Tara Oceans Science
@taraoceans-science.bsky.social
Highlights and sharing of the science and research from the Tara Oceans expeditions.
Publication list: https://t.co/TCbLXqT0oE
Publication list: https://t.co/TCbLXqT0oE
Reposted by Tara Oceans Science
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Tara Oceans Science
Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions academic.oup.com/nar/advance-... #jcampubs 🌊
Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions
Abstract. Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notabl
academic.oup.com
November 1, 2025 at 7:35 AM
Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions academic.oup.com/nar/advance-... #jcampubs 🌊
Reposted by Tara Oceans Science
Excited to introduce Auxenochlorella as a new algal reference organism for fundamental plant science and bioengineering. A paper in two parts: a genetic toolkit for site-specific genomic manipulation, paired with the most unusual genome I’ve ever worked on
academic.oup.com/plcell/artic...
academic.oup.com/plcell/artic...
Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella
Auxenochlorella, green algae shaped by evolutionary forces acting on vegetative diploids, are amenable to discovery research and bioengineering via efficie
academic.oup.com
November 1, 2025 at 8:56 AM
Reposted by Tara Oceans Science
Forams are super cute, but some of them are just spooky 🎃Did you know some forams make their shells gluing “skeletons” of other fossils?
November 1, 2025 at 12:35 PM
Reposted by Tara Oceans Science
Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n
#ProtistsOnSky
tinyurl.com/2zxaund7
#ProtistsOnSky
tinyurl.com/2zxaund7
October 31, 2025 at 3:27 PM
Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n
#ProtistsOnSky
tinyurl.com/2zxaund7
#ProtistsOnSky
tinyurl.com/2zxaund7
Reposted by Tara Oceans Science
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
October 31, 2025 at 2:42 PM
🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky
www.cell.com/cell/fulltex...
Reposted by Tara Oceans Science
I've written a piece about great new article by @thibautbrunet.bsky.social, Chantal Combredet & Mylan Ansel. (www.cell.com/cell-reports... )
theconversation.com/how-the-firs...
theconversation.com/how-the-firs...
How the first animals evolved – a new clue from a tiny relative
Meet the choanoflagellates - the microscopic cousins of animals.
theconversation.com
October 29, 2025 at 3:04 PM
I've written a piece about great new article by @thibautbrunet.bsky.social, Chantal Combredet & Mylan Ansel. (www.cell.com/cell-reports... )
theconversation.com/how-the-firs...
theconversation.com/how-the-firs...
Reposted by Tara Oceans Science
🚨NOTICE TO OUR USERS🚨
The Data Portal will soon replace the Genome Portal.
Portal users can book a session with our team for technical help, feedback or a guided walk-through of the new Data Portal. 🖥️🧬 🌱🦠🍄🧪
More information: jgi.doe.gov/analyze-data...
The Data Portal will soon replace the Genome Portal.
Portal users can book a session with our team for technical help, feedback or a guided walk-through of the new Data Portal. 🖥️🧬 🌱🦠🍄🧪
More information: jgi.doe.gov/analyze-data...
JGI Portals | Joint Genome Institute
Our data platforms are a key resource for the broader scientific community and require constant developments to meet the ever-changing demands of our users.
jgi.doe.gov
October 27, 2025 at 6:57 PM
🚨NOTICE TO OUR USERS🚨
The Data Portal will soon replace the Genome Portal.
Portal users can book a session with our team for technical help, feedback or a guided walk-through of the new Data Portal. 🖥️🧬 🌱🦠🍄🧪
More information: jgi.doe.gov/analyze-data...
The Data Portal will soon replace the Genome Portal.
Portal users can book a session with our team for technical help, feedback or a guided walk-through of the new Data Portal. 🖥️🧬 🌱🦠🍄🧪
More information: jgi.doe.gov/analyze-data...
Reposted by Tara Oceans Science
The idea that emissions can be offset through projects that claim to avoid releases or to remove carbon dioxide from the atmosphere is fatally flawed
go.nature.com/4925W5G
go.nature.com/4925W5G
Carbon credits are failing to help with climate change — here’s why
The idea that emissions can be offset through projects that claim to avoid releases or to remove carbon dioxide from the atmosphere is fatally flawed.
go.nature.com
October 14, 2025 at 1:32 PM
The idea that emissions can be offset through projects that claim to avoid releases or to remove carbon dioxide from the atmosphere is fatally flawed
go.nature.com/4925W5G
go.nature.com/4925W5G
Reposted by Tara Oceans Science
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
October 5, 2025 at 10:35 AM
Latest from ours: www.cell.com/cell-reports...
