Savvas Paragkamian

Genomic divergence across the tree of life | PNAS Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed. Bu...

Genomic divergence across the tree of life 🧪🌐https://www.pnas.org/doi/10.1073/pnas.2319389122

Can synthetic biology help save endangered ecosystems?
Our new paper with @vmaull.bsky.social explores how engineered genes can spread through soil microbes.
We model how synthetic gene transfer can support biodiversity. @vdlorenzo.bsky.social @guimaguade.bsky.social www.biorxiv.org/content/10.1...

MVIF fellows

and first task done!!

✅ to hug @cpavloud.bsky.social after many many #MVIF events working together (online)

@microbiomevif.bsky.social

📢 Dryad & @openrxiv.bsky.social are excited to announce a new partnership & integration. Beginning today, authors posting #preprints to @biorxivpreprint.bsky.social will have the option to upload #opendata to Dryad at the same time.

Read more ➡️ bit.ly/4nHtcdA

#preprint #openaccess #datasharing

Can science ever escape its demons? Enjoying these three brilliant books by historian of science Jimena Canales. They remind us that science isn’t a straight line. History, time, imagination, they're all up for grabs. @gemmadlc.bsky.social @jordipinero.bsky.social @seanmcarroll.bsky.social

Mediterranean olive groves🫒, which have long been symbols of tradition and culinary heritage🫘🥘 are threaten by serious erosion rates of 29-47 tons per ha annually. Read the Nature Article @soilolive.bsky.social .
t.co/BUnwiZePKe

Can cellular life be created in the lab? We are not yet there, but clearly getting closer! Check this paper where a new scenario for protocell replication is presented by Job Boekhoven and co-workers @manlius.bsky.social www.cell.com/chem/pdf/S24...

What is emergence? This is one of the most central ingredients of complexity, and a challenging one to formalize. Here's a paper by @seanmcarroll.bsky.social & Achyth Parola that attempts to classify different forms of emergence. @manlius.bsky.social @sfiscience.bsky.social arxiv.org/pdf/2410.15468

New Physics-Inspired Proof Probes the Borders of Disorder | Quanta Magazine For decades, mathematicians have struggled to understand matrices that reflect both order and randomness, like those that model semiconductors. A new method could change that.

Mathematicians have made an advance toward understanding the gray areas between order and disorder.

A diverse and distinct microbiome inside living trees - Nature Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...

Really exciting and important tree microbiome paper published in @nature.com ‘A diverse and distinct microbiome inside living trees’ 👏 www.nature.com/articles/s41...

Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series - Scientific Data Scientific Data - Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series

Do you like coastal/estuarine microbiology, time-series data, and/or metagenomics? Have we got a dataset for you #NSFfunded

Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs

You can watch Hadley's keynote at this link: www.youtube.com/live/ctc2kx3...

#useR2025

New Method Is the Fastest Way To Find the Best Routes | Quanta Magazine A canonical problem in computer science is to find the shortest route to every point in a network. A new approach beats the classic algorithm taught in textbooks.

For the past four decades, finding the fastest route to every destination in a network involved sorting the routes by distance. This meant that algorithms could only work as quickly as they could sort. No longer.

Climate warming fuels the global antibiotic resistome by altering soil bacterial traits - Nature Ecology & Evolution A combination of metagenomic data from experimental and natural warming with microbial culturing experiments shows that warming increases the potential of evolution of antibiotic resistance in soil ba...

Lin et al.
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits

www.nature.com/articles/s41...

Just about to push a big update to our R package TaxSEA where we've spent a lot of time collating data from the BacDive database so it's readily usable in a metagenomics analysis. See example below from the HMP IBD data. #metagenomics #bioinformatics #microbiome #microbiota

#DYK?

🌱 Of 30 000 edible plant species, just 30 feed the world.

🥣 And 5 grains (rice, wheat, maize, millet, sorghum) provide 60% of global calories!

