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...

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

biorxiv.org

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!

Alvaro San Millan@sanmillan.bsky.social · 2y ago

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...

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/...

Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes www.pnas.org/doi/10.1073/... #jcampubs

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

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

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

biorxiv.org

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/

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 3y ago

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

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

biorxiv.org

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....

Can we predict AMR evolution?? We sure can try! New study published today in PNAS 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

Quanta Magazine@quantamagazine.org · 3y ago

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.

… and an excellent companion article (to the repost 👇) from @quantamagazine.bsky.social. Super cool work! 🧪

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...

quantamagazine.org

Andrei Papkou@biobarkologist.bsky.social · 3y ago

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/...

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

biorxiv.org

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/...