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
This is two stories in one: a case study/cautionary tale on developing genetic tools in new organisms, and the first hint at a gene regulatory network for choanoflagellate multicellular development (which turn out to involve a Hippo/YAP/ECM loop!) A 🧵
Reposted by Tara Oceans Science
Happy Ctenophore Day!
🐙🦑🧪
🐙🦑🧪
October 4, 2025 at 7:36 AM
Happy Ctenophore Day!
🐙🦑🧪
🐙🦑🧪
Reposted by Tara Oceans Science
Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching
We introduce Mapping-friendly Sequence Reduction (MSR) sketches, a sketching method for high-fidelity (HiFi) long reads, and Alice, an assembler that operates directly on these sketches. MSR produces ...
www.biorxiv.org
October 3, 2025 at 2:51 PM
Our preprint on our new metagenomic HiFi assembler Alice is out 🥳 Based on a *new sketching method* (🧵1/6)
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
👉 Preprint www.biorxiv.org/content/10.1...
👉 Github github.com/rolandfaure/...
Reposted by Tara Oceans Science
The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.
OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4
October 1, 2025 at 1:14 PM
The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.
Reposted by Tara Oceans Science
EcoFoldDB: Protein Structure‐Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
EcoFoldDB: Protein Structure‐Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale
EcoFoldDB provides a curated database of protein structures for ecologically important microbial traits. Its companion annotation pipeline (EcoFoldDB-annotate) employs rapid structural homology searc...
enviromicro-journals.onlinelibrary.wiley.com
September 18, 2025 at 2:01 AM
EcoFoldDB: Protein Structure‐Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
Reposted by Tara Oceans Science
A genomic view of Earth’s biomes www.nature.com/articles/s41...
A genomic view of Earth’s biomes - Nature Reviews Genetics
Genome-wide approaches have uncovered the vast microbial and viral diversity across ecosystems. This Review explores advances in metagenomics, single-cell sequencing and functional profiling to elucid...
www.nature.com
September 18, 2025 at 3:35 AM
A genomic view of Earth’s biomes www.nature.com/articles/s41...
Here's a new paper that stresses the importance of microbes not only for human health but for planetary health in general, performing all sorts of essential activities at global scale : Incorporating microbiomes into the One Health Joint Plan of Action | mBio journals.asm.org/doi/10.1128/...
Incorporating microbiomes into the One Health Joint Plan of Action | mBio
One Health is a well-established concept that is now more crucial than ever in tackling
modern challenges of zoonotic diseases, antimicrobial resistance, and climate- and
environment-related health th...
journals.asm.org
September 9, 2025 at 1:04 PM
Here's a new paper that stresses the importance of microbes not only for human health but for planetary health in general, performing all sorts of essential activities at global scale : Incorporating microbiomes into the One Health Joint Plan of Action | mBio journals.asm.org/doi/10.1128/...
Reposted by Tara Oceans Science
It being Sunday, and having been to the #Vatican in support of Pope Francis's environmental work, here's my news to me good news for Sept 7 #EarthOptimism #BeyondTheObituaries www.reuters.com/sustainabili...
Pope Leo, in climate push, to open Vatican-run ecological training centre
Pope Leo will open a new Vatican-run ecological training centre in the Italian countryside on Friday, in an initiative Catholic officials say is meant to encourage world leaders to address global climate change.
www.reuters.com
September 7, 2025 at 4:07 PM
It being Sunday, and having been to the #Vatican in support of Pope Francis's environmental work, here's my news to me good news for Sept 7 #EarthOptimism #BeyondTheObituaries www.reuters.com/sustainabili...
Reposted by Tara Oceans Science
Catastrophic tipping point in Antarctica already happening
A "rapid and substantial slowdown" of ocean currents has already begun
Warming waters will further reduce Krill and phytoplankton populations and starve emperor penguins
Sea levels will rise
www.dw.com/en/antarctic...
