Reposted by Akos NyergesJase Gehring @skyjase.bsky.social · 19/09/2026My friends started Novome. The story of their clinical failure is fascinating. Immediately what I thought about at the top of Akos‘ thread. Cool stuff 021
Akos Nyerges @akosnyerges.bsky.social · 19/09/2026Proud and excited to share our first preprint 🚀 in which we • create a high-fitness firewalled organism, • that stably colonizes the mouse gut for >100 days, • resists all tested phages in the gut, • and blocks horizontal gene transfer. + A new method: Chimera genomes to tailor existing synthetic 33315
Reposted by Akos NyergesVictor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 07/09/2026If we keep on advocating the benefits of Eng Microbes for Env Release with the same arguments that we had for 50 yr, no wonder we will also get the same social backlash. A new narrative is badly needed focused on partnership & stewardship—not just containment & control dx.doi.org/10.1111/1751...dx.doi.orgEnvironmental Release of Genetically Intervened Microorganisms: Towards a New NarrativeFrom control to partnership: Rethinking the environmental release of laboratory-trained microorganisms for bioremediation. 0114
Akos Nyerges @akosnyerges.bsky.social · 24/07/2026careers.harvard.edu/job/research...careers.harvard.eduResearch Assistant I 000
Reposted by Akos NyergesbioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 17/07/2026Synthesis of Ultra-Large Fibrous Proteins from Bacteria via a Looped-Translation System www.biorxiv.org/content/10.64898/20… 032
Reposted by Akos NyergesManuel Kleiner @manuelkleiner.bsky.social · 10/07/2026The type and amount of bacterial DNA carried by virus-like particles in the gut microbiome is simply mind-boggling. Amazing work by PhD candidate Jessie Maier in my group and collaborators @duerkoplab.bsky.social and Ben Callahan www.biorxiv.org/content/10.6...biorxiv.orgPerturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiomeHorizontal gene transfer (HGT) is a driving force in microbial evolution that allows community members to rapidly evolve to cope with environmental stressors and competition. Despite the importance of... 13516
Reposted by Akos NyergesVivek Mutalik @vivekmutalik.bsky.social · 27/06/2026New preprint!! 🎉 A cool collaborative work with @copabio.bsky.social and Chase Beisel teams on the phage editing technology. @sarshad.bsky.social led the work from our side to validate & characterize the lib. #phage #phagesky www.biorxiv.org/content/10.6... Work supported by: phagefoundry.orgbiorxiv.orgTargeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomesGenetic manipulation of bacteriophages is essential for interrogating phage biology and advancing antimicrobial therapies. However, current genome editing approaches can be inefficient, require multip... 14914
Reposted by Akos NyergesMichael Baym @baym.lol · 25/06/2026Latest work from my lab, in which @amycrobes.bsky.social probes the evolutionary consequences of prophages potentiating death at otherwise sublethal antibiotic doses 25021
Reposted by Akos NyergesJames Lloyd 🧬 @jamespblloyd.bsky.social · 23/06/2026Recording the codons of E. coli might not be as simple or uneventful as one might imagine Probing the limits of genetic recoding using multi-omics-guided evolution www.nature.com/articles/s41...nature.comProbing the limits of genetic recoding using multi-omics-guided evolution - Nature CommunicationsCodon recoding is often lethal for microbes, and how recoding impacts fitness remains poorly explored. Here the authors construct six partially recoded E. coli strains bearing up to 45% of a synthetic... 011
Akos Nyerges @akosnyerges.bsky.social · 18/06/2026I'm hiring a research tech soon for my lab at Harvard Med, starting this fall. We'll work on designing microbes and proteins with New-to-Nature functions. Ideal for a recent grad seeking hands-on research & opportunity to publish before PhD. Job ad soon. Reposts much appreciated! 210
Reposted by Akos NyergesKamila Naxerova @naxerova.bsky.social · 16/06/2026Please join us in NH (perfect place to be in August!) for this inspiring conference organized by @petrovadmitri.bsky.social and Joy Bergelson. Very interdisciplinary, so I look forward to learning tons of new concepts. www.grc.org/function-of-...grc.orgFunction of Evolving Systems - Gordon Research ConferencesGRC presents Function of Evolving Systems, a conference on . 064
Akos Nyerges @akosnyerges.bsky.social · 04/06/2026Generating E. coli 0.5 controlled by a half-sized genome www.biorxiv.org/content/10.6...biorxiv.org 010
Reposted by Akos NyergesbioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 01/06/2026Thousandfold Expansion Microscopy www.biorxiv.org/content/10.64898/20… 011
Reposted by Akos NyergesbioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 26/05/2026Artificial initiation codons and engineered initiator tRNAs enable N-terminal noncanonical amino acid incorporation in intact cell-free translation systems www.biorxiv.org/content/10.64898/20… 011