It's time to diversify our plate. 🥬🍠

fao.org/seeds/en

How Can Math Protect Our Data? | Quanta Magazine Mary Wootters discusses how error-correcting codes work, and how they are essential for reliable communication and storage.

Today, error-correcting codes are operating behind the scenes everywhere your data is stored or transmitted — even on Netflix. Tune in to The Joy of Why:
www.quantamagazine.org/how-can-math...

Have you explored the NMDC Field Notes mobile app yet? Check out our new tutorial video for a quick walkthrough! buff.ly/Dohg4gH 🧪

Protein Structure Informed Bacteriophage Genome Annotation with Phold Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

www.biorxiv.org/content/10.1...

Viromics approaches for the study of viral diversity and ecology in microbiomes Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

How Distillation Makes AI Models Smaller and Cheaper | Quanta Magazine Fundamental technique lets researchers use a big, expensive “teacher” model to train a “student” model for less.

A fundamental technique in AI lets researchers transfer knowledge from a large, expensive “teacher” model to a smaller, cheaper “student” model.

What can be predicted when dealing with the real world? What are the limits of prediction? Watch this fantastic talk by @evamirandag.bsky.social on the nature of undecidability. With Turing, fluid turbulence, computation, chaos theory and ... rubber ducks www.youtube.com/watch?v=FsJ8...

llms-for-R.md GitHub Gist: instantly share code, notes, and snippets.

Thanks to everyone who responded to my question about what folks should know about using LLMs to generate #rstats: I've summarised the feedback with a few of my thoughts at gist.github.com/hadley/77d42...

YouTube video by National Microbiome Data Collaborative Validating and submitting metadata through the NMDC Submission Portal - 2025 tutorial video

Check out our updated tutorial video for the NMDC Submission Portal and learn how it can help you record, validate, and submit the metadata relating to your microbiome samples! www.youtube.com/watch?v=BV8U...

The #BHLTransition is underway! ⛵ We’re charting the course to a strong and sustainable future for the Biodiversity Heritage Library. Read our latest update and, if you have visionary ideas about how BHL can evolve and grow, get in touch 🚀: blog.biodiversitylibrary.org/2025/07/bhl-...

Hiring/Seeking a *permanent* programmer in ecological modelling at my lab @unibonn.bsky.social. We mechanistically model plant communities, island biogeography, species range dynamics, eco-evolutionary feedbacks, diversity gradients, tropical forests, vascular epiphytes. Pls rt! shorturl.at/Bzzdt

BHL Transition Update #2 Help us shape the future of the Biodiversity Heritage Library The Biodiversity Heritage Library (BHL) is at a turning point. After nearly two decades of calling the Smithsonian Institution home, BH…

Thank you to everyone who has shared & responded to our Call for Support thus far. Our Call proposes a more distributed & sustainable future where BHL is shared across multiple hosts supported by multiple funding sources. Find out more: blog.biodiversitylibrary.org/2025/06/tran... 🌱 📖 🧪 🌏 #ILoveBHL

A red flower on a green stem withe the words: BHL Call for support now open overlayed.

📢 The #BiodiversityHeritageLibrary is entering a bold new chapter – and we need your help! Today we release our official Call for Support. We’re seeking new hosts for BHL’s staff, infrastructure, and services. Learn more: blog.biodiversitylibrary.org/2025/06/tran... #BHLTransition #ILoveBHL

How can we build a general theory of mutualistic communities? After five years, we finally completed a new Neutral Theory of Cooperation that is fully solved analytically and displays remarkable properties @jordipinero.bsky.social @artemyte.bsky.social @manlius.bsky.social arxiv.org/abs/2506.09737

Information, complexity, evolution and computation are connected in profound ways. How? Algorithmic information theory is one fundamental piece of the puzzle. Here's one of the classic papers, by the great Russian mathematician Andrey Kolmogorov complexityexplorer.s3.amazonaws.com/Epistemologi...