A "rapid and substantial slowdown" of ocean currents has already begun
Warming waters will further reduce Krill and phytoplankton populations and starve emperor penguins
Sea levels will rise
www.dw.com/en/antarctic...
Antarctic ice loss could have 'catastrophic' impact – DW – 08/21/2025
A study warned that Antarctic ice loss could cause more warming in the region and beyond, and could push some marine species toward extinction.
www.dw.com
August 22, 2025 at 5:35 PM
Catastrophic tipping point in Antarctica already happening
A "rapid and substantial slowdown" of ocean currents has already begun
Warming waters will further reduce Krill and phytoplankton populations and starve emperor penguins
Sea levels will rise
www.dw.com/en/antarctic...
A "rapid and substantial slowdown" of ocean currents has already begun
Warming waters will further reduce Krill and phytoplankton populations and starve emperor penguins
Sea levels will rise
www.dw.com/en/antarctic...
Reposted by Tara Oceans Science
This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered
July 31, 2025 at 3:38 PM
This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered
Reposted by Tara Oceans Science
Just out: metagenomics with internal standards yields phylogenetically resolved genome ("~cell") counts of bacteria, archaea, and photosynthetic eukaryotes per L of seawater, over the AMT29 Atlantic transect, via "single copy" genes (recA, radA, psbO). Compares with microscopy and flow cytometry.
Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes #USC_MEB #jcampubs 🌊 academic.oup.com/ismecommun/a...
Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes
Abstract. High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequenci
academic.oup.com
July 31, 2025 at 1:29 AM
Just out: metagenomics with internal standards yields phylogenetically resolved genome ("~cell") counts of bacteria, archaea, and photosynthetic eukaryotes per L of seawater, over the AMT29 Atlantic transect, via "single copy" genes (recA, radA, psbO). Compares with microscopy and flow cytometry.
Reposted by Tara Oceans Science
A dinoflagellate-infecting giant virus with a micron-length tail www.biorxiv.org/content/10.1...
July 30, 2025 at 2:02 PM
A dinoflagellate-infecting giant virus with a micron-length tail www.biorxiv.org/content/10.1...
Reposted by Tara Oceans Science
Characterizing organisms from three domains of life with universal primers from throughout the global ocean www.nature.com/articles/s41...
July 22, 2025 at 10:02 AM
Characterizing organisms from three domains of life with universal primers from throughout the global ocean www.nature.com/articles/s41...
Reposted by Tara Oceans Science
For my science column in this week's Listener, I talked to polar governance expert Alan Hemmings about the #Antarctic Treaty, geopolitics and emperors 🐧 current issue in shops now, online soon 🌎🇦🇶
July 21, 2025 at 5:15 AM
For my science column in this week's Listener, I talked to polar governance expert Alan Hemmings about the #Antarctic Treaty, geopolitics and emperors 🐧 current issue in shops now, online soon 🌎🇦🇶
Reposted by Tara Oceans Science
Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
AlphaFold - A practical guide
AlphaFold - A practical guide
www.ebi.ac.uk
July 21, 2025 at 3:33 PM
Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
Reposted by Tara Oceans Science
Even if you can’t attend this course in person, the online course materials are free and SO useful (I used this GitHub to plan out content for my new -Omics grad course)
#stamps2025
Metagenomics intro I: sampling & presence/absence
II: bioinformatics techniques for measuring genomes in metagenomes
III: reference-based metagenome interpretation & enhancing reference catalogs
IV: comprehensive metagenome content analysis and the challenge of bacterial strains
Metagenomics intro I: sampling & presence/absence
II: bioinformatics techniques for measuring genomes in metagenomes
III: reference-based metagenome interpretation & enhancing reference catalogs
IV: comprehensive metagenome content analysis and the challenge of bacterial strains
STAMPS 2025 tutorials - intro to metagenomics · Issue #3734 · sourmash-bio/sourmash
Metagenomics intro I: sampling & presence/absence Metagenomics intro II: bioinformatics techniques for measuring genomes in metagenomes Metagenomics intro III: reference-based metagenome interpreta...
github.com
July 18, 2025 at 5:11 PM
Even if you can’t attend this course in person, the online course materials are free and SO useful (I used this GitHub to plan out content for my new -Omics grad course)