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Molecular Systems Biology

@molsystbiol.org
733 followers 362 following 82 posts

#OpenAccess @embopress.org journal publishing pioneering research in systems & synthetic biology, systems medicine

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Molecular Systems Biology @molsystbiol.org · 11/09/2026
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
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Dr Hannah Tompkins @hetompkins.bsky.social · 24/07/2026
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...
link.springer.com
Extracellular matrix phenotyping by imaging mass cytometry defines distinct cellular matrix environments associated with allergic airway inflammation - Molecular Systems Biology
The extracellular matrix (ECM) forms the scaffold in which cells reside and interact. The composition of this scaffold guides the development of local immune responses and tissue function. With the ad...
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Cameron Martino @cameronmartino.bsky.social · 18/08/2026
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...
link.springer.com
Joint-RPCA: domain-aware multi-omics integration for systems microbiology - Molecular Systems Biology
Integrating multi-omics data is essential for microbiome research, as microbial communities are shaped by and respond to interdependent processes, including taxonomic composition, metabolite productio...
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Molecular Systems Biology @molsystbiol.org · 24/07/2026
Evolutionary modeling of chemotherapy-resistant cells show combination chemo+disulfiram treatment reduces resistance more than sequential therapy ➡️ link.springer.com/article/10.1...
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Qi Chen @qichen-lab.bsky.social · 20/07/2026
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...
link.springer.com
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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Molecular Systems Biology @molsystbiol.org · 14/07/2026
authors developed computational framework VEFill to impute missing deep mutational scanning (DMS) scores for variant effect prediction ➡️ link.springer.com/article/10.1...
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Molecular Systems Biology @molsystbiol.org · 03/07/2026
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
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Marco Fumasoni @marcofumasoni.bsky.social · 12/06/2026
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
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Molecular Systems Biology @molsystbiol.org · 12/06/2026
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
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Molecular Systems Biology @molsystbiol.org · 03/06/2026
a modular chemical surface‑functionalization method was developed by attaching diverse azide‑tagged groups to microbes ➡️ link.springer.com/article/10.1...
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Molecular Systems Biology @molsystbiol.org · 05/05/2026
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
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Delphine Merino @delphine-merino.bsky.social · 12/02/2026
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!
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Molecular Systems Biology @molsystbiol.org · 24/04/2026
authors developed a modular chemical surface‑functionalization method by attaching diverse azide‑tagged groups to microbes ➡️ link.springer.com/article/10.1...
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Molecular Systems Biology @molsystbiol.org · 22/04/2026
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...
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Molecular Systems Biology @molsystbiol.org · 21/04/2026
@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...
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Molecular Systems Biology @molsystbiol.org · 20/04/2026
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...
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Molecular Systems Biology @molsystbiol.org · 17/04/2026
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...
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Molecular Systems Biology @molsystbiol.org · 17/04/2026
engineered chromosome fusions reveal constraints on chromosome length due to spindle axis length ➡️ link.springer.com/article/10.1...
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Molecular Systems Biology @molsystbiol.org · 17/04/2026
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
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Molecular Systems Biology @molsystbiol.org · 24/03/2026
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...
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Molecular Systems Biology @molsystbiol.org · 24/03/2026
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...
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Picotti Lab @picottilab.bsky.social · 17/03/2026
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
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Molecular Systems Biology @molsystbiol.org · 06/03/2026
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
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Oded Rechavi @odedrechavi.bsky.social · 26/02/2026
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 👇👇👇🔥).
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Csaba Pal Laboratory @csabapallab.bsky.social · 05/02/2026
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
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Elvin Maharramov @m-elvin.bsky.social · 10/02/2026
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
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Molecular Systems Biology @molsystbiol.org · 03/02/2026
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...
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Molecular Systems Biology @molsystbiol.org · 03/02/2026
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
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Comparative genomics group IRB-BSC Barcelona (PI: Toni Gabaldón) @gabaldonlab.bsky.social · 18/01/2026
📣 #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...
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Fran Supek @fransupek.bsky.social · 02/02/2026
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...
Figure 1: Data modalities of genomic language models. From review article "The DNA dialect: a comprehensive guide to pretrained genomic language models" by Veiner and Supek.
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Molecular Systems Biology @molsystbiol.org · 19/12/2025
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
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Rahul K @theresearch.bsky.social · 07/11/2025
On overflow #metabolism 🧪
embopress.org
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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Mann Lab @mannlab.bsky.social · 16/12/2025
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...
link.springer.com
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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Amir Mitchell @amitchell.bsky.social · 17/12/2025
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...
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Molecular Systems Biology @molsystbiol.org · 17/11/2025
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
keysym.us
Microbiome Metabolism and Metabolites: Discovery and Function in Health and Disease | Keystone Symposia
Join us at the Keystone Symposia on Microbiome Metabolism and Metabolites: Discovery and Function in Health and Disease, January 2026, in Banff, with field leaders!
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Molecular Systems Biology @molsystbiol.org · 07/11/2025
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
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EMBO Press @embopress.org · 23/10/2025
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
keysym.us
Microbiome Metabolism and Metabolites: Discovery and Function in Health and Disease | Keystone Symposia
Join us at the Keystone Symposia on Microbiome Metabolism and Metabolites: Discovery and Function in Health and Disease, January 2026, in Banff, with field leaders!
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Grosshans Lab @labgrosshans.bsky.social · 10/10/2025
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
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Ozren Bogdanovic @obog.bsky.social · 14/10/2025
Now out in @molsystbiol.org www.embopress.org/doi/full/10....
embopress.org
A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation | Molecular Systems Biology
imageimageA multiomics study of zebrafish spermatogenesis integrating scRNA-seq, scATAC-seq, and base-resolution DNA methylomes defines the chromatin and transcriptional states of germ cells, revealin...
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Molecular Systems Biology @molsystbiol.org · 07/10/2025
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
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Joe Grove @grovearmada.bsky.social · 26/09/2025
🚨 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 🧪 🦠
viro3d.cvr.gla.ac.uk
Viro3D
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Jeremie Roux @jrxlab.bsky.social · 01/10/2025
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....
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Adlung Lab @adlunglab.com · 03/10/2025
🏎️ 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... 🧪
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Emmanuel Levy's lab @elevylab.bsky.social · 05/10/2025
@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!
This month's cover highlights the article Mutation-induced filaments of folded proteins are inert and non-toxic in a cellular system by Emmanuel Levy, Hector Garcia-Seisdedos and colleagues. Yeast cells harboring mutation-induced filaments of folded proteins or “agglomerates”. The filaments appear large and disruptive, but surprisingly, Levin et al. reveal they are largely inert and non-toxic, unlike aggregates of misfolded proteins.
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Emmanuel Levy's lab @elevylab.bsky.social · 16/09/2025
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...
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Biology-UNIGE @biology-unige.bsky.social · 17/09/2025
👏 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
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Marco Trizzino @marcotrizzino.bsky.social · 22/09/2025
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....
embopress.org
Hominoid-specific transposable elements reshaped neural crest migration in craniofacial development | Molecular Systems Biology
imageimageHominoid-specific transposable elements function as enhancers in cranial neural crest cells, fine-tuning gene expression and migration. Their activity may underlie regulatory innovations in ...
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Molecular Systems Biology @molsystbiol.org · 08/09/2025
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
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Biomedical Picture of the Day BPoD @bpodaily.bsky.social · 29/08/2025
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
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CNRS Biologie @cnrsbiologie.bsky.social · 01/09/2025
#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
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