Sign in

Stefan O. Bassler

@stefanbassler.bsky.social
516 followers 1.3K following 6 posts

Evolutionary Systems Biology of Aging, @typaslab.bsky.social @embl.org PhD & Bridging Excellence Postdoc (LifeScienceAlliance) with @petrovadmitri.bsky.social & Steinmetz lab @stanford.edu and Aulehla lab @embl.org

PostsRepliesMedia
Reposted by Stefan O. Bassler
Mark Bitter @markcbitter.bsky.social · 01/10/2026
New Perspective w/ @petrovadmitri.bsky.social and Paul Schmidt! We ask what evolution-in-action studies tell us about an old question: what genetic variation matters for fitness, and what maintains it? ecoevorxiv.org/repository/v...
ecoevorxiv.org
Common, consequential, and actively maintained: a neo-balance view of genetic variation
14528
Reposted by Stefan O. Bassler
Kate Baker @ksbakes.bsky.social · 25/09/2026
We have an open Assistant/Associate Professor position in Pathogen Biology at the Department of Genetics - come and join us! 🦠 🧫 🧬https://www.cam.ac.uk/jobs/assistantassociate-professor-in-pathogen-genetics-pc51175
cam.ac.uk
Assistant/Associate Professor in Pathogen Genetics
Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...
03970
Reposted by Stefan O. Bassler
Sasha (Alexandra) Khristich @khristich.bsky.social · 22/09/2026
I’m excited to share our preprint with @oliviamghosh.bsky.social, where we explore what it takes to ‘win’ in long-term evolutionary competition: www.biorxiv.org/content/10.1...
biorxiv.org
Adaptive evolution can overwrite initial natural fitness variation only in highest-fitness yeast isolates
The fitness of an organism determines its likelihood of succeeding in short-term competition, but many other factors can influence its long-term success. In this study, we investigate the relative con...
13929
Reposted by Stefan O. Bassler
EMBL @embl.org · 15/09/2026
Scientists have determined the highest-resolution protein structure obtained to date. Using advanced X-ray crystallography techniques at EMBL Hamburg's P14 beamline, the team solved the structure of an archaeal protein at an astonishing 0.43 Ångström resolution. www.embl.org/news/science...
embl.org
Every electron counts: most detailed protein structure to date revealed | EMBL
Researchers have used advanced X-ray crystallography methods to determine the structure of an archaeal protein at unprecedented resolution
0237
Reposted by Stefan O. Bassler
Bernard Kim @bernardkim.bsky.social · 15/09/2026
Princeton EEB is running a very broad faculty search at the Assistant Professor level. Please consider applying to join us! This is a wonderful, collaborative, cohesive department with diverse interests and amazing colleagues. apply.interfolio.com/193474
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
099104
Reposted by Stefan O. Bassler
Karen Shih @karenyshih.bsky.social · 28/08/2026
Really excited to share that work from my PhD is now on bioRxiv! We ask: Is the transcriptional response to high tumor mutational burden (TMB) consistent across cancers, or does it vary by cancer type? www.biorxiv.org/content/10.6...
biorxiv.org
Transcriptional Response to Tumor Mutational Burden Is Consistent Across Cancer Types
Tumor mutational burden (TMB) shapes tumor transcriptional state, but studies typically describe this response as an average effect pooled across cancer types. Whether that average reflects a consiste...
2106
Reposted by Stefan O. Bassler
Savitski Lab @savitski-lab.bsky.social · 20/08/2026
1/5 How much phosphorylation can a single kinase deposit? In our new study with @typaslab.bsky.social out in @nature.com, phage T7's kinase (T7K) modifies almost all the E. coli proteome + more densely than all ~500 kinases do our own proteomes 🤯 www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
58733
Reposted by Stefan O. Bassler
EMBL @embl.org · 20/08/2026
A single phage enzyme can target thousands of bacterial proteins, shutting down host defences, a new EMBL study shows. The study provides novel insights into bacteria-virus interactions and opens up new possibilities for bioengineering for phage therapy. www.embl.org/news/science...
