It’s finally out! Together with @embopress.org and @reviewcommons.org, we conducted a structured side-by-side comparison of human peer review and our AI scientific review (see thread 👇👇👇🔥).

Excited to share our collaborative work led by the Szilvia Juhasz and Mate Manczinger @matemanc.bsky.social labs: #cancer mutations converge into five protein-level “fingerprints” that shape tumor immune visibility. Mutation burden alone fails to predict #immunotherapy response! @molsystbiol.org

Great work from the Juhasz and Manczinger @matemanc.bsky.social labs! This study reveals five protein-level mutation “fingerprints” that influence tumor immune visibility, beyond mutation burden alone. #Cancer #Immunotherapy @molsystbiol.org

iPS2-seq is a clone-aware platform for #singlecell loss-of-function screening in #hiPSCs and derivatives including #organoids, here revealing SMAD2 role in cardiac progenitor specification from @berterolab.bsky.social @mendjanlab.bsky.social #functionalgenomics ➡️ link.springer.com/article/10.1...

2/2026 Issue ➡️ link.springer.com/journal/4432... expansion microscopy, spatial omics and gene networks, cell population control by cell cycle, #IBD heterogeneity, aging monkey lipid signatures Cover: single-cell loss-of-function screening in human pluripotent stem cells from @berterolab.bsky.social

📣 #paper "Uncovering actionable trade-offs of antifungal resistance in a yeast pathogen" Check out our new publication in @molsystbiol.org where we systematically map stress-related trade-off associated with drug resistance in Candida glabrata (N. glabratus) link.springer.com/article/10.1...

On the heels of the release of #AlphaGenome, we have written up a review on 🧬genomic language models for DNA/RNA, out in EMBO @molsystbiol.org journal 🔖"The DNA dialect: a comprehensive guide to pretrained genomic language models" by Marcell Veiner👏 & yours truly👇 link.springer.com/article/10.1...

12/2025 Issue ➡️ link.springer.com/journal/4432... MSB 20th anniversary editorial, transposable elements in human craniofacial development, engineered paediatric tumor models, personalized signalling models, and more Cover (www.scistories.com): ancestry shapes prostate tumour methylation patterns

On overflow #metabolism 🧪

We can know more than we can tell, but now Al can capture it. Our multimodal agent analyzes lab videos to generate protocols & catch common lab errors. Preserving tacit knowledge in proteomics. Now in @molsystbiol.org @patiskowronek.bsky.social #Google link.springer.com/10.1038/s443...

We just published in @molsystbiol.org with the Mugler lab (UPitt) on bacterial population dynamics during tumor colonization (mouse model). Our study was guided by a Luria–Delbrück-style idea: infer mechanism from statistics (1/7) 🧪🦠 doi.org/10.1038/s443...

Early Registration deadline Nov 20th for @keystonesymposia.bsky.social #Microbiome Metabolism & #Metabolites, joint with Human #Microbiome, Jan 19-23 in Banff! See upcoming deadlines: keysym.us/KSMicroMetab26 keysym.us/KSMicrobiome26 #KSMicroMetab26 #KSMicrobiome26

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