11/2025 Issue ➡️ www.embopress.org/toc/17444292... overflow metabolism, asymptomatic malaria, yeast variation, conserved PPI interfaces, persisters, base editing, immune signatures and cell patterning, viral protein structure prediction, GRN tool Cover: vascular site-specific regulatory enhancers

Explore emerging research with field leaders @keystonesymposia.bsky.social #Microbiome Metabolism & #Metabolites, this January in Banff! @molsystbiol.org scientific editor Poonam Bheda will attend. Early registration deadline is Nov 20th => keysym.us/KSMicroMetab26 #KSMicroMetab26

Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n

Now out in @molsystbiol.org www.embopress.org/doi/full/10....

10/2025 Issue ➡️ www.embopress.org/toc/17444292... reduced genomes, adaptive mutations under stress, xenobiotics and gut microbiome, DMS analysis, TF effector metabolites Cover: proteins can agglomerate with limited impact on cell by @elevylab.bsky.social

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

Our latest paper just came out in Molecular Systems Biology ! Transition between cell states of sensitivity reveals molecular vulnerability of drug-tolerant cells @molsystbiol.org www.embopress.org/doi/full/10....

🏎️ We wrote a N&Vs on the great new work from Shalev Itzkovitz lab in @molsystbiol.org. Barkai et al. calculate a turnover score and map it into spatial transcriptomics maps of intestinal tissues, informing us about dynamic biological processes in static atlases: www.embopress.org/do... 🧪

@molsystbiol.org picked a neat cover for this month's issue 🙃 - Great work from Tal Levin, Hector Garcia-Seisdedos, many more colleagues (doi.org/10.1038/s443...) and great matching cover, too!

Years ago we discovered that missense mutations in homomeric proteins often induces their supramolecular assembly, as in the 📽️👇 - Are such aberrant assemblies of *folded* proteins toxic? Surprisingly, NO. Cells are amazingly robust systems! Paper now online @molsystbiol.org doi.org/10.1038/s443...

👏 Congratulations @elevylab.bsky.social for your latest publication in @molsystbiol.org: Mutation-induced filaments of folded proteins are inert and non-toxic in a cellular system @mocel.bsky.social #UNIGE

Our study on the role of LTR5HS and SVAs in regulation of human neural crest migration is now published as peer-reviewed paper on @molsystbiol.org! Congrats to first author brilliant postdoc Laura Deelen, and all the authors involved! @imperialsci.bsky.social www.embopress.org/doi/full/10....

9/2025 Issue ➡️ www.embopress.org/toc/17444292... mutational bursts in subsets of yeast, directed evolution with optogenetics, mouse gut biosensor screening, gene program dysregulation analysis Cover: AlphaDesign to generate various protein structures, e.g. protein site-specific binders and oligomers

Identifying genes essential to survival of bacteria Mycoplasma pneumoniae – the relevant new treatment targets 📷 ‪Maria Lluch-Senar, research Samuel Miravet-Verde & Raul Burgos et al Serrano lab @crg.eu in @molsystbiol.org ➡️ bpod.org.uk/archive/2025... with @rooph.bsky.social

#ResultatScientifique 🔎 | Saviez-vous que l’IA peut aider à prévoir comment un organisme réagit à son environnement ? Des scientifiques utilisent la levure comme modèle et réussissent à prédire plus de 200 traits grâce au machine learning ✍️ @litinice.bsky.social 📕 @molsystbiol.org | buff.ly/MliXXKz

A. Mardinoglu et al. explore how AI + systems biology are transforming multi-omics integration for precision health and medicine ➡️ www.embopress.org/doi/full/10....

AlphaDesign uses hallucination + sequence generation to create diverse proteins—from monomers to oligomers to site-specific binders ➡️ www.embopress.org/doi/full/10....

generative AI model PerturbNet predicts changes in gene expression and cell state in response to unseen chemical and genetic perturbations ➡️ www.embopress.org/doi/full/10....

8/2025 Issue ➡️ www.embopress.org/toc/17444292... spatial metabolomics, protein compensation upon gene loss, ancient yeast gene family evolution, prion-like protein fibrils in the gut Cover: PerturbNet deep generative model predicts states of cells perturbed by chemicals or genetics

Excited to share the latest paper from the Riglar lab @imperialinfect.bsky.social & @crick.ac.uk. We use #synbio for biosensor discovery in our quest to build 'smart probiotics' to sense and treat disease. Well done @clare-r.bsky.social et al! Thanks to @wellcometrust.bsky.social for funding!

@skamrad.bsky.social @kiranrpatil.bsky.social show xenobiotics impact growth of gut bacteria and their metabolic homeostasis by affecting amine metabolism ➡️ www.embopress.org/doi/full/10....

@mariananatalin6.bsky.social @marcofumasoni.bsky.social show evolutionary repair in response to DNA replication stress in yeast is predictable and consistent across different environments #CompensatoryEvolution #NutrientAvailability #ReplicationStress #GxE ➡️ www.embopress.org/doi/full/10....

A bacterial synthetic memory system is used to enhance screening for new biosensors in the mouse gut by @driglar.bsky.social @clare-r.bsky.social ➡️ www.embopress.org/doi/full/10....

integrated temporally resolved transcriptomic, proteomic, and secretomic profiling of human kidney mesenchymal cells from @savitski-lab.bsky.social @saezlab.bsky.social @miraburtscher.bsky.social identify dynamic changes upon TGF-beta stimulation ➡️ www.embopress.org/doi/full/10....

Latent Graph-based individuAl Causal Effect Estimation (LaGrACE) is a new method from @benoslab.bsky.social lab to uncover gene program dysregulation and disease subtypes ➡️ www.embopress.org/doi/full/10....

