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...
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.
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
#Microbiome and #Metabolism are among key areas of interest across @embopress.org journals. Contact us if you are attending the meeting and interested in discussing with scientific editor Poonam Bheda from @molsystbiol.org.
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
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... 🧪
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.
@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....
