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Adrià Auladell

@adriaula.bsky.social
1.3K followers 539 following 173 posts

Bioinformatics and marine microbial ecology. Right now focused mainly protists + metatranscriptomics! Open science. He/Him/His.

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Reposted by Adrià Auladell
Jess Holz @jessholz.bsky.social · 15/03/2026
This was a Stentor timelapse we made earlier this week from her trip to Boston (which she also had to crowdfund). She was magically able to locate one ‘on demand’ despite that I very rarely find one in Boston. She also brought me samples from all the way up the east coast. #sciart #microscopy
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Kenneth Dumack @dumack.bsky.social · 05/04/2026
We all know #fungi are the dominant microbial #eukaryotes in #forest #soils… or are they really? In our new paper, we revisited 51 forest metatranscriptomes from 4 European and North American forest regions - and found that protistan predators outshine fungi in activity!
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 04/02/2026
I am doing a short workshop in this symposium (quoted below) for folks in and around Leipzig. Here's the abstract. I really indulged myself with this one. A Guerilla Approach to Scientific Workflow:
Title: A Guerilla Approach to Scientific Workflow

Abstract: Taking inspiration from guerilla warfare, I will introduce a framework for managing scientific research that addresses the complexity of research while advancing goals of transparency and reliability. Real science is complex, and there is no single scientific method. It is a chaotic network of theories, data, models, graphs, comparisons, summaries, and narratives. A flaw in any part can ruin everything. How can small teams of researchers challenge this complexity and emerge victorious? More statistical training is not enough. More resources is not enough. Lawrence of Arabia once said, "Guerrilla warfare is more intellectual than a bayonet charge." And this is how we too will proceed. Instead of confronting the complexity directly, with more money and more people and more data and more meta-analyses, we must develop a SCIENTIFIC WORKFLOW that subdivides, analyzes, and transparently justifies our individual research projects. The tools to do this already exist, and individual researchers can become scientific guerillas today to improve their chances of victory.
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Richard Lenski @relenski.bsky.social · 20/01/2026
Looking for something new to integrate into an #evolution or #microbiology course? Useful for lectures, labs, homework? Have a look at our STEPS program, which simulates bacterial evolution, including the #LTEE. Easy web-based interface & lab manual w/ exercises to help develop students' intuition.
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Daniel Podlesny @podlesny.bsky.social · 02/12/2025
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
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Luis Pedro Coelho @luispedrocoelho.bsky.social · 17/01/2026
I woke up to some very sad news... Peer was a giant of bioinformatics and computational biology and an inspiring mentor to everyone who had been in his group. I find myself repeating things he said all the time and will probably keep doing so for the rest of my life www.embl.org/news/embl-an...
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
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Daan Speth @daanspeth.bsky.social · 26/01/2026
With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o. More info: globdb.org/news Thanks #anvio team! 🖥️🧬🦠
globdb.org
News | GlobDB
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Adrià Auladell @adriaula.bsky.social · 23/01/2026
amazing work!
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Paul Carini @uncultured.carinilab.com · 22/01/2026
Excited to see this published! A big part of why SAR11 is so tricky to grow like "normal" microbes.
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Nature @nature.com · 14/01/2026
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers go.nature.com/4sEMwLH
go.nature.com
Genomic clues to the origin of eukaryotic cells
How did eukaryotic cells with complex architecture evolve from simpler prokaryotic cells? DNA analyses offer possible answers.
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Seva @seva.bsky.social · 13/01/2026
I just finished a three-year term as an editor at an international relations journal. I began at the start of the LLM era but ended right in the middle of it. Our volume of submissions tripled and our desk reject rate rose to 75%. I have some thoughts. open.substack.com/pub/hegemon/...
open.substack.com
The Age of Academic Slop is Upon Us
what happens when AI automates "normal science"?
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Adrià Auladell @adriaula.bsky.social · 14/01/2026
damnnnnnn
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Hannah Reich @hannahgreich.bsky.social · 11/01/2026
It's that time of year again! I'm looking for suggestions of 'emerging' model organisms for my #CellBio course's final proj: Organism nomination form here (links to blog on proj info): forms.office.com/r/v8zYgqVe8W #cellbiology #biology #academicsky #microsky #archaeasky #protistsonsky 🧪 (1/n)
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Thomas Lin Pedersen @thomasp85.com · 13/01/2026
Cleaning up the desktop on my laptop and found this #ggplot2 #rstats
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Anne Walraven @annewalraven.bsky.social · 08/01/2026
Thought I would share an SEM image of a Meringosphaera I picked at Klubban (West Coast of Sweden) for my first post on Bluesky :) #protistsonsky
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Miguel Méndez Sandín @sandinmm.eurosky.social · 15/12/2025
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...
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Noah Fierer @noahfierer.bsky.social · 06/01/2026
New paper up - inspired by the periodic table of the elements, we attempted to organize bacterial diversity in genome-inferred trait space academic.oup.com/ismej/advanc...
academic.oup.com
Constructing a “periodic table” of bacteria to map diversity in trait space
Abstract. Despite an ever-expanding number of bacterial taxa being discovered, many of these taxa remain uncharacterized with unknown traits and environmen
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Germán Bonilla-Rosso @germusthermophilus.bsky.social · 20/12/2025
🖥🧬🦠
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Jelena Godrijan 🫧❾🌊🦋 @godi.bsky.social · 05/11/2025
🚀 New in @natmicrobiol.nature.com EMCG — droplet-based single-particle genomics method 🧬⚠️Sequencing marine microbes one by one — in nL of seawater! Ultra-high resolution — no culture, no bulk averaging. A new way to see the invisible 🫥 🌊 rdcu.be/eOsUF #protistsonsky @bigelowlab.bsky.social
rdcu.be
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.
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Evgenii Protasov @evgenii-protasov.bsky.social · 09/11/2025
A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists(Amoebozoa and Rhizaria) #protists #eukaryotes #amoeba onlinelibrary.wiley.com/doi/10.1111/...
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Kasia Piwosz @piwoszomonas.bsky.social · 31/10/2025
Our new paper on what heterotrophic nanoflagellates do in nature doi.org/10.1111/1462... or www.biorxiv.org/cgi/content/.... Data available at doi.org/10.5281/zeno.... Funded by @ncn.gov.pl #ProtistsOnSky
doi.org
High‐Temporal Resolution of Microbial Food Web Dynamics and Structure During Phytoplankton Blooms in the Baltic Sea
Heterotrophic nanoflagellates are typically considered to be bacterial grazers, but some are actually omnivores and predators, both eating also other eukaryotes. Thanks to a high-frequency sampling c...
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Maria Carlos Oliveira @mariacoliveira.bsky.social · 28/10/2025
I had the honor of designing a field guide that spotlights 222 species of pollinators in Portugal. These creatures play a vital role in our ecosystems, supporting over 75% of agricultural crops. Yet, their populations are declining, a reality that makes this guide more urgent than ever.
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Tom Emery @drtomemery.bsky.social · 22/10/2025
Applications for MCSA are up 64%! 50% now come from outside the EU. Trump effect? The European Research market just got a hell of a lot more crowded. EU should turn on the tap marie-sklodowska-curie-actions.ec.europa.eu/news/msca-po...
marie-sklodowska-curie-actions.ec.europa.eu
MSCA Postdoctoral Fellowships 2025 receives record number of 17,058 proposals
This year’s annual MSCA Postdoctoral Fellowships call has attracted considerable interest from the research community with 17,058 proposals submitted.
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Adrià Auladell @adriaula.bsky.social · 03/11/2025
a huge effort and a huge service!
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Sebastian Schmidt @tsbschm.bsky.social · 31/10/2025
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-...
academic.oup.com
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
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Brett "Solidarity 2026" Banditelli @banditelli.org · 02/08/2025
Perfect bird design 10/10 peak A+ no notes #birds 🗺️
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Snowden St. @snowden.st · 11/04/2024
Maybe my favorite Food Map, ever.
A map from the Economist, of how dumplings spread from Italy to Japan by way of the Mongolian Empire
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Darakhshan Nehal @darakhshann.bsky.social · 28/10/2025
Just learned you can convert JPG to PNG in R with {magick}. Did you know this? #rstats
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angela oliverio @oliverio.bsky.social · 23/10/2025
This was such a neat study it got posted twice on our 'cool papers' channel in lab slack 😅 #ProtistsonSky
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Pawel Burkhardt @pawelburkhardt.bsky.social · 27/10/2025
First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience Our latest in @natrevneuro.nature.com Link: rdcu.be/eMX3E @jeffcolgren.bsky.social @msarscentre.bsky.social
rdcu.be
The evolutionary origins of synaptic proteins and their changing roles in different organisms across evolution
Nature Reviews Neuroscience - Recent studies have shed further light on the evolutionary origins of chemical synapses, In this Review, Colgren and Burkhardt explore how ancient proteins were...
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A. Murat Eren (Meren) @merenbey.bsky.social · 23/10/2025
Read the annual report from @elife.bsky.social: elifesciences.org/inside-elife... I welcome that eLife is no longer indexed by SCIE. And I admire that they have not backed away from their innovative model, which makes me even more motivated to send our best work to eLife.
elifesciences.org
Annual Report: 2024 in review
In 2024, eLife continued with its efforts to make peer review and publishing better for science and scientists.
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Xavier Grau-Bové 🌾 @xgrau.bsky.social · 24/10/2025
«A global coral phylogeny reveals resilience and vulnerability through deep time» This looks great. Figure 2 is textbook material! www.nature.com/articles/s41...
Partial snapshot of Figure 2 from the linked paper, showing the distribution of lineage ages for various coral taxonomic categories (from order Scleractinia to various families), together with environmental variables along the same timeline and reconstructed ancestral states for various traits (coloniality, symbiotic relationships, depth...).
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A. Murat Eren (Meren) @merenbey.bsky.social · 22/10/2025
Please share this with anyone who may be interested in a post-doc in Germany: jobs.awi.de/Vacancies/20... This is quite an exciting opportunity to push the boundaries of what is known regarding the molecular basis of the formation and demise of photosymbiotic relationships in marine habitats.
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 22/10/2025
Sprache der Dichter und Denker (languagelog.ldc.upenn.edu/nll/?p=71740)
While native English speakers in the UK and Spanish speakers in Spain rattled off an average of 16 words, Germans more than tripled this with an average of 53 words ranging from intelligenzallergiker, a person allergic to intelligence, to hodenkobold, or “testicle goblin”, someone who is being annoying
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Sarah J Tucker @sjtucker.bsky.social · 20/10/2025
I'm delighted our paper is out: doi.org/10.1093/isme... With new SAR11 isolate genomes and time-series metagenomes, we reveal coastal and offshore SAR11 ecotypes, identify associated metabolic traits, and pinpoint selective gene sweeps as a likely evolutionary driver to niche partitioning. 🌊🦠
doi.org
Habitat-specificity in SAR11 is associated with a few genes under high selection
Abstract. The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages
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Dan Quintana @dsquintana.bsky.social · 22/10/2025
LLMs can be useful for some things, but simulating human research participant responses isn’t one of them
However, recent work demonstrates that demographically prompted LLMs cannot accurately simulate diverse identities. Prompted LLMs are more likely to represent majority groups' stereotypes about minority groups than minority groups' own standpoints [12,13]. For instance, one study [13] prompted LLMs with the identity of Black woman. GPT-4 started generations with phrases such as 'Hey girl' and
'Oh, honey'; Llama-2 started nearly every response with 'Oh, girl', and used phrases including I'm like, YAASSSSS' and 'That's cray, hunty!' In addition, demographic prompting flattens diverse identities into narrow categories, limiting researchers' ability to observe and understand diversity within those categories [13,55]. Demographic prompting misrepresents people who are chronically under-represented in cognitive science research, a form of representational harm [56].
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Christian Kost @kostchristian.bsky.social · 15/10/2025
#microsky #mevosky @spp2389.bsky.social A PhD position is available in my lab to work on: Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria. Please RT Deadline: 12.11.25 More infos 👇 shorturl.at/rAKAT
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Prof Anna Watts @profannawatts.bsky.social · 09/10/2025
Lol the Nobels can't even acknowledge women's contribution to discovery. But sure let's acknowledge The Machines.