OptoRep continuous directed evolution method employs an optogenetic system to evolve proteins with new essential functions from the lab of @javalospu.bsky.social ➡️ www.embopress.org/doi/full/10....

reactant and product metabolite ratios revealed metabolic pathways differences between cancer subtypes and noncancer cell lines by @hoylipidlab.bsky.social @sydneyprecisionds.bsky.social @nancyts.bsky.social ➡️ www.embopress.org/doi/full/10....

prion-like proteins in the worm gut can form amyloid fibrils and are linked to memory impairment and oxidative stress #Amyloid #Prion #Neurodegeneration #Microbiome #Gut #UABBarcelona ➡️ www.embopress.org/doi/full/10....

Enzyme kinetic data mapped onto a yeast genome-scale metabolic model reveals interactions between enzymes and metabolites/metabolic reactions ➡️ www.embopress.org/doi/full/10....

7/2025 Issue ➡️ www.embopress.org/toc/17444292... proteomics of human protein complexes and colorectal tumors, cryptic antimicrobial peptides, transferable plasmids, gene buffering, metabolic pathway crosstalk Cover (www.scistories.com): 3D genome variance between homologous heterozygous chromosomes

Incredibly proud of our latest publication in @molsystbiol.org led by @nancyts.bsky.social in collab w/ Jean Yang and Lake-Ee Quek - www.embopress.org/doi/full/10.... We curated targeted metabolomic data into pathway-centric ratios and identified subclusters of cancer cells with distinct features.

The work of brilliant PhD student @mariananatalin6.bsky.social is now out in @molsystbiol.org! We asked how nutrients shape compensatory evolution to DNA replication stress. We find changes in physiology and adaptation rates, yet core genetic adaptation remains robust! See her thread for details!👇

Big shout-out to @reviewcommons.org for finding four thorough, constructive reviewers, and to @molsystbiol.org & @embopress.org for a smooth journal transition and editorial process!

Happy to share our new comment on How #spatial #metabolomics is transforming #microbiology and gives insights into #microbe-microbe and #host-microbe interactions. #OpenAccess in @molsystbiol.org @crc1182.bsky.social @uni-kiel.de @mpimarinemicrobio.bsky.social doi.org/10.1038/s443...

#IQFPaper Mining the heparinome for cryptic antimicrobial peptides that selectively kill Gram-negative bacteria. Published in @molsystbiol.org Collaboration with #UABBarcelona @upf.edu @vallhebron.com @ciberisciii.bsky.social bit.ly/3ZxGBLi

Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes. www.embopress.org/doi/full/10....

Anjan's paper out in @molsystbiol.org. Main question: How are the molecular interaction networks inside cancer cells robust to the deletion of protein coding genes? One mechanism: increased protein abundance of a paralog (duplicate gene) www.embopress.org/doi/full/10....

6/2025 Issue ➡️ www.embopress.org/toc/17444292... spatial proteomics, metabolic reactions in coronary artery disease, gastrointestinal cancer super-enhancer, #T2D metabolic modeling Cover: resources for human solute carrier superfamily @supertifurgalab.bsky.social @giuliosupertifurga.bsky.social

Proteomics-driven subtyping of pre-metastatic colorectal cancer reveals CAVIN1 as a key player in relapse ➡️ www.embopress.org/doi/full/10....

A novel computational method for gene buffering prediction using DepMap data ➡️ www.embopress.org/doi/full/10....

A novel super-enhancer driving MYB expression identified in gastrointestinal cancers ➡️ www.embopress.org/doi/full/10....

New research reveals that metabolic reactions can amplify or buffer the impact of coronary artery disease risk alleles on susceptibility ➡️ www.embopress.org/doi/full/10....

Fabian Coscia @coscialab.bsky.social & Peter Horvath explore cutting-edge advances in spatial proteomics and highlight their translational potential in medicine ➡️ www.embopress.org/doi/full/10....

Paper(s) alert from our RESOLUTE project – In a compilation of four papers in @molsystbiol.org we show how we were deciphering cellular logistics and present a comprehensive systematic blueprint of chemical transport pathways with #SoluteCarrier transporters

A comprehensive human solute carrier (#SLC) transporter database annotating substrates, classifying SLCs, revealing potential disease associations from @supertifurgalab.bsky.social @giuliosupertifurga.bsky.social @oeaw.bsky.social ky.social @ihieurope.bsky.social ➡️ www.embopress.org/doi/full/10....

A systematic proteomics-based protein-protein interaction mapping of the human solute carrier (SLC) transporter superfamily by @supertifurgalab.bsky.social as part of @ihieurope.bsky.social ➡️ www.embopress.org/doi/full/10....

@kaletalab.bsky.social lab metabolic model reveals diminished exchange of nutrients between host and gut microbiome in diabetes with more competition in microbial communities upon elevated glucose ➡️ www.embopress.org/doi/full/10....

1/5 🎉 Excited to share our new paper on genome-scale metabolic modeling of the gut microbiome in type 2 diabetes! Huge thanks to former Postdoc Samer Kadibalban and the whole team for driving this work. www.embopress.org/doi/full/10....

ER+ breast cancer resistance is associated with a shift towards ERBB growth factor mediated proliferation and away from estrogen signaling ➡️ www.embopress.org/doi/full/10....

A bacterial metacommunity model predicted that reducing spatial entropy increased plasmid transfer, validated in heterogeneous E. coli populations and antibiotic resistance gene data in low-entropy environment microbes ➡️ www.embopress.org/doi/full/10....