Molecular Systems Biology

10/2026 Issue ➡️ link.springer.com/journal/4432... proteome remodeling, RNA fragmentation dynamics, protein complex assembly buffering genetic variation, macrophage ligand detection Cover: live tumor tissue microscopy and modeling reveals collagen matrix organizes immunosuppressive myeloid cells

Scientific Editor for Molecular Systems Biology, Poonam Bheda, will be attending #LorneGenome2027 on 14–17 February in Lorne, Victoria. Connect with her at the meeting to discuss your genome science! www.lornegenome.org

9/2026 Issue ➡️ link.springer.com/journal/4432... #XLMS analysis, multi-omics integration, skeletal muscle insulin resistance, sweeteners affect gut microbes, nonenzymatic protein functions Cover: E. coli engineered to swarm in various patterns

New paper alert 🔬📣 Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation | @molsystbiol.org 🔗 doi.org/10.1038/s443...

New addition to the toolbox for multi-omics link.springer.com/article/10.1... in @molsystbiol.org available in python github.com/biocore/geme... and R microbiome.github.io/mia/referenc...

Evolutionary modeling of chemotherapy-resistant cells show combination chemo+disulfiram treatment reduces resistance more than sequential therapy ➡️ link.springer.com/article/10.1...

A tRNA/rRNA can be cleaved into different small RNAs with distinct functions depending on the cut site, yet abundance-based small RNA analysis is blind to it. Tong Zhou & us built a tool to read that hidden layer. Meet qMAP & the 'RNA fragmentome' @molsystbiol.org link.springer.com/article/10.1...

authors developed computational framework VEFill to impute missing deep mutational scanning (DMS) scores for variant effect prediction ➡️ link.springer.com/article/10.1...

7/2026 Issue ➡️ link.springer.com/journal/4432... spatially-informed RNA velocity, cell identity and metabolomics, breast cancer combination therapy, B cell differentiation #GRNs, single-cell omics ensemble learning Cover: #morphodynamic features predict epithelial fate @kuba-sedzinski.bsky.social

A lively and honest panel on funding and publishing interdisciplinary research, featuring Poonam Bheda @embopress.org @molsystbiol.org, Dario Corradini @apsphysics.bsky.social and Guntram Bauer @hfspo.bsky.social

6/2026 Issue ➡️ link.springer.com/journal/4432... plasmid-free protein engineering, #DMS analysis, microbial surface functionalization, glioma cell interactions, viral mimic evolution Cover: generative AI for antibiotic synthesis design by Jonathan Stokes and @jameszou.bsky.social labs

a modular chemical surface‑functionalization method was developed by attaching diverse azide‑tagged groups to microbes ➡️ link.springer.com/article/10.1...

5/2026 Issue ➡️ link.springer.com/journal/4432... melanoma drug response, #Parkinson's and cancer signatures, human nucleosome patterns, epigenetic changes during aging, single-cell state transitions Cover: solid and liquid biopsies capture intratumoral heterogeneity @delphine-merino.bsky.social lab

Thrilled to share this new manuscript, showcasing how genetic tags can be leveraged to map the clonal makeup of solid and liquid biopsies - opening new avenues to study DNA shedding and clonal dynamics!

authors developed a modular chemical surface‑functionalization method by attaching diverse azide‑tagged groups to microbes ➡️ link.springer.com/article/10.1...

authors developed a computational tool, State Transition Inference using Cross-cell Correlations (STICCC), to predict both net and reversible cell state transitions using a #GRN and single-cell gene expression data ➡️ link.springer.com/article/10.1...

@matemanc.bsky.social lab shows that amino acid substitutions in cancer can be grouped into five recurrent signatures, and the individual properties of these signatures can shape tumor microenvironment ➡️ link.springer.com/article/10.1...

chemical mapping generated human single-base-pair–resolution nucleosome positioning maps during interphase and metaphase, revealing widespread nucleosome repositioning at gene regulatory regions across the cell cycle ➡️ link.springer.com/article/10.1...

gene dosage is variably buffered by protein abundance in cancer, with buffering capacity linked to altered oncogenic potential and altered drug sensitivity ➡️ link.springer.com/article/10.1...

engineered chromosome fusions reveal constraints on chromosome length due to spindle axis length ➡️ link.springer.com/article/10.1...

4/2026 Issue ➡️ link.springer.com/journal/4432... chromosome length limits, infection affects human tRNAs, fitness costs to antifungal resistance, protein buffering of aneuploidy, Dictyostelid genome editing Cover: Pooled-AlphaFold3 reveals folding complexes more accurate than a pairwise approach

fitness costs are associated with acquired antifungal resistance in N. glabratus, and these trade-offs can be targeted by drugs as shown by @gabaldonlab.bsky.social ➡️ link.springer.com/article/10.1...

protein conformational changes are detected on a proteome-wide scale in live cells by LiP-MS method from @picottilab.bsky.social, which they use to show changes in biomolecular condensates upon arsenite stress ➡️ link.springer.com/article/10.1...

Our paper on disease mechanisms in synucleinopathies, led by Tetiana Serdiuk, is out at Molecular Systems Biology. #proteomics #structuralproteomics #neurodegeneration #Parkinsons #alphasynuclein #structuralbiology #ethz @imsb-eth.bsky.social @molsystbiol.org

3/2026 Issue ➡️ link.springer.com/journal/4432... genomic language models, proteomics practices, host-microbiome, bacterial tumor colonization, pooled single-cell screening, scRNA-seq clustering Cover (www.scistories.com): @picottilab.bsky.social probed in-cell protein structural changes

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