Illustration depicting how T7 kinase, a phage enzyme, modifies many proteins inside an infected bacterium, helping shut down its defence mechanisms. Credit: Daniela Velasco/EMBL
2216
Reposted by Stefan O. Bassler
Typas Lab @typaslab.bsky.social · 20/08/2026
Excited to share our paper with @savitski-lab.bsky.social, led by @tarabartolec.bsky.social, Karin Mitosch & Clément Potel, out now in @nature.com. We show that T7 phage broadly disables bacterial defenses using a unique ‘loose cannon’ protein kinase. www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
47739
Reposted by Stefan O. Bassler
Typas Lab @typaslab.bsky.social · 10/08/2026
Join us at EMBL Heidelberg from 8–10 Dec 2026 for the conference “Gut Microbe Function” and explore the latest advances in the field. Submit your abstract, register, and join the discussion! 📝Abstract deadline 15 Sep 2026 📍On-site registration deadline 27 Oct 2026 www.embl.org/about/info/c...
embl.org
Unlocking the functional diversity of gut microbiomes
0125
Reposted by Stefan O. Bassler
Typas Lab @typaslab.bsky.social · 29/04/2026
Check our new preprint by Knopp M. et al.! Human gut microbiomes can impose strong +/- selection for resistant versions of resident opportunistic pathogens. In the case we follow up, selection is driven by altered carbohydrate utilisation that the resistant mutant evolves. doi.org/10.64898/202...
doi.org
12917
Reposted by Stefan O. Bassler
Savitski Lab @savitski-lab.bsky.social · 11/02/2026
Rewiring of oncogenic signaling in #DrugResistance is a moving target. In our new study, we used biophysical phosphoproteomics to investigate #BRAF mutant cancer, linking phosphorylation changes to protein function and #MolecularMechanisms through #Multi-Omics integration. tinyurl.com/funsignaling
13113
Reposted by Stefan O. Bassler
Mateus lab @mateuslab.com · 08/08/2026
Bolor's paper is now out! Read the final story here: www.nature.com/articles/s41... See below 👇 for the main highlights
nature.com
Systematic profiling of growth interactions in human gut microbiome species - Nature Communications
Here, Buyanbadrakh et al. systematically map growth interactions among gut bacteria, revealing predominantly inhibitory effects, and identifying extracellular vesicles and pH modulation as mechanisms ...
23411
Reposted by Stefan O. Bassler
Mateus lab @mateuslab.com · 22/12/2025
New preprint from the lab is out! 🥳 We systematically profiled all pairwise growth interactions between 36 representative human gut microbiome strains, and delved deeper into the molecular mechanisms behind specific growth interactions. www.biorxiv.org/content/10.6... 👇
biorxiv.org
Systematic profiling of growth interactions in human gut microbiome species
Microbial interactions shape the composition and stability of the human gut microbiome. Yet, the molecular mechanisms underlying these relationships remain poorly understood. Here, we systematically p...
11813
Reposted by Stefan O. Bassler
Miki Ebisuya @ebisuyamiki.bsky.social · 13/08/2026
New paper from the lab! authors.elsevier.com/sd/article/S... We find that protein degradation is broadly slower in human segmentation clock cells than in mouse cells, regardless of the degradation pathway or protein category! 1/
authors.elsevier.com
Systematic differences in protein stability underlie species-specific developmental tempo
Human embryonic development proceeds more slowly than in mice. The segmentation clock offers a tractable model for studying species-specific developme…
49127
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 23/07/2026
I am very excited about a new paper from our lab by @nicole-nova.bsky.social and @kasolari.bsky.social on the persistence of CDV in wild populations. Our first foray into evolution and ecology of infectious disease. 1/n
153
Reposted by Stefan O. Bassler
Nicole Nova @nicole-nova.bsky.social · 23/07/2026
A fundamental question in disease ecology remains unresolved: How can an acute, immunizing virus persist in nature? Theory says viruses like measles need huge pools of susceptible hosts. Our new preprint offers an answer. www.biorxiv.org/content/10.6...
biorxiv.org
Persistent, Multi-Species Outbreaks and Long-Range Transmissions of a Measles-Like Virus
Canine distemper\---|a measles-like disease with high mortality and presently without a cure\---|poses a major threat to wild and domestic carnivores globally. Domestic dogs are generally considered t...
12114
Reposted by Stefan O. Bassler
Jesse Engreitz @jengreitz.bsky.social · 15/07/2026
An encyclopedia of enhancer-gene regulatory interactions — online today! nature.com/articles/s4158… Now with an improved model, expanded maps across 1400+ biosamples, larger validation CRISPR datasets, and guidance on applying the model 1/
nature.com
12911
Reposted by Stefan O. Bassler
Jesse Engreitz @jengreitz.bsky.social · 19/09/2025
New preprint from our lab! What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells? Find out here: www.biorxiv.org/content/10.1... 👇 1/
bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq
16018
Reposted by Stefan O. Bassler
Andreas Gschwind @argschwind.bsky.social · 15/07/2026
Thrilled to share that our ENCODE enhancer–gene mapping paper is now out in Nature! An encyclopedia of human enhancer–gene regulatory interactions: www.nature.com/articles/s41... Thread 👇 1/
nature.com
An encyclopedia of human enhancer–gene regulatory interactions - Nature
An encyclopedia of more than 92 million enhancer–gene regulatory interactions created as part of the ENCODE4 project provides a valuable resource for future studies of gene regulation and human geneti...
