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Reposted by James Kosmopoulos

Ashish Malik @ashish-malik.bsky.social · 23d

📢 Funded PhD opportunities for UK candidates in beautiful Edinburgh. Get in touch if you're interested in a PhD on understanding the mechanisms of soil carbon cycling and the role of microbes. We work in different ecosystems: peatlands, forests and agricultural soils. Please repost/spread the word.

Poster showing the following text: PhD in microbial mechanisms of soil carbon cycling. Soil microbes shape the global carbon cycle in life and death. We study the effect of aboveground land management on belowground soil carbon cycling processes. We aim create a scalable understanding of microbial processes from single cells to populations to communities to ecosystems. Pictures with text: peatland restoration, sustainable agriculture and woodland regeneration.

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

You might still... but probably to ask you "Have you tried the Nug-ee's?"

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

@urineri.bsky.social Have you seen this new sequence aligner? I wonder if its approach would help mitigate some of the alignment issues you pointed out in your preprint on spacer-protospacer alignments.

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

Your support means the world to us. Thank you for helping my family take these steps together!

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

Please donate whatever you can to our team (Team Kosmo!) to stand with us and my dad in our effort to build a better future for people with Parkinson's. Here's the link to donate: secure.parkinson.org/site/TR/Movi...

Parkinson's Foundation: Keep on Moving!

The Parkinson's Foundation Moving Day Walk is a fun, inspiring fundraising event that unites families, friends and communities in the fight against Parkinson's disease. Held in cities across the Unite...

secure.parkinson.org

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

My goal is to raise $500 by October 5th. Every dollar raised goes directly to the Parkinson's Foundation, funding research, improving care, and providing resources that make a real difference for families like ours.

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

I'm so proud of how he's faced it by staying active, raising awareness, and by doing what he does best: (1) being a great dad, and (2) being a very talented DJ who brings people together, making them dance, and showing that you don't have to let life's hurdles stop you from doing what you love.

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James Kosmopoulos @kosmopoulos.bsky.social · 23d

This past year, my dad was diagnosed with Parkinson's disease. On October 5th, our family will walk together as Team Kosmo at Moving Day Chicago to celebrate his strength and support everyone living with Parkinson's.

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Reposted by James Kosmopoulos

Karthik Anantharaman @karthik-a.bsky.social · Aug 29

New review paper on metabolic handoffs in microbiomes led by PhD student Katie Klier.

We define major types of metabolic handoffs, examine their drivers and benefits, & describe their importance in different complex microbial systems and environments.

www.sciencedirect.com/science/arti...

An updated view of metabolic handoffs in microbiomes

From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and …

www.sciencedirect.com

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James Kosmopoulos @kosmopoulos.bsky.social · Aug 28

Thank you for the validation 🍄

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James Kosmopoulos @kosmopoulos.bsky.social · Aug 27

Am I proud that I made an impulse buy? No. Am I okay with it because it was only $20 for a special series set of Canadian stamps with fungi and lichen? Yes.

CTV News Kitchener @ctvnewskitchener.bsky.social · Aug 27

Canada Post features fungi and lichen in new stamp series - Canada Post has unveiled its new stamp collection Wednesday featuring fungi and lichens found in the country.

Canada Post features fungi and lichen in new stamp series

Canada Post has unveiled its new stamp collection Wednesday featuring fungi and lichens found in the country.

bit.ly

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Reposted by James Kosmopoulos

Karthik Anantharaman @karthik-a.bsky.social · Aug 27

New paper alert! We suggest caution in the analyses of viral auxiliary metabolic genes and propose a new overarching term - 'auxiliary viral genes' (AVGs) to describe different types of such genes. @simrouxvirus.bsky.social #phagesky #Microsky www.nature.com/articles/s41...

A call for caution in the biological interpretation of viral auxiliary metabolic genes - Nature Microbiology

This Perspective discusses virus-encoded auxiliary metabolic genes and provides a framework for the biological interpretation of these genes.

www.nature.com

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James Kosmopoulos @kosmopoulos.bsky.social · Aug 11

Looks like RFK Jr needs a lesson in viral taxonomy @evelienadri.bsky.social!!

Colin Carlson @colincarlson.bsky.social · Aug 8

RFK has announced that he is developing a vaccine against all viruses. Yes, every single one. The whole, uh, "phylum"

RFK Jr: “We're developing a universal vaccine at NIH which is a vaccine that addresses the entire phylum of viruses.”

