iiinova — where your digital self keeps evolving

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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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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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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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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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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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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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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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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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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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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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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Molecular Systems Biology @molsystbiol.org · 08/08/2025

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....

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Molecular Systems Biology @molsystbiol.org · 08/08/2025

AlphaDesign uses hallucination + sequence generation to create diverse proteins—from monomers to oligomers to site-specific binders ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 04/08/2025

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....

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Molecular Systems Biology @molsystbiol.org · 04/08/2025

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

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

@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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

@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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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....

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Molecular Systems Biology @molsystbiol.org · 03/07/2025

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

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Molecular Systems Biology @molsystbiol.org · 03/06/2025

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

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Molecular Systems Biology @molsystbiol.org · 19/05/2025

Proteomics-driven subtyping of pre-metastatic colorectal cancer reveals CAVIN1 as a key player in relapse ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 19/05/2025

A novel computational method for gene buffering prediction using DepMap data ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 19/05/2025

A novel super-enhancer driving MYB expression identified in gastrointestinal cancers ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 19/05/2025

New research reveals that metabolic reactions can amplify or buffer the impact of coronary artery disease risk alleles on susceptibility ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 19/05/2025

Fabian Coscia @coscialab.bsky.social & Peter Horvath explore cutting-edge advances in spatial proteomics and highlight their translational potential in medicine ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 15/05/2025

A comprehensive human solute carrier (#SLC) transporter database annotating substrates, classifying SLCs, revealing potential disease associations from @supertifurgalab.bsky.social @giuliosupertifurga.bsky.social @oeaw.bsky.social ky.social @ihieurope.bsky.social ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 15/05/2025

A systematic proteomics-based protein-protein interaction mapping of the human solute carrier (SLC) transporter superfamily by @supertifurgalab.bsky.social as part of @ihieurope.bsky.social ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 15/05/2025

@kaletalab.bsky.social lab metabolic model reveals diminished exchange of nutrients between host and gut microbiome in diabetes with more competition in microbial communities upon elevated glucose ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 15/05/2025

ER+ breast cancer resistance is associated with a shift towards ERBB growth factor mediated proliferation and away from estrogen signaling ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 15/05/2025

A bacterial metacommunity model predicted that reducing spatial entropy increased plasmid transfer, validated in heterogeneous E. coli populations and antibiotic resistance gene data in low-entropy environment microbes ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 15/05/2025

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

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Molecular Systems Biology @molsystbiol.org · 08/05/2025

A model for distinguishing between adaptive and non-adaptive explanations for multiple isoforms of a gene ➡️ www.embopress.org/doi/full/10....

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