Evolutionary modeling of chemotherapy-resistant cells show combination chemo+disulfiram treatment reduces resistance more than sequential therapy ➡️ link.springer.com/article/10.1...
Molecular Systems Biology
@molsystbiol.org
#OpenAccess @embopress.org journal publishing pioneering research in systems & synthetic biology, systems medicine
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...
qMAP decodes RNA fragmentation dynamics in development and disease - Molecular Systems Biology
Noncanonical small RNAs, such as tRNA-derived (tsRNAs) and rRNA-derived (rsRNAs) fragments, are more abundant than microRNAs and arise from selective cleavage events rather than random degradation. Wh...
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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!
ONJ Cancer Research Institute@onjcri.org.au · 6mo agoResearchers from ONJCRI, WEHI and Peter Mac have discovered that DNA barcoding can be used to track cancer cells in solid and liquid biopsies. In a world-first, the team were able to detect the DNA barcodes shed by the primary tumour in plasma samples. ➡️ https://ow.ly/fcK550Yc0WN
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
Máté Manczinger@matemanc.bsky.social · 6mo agoOur new paper is out: Five dominant amino acid substitution signatures shape tumour immunity link.springer.com/article/10.1... Thread 🧵⬇ #cancer #tumor #immunity #immunotherapy #oncology
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
Máté Manczinger@matemanc.bsky.social · 6mo agoOur new paper is out: Five dominant amino acid substitution signatures shape tumour immunity link.springer.com/article/10.1... Thread 🧵⬇ #cancer #tumor #immunity #immunotherapy #oncology
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 🧪
Overflow metabolism in bacterial, yeast, and mammalian cells: different names, same game | Molecular Systems Biology
EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.
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Molecular Systems Biology@molsystbiol.org · 9mo ago11/2025 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
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...
Multimodal AI agents for capturing and sharing proteomics laboratory practice - Molecular Systems Biology
Molecular Systems Biology - A multimodal AI laboratory agent was developed to capture and communicate proteomics experimental practices by linking written protocols with hands-on laboratory work...
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Mann Lab@mannlab.bsky.social · 10mo agoHow much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google. Preprint: www.biorxiv.org/content/10.1... @patiskowronek.bsky.social explains👇