“It's a vaccine that mimics natural immunity and it is effective against any kind of mutation.”

“We believe it's gonna be effective against not only coronaviruses but also flu.”

“And it's gonna be a much safer and a much more effective vaccine.”

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Reposted by James Kosmopoulos

George Bouras @gbouras13.bsky.social · Aug 8

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...

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

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Reposted by James Kosmopoulos

Ashish Malik @ashish-malik.bsky.social · Aug 4

📢 New preprint on work by my first PhD student William Pallier.

Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration.

We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health.

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

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Reposted by James Kosmopoulos

Susie Grigson @susiegriggo.bsky.social · Jul 30

🚨 New preprint 🚨

My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky

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

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

www.biorxiv.org

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James Kosmopoulos @kosmopoulos.bsky.social · Jul 28

Used any new tools or databases (released in the past ~year) for #metagenomics or #viromics? Found something especially useful- or seen recent insights using old methods? Reply with your favorites! I'm trying to compile a list of new resources and approaches.

James Kosmopoulos @kosmopoulos.bsky.social · Jul 26

Looks like a very useful database for classifying fungal sequences in soil metagenomes. Makes me realize I’ve probably overlooked a lot of fungal DNA in my soil datasets! www.biorxiv.org/content/10.1...

Improved detection of fungi and uncultivated microorganisms in soil metagenomes using a comprehensive genome database

Soils harbor diverse microbial communities crucial for ecosystem functioning, but poor genomic representation of many uncultured soil microorganisms limits the utility of existing databases to address...

www.biorxiv.org

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James Kosmopoulos @kosmopoulos.bsky.social · Jul 24

I've been playing with sylph and pavian all day today. Very neat tools, and excellent incorporation of databases!

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Reposted by James Kosmopoulos

Morgan Sobol @msobol.bsky.social · Jul 23

My postdoc position is open again! If you’re interested and did not get your application in last time, please send one by end of this week! Start date asap, latest by end of Fall. ‼️

Morgan Sobol @msobol.bsky.social · May 28

🚨 I’m hiring a postdoc for Fall 2025 with experience in microbial ‘omics data analysis and phylogenetics/genomics. Projects will be centered around ancient microbial ecology & evolution. Click here for more information: bpb-us-e1.wpmucdn.com/wp.txstate.e...

Please share, thank you 🙏🏻

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Reposted by James Kosmopoulos

Nature Reviews Genetics @natrevgenet.nature.com · Jul 21

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

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Reposted by James Kosmopoulos

Rauf Salamzade @raufs.bsky.social · Jul 11

Great to see our manuscript on skDER & CiDDER - programs for selection of representative microbial genomes - now published.

Please give them a try and if you have any feature requests or issues, just let us know.

www.microbiologyresearch.org/content/jour...

github.com/raufs/skDER

skDER and CiDDER: two scalable approaches for microbial genome dereplication

An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping...

www.microbiologyresearch.org

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Reposted by James Kosmopoulos

Angel J Hernández Viera @angeljhv.bsky.social · Jul 10

I'm excited to announced that the version of record of this article is out in @elife.bsky.social. With the other first coauthor My Tran, we found that phage resistance cause reduced beta-lactam resistance and reduced virulence phenotypes in diverse MRSA strains.

elifesciences.org/articles/102...

Bacteriophage infection drives loss of β-lactam resistance in methicillin-resistant Staphylococcus aureus

In methicillin-resistant Staphylococcus aureus, evolution of bacteriophage resistance causes trade-offs that re-sensitize the bacteriato β-lactam antibiotics.

elifesciences.org

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Reposted by James Kosmopoulos

Rafal Mostowy @rafalmostowy.bsky.social · Jun 26

This work was equally driven by two PhD students, Aleksandra Otwinowska (experiments) and Janusz Koszucki (bioinformatics). Check out the preprint or DM if you want to learn more.
www.biorxiv.org/content/10.1...

Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes

Understanding host-range determinants in temperate bacteriophages is critical for elucidating phage-host co-evolution and advancing phage therapies. We analysed 3,900 Klebsiella genomes from diverse e...

www.biorxiv.org

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James Kosmopoulos @kosmopoulos.bsky.social · Jun 16

Loved this episode!

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