Savvas Paragkamian
@sparagkamian.bsky.social
Looking for different ways to explore nature, with ropes, dance, pictures and friends
Reposted by Savvas Paragkamian
📢Coming up, workshop at #Behaviour2025 on our swaRmverse package!
🗓️Tue 26/8, 13:10–14:40
💻Theory & R practical (feel free to bring your data)
🎯Discussion on comparative analysis & metrics
🙏Come & recommend features for version 2.0!
👉RSVP on the app
More info: behaviourindia2025.in/workshops.html
🗓️Tue 26/8, 13:10–14:40
💻Theory & R practical (feel free to bring your data)
🎯Discussion on comparative analysis & metrics
🙏Come & recommend features for version 2.0!
👉RSVP on the app
More info: behaviourindia2025.in/workshops.html
August 19, 2025 at 3:05 PM
📢Coming up, workshop at #Behaviour2025 on our swaRmverse package!
🗓️Tue 26/8, 13:10–14:40
💻Theory & R practical (feel free to bring your data)
🎯Discussion on comparative analysis & metrics
🙏Come & recommend features for version 2.0!
👉RSVP on the app
More info: behaviourindia2025.in/workshops.html
🗓️Tue 26/8, 13:10–14:40
💻Theory & R practical (feel free to bring your data)
🎯Discussion on comparative analysis & metrics
🙏Come & recommend features for version 2.0!
👉RSVP on the app
More info: behaviourindia2025.in/workshops.html
Reposted by Savvas Paragkamian
What is the origin of diversity in allometric laws scaling across species? Check our new paper led by Andrea Tabi where
we propose a new theory of metabolic scaling grounded in thermodynamics and stochastic fluctuations at the cellular level.
www.biorxiv.org/content/10.1...
we propose a new theory of metabolic scaling grounded in thermodynamics and stochastic fluctuations at the cellular level.
www.biorxiv.org/content/10.1...
November 9, 2025 at 2:39 AM
What is the origin of diversity in allometric laws scaling across species? Check our new paper led by Andrea Tabi where
we propose a new theory of metabolic scaling grounded in thermodynamics and stochastic fluctuations at the cellular level.
www.biorxiv.org/content/10.1...
we propose a new theory of metabolic scaling grounded in thermodynamics and stochastic fluctuations at the cellular level.
www.biorxiv.org/content/10.1...
Reposted by Savvas Paragkamian
Genomic divergence across the tree of life 🧪🌐https://www.pnas.org/doi/10.1073/pnas.2319389122
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...
www.pnas.org
September 27, 2025 at 9:21 AM
Genomic divergence across the tree of life 🧪🌐https://www.pnas.org/doi/10.1073/pnas.2319389122
Reposted by Savvas Paragkamian
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...
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...
September 24, 2025 at 9:11 AM
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...
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...
Reposted by Savvas Paragkamian
and first task done!!
✅ to hug @cpavloud.bsky.social after many many #MVIF events working together (online)
@microbiomevif.bsky.social
✅ to hug @cpavloud.bsky.social after many many #MVIF events working together (online)
@microbiomevif.bsky.social
September 22, 2025 at 9:39 AM
and first task done!!
✅ to hug @cpavloud.bsky.social after many many #MVIF events working together (online)
@microbiomevif.bsky.social
✅ to hug @cpavloud.bsky.social after many many #MVIF events working together (online)
@microbiomevif.bsky.social
Reposted by Savvas Paragkamian
📢 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
Read more ➡️ bit.ly/4nHtcdA
#preprint #openaccess #datasharing
September 18, 2025 at 4:13 PM
📢 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
Read more ➡️ bit.ly/4nHtcdA
#preprint #openaccess #datasharing
Reposted by Savvas Paragkamian
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
September 13, 2025 at 4:54 PM
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
Reposted by Savvas Paragkamian
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
t.co/BUnwiZePKe
September 13, 2025 at 9:11 AM
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
t.co/BUnwiZePKe
Reposted by Savvas Paragkamian
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...
August 30, 2025 at 1:06 PM
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...
Reposted by Savvas Paragkamian
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
August 17, 2025 at 3:50 PM
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
Reposted by Savvas Paragkamian
Mathematicians have made an advance toward understanding the gray areas between order and disorder.
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.
www.quantamagazine.org
August 15, 2025 at 8:05 PM
Mathematicians have made an advance toward understanding the gray areas between order and disorder.
Reposted by Savvas Paragkamian
Really exciting and important tree microbiome paper published in @nature.com ‘A diverse and distinct microbiome inside living trees’ 👏 www.nature.com/articles/s41...
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...
www.nature.com
August 11, 2025 at 5:20 PM
Really exciting and important tree microbiome paper published in @nature.com ‘A diverse and distinct microbiome inside living trees’ 👏 www.nature.com/articles/s41...
Reposted by Savvas Paragkamian
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
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
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
www.nature.com
August 11, 2025 at 4:37 PM
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
Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series www.nature.com/articles/s41... #jcampubs
Reposted by Savvas Paragkamian
August 8, 2025 at 4:34 PM
Reposted by Savvas Paragkamian
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.
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.
www.quantamagazine.org
August 8, 2025 at 7:05 PM
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.
Reposted by Savvas Paragkamian
Lin et al.
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
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...
www.nature.com
August 6, 2025 at 8:50 PM
Lin et al.
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
Climate warming fuels the global antibiotic resistome by altering soil bacterial traits
www.nature.com/articles/s41...
Reposted by Savvas Paragkamian
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
August 7, 2025 at 2:50 AM
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
Reposted by Savvas Paragkamian
#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
🌱 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
August 7, 2025 at 10:24 AM
#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
🌱 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
Reposted by Savvas Paragkamian
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...
www.quantamagazine.org/how-can-math...
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.
www.quantamagazine.org
August 7, 2025 at 3:16 PM
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...
www.quantamagazine.org/how-can-math...
Reposted by Savvas Paragkamian
Have you explored the NMDC Field Notes mobile app yet? Check out our new tutorial video for a quick walkthrough! buff.ly/Dohg4gH 🧪
August 7, 2025 at 8:21 PM
Have you explored the NMDC Field Notes mobile app yet? Check out our new tutorial video for a quick walkthrough! buff.ly/Dohg4gH 🧪
Reposted by Savvas Paragkamian
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 8, 2025 at 7:11 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Savvas Paragkamian
New online! Viromics approaches for the study of viral diversity and ecology in microbiomes
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.
www.nature.com
July 21, 2025 at 6:34 PM
New online! Viromics approaches for the study of viral diversity and ecology in microbiomes
Reposted by Savvas Paragkamian
A fundamental technique in AI lets researchers transfer knowledge from a large, expensive “teacher” model to a smaller, cheaper “student” model.
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.
www.quantamagazine.org
July 19, 2025 at 10:04 PM
A fundamental technique in AI lets researchers transfer knowledge from a large, expensive “teacher” model to a smaller, cheaper “student” model.
Reposted by Savvas Paragkamian
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...
July 20, 2025 at 2:19 PM
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...
Reposted by Savvas Paragkamian
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...
llms-for-R.md
GitHub Gist: instantly share code, notes, and snippets.
gist.github.com
July 11, 2025 at 8:34 PM
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...