Akos Nyerges

Pivot Fellowship Pivot Fellowship on Simons Foundation

www.simonsfoundation.org/grant/pivot-... - a terrific opportunity for a cross-disciplinary focused postdoc training

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2 Nature Methods - AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments,...

Our paper with @sokrypton.org using AlphaFold2 to predict small-molecule binding sites in proteins is now out in Nature Methods! 🧵
rdcu.be/e7SnX
www.nature.com/articles/s41...

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

Happy 38th birthday to the #LTEE!
#BOTD in 1988.
Keep on evolving!

#science #evolution #microbiology

I’m looking to hire a research technician for my lab at Harvard & DFCI, who would primarily work in the wet lab expressing and characterizing designed proteins, starting this summer. A great role for a recent college grad looking for an immersive research experience before grad school.

And save >80% on the cost by pooling 6 or more plasmids into a single sample using our free SAVEMONEY algorithm!

elifesciences.org/articles/88794

colab.research.google.com/github/Masaa...

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

@science.org Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation | Science www.science.org/doi/10.1126/...

Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial - Nature Medicine In a phase 2 trial evaluating healthy donor fecal microbial transplantation plus either anti-PD-1 in patients with non-small cell lung cancer or anti-PD-1 and anti-CTLA-4 in patients with melanoma, en...

#NatMicroPicks

FMT for cancers in clinic! 💩🦠🦀⚕️

Three different clinical trials report activity of faecal microbiota transplant against cancer

#MicroSky #CancerSky

www.nature.com/articles/s41...
www.nature.com/articles/s41...

A 28-year evolution experiment on Burkholderia pseudomallei survival in nutrient-depleted sterile water https://www.biorxiv.org/content/10.64898/2026.02.06.704356v1

Feel like doing a SynBio PhD in Spain? Check this offer, many fellowships available 👉🏻 lifehub.csic.es/synbio-cofund/

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBio Names matter; they are not mere labels. They operate as anchors of memory, social coordinates, and references of collective identity. When a name becomes established through long-term use and broad ad...

How do you react when your favorite microbe is renamed by taxonomists who are completely outside your field—and who ignore the community that actually works with it? Here is our clear answer re the case of Pseudomonas putida KT2440 👉🏻 journals.asm.org/doi/10.1128/...

Mammalian genome writing: Unlocking new length scales for genome engineering The ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…

Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social!

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

Expanding the Genetic Code of an Animal with Two Non-Canonical Amino Acids https://www.biorxiv.org/content/10.64898/2026.01.20.700547v1

We are accepting applications for up to 3 Peggy Cotter Travel Awards ($1,650 each) to support early-career professionals attending ASM Microbe 2026. Apply by Feb 16, 2026 by emailing a 1-page letter to jegoff@esf.edu. ASM membership required; branch membership may be completed once that is live.

NSF seeks public input on its Fiscal Year (FY) 2026–2030 NSF Strategic Plan

NSF needs to hear from you. Among other points, I suggested: keep politics out of science; stop using the threat of cancelling scientific grants to try to control universities; increase NSF funding for fundamental research. Pls send around. Deadline is January 27. Thanks
www.nsf.gov/od/updates/n...

Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE Accurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav...

OpenFE is ready for production! chemrxiv.org/engage/chemr...

In collaboration with our industry partners, we ran benchmarking simulations of our hybrid-topology RBFE protocol on a large collection of both public and private protein-ligand binding datasets.

#compchem

CSP Functional Genomics | Joint Genome Institute The CSP Functional Genomics call is to enable users to perform state-of-the-art functional genomics research and to help them translate genomic information into biological function.

The deadline for our FY26 Functional Genomics call is 1/29/26 👀

We're seeking projects that leverage our DNA synthesis and omics capabilities to enhance understanding of gene and genome function: jointgeno.me/CSPFunctionalGenomics

@berkeleylab.lbl.gov @biosci.lbl.gov @nigelmouncey.bsky.social

NEW INTERIM USDA REGS GONNA DROP IN MARCH!!!

www.reginfo.gov/public/do/eA...

Time to leverage SynBio for tacking environmental pollution. But releasing bioengineered microorganisms still raises alarms. A new narrative is badly needed: bacteria for bioremediation are not alien intrusions but laboratory-trained extensions of life’s creativity link.springer.com/10.1038/s443...

The changing roles of Escherichia coli Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

"The changing roles of Escherichia coli" -- a short essay by yours truly.

rdcu.be/eVtXT

A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...

Confirmation of the new triage line at 65-70% of proposals. Introduction of a new “competitive but ND” class to permit exception pay pickups.

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...

Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!

Public access to the first fly connectome that spans the whole CNS - BANC!: codex.flywire.ai?dataset=banc

Different from prior connectomes - it is brain + cord (think spinal cord)

We use it to ‘embody’ the system and find it resembles ‘subsumption architecture’ doi.org/10.1101/2025...

Wilkinson Lab We discover and study reverse transcriptases

The Wilkinson Lab is open for science! @mskcancercenter.bsky.social

🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬

annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)

Hijacking a bacterial ABC transporter for genetic code expansion - Nature Bacterial ATP-binding cassette (ABC) transporters can be utilized and engineered to transport non-canonical amino acids into Escherichia coli for highly efficient synthesis of proteins with novel func...

🚨Our paper is out! 🥳
Hijacking a bacterial ABC transporter for efficient genetic code expansion.
Many congrats to everyone involved - a multi-year effort led by @taruniype.bsky.social @maxfottner.bsky.social
www.nature.com/articles/s41...

it all started years ago with a failed experiment
🧵👇 1/9

Biosecurity Really: A Strategy for Victory Current trends make clear that biosecurity will become much more challenging over the next several years. We must act strategically to secure biology—before it becomes a general-purpose technology. Dr...

The recently published report on Biosecurity by Drew Endy et al in the context of contemporary & future Biotech & SynBio is worth every word. Check it out 👉🏻 www.hoover.org/research/bio...