Theoretical Biophysics

Magnetotactic bacteria optimally navigate natural pore networks Diverse magnetotactic bacteria are adapted to the local geomagnetic field and grain size to maximize their swimming speed through the pore space.

Magnetotactic bacteria swim along geomagnetic field lines to navigate sediments. Using microfluidics and simulations, this study shows their motility is optimised, revealing how evolution fine-tunes life for challenging environments.

Dynamic Gene Regulatory Network Inference with Interpretable, Biophysically-Motivated Neural ODEs
doi.org/10.1101/2025...

Deciphering Global Patterns of Marine Microbial Community Assembly and Network Stability https://www.biorxiv.org/content/10.1101/2025.09.19.677047v1

🚨Starting in 30 minutes (Friday 12/09 15:30 EU), Susann Müller (UFZ Leipzig) will present the talk

Ecological forces dictate microbial community assembly processes in bioreactor systems

at the Population Dynamics Seminars. Subscription sites.google.com/view/popdyn/

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism Transcription factors (TFs) may activate or repress gene expression through an interplay of different mechanisms, including RNA polymerase (RNAP) recruitment, exclusion, and initiation. However, depen...

E. coli transcription factors regulate promoter activity by a universal, homeostatic mechanism | Science www.science.org/doi/10.1126/...

🚨 PopDyn is back! Tomorrow, Friday 12/09 15:30 EU, Susann Müller (UFZ Leipzig) will present the talk

Ecological forces dictate microbial community assembly processes in bioreactor systems

at the Population Dynamics Seminars. Subscription sites.google.com/view/popdyn/

The 2026 Complexity Postdoctoral Fellowships applications are open, offering early-career scholars intellectual freedom, transdisciplinary collaboration with leading researchers, and a competitive salary with research and collaboration funds.

Deadline: Oct 1, 2025
Apply: santafe.edu/sfifellowship

Ilya Nemenman, Pankaj Mehta: Randomness with constraints: constructing minimal models for high-dimensional biology https://arxiv.org/abs/2509.03765 https://arxiv.org/pdf/2509.03765 https://arxiv.org/html/2509.03765

Please repost!

We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky

University Lecturer in Biostatistics University Lecturer in Biostatistics

We are recruiting‼️A permanent university lecturer position in BIOSTATISTICS is available at @helsinki.fi Faculty of Biological and Environmental Sciences. Great colleagues, excellent infrastructures and startup support 🙌🏻
DL 14 September

jobs.helsinki.fi/job/Helsinki...

Happy to see this paper finally out in @pnas.org!

#phage #microbiology #MicroSky #VirEvol 🦠 🧫 🔬

Gift link: www.pnas.org/eprint/YYDZ9...

Disentangling the cost of gene expression
doi.org/10.21203/rs....

🚨 Friday 12/09 15:30 EU, Susann Müller (UFZ Leipzig) will present the talk

Ecological forces dictate microbial community assembly processes in bioreactor systems

at the Population Dynamics Seminars. Subscription sites.google.com/view/popdyn/

Another #preprint: "Elasticity and plasticity of epithelial gap closure", from the #PhD work of Maryam Setoudeh:

arxiv.org/abs/2509.05110

This one required a lot of (I think) beautiful #mechanics!

@mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social

closing at the end of this week!

We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!

Nonlinear memory in cell-division dynamics across species | PNAS Regulation of cell growth and division is essential to achieve cell-size homeostasis. Recent advances in imaging technologies, such as “mother mach...

Nonlinear memory in cell-division dynamics across species

#PNAS by Shijie Zhang, Chenyi Fei, and Jörn Dunkel

www.pnas.org/doi/10.1073/...

How did differentiation evolve to allow for complex multicellular systems? In this @cp-trendsecolevo.bsky.social‬ paper, Boolean networks are used to answer long-standing questions in the evolution of cell type diversity. @wcratcliff.bsky.social d1wqtxts1xzle7.cloudfront.net/115269531/j....

