Petar Penev
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ppenev.bsky.social
Petar Penev
@ppenev.bsky.social
160 followers 130 following 4 posts
Senior bioinformatics scientist @ Eligo
Metagenomics, protein evolution, ribosomes, and recently microbiome and its role in health.

https://orcid.org/0000-0002-9027-3824
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Reposted by Petar Penev
andrejakust.bsky.social
🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes.

Check it out: doi.org/10.1093/isme...
July 11, 2025 at 1:08 PM
Reposted by Petar Penev
bethanykolody.bsky.social
Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org
July 10, 2025 at 7:29 PM
Reposted by Petar Penev
lingdong-shi.bsky.social
Happy to share our recent work on rRNA processing and conformation: www.biorxiv.org/content/10.1...

Huge thanks to @ppenev.bsky.social @Amos Nissley @Dipti Nayak @Rohan Sachdeva @jhdcate.bsky.social @Jill Banfield @banfieldlab.bsky.social !!
Circular 23S rRNA within archaeal ribosomes
The ribosomal RNAs (rRNAs) that form the core of ribosomes are believed to occur as linear molecules. Here, we investigated rRNAs from diverse and mostly uncultivated archaea and found evidence that, ...
www.biorxiv.org
April 29, 2025 at 2:34 AM
Reposted by Petar Penev
bethanykolody.bsky.social
I’m very excited to finally share the results of a passion project that has been on my mind for nearly a decade. You can find the pre-print below, but what follows is the saga of how this project came to be:
January 15, 2025 at 7:22 PM
Reposted by Petar Penev
archaeal.bsky.social
After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social

rdcu.be/d5put

A thread…
Two decades of bacterial ecology and evolution in a freshwater lake
Nature Microbiology - A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response...
rdcu.be
January 3, 2025 at 11:44 AM
Reposted by Petar Penev
alexjprobst.bsky.social
#PhD #position #alert

2 bioinfo PhD positions @ProbstLab @RESIST_CRC
#1 on microbial & epigenetic stress response in rivers
tinyurl.com/bdf8eu5a
#2 on virus-host stress response in rivers
tinyurl.com/43cjd6es (supervision Moraru)

Please share!
Stellenausschreibung
tinyurl.com
December 19, 2024 at 4:37 PM
Reposted by Petar Penev
acritschristoph.bsky.social
the tool of the elite bioinformatician
December 10, 2024 at 5:38 PM
Reposted by Petar Penev
cgemcci.bsky.social
📰 Hot off the press at @naturecomms.bsky.social:
RNA language models predict mutations that improve RNA function
www.nature.com/articles/s41...

Congrats to @kshulgina.bsky.social @jhdcate.bsky.social and coauthors on a great C-GEM + @innovativegenomics.bsky.social collaboration! #NSFfunded #RNAsky
A red ribosome in front of a figure showing the phylogenetic relationships between organisms in GARNET with information on growth temperatures and ribosome sequences
December 5, 2024 at 10:58 PM
Reposted by Petar Penev
lauraeme.bsky.social
Excited to have our review 'Archaea and the origin of eukaryotes' in the @NatureRevMicro special issue celebrating the 40th anniversary of Woese and Fox's paper! With @anjspa1 @cstairs J. Lombard and @Ettema_lab
https://www.nature.com/articles/nrmicro.2017.133
November 16, 2024 at 5:43 PM
Reposted by Petar Penev
microyunha.bsky.social
Hello 🦋 #protein / #microbio / #BioML community! We are excited to release Gaia🌎, a context-aware protein search tool, extending protein search and discovery capabilities beyond sequence and structure, to include *genomic context*. Search your favorite protein sequences with on gaia.tatta.bio
November 19, 2024 at 3:07 PM
Reposted by Petar Penev
jeffinerca.bsky.social
Great job opportunity in my hometown! Pgh is a fantastic city.
costasamaras.com Costa Samaras @costasamaras.com · Nov 17
Tenure Track Faculty Opening at Carnegie Mellon in Decarbonization, Climate Change Adaptation, & Related Fields. Please share airb your networks or consider applying. One reason I left a think tank for CMU is because CMU has a lot of folks working on energy & climate. 🔌💡 apply.interfolio.com/154848
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 17, 2024 at 3:29 PM
Reposted by Petar Penev
jeffinerca.bsky.social
And then there was one…
Celebrating the final ‘cosm harvest from our 7th/last 13CO2 experiment of 2024. We’re studying how the psY gene affects CH4 fluxes and soil C cycles.
Much gratitude to Rina Estera, Flor Ercoli, Pam Ronald Lab, Dave Savage Lab & many others @innovativegenomics.bsky.social
A single soil megacosm holding a rice plant, surrounded by racks in a greenhouse A pile of cut apart, discarded soil megacosm containers, and one blue lab glove, inside a greenhouse. Three researchers cutting apart a one meter tall megacosm of soil on a table. Two researchers standing in front of megacosms holding rice plants, next to equipment for measuring photosynthesis, inside a greenhouse.
November 15, 2024 at 7:19 AM
Reposted by Petar Penev
lauraeme.bsky.social
Fully Funded PhD Opportunity in Evolutionary Biology at the U of Rhode Island. Join us to explore the origin and early evolution of eukaryotes using cutting-edge comparative (meta)genomics and molecular evolution approaches. Applications are due December 15th. Contact me ASAP at laura.eme@uri.edu
November 15, 2024 at 6:10 PM
Reposted by Petar Penev
symbiosisrox.bsky.social
We are searching for a postdoc to join our team, focused on anaerobic ciliate-methanogen symbiosis. Please share widely!
October 24, 2024 at 3:01 PM
Reposted by Petar Penev
claudiaalcar.bsky.social
New paper out! We found evidence of sporadic domain insertion events that affected protein-coding genes hundreds of million years ago. These insertions were retained by the DNA-dependent RNA polymerase in bacteria and by ribosomal protein uL10 in archaea.