Headline from an article in Nature this week that states "Prizes must recognize machine contributions to discovery. The future of science will be written by humans and machines together. Awards should reflect that reality."
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Jelena Godrijan 🫧❾🌊🦋 @godi.bsky.social · 07/10/2025
They are architects of the sea, engineers of the air—capturing carbon, atom by atom. While you breathe, they build. While you sleep, they safeguard our climate. #InvisibleHeroes #OceanGuardians #ClimateWarriors #protistsonsky Illustrations by Rosie Sheward
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John Dolan @tintinnman.bsky.social · 08/10/2025
Victor Hensen coined the term "Plankton" in 1887. By 1910 it was an industry (still is)! Steuer's book ran 722 pages!
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Steven Robbins @stevenjrobbins.bsky.social · 06/10/2025
Curious, if someone wanted to annotate a large set of MAGs with KEGG, PFAM, CAZY, and then do some statistical comparison, how would you do that these days? Back in the day I loved EnrichM, but the backend databases for KEGG, etc, are woefully out of date now.
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Alejandro Rodríguez-Gijón @alejandrorgijon.bsky.social · 06/10/2025
I am extremely happy to share our latest manuscript "Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance". This project started back in 2021-2022 and after a long time, it sees the light today! www.nature.com/articles/s41...
nature.com
Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance - Scientific Reports
Scientific Reports - Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance
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Oliver Schwengers @oschwengers.bsky.social · 06/10/2025
Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)
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Adrià Auladell @adriaula.bsky.social · 06/10/2025
"Put simply, this is bad science. Research that can’t be verified can’t be trusted. Research that can’t be built upon can’t advance knowledge." This is great! pracheeac.substack.com/p/scholarly-...
pracheeac.substack.com
Scholarly Communication Is a Research Problem. This Means You.
Scholarly Communication Is a Research Problem.
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Jelena Godrijan 🫧❾🌊🦋 @godi.bsky.social · 05/10/2025
⚠️New paper ➡️ isolating >600 freshwater microbes using dilution-to-extinction and low-nutrient, lake-mimicking media. 🤯Expands cultured diversity to ~70 % of detected genera and enables physiological studies of streamlined oligotrophs. 🔗 www.nature.com/articles/s41... #protistsonsky
nature.com
Bringing the uncultivated microbial majority of freshwater ecosystems into culture - Nature Communications
A large fraction of aquatic bacteria remains uncultured. Here, the authors cultivated 627 strains of abundant freshwater bacteria from 14 European lakes, thus generating a collection that includes many previously uncultured, oligotrophic bacteria that may serve as model organisms.
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John Burns @burnsajohn.bsky.social · 02/10/2025
I've seen this several times: when Acantharians get big enough they like to eat tintinnids. And they always orient with the lorica opening pointed in: like they are slurping up a little jello shot. That glass house can't protect you from these weird predators little ciliate! 🦑 #protistsonsky
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John Burns @burnsajohn.bsky.social · 30/09/2025
The radiolarian hipster says to the diatoms "I was a spiky glass cell before it was cool" (first radiolarians appeared ~500 million years ago; first diatoms ~200 million years ago). But the diatoms grow *much* faster. No one even knows how radiolarians grow at all! They don't seem to eat diatoms 😅
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Science Vs @sciencevs.bsky.social · 01/10/2025
This moment from our latest episode with science writer @edyong209.bsky.social is 🔥 We asked Ed — how do we talk up the benefits of science in the face of government cuts? He told us that's the wrong approach. 🧪 Listen wherever, or watch on Spotify 👇 open.spotify.com/episode/7Evh...
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Richard Sever @richardsever.bsky.social · 01/10/2025
Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵
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Brian J. Enquist @bjenquist.bsky.social · 01/10/2025
Classic macroecological laws-long held as signatures of biological systems-also emerge in economic and geological systems. The real signal lies not in the static universal patterns, but in how those patterns shift with scale 🌐🧪 #scaling #macroecology journals.plos.org/plosone/arti...
journals.plos.org
Separating Macroecological Pattern and Process: Comparing Ecological, Economic, and Geological Systems
Theories of biodiversity rest on several macroecological patterns describing the relationship between species abundance and diversity. A central problem is that all theories make similar predictions f...
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