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

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

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...

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...

link.springer.com

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...

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...

link.springer.com

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...

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...

link.springer.com

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 · 9mo ago

Researchers 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 · 9mo ago

Our 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 · 9mo ago

Our 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