Andrei Papkou
@biobarkologist.bsky.social
Evolutionary biologist
Reposted by Andrei Papkou
New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
March 2, 2024 at 7:53 PM
New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Andrei Papkou
Excited to share the first preprint from my lab, collaborating with the fantastic @sanmillan.bsky.social 's lab, led by the amazing Jorge Sastre. We've demonstrated how insertion sequences encoded in plasmids promote bacterial adaptation. This project has been incredibly fun!
New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
March 3, 2024 at 2:16 PM
Excited to share the first preprint from my lab, collaborating with the fantastic @sanmillan.bsky.social 's lab, led by the amazing Jorge Sastre. We've demonstrated how insertion sequences encoded in plasmids promote bacterial adaptation. This project has been incredibly fun!
Nice systematic study of all synonymous substitution in 30 E. coli finding that substantial fitness effects are common under strong selection
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
January 24, 2024 at 9:57 AM
Nice systematic study of all synonymous substitution in 30 E. coli finding that substantial fitness effects are common under strong selection
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Andrei Papkou
Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes www.pnas.org/doi/10.1073/... #jcampubs
January 23, 2024 at 2:16 PM
Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes www.pnas.org/doi/10.1073/... #jcampubs
Reposted by Andrei Papkou
Announcing the Social Lives of Viruses 2024!
Do you study social evolution in viruses? Do you want to?
Join us in Puerto Rico this June for a 50-person meeting dedicated to viral sociality. All costs covered.
Apply here: forms.gle/sHTEcHJjryDh...
#ViroSky
#MicroSky
#EvoSky
#SocialViruses
Do you study social evolution in viruses? Do you want to?
Join us in Puerto Rico this June for a 50-person meeting dedicated to viral sociality. All costs covered.
Apply here: forms.gle/sHTEcHJjryDh...
#ViroSky
#MicroSky
#EvoSky
#SocialViruses
January 22, 2024 at 8:34 PM
Announcing the Social Lives of Viruses 2024!
Do you study social evolution in viruses? Do you want to?
Join us in Puerto Rico this June for a 50-person meeting dedicated to viral sociality. All costs covered.
Apply here: forms.gle/sHTEcHJjryDh...
#ViroSky
#MicroSky
#EvoSky
#SocialViruses
Do you study social evolution in viruses? Do you want to?
Join us in Puerto Rico this June for a 50-person meeting dedicated to viral sociality. All costs covered.
Apply here: forms.gle/sHTEcHJjryDh...
#ViroSky
#MicroSky
#EvoSky
#SocialViruses
Reposted by Andrei Papkou
Our latest paper out today led by the incomparable Jukka Corander.
Using longitudinal antibiotic use and genomic data, we show that antibiotic use does not determine the success of E. coli lineages causing BSI.
www.sciencedirect.com/science/arti...
1/2
Using longitudinal antibiotic use and genomic data, we show that antibiotic use does not determine the success of E. coli lineages causing BSI.
www.sciencedirect.com/science/arti...
1/2
January 12, 2024 at 8:50 AM
Our latest paper out today led by the incomparable Jukka Corander.
Using longitudinal antibiotic use and genomic data, we show that antibiotic use does not determine the success of E. coli lineages causing BSI.
www.sciencedirect.com/science/arti...
1/2
Using longitudinal antibiotic use and genomic data, we show that antibiotic use does not determine the success of E. coli lineages causing BSI.
www.sciencedirect.com/science/arti...
1/2
Reposted by Andrei Papkou
Quantifying the strength of viral fitness tradeoffs between hosts: A meta-analysis of pleiotropic fitness effects https://www.biorxiv.org/content/10.1101/2023.12.16.571995v1
Quantifying the strength of viral fitness tradeoffs between hosts: A meta-analysis of pleiotropic fitness effects https://www.biorxiv.org/content/10.1101/2023.12.16.571995v1
The range of hosts a given virus can infect is widely presumed to be limited by tradeoffs in fitness
www.biorxiv.org
December 17, 2023 at 2:35 AM
Quantifying the strength of viral fitness tradeoffs between hosts: A meta-analysis of pleiotropic fitness effects https://www.biorxiv.org/content/10.1101/2023.12.16.571995v1
Reposted by Andrei Papkou
Excited to share our new preprint! w @jfriedman.bsky.social #Microsky#evosky
We tackle a simple question - How much of species evolution depends on the presence of other species?
Bottom line: Most evolutionary changes were robust across strains that evolved with different biotic partners 1/
We tackle a simple question - How much of species evolution depends on the presence of other species?
Bottom line: Most evolutionary changes were robust across strains that evolved with different biotic partners 1/
Evolution in microbial microcosms is highly parallel regardless of the presence of interacting species https://www.biorxiv.org/content/10.1101/2023.12.14.571477v1
Evolution in microbial microcosms is highly parallel regardless of the presence of interacting species https://www.biorxiv.org/content/10.1101/2023.12.14.571477v1
During laboratory evolution, replicate bacterial populations often follow similar trajectories, thus
www.biorxiv.org
December 17, 2023 at 1:10 PM
Excited to share our new preprint! w @jfriedman.bsky.social #Microsky#evosky
We tackle a simple question - How much of species evolution depends on the presence of other species?
Bottom line: Most evolutionary changes were robust across strains that evolved with different biotic partners 1/
We tackle a simple question - How much of species evolution depends on the presence of other species?
Bottom line: Most evolutionary changes were robust across strains that evolved with different biotic partners 1/
Reposted by Andrei Papkou
A joint embedding of protein sequence and structure enables robust variant effect predictions https://www.biorxiv.org/content/10.1101/2023.12.14.571755v1
A joint embedding of protein sequence and structure enables robust variant effect predictions https://www.biorxiv.org/content/10.1101/2023.12.14.571755v1
The ability to predict how amino acid changes may affect protein function has a wide range of applic
www.biorxiv.org
December 16, 2023 at 12:48 PM
A joint embedding of protein sequence and structure enables robust variant effect predictions https://www.biorxiv.org/content/10.1101/2023.12.14.571755v1
Reposted by Andrei Papkou
New call for postdoc fellowships from the 🇪🇸 govt.
My brilliant colleague Cristina Vieitez and I are happy to jointly sponsor candidates who'd like to join us in beautiful Salamanca & develop methods for characterizing and optimizing microbial consortia. More info ⬇️.
www.aei.gob.es/convocatoria....
My brilliant colleague Cristina Vieitez and I are happy to jointly sponsor candidates who'd like to join us in beautiful Salamanca & develop methods for characterizing and optimizing microbial consortia. More info ⬇️.
www.aei.gob.es/convocatoria....
December 16, 2023 at 12:34 PM
New call for postdoc fellowships from the 🇪🇸 govt.
My brilliant colleague Cristina Vieitez and I are happy to jointly sponsor candidates who'd like to join us in beautiful Salamanca & develop methods for characterizing and optimizing microbial consortia. More info ⬇️.
www.aei.gob.es/convocatoria....
My brilliant colleague Cristina Vieitez and I are happy to jointly sponsor candidates who'd like to join us in beautiful Salamanca & develop methods for characterizing and optimizing microbial consortia. More info ⬇️.
www.aei.gob.es/convocatoria....
Reposted by Andrei Papkou
Can we predict AMR evolution?? We sure can try! New study published today in PNAS
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
December 14, 2023 at 9:09 PM
Can we predict AMR evolution?? We sure can try! New study published today in PNAS
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
An amazing piece in @quantamagazine.bsky.social by Veronique Greenwood about our recent article. High accessibility of fitness landscapes explained in a very accessible way
If evolution can be likened to mountains and valleys of fitness, the complexity of genetics makes the landscape into a high-dimensional plane. That makes more trails for natural selection.
Evolving Bacteria Can Evade Barriers to ‘Peak’ Fitness | Quanta Magazine
Paradoxically, natural selection can sometimes seem to block organisms from evolving useful adaptations. But a new study of “fitness landscapes” and antibiotic resistance in bacteria shows that li...
www.quantamagazine.org
November 30, 2023 at 10:51 AM
An amazing piece in @quantamagazine.bsky.social by Veronique Greenwood about our recent article. High accessibility of fitness landscapes explained in a very accessible way
Reposted by Andrei Papkou
… and an excellent companion article (to the repost 👇) from @quantamagazine.bsky.social. Super cool work! 🧪
November 28, 2023 at 11:00 PM
… and an excellent companion article (to the repost 👇) from @quantamagazine.bsky.social. Super cool work! 🧪
Reposted by Andrei Papkou
Spurred on by ribosome profiling and other cool methods, translation elongation has grown into a whole field with new surprises all the time (and new relevance for vaccine mRNAs!). Here’s our latest on why synonymous codons aren’t all the same. (Thread) www.biorxiv.org/content/10.1...
Codon optimality modulates protein output by tuning translation initiation
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
November 29, 2023 at 7:07 AM
Spurred on by ribosome profiling and other cool methods, translation elongation has grown into a whole field with new surprises all the time (and new relevance for vaccine mRNAs!). Here’s our latest on why synonymous codons aren’t all the same. (Thread) www.biorxiv.org/content/10.1...
New in Science with @jaescudero.bsky.social . A combinatorially complete fitness landscape with >260.000 E.coli genotypes shows unexpected properties. Despite ~500 fitness peaks in this landscape, adaptive evolution can easily navigate to highest fitness peaks www.science.org/doi/10.1126/...
A rugged yet easily navigable fitness landscape
A high number of genetic fitness peaks does not impair adaptive evolution in a large empirical fitness landscape.
www.science.org
November 24, 2023 at 1:29 PM
New in Science with @jaescudero.bsky.social . A combinatorially complete fitness landscape with >260.000 E.coli genotypes shows unexpected properties. Despite ~500 fitness peaks in this landscape, adaptive evolution can easily navigate to highest fitness peaks www.science.org/doi/10.1126/...