James Kosmopoulos
@kosmopoulos.bsky.social
Microbiology PhD candidate in the Anantharaman Lab at UW-Madison | Exploring viral community ecology in soils & developing bioinformatics tools for #viromics 🧬🦠 | he/him
Pinned
Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
pubs.acs.org
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Reposted by James Kosmopoulos
#Virus discovery has accelerated but linking viruses to hosts is hard. @sullivan-lab.bsky.social use synthetic #microbiomes to optimize & benchmark #Hi-C for virus-host linkage inference, applying this to existing #soil data to reveal 100s of novel linkages @plosbiology.org 🧪 plos.io/3MlAENO
November 25, 2025 at 2:05 PM
#Virus discovery has accelerated but linking viruses to hosts is hard. @sullivan-lab.bsky.social use synthetic #microbiomes to optimize & benchmark #Hi-C for virus-host linkage inference, applying this to existing #soil data to reveal 100s of novel linkages @plosbiology.org 🧪 plos.io/3MlAENO
Surely SOMEBODY mourns the wicked
November 24, 2025 at 3:53 PM
Surely SOMEBODY mourns the wicked
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
pubs.acs.org
November 20, 2025 at 9:24 PM
Viral "dark matter" dominates the virosphere. In this review by me & @karthik-a.bsky.social, we synthesize what's known, highlight major gaps, and outline paths forward for illuminating viral protein functions in diverse ecosystems.
Reposted by James Kosmopoulos
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Reposted by James Kosmopoulos
📢 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.
September 16, 2025 at 4:25 PM
📢 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.
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.
September 15, 2025 at 5:52 PM
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.
Reposted by James Kosmopoulos
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...
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
August 29, 2025 at 1:30 PM
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...
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...
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.
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
August 27, 2025 at 3:42 PM
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.
Reposted by James Kosmopoulos
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
August 27, 2025 at 12:24 PM
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...
Looks like RFK Jr needs a lesson in viral taxonomy @evelienadri.bsky.social!!
RFK has announced that he is developing a vaccine against all viruses. Yes, every single one. The whole, uh, "phylum"
August 11, 2025 at 12:40 AM
Looks like RFK Jr needs a lesson in viral taxonomy @evelienadri.bsky.social!!
Reposted by James Kosmopoulos
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 James Kosmopoulos
📢 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...
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...
August 4, 2025 at 4:31 PM
📢 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...
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...
Reposted by James Kosmopoulos
🚨 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...
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
July 30, 2025 at 6:01 AM
🚨 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...
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...
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.
July 28, 2025 at 4:55 PM
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.
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
July 26, 2025 at 5:52 PM
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...
Reposted by James Kosmopoulos
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. ‼️
🚨 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 🙏🏻
Please share, thank you 🙏🏻
July 23, 2025 at 2:39 AM
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. ‼️
Reposted by James Kosmopoulos
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 James Kosmopoulos
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
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
July 11, 2025 at 8:14 PM
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
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
Reposted by James Kosmopoulos
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...
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
July 10, 2025 at 6:36 PM
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...
elifesciences.org/articles/102...
Reposted by James Kosmopoulos
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...
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
June 26, 2025 at 7:13 AM
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...
www.biorxiv.org/content/10.1...
Reposted by James Kosmopoulos
#MicroSky
with this author, karen lloyd, this is sure to be an entertaining read. and an exciting one at that...
with this author, karen lloyd, this is sure to be an entertaining read. and an exciting one at that...
Hunting extreme microbes that redefine the limits of life
book by @karenlloyd.bsky.social #usc_earth #usc_meb
www.nature.com/articles/d41...
book by @karenlloyd.bsky.social #usc_earth #usc_meb
www.nature.com/articles/d41...
Hunting extreme microbes that redefine the limits of life
An adventurous survey of inhospitable habitats unearths extraordinary organisms that pose challenging research questions.
www.nature.com
May 13, 2025 at 3:19 PM
#MicroSky
with this author, karen lloyd, this is sure to be an entertaining read. and an exciting one at that...
with this author, karen lloyd, this is sure to be an entertaining read. and an exciting one at that...
Reposted by James Kosmopoulos
Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection https://www.biorxiv.org/content/10.1101/2025.05.06.652306v1
May 11, 2025 at 12:47 AM
Tool Choice drastically Impacts CRISPR Spacer-Protospacer Detection https://www.biorxiv.org/content/10.1101/2025.05.06.652306v1
Reposted by James Kosmopoulos
Excited to share our lab's latest work led by PhD student
@maggielangwig.bsky.social
describing the ecology and evolution of viruses in globally distributed hydrothermal vents.
www.nature.com/articles/s41...
@maggielangwig.bsky.social
describing the ecology and evolution of viruses in globally distributed hydrothermal vents.
www.nature.com/articles/s41...
Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems - Nature Communications
Viruses are pivotal players in deep-sea hydrothermal vents, shaping microbiomes by preying on key hosts. Through a global-scale analysis of vent viruses and their interactions, this study reveals that...
www.nature.com
May 5, 2025 at 6:18 AM
Excited to share our lab's latest work led by PhD student
@maggielangwig.bsky.social
describing the ecology and evolution of viruses in globally distributed hydrothermal vents.
www.nature.com/articles/s41...
@maggielangwig.bsky.social
describing the ecology and evolution of viruses in globally distributed hydrothermal vents.
www.nature.com/articles/s41...
Reposted by James Kosmopoulos
Engineering bacteriophages through deep mining of metagenomic motifs www.science.org/doi/full/10.... #jcampubs
Engineering bacteriophages through deep mining of metagenomic motifs
We unlock the potential encoded in phage metagenomes to engineer phages to change host range and kill pathogenic bacteria.
www.science.org
April 21, 2025 at 3:30 PM
Engineering bacteriophages through deep mining of metagenomic motifs www.science.org/doi/full/10.... #jcampubs
Reposted by James Kosmopoulos
Abrupt termination of research doesn't stop waste, it CREATES waste! We call on @hhsgov.govmirrors.com to restore the funding without delay! #Cuts2Science
CLS Calls on the Trump Administration to Restore Research Funding - The Coalition for the Life Sciences
On April 14, 2025, CLS Chair Jo Handelsman and Exec Director Adrienne Hallett sent a letter outlining the tremendous consequences of terminating research and asking that it be reinstated.
www.coalitionforlifesciences.org
April 15, 2025 at 2:52 PM
Abrupt termination of research doesn't stop waste, it CREATES waste! We call on @hhsgov.govmirrors.com to restore the funding without delay! #Cuts2Science