18041
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 15/07/2026
Cannot be more excited about the lineup for the inaugural Function of Evolving Systems GRC conference I am co-organizing with the amazing Joy Bergelson. Less than a month away: August 9 - 14, 2026. Still a few spots left! And do check out the amazing list of speakers: www.grc.org/function-of-...
grc.org
2026 Function of Evolving Systems Conference GRC
The 2026 Gordon Research Conference on Function of Evolving Systems will be held in Waterville Valley, New Hampshire. Apply today to reserve your spot.
43926
Reposted by Stefan O. Bassler
Tadashi Fukami @fukamit.bsky.social · 18/06/2026
Mountain lion and trophic cascades at Jasper Ridge Biological Preserve ('Ootchamin 'Ooyakma) in California news.stanford.edu/stories/2026...
1102
Reposted by Stefan O. Bassler
Typas Lab @typaslab.bsky.social · 12/03/2026
How can we tap into the enormous functional diversity of microbes on this planet? Join us at EMBL Heidelberg (8–10 Dec 2026) to learn about ongoing efforts to decode gene function and organisation in human gut microbes, and present your science.
13829
Reposted by Stefan O. Bassler
Max-Planck-Gesellschaft @maxplanck.de · 01/04/2026
Neue #Antibiotika werden für den Kampf gegen resistente Krankheitserreger dringend gebraucht. Helge Bode und Tobias Erb vom Max-Planck-Institut für terrestrische Mikrobiologie haben neue Wege gefunden, diese schneller über molekulare Fertigungsstraßen herzustellen www.mpg.de/26296724/neu... #Medizin
mpg.de
Neue Antibiotika wie am Fließband
Helge Bode und Tobias Erb vom Max-Planck-Institut für terrestrische Mikrobiologie haben neue Wege gefunden, Peptide für die Medizin herzustellen
0123
Reposted by Stefan O. Bassler
European Research Council (ERC) @erc.europa.eu · 01/04/2026
How do trees build the molecules they need to grow? ERC-funded research led by Wout Boerjan at VIB is mapping metabolic pathways in poplar trees using large-scale genetic and chemical analysis. 👉 t.co/PG1QIYRfQv #PlantScience
091
Reposted by Stefan O. Bassler
Olivia Ghosh @oliviamghosh.bsky.social · 30/03/2026
Really excited that this major work from my PhD is finally published in @plosbiology.org ! In it, we were trying to tackle a fundamental question in evolution - how do genetic mutations map onto evolutionary fitness? (1/n) journals.plos.org/plosbiology/...
journals.plos.org
Genotype-fitness mapping of adaptive mutants reveals shifting low-dimensional structure across divergent environments
Predicting the effect of a genetic mutation on fitness is a major challenge in evolutionary biology. This study uses fitness effects of a large collection of adaptive yeast mutants in multiple lab env...
28339
Reposted by Stefan O. Bassler
Maria Bernabeu @mariabernabeu.bsky.social · 07/08/2025
We are happy to show one ourt first exciting papers. We have developed a blood-brain barrier model to study the disruptive effects caused by the malaria parasite, Plasmodium falciparum. First, congratulations to the fearless @liviapiatti.bsky.social and @alinabatzi.bsky.social rdcu.be/ezBl7
rdcu.be
Plasmodium falciparum egress disrupts endothelial junctions and activates JAK-STAT signaling in a microvascular 3D blood-brain barrier model
Nature Communications - Here the authors show that Plasmodium falciparum egress products disrupt endothelial barrier and activate JAK-STAT and interferon type response in a 3D blood-brain barrier...
27222
Reposted by Stefan O. Bassler
James Hemker @jahemker.bsky.social · 11/03/2026
Proud that this work is now published! We hope it helps orient future #Nanopore long-read sequencing studies hunting for structural variants Also really happy to share eight new high-coverage (>100x) long-read read pools and assemblies with the #Drosophila community! doi.org/10.1093/g3jo...
doi.org
Manual validation finds ultra-long-read sequencing best enables faithful, population-level structural variant calling in Drosophila melanogaster euchromatin with nanopore
Abstract. The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of popul
04121
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 11/03/2026
Very proud of this contribution. Beautiful and hyper careful work by @jahemker.bsky.social showing that not all long read assembles are created equal and at times it really does matter to have enough not just long but very long reads. Curious what you all think!
0174
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 06/03/2026
Very proud of this paper, now officially out at PRX LIFE journals.aps.org/prxlife/abst.... Here @mrazo.bsky.social shows that geometry-aware autoencoder architecture can discover low dimensional phenotypic spaces traversed by evolution. 1/2
scholar.google.com
1197
Reposted by Stefan O. Bassler
Joao Pedro Magalhaes @jpsenescence.bsky.social · 06/03/2026
Excited to share our new preprint on multi-omics signatures of accelerated PhenoAge. By integrating plasma proteomics and metabolomics, we identified pathways associated with faster aging, including immune-inflammatory activity. www.medrxiv.org/content/10.6...
medrxiv.org
Integrative Proteomic and Metabolomic Signatures of Accelerated PhenoAge in the UK Biobank
Aging is accompanied by molecular changes across multiple biological systems that contribute to functional decline and increased disease risk, but the underlying mechanisms and inter-individual variat...
073
Reposted by Stefan O. Bassler
EMBL @embl.org · 05/03/2026
Is the linear map of cell signaling a myth? New research suggests the reality of cellular networks is more complex. @savitski-lab.bsky.social & @saezlab.bsky.social combined experimental and computational expertise to test how we map kinase–substrate interactions. www.nature.com/articles/s41...
nature.com
Benchmarking EGF signaling pathway inference using phosphoproteomics and kinase-substrate interactions - Nature Communications
To what extent can large-scale approaches accurately reconstruct classic signaling pathways? Here, authors revisit the EGF pathway using phosphoproteomics and kinase-substrate interactions
0104
Reposted by Stefan O. Bassler
allen institute @alleninstitute.org · 25/02/2026
Applications for our Next Generation Leaders program are open! For 3 years, accepted early career scientists will join a supportive network and contribute to our research initiatives. Apply by Mar. 31: bit.ly/3OjzdRa 📸 Photo by NGL Alum @bjmarlin.bsky.social
0114
Stefan O. Bassler @stefanbassler.bsky.social · 23/02/2026
The increased mutation rate of DNA-repair–deficient mutators accelerates resistance evolution in bacteria and cancer. In a great collaboration with @mulkern.bsky.social, we find that DNA-damaging antibiotics can turn this advantage into a liability—but only for certain genotypes.
1125
Reposted by Stefan O. Bassler
Helmholtz-Zentrum für Infektionsforschung (HZI) @helmholtzhzi.bsky.social · 20/02/2026
Are you a game changer in infection research? Apply for a HUMAN junior research group leader position (with professorship and tenure options) at the HZI by March 30! Infection Biology: jobs.helmholtz-hzi.de/job/Braunsch... AI in Health and Infection Research: jobs.helmholtz-hzi.de/job/Braunsch...
Text: We seek: Game changers in infection research; Human Microbe Alliance for Universal Health (HUMAN) program; in the background a night sky with a shooting star and an electron micrograph of different bacteria
054
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 19/02/2026
The next BAPG has been announced! April 11 at Davis organized by the inimitable @jrossibarra.bsky.social! bapg-conference.github.io
bapg-conference.github.io
BAPG Spring 2026
Bay Area Population Genomics Conference
02114
Reposted by Stefan O. Bassler
EMBL @embl.org · 19/02/2026
EMBL International PhD Programme - summer recruitment 2026! 👀 Research groups across EMBL are recruiting now! www.embl.org/about/info/e... Don’t miss this opportunity to receive dedicated mentoring while doing interdisciplinary research.
01213
Reposted by Stefan O. Bassler
Helmholtz-Zentrum für Infektionsforschung (HZI) @helmholtzhzi.bsky.social · 29/01/2026
Join the HZI as a Junior Research Group Leader at @helmholtz-hiri.bsky.social or @helmholtzhips.bsky.social! We’re seeking exceptional postdocs for the @helmholtz.de Investigator Groups program. Shape cutting-edge research in infection biology & apply by Feb 15! jobs.helmholtz-hzi.de/job/Saarbr%C...