Reposted by Akos NyergesDr Kathleen Millen @neurodevkathy.bsky.social · 20/05/2026🚨🧪🧵URGENT INPUT NEEDED: NIH asks input for next strategic plan-including emphasis on non-animal models (NAMs) to replace animals. Per NIH insider, anti-animal responses now outnumber scientists 200-700x. Please please provide input. Deadline: May 26, 11:59 PM ET. grants.nih.gov/news-events/...grants.nih.govNIH Seeks Input on Framework for Next NIH-Wide Strategic Plan | Grants & Funding 45996
Reposted by Akos NyergesMolly Schumer @mollyschumer.bsky.social · 12/05/2026Do you know any students who are planning to apply to graduate school this cycle? Encourage them to apply to the Biology Preview Program! We provide intensive workshops to help students w/ their applications + 1:1 mentorship. 14759
Reposted by Akos NyergesRicard Solé @ricardsole.bsky.social · 12/05/2026Can engineered mirror life become a threat to humans or the biosphere itself? Despite some recent claims, a life form created in the test tube may be doomed to fail when confronted with established ecosystems. Check our new paper where we do the maths. www.biorxiv.org/content/10.6... 12913
Reposted by Akos NyergesOpenBind @openbind.bsky.social · 06/05/2026#OpenBind announces its first data drop marking a major milestone for AI‑Enabled #DrugDiscovery! It’s the first initiative to generate open, AI‑ready datasets for protein–drug complexes, produced continuously & at industrial scale to enable the next generation of #AI models. loom.ly/eIrsqqg 1168
Reposted by Akos NyergesRichard Lenski @relenski.bsky.social · 01/05/2026The Barrick & Lenski Labs in Dept of Microbiology, Genetics, & Immunology at Michigan State Univ seek a Research Assistant II to manage their research operations and participate in projects related to microbial evolution and synthetic biology. See details below. careers.msu.edu/jobs/researc...careers.msu.eduResearch Assistant II - East Lansing, Michigan, United StatesPosition Summary The Barrick and Lenski Labs in the Department of Microbiology, Genetics, & Immunology at Michigan State University are seeking a Research Assistant II to manage their research ope... 03555
Reposted by Akos NyergesDavid Bikard @dbikard.bsky.social · 17/04/2026Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social ! 08236
Reposted by Akos NyergesXiaojing Gao @synbiogaolab.bsky.social · 18/04/2026Don't feel bad about missing the mSBW abstract deadline. We have extended it! We also keep the registration fee affordable ($150 for students) so that mammalian synbio-curious trainees can check it out, especially if you are in the Atlanta area. Meeting link below: 111
Reposted by Akos NyergesVivek Mutalik @vivekmutalik.bsky.social · 21/03/2026Excited to share this review🔔, we spent sometime thinking about phage–microbiome–immune–oncology axis for phage therapy in cancer! #phage #phagesky Phage therapy in oncology: opportunities for cancer prevention and treatment: Trends in Molecular Medicine www.cell.com/trends/molec...cell.comPhage therapy in oncology: opportunities for cancer prevention and treatmentBacteriophages (phages) are emerging as programmable biological therapeutics in oncology, extending beyond their traditional antimicrobial applications. This review proposes a phage–microbiome–immune–... 0116
Reposted by Akos NyergesAI x Bio Discovery @aixbiobot.bsky.social · 19/03/2026RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols [new] identifies ORFs recovering protocol biases and codon-level occupancy from Ribo-seq data to adjust profiles. 011
Reposted by Akos NyergesJason Stajich @hyphaltip.bsky.social · 15/03/2026www.simonsfoundation.org/grant/pivot-... - a terrific opportunity for a cross-disciplinary focused postdoc trainingsimonsfoundation.orgPivot FellowshipPivot Fellowship on Simons Foundation 068
Reposted by Akos NyergesVivek Mutalik @vivekmutalik.bsky.social · 15/03/2026New 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 36232
Reposted by Akos NyergesNick Polizzi @nickpolizzi.bsky.social · 11/03/2026Our 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...rdcu.beAF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2Nature 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,... 16921
Reposted by Akos NyergesMart Krupovic @mkrupovic.bsky.social · 03/03/2026With 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 5250106
Reposted by Akos NyergesRichard Lenski @relenski.bsky.social · 24/02/2026Happy 38th birthday to the #LTEE! #BOTD in 1988. Keep on evolving! #science #evolution #microbiology 418645
Reposted by Akos NyergesNick Polizzi @nickpolizzi.bsky.social · 20/02/2026I’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. 11113
Reposted by Akos NyergesJeremy Baskin @jeremybaskin.bsky.social · 15/02/2026And 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...elifesciences.orgBarcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencingSAVEMONEY is a computational tool that guides users to mix plasmids prior to nanopore sequencing, reducing the effective cost of whole-plasmid sequencing to below that of Sanger sequencing. 810234
Reposted by Akos NyergesDi Jiang @dijiang319.bsky.social · 14/02/2026@science.org Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation | Science www.science.org/doi/10.1126/...science.orgMechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptationTranscriptional 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... 13812
Reposted by Akos NyergesNature Microbiology @natmicrobiol.nature.com · 07/02/2026#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...nature.comFecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial - Nature MedicineIn 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... 0134
Reposted by Akos NyergesbioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 07/02/2026A 28-year evolution experiment on Burkholderia pseudomallei survival in nutrient-depleted sterile water www.biorxiv.org/content/10.64898/20… 0145
Reposted by Akos NyergesVictor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 06/02/2026Feel like doing a SynBio PhD in Spain? Check this offer, many fellowships available 👉🏻 lifehub.csic.es/synbio-cofund/ 02021
Reposted by Akos NyergesDavid Bikard @dbikard.bsky.social · 28/01/2026🚨 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...research.pasteur.frPostdoctoral position - Synthetic Biology / Bacterial Immunity - ResearchThe 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... 07481
Reposted by Akos NyergesVictor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 27/01/2026How 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/...journals.asm.orgThe disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe | mBioNames 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... 23314
Reposted by Akos NyergesSudarshan Pinglay @sudpinglay.bsky.social · 23/01/2026Happy 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...sciencedirect.comMammalian genome writing: Unlocking new length scales for genome engineeringThe ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab… 2219
Reposted by Akos NyergesbioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 21/01/2026Expanding the Genetic Code of an Animal with Two Non-Canonical Amino Acids www.biorxiv.org/content/10.64898/20… 042
Reposted by Akos NyergesCNY ASM @cnyasm.bsky.social · 19/01/2026We 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. 11122
Reposted by Akos NyergesPam Ronald @pcronald.bsky.social · 17/01/2026NSF 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...nsf.govNSF seeks public input on its Fiscal Year (FY) 2026–2030 NSF Strategic Plan 16756
Reposted by Akos NyergesOpen Free Energy @openfree.energy · 18/12/2025OpenFE 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. #compchemchemrxiv.orgLarge-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFEAccurately measuring compound binding affinities is key to driving the pharmaceutical development process. Rigorous physics-based in silico approaches, particularly alchemical free energy methods, hav... 1178
Reposted by Akos NyergesJoint Genome Institute @jgi.doe.gov · 08/01/2026The 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 jgi.doe.govCSP Functional Genomics | Joint Genome InstituteThe 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. 021
Reposted by Akos NyergesSebastian S. Cocioba @atinygreencell.bsky.social · 04/01/2026NEW INTERIM USDA REGS GONNA DROP IN MARCH!!! www.reginfo.gov/public/do/eA... 061
Reposted by Akos NyergesVictor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 03/01/2026Time 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... 2116
Reposted by Akos NyergesRichard Lenski @relenski.bsky.social · 19/12/2025"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXTrdcu.beThe changing roles of Escherichia coliNature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways. 116359
Reposted by Akos NyergesCarl Zimmer @carlzimmer.com · 06/12/2025A 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...doi.orgRedirecting 4130971251
Reposted by Akos NyergesDrug Monkey @drugmonkey.bsky.social · 24/11/2025Confirmation of the new triage line at 65-70% of proposals. Introduction of a new “competitive but ND” class to permit exception pay pickups. 42921
Reposted by Akos NyergesMichael Baym @baym.lol · 20/11/2025Hot 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/...science.orgIntracellular competition shapes plasmid population dynamicsFrom populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g... 11437199
Reposted by Akos NyergesMichael Baym @baym.lol · 20/11/2025Brand 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! 26328
Reposted by Akos NyergesAlexander Shakeel Bates @asbates.bsky.social · 02/08/2025Public 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... 38835