onlinelibrary.wiley.com/doi/full/10....
BEAN and HABAS: Polyphyletic insertions in the DNA‐directed RNA polymerase
The β and β′ subunits of the RNA polymerase (RNAP) are large proteins with complex multi-domain architectures that include several insertional domains. Here, we analyze the domain organizations of RN....
onlinelibrary.wiley.com
October 30, 2024 at 9:02 AM
Reposted by Petar Penev
dbikard.bsky.social
Reposting this here: Two years ago we published the discovery of hotspots of novel anti-phage defense systems in the genome of P4 phage satellites, including a mysterious Phage Anti-Restriction Induced System (PARIS). We have now published the mechanism in @Nature www.nature.com/articles/s41...
A virally encoded tRNA neutralizes the PARIS antiviral defence system - Nature
Structural and functional studies reveal how viral proteins trigger the phage antirestriction induced system (PARIS) to degrade host tRNA and how viral tRNAs suppress the PARIS nuclease and thereby ov...
www.nature.com
November 14, 2024 at 4:07 PM
Reposted by Petar Penev
archaeal.bsky.social
Many years in the making, our new paper in collaboration with the Banfield lab.

- Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

microbiomejournal.biomedcentral.com/articles/10....
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sul...
Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse ...
microbiomejournal.biomedcentral.com
January 26, 2024 at 5:54 PM
Reposted by Petar Penev
alexjaf.bsky.social
first post on ~here~ to highlight the work of former Banfield lab undergrad @jettliu.bsky.social out today in mBio, examining the genetic characteristics of phages of CPR bacteria: journals.asm.org/doi/10.1128/...
Host translation machinery is not a barrier to phages that interact with both CPR and non-CPR bacter...
Here, we profiled putative phages of Saccharibacteria, which are of particular importance as Saccharibacteria influence some human oral diseases. We additionally profiled putative phages of Gracilibac...
journals.asm.org
November 27, 2023 at 3:48 PM
Reposted by Petar Penev
wcratcliff.bsky.social
Hey, we have a new paper out! In collaboration with Brian Hammer's group, we examine how E. coli evolves to *resist* being killed by the Type 6 Secretion System (basically a microbial poison-tipped spear attack).

www.cell.com/iscience/ful...
Trade-offs constrain adaptive pathways to the type VI secretion system survival
Bacteriology; Biological sciences; Evolutionary mechanisms
www.cell.com
November 17, 2023 at 9:13 PM
Reposted by Petar Penev
archaeal.bsky.social
The father of Archaea examines Asgards!

www.hindawi.com/journals/arc...
It has been proposed that the superphylum of Asgard Archaea may represent a historical link between ...
Ribosomal Protein Cluster Organization in Asgard Archaea
www.hindawi.com
October 3, 2023 at 5:04 PM
Reposted by Petar Penev
methanojen.bsky.social
Our latest work on bacterial methane clathrate proteins in collaboration with @raquellieberman.bsky.social is featured in this article ! research.gatech.edu/seafloor-spa...
From Seafloor to Space: New Bacterial Proteins Shine Light on Climate and Astrobiology | Research
Gigatons of greenhouse gas are trapped under the seafloor, and that’s a good thing. Around the coasts of the continents, where slopes sink down into the sea, tiny cages of ice trap methane gas, prev...
research.gatech.edu
September 26, 2023 at 3:45 PM
Reposted by Petar Penev
benadler.bsky.social
I’m really excited to share our new pre-print “Genome-wide Characterization of Diverse Bacteriophages Enabled by RNA-Binding CRISPRi”, with co-first author Muntathar Al-Shimary  from the Doudna and the newly-minted Cress labs!
www.biorxiv.org/content/10.1...
September 19, 2023 at 8:13 PM
Reposted by Petar Penev
martinsteinegger.bsky.social
Our work on clustering the 214M AlphaFold protein structure was published in @Nature. We identified 2.3M clusters using our fast structure cluster algorithm and analysed its annotations, evolution and novel domains. Work with Pedro Beltrao. 1/n
📄 www.nature.com/articles/s41...
💾 cluster.foldseek.com
Clustering-predicted structures at the scale of the known protein universe - Nature
The novel Foldseek clustering algorithm defines 2.30 million clusters of AlphaFold structures, identifying remote structural similarity of human immune-related proteins in prokaryotic species.
www.nature.com
September 13, 2023 at 3:04 PM
Reposted by Petar Penev
valdeanda.bsky.social
Excited for my first Blue Skye post! 🚀
Our latest paper from the Baker lab is out today in mBio!
Interested in ocean hydrocarbon degradation & SIP-metagenomics?
Check this out!
👇
journals.asm.org/doi/10.1128/...
@archaeal.bsky.social
September 13, 2023 at 5:45 PM
Reposted by Petar Penev
acritschristoph.bsky.social
www.cell.com/cell/fulltex...
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and...
Discovery and exploitation of natural competence in Patescibacteria enables visualization of the bacterial epibiont lifecycle and dissection of its genetic underpinnings.
www.cell.com
September 8, 2023 at 3:09 PM