Call for the position as Helmholtz Junior Research Group Leaders at the Helmholtz Institute for RNA-based Infection Research or Helmholtz Institute for Pharmaceutical Research Saarland
21110
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 29/01/2026
Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social
grc.org
14839
Reposted by Stefan O. Bassler
Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut @leibnizfli.bsky.social · 16/01/2026
📢 Prof. Dr. Dmitri Petrov from the School of Humanities and Science | Department of Biology, Stanford University, will give a lecture on “Barcoding Fitness Landscapes of Tumorigenesis” at the @leibnizfli.bsky.social on January 22, 2026. 👉 More information: bit.ly/4pGtqSu
022
Reposted by Stefan O. Bassler
Leibniz-Institut für Alternsforschung - Fritz-Lipmann-Institut @leibnizfli.bsky.social · 22/01/2026
➡️ Prof. Dr. Dmitri Petrov from the School of Humanities and Science | Department of Biology, Stanford University, spoke today at the @leibnizfli.bsky.social about “Barcoding Fitness Landscapes of Tumorigenesis”. Before he gave his lecture, we had the opportunity to interview him. 🎤 bit.ly/4r66mxG
youtu.be
Interview with Prof. Dr. Dmitri Petrov
YouTube video by Leibniz-Institut für Alternsforschung - FLI e.V.
022
Reposted by Stefan O. Bassler
Emma Dann @emmamarydann.bsky.social · 05/01/2026
Together with @ronghuizhu.bsky.social, we are thrilled to present our new perturb-seq study of 22M primary CD4+ T cells, across donors and timepoints – the result of a decade-long collaboration between the Marson @marsonlab.bsky.social and Pritchard @jkpritch.bsky.social labs 🧵 tinyurl.com/gwt2025
tinyurl.com
Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits
Gene regulatory networks encode the fundamental logic of cellular functions, but systematic network mapping remains challenging, especially in cell states relevant to human biology and disease. Here, ...
26529
Reposted by Stefan O. Bassler
Maerkl Lab @maerkl-lab.bsky.social · 18/12/2025
Saeed's latest paper is now out on bioRxiv: "PURE makes PURE: reconstitution of the PURE cell-free system from self-synthesized non-ribosomal proteins" www.biorxiv.org/content/10.6...
biorxiv.org
PURE makes PURE: reconstitution of the PURE cell-free system from self-synthesized non-ribosomal proteins
Building a universal biochemical constructor, an autonomously self-replicating biochemical system, is a major challenge in synthetic biology. The PURE cell-free system is an ideal starting point for e...
041
Reposted by Stefan O. Bassler
José Aguilar-Rodríguez @jaguilarrod.bsky.social · 05/12/2025
Excited to co-organize with @weieli.bsky.social a symposium at SMBE 2026 on how synthetic & systems biology can illuminate the molecular mechanisms of evolution. Honored to have @christianlandry.bsky.social as invited speaker! Join us!
1147
Reposted by Stefan O. Bassler
Jana Helsen @helsenjana.bsky.social · 26/11/2025
How do new centromeres evolve while staying compatible with the division machinery? Discover it in our new Nature paper! We show centromeres transition gradually via a mix of drift, selection, and sex, reaching new states that still work with the kinetochore. 👉 doi.org/10.1038/s41586-025-09779-1
818584
Reposted by Stefan O. Bassler
Sophie Jean Walton @sophiejwalton.bsky.social · 11/11/2025
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...
biorxiv.org
310949
Reposted by Stefan O. Bassler
Dmitri Petrov @petrovadmitri.bsky.social · 20/10/2025
For population genetics and evolutionary biology folks in the Bay Area: the next BAPG will be hosted by Stanford CEHG and the Petrov lab at Stanford on 12/6. Registration is free but required. The deadline for talk submission is Nov. 16. Hope to see you soon! Pls RT! docs.google.com/forms/d/e/1F...
docs.google.com
14031
Reposted by Stefan O. Bassler
Christophe Dessimoz @dessimoz.bsky.social · 23/10/2025
Job alert🚨📢! Join us as Director of the SIB Centre for Pathogen Bioinformatics, on a topic where global collaboration is particularly important, in a highly stimulating environment. This is a research infrastructure leadership position. Apply or spread the word! apply.refline.ch/499599/0346/...
apply.refline.ch
Director, Center for Pathogen Bioinformatics
The Centre for Pathogen Bioinformatics (CPB) is a unit of SIB which offers expertise and services in pathogen bioinformatics, computational molecular epidemiology and related multi-site project manage...
0716
Reposted by Stefan O. Bassler
José Aguilar-Rodríguez @jaguilarrod.bsky.social · 22/10/2025
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...
biorxiv.org
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
516884