Höllring, K., Nuić, L., Rogić, L., ..., Hubert, M., & Smith, A. S. (2024). Capturing the mechanosensitivity of cell proliferation in models of epithelium. Proceedings of the National Academy of Sciences of the United States of America, 121(45), e2308126121. #EpithelialMechanics
buff.ly/cCmDwwk

Modeling predicts that metabolic diversity increases the ecological impacts of weapon gene transfer. Modeling scenarios for each column are shown across the top row. Bottom row: Example dynamics of the strains (attacker, target, transconjugant) during a contest using parameters that correspond to the cross (X) shown in the parameter sweeps directly below.

#Bacteria use weapons to outcompete rivals, but what happens if they're transferred? @prokaryota.bsky.social @jdpal.bsky.social &co show that HGT of toxin #plasmids is rare but recipients can thrive under relaxed nutrient competition, reshaping bacterial warfare @plosbiology.org 🧪 plos.io/43vC3X7

Structuring complexity by mapping the possible in microbial ecosystems

-in Current Opinion in Microbiology from @dbajic.bsky.social

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

🚨 New call for preLighters!🚨

Help us highlight the most exciting biological #preprints. Share your insights, build your profile, and be part of a supportive community! 🌍

Interested? Apply today & help shape the future of science publishing! 📢

More info: prelights.biologists.com/news/join-th...

PMMH seminar.
Friday 05/09 at 11:00 in the meeting room
You may also watch on Zoom (link upon request).

Irène Nagle of TU Delft, Netherlands

Mechanics of collagen networks with active cellular inclusions

Quantification and Determination of Compatible Bacterial Consortia This study presents a mathematical model to identify compatible bacterial consortia by analysing antagonistic and coexistence relationships. Introducing the Bacterial Coexistence Index (BCI), it eval....

Quantification and Determination of Compatible Bacterial Consortia

in #MicrobialBiotech

enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....

mvif season 5 keynotes

Season 5 is going to start 🔜

Check out the program and
feel free to join the keynotes by presenting your work–abstract submission is open www.microbiome-vif.org/en-US/-/info...

@kathlemon.bsky.social ‬ @saramitri.bsky.social @simrouxvirus.bsky.social @halllab.bsky.social @deepaagashe.bsky.social

Bayesian parameter inference for epithelial mechanics Cell-based mechanical models, such as the Cell Vertex Model (CVM), have proven useful for studying the mechanical control of epithelial tissue dynamic…

Link to her first first-author paper, Bayesian Parameter Inference for Epithelial Mechanics: www.sciencedirect.com/science/arti...

GitHub - Sugimuralab/BayesianForceInference_GoogleColab Contribute to Sugimuralab/BayesianForceInference_GoogleColab development by creating an account on GitHub.

Bayesian Force Inference is now on GitHub!
Together with GetVertex, an ImageJ/Fiji plugin for extracting input data from skeletonized images, this enables code-free quantification of forces during epithelial development.
github.com/Sugimuralab/...

Decoding how higher-order network interactions shape contagion dynamics - Journal of Mathematical Biology Complex contagion models that involve contagion along higher-order structures, such as simplicial complexes and hypergraphs, yield new classes of mean-field models. Interestingly, the differential equ...

Fun collaborative project with Istvan Z. Kiss (London) and Peter Simon to understand how higher-order interactions affect the dynamics of contagion processes now out in J Math Bio: doi.org/10.1007/s002...

Striatal Gradient in Value-Decay Explains Regional Differences in Dopamine Patterns and Reinforcement Learning Computations Dopamine has been suggested to encode reward-prediction-error (RPE) in reinforcement learning (RL) theory but also shown to exhibit heterogeneous patterns depending on regions and conditions: some exh...

This paper in J Neuroscience provides evidence that some of the heterogeneity in dopamine signals in the striatum is related to value decay - interesting idea, I hadn't encountered this before:

www.jneurosci.org/content/45/3...

🧠📈 🧪 #NeuroAI

Beneath the surface of the sum When genetic interactions matter and when they don't

I wrote about gene-gene interactions (epistasis) and the implications for heritability, trait definitions, natural selection, and therapeutic interventions. Biology is clearly full of causal interactions, so why don't we see them in the data? A 🧵: