t look like that happens at a high rate.
Mainly troubling if the Dorado demultiplexing/trimming leads to an appreciable % of reads demtiplexed into the wrong sample before PoreChop, but doesn’t look like that happens at a high rate.
Reposted by Steven Robbins
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
October 22, 2025 at 3:39 PM
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
Reposted by Steven Robbins
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 21, 2025 at 1:38 PM
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
Reposted by Steven Robbins
How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬
October 20, 2025 at 6:15 PM
How I like my @nanoporetech.com runs 🟩💚🟩🚀🧬
Reposted by Steven Robbins
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
September 24, 2025 at 8:30 PM
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
Reposted by Steven Robbins
Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....
EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles
peercommunityjournal.org
October 18, 2025 at 7:58 AM
Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....
Reposted by Steven Robbins
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 10:28 AM
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