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Aida Abiad, Alex Arenas, Ágnes Backhausz, József Balogh, Christopher R S Banerji, Sergio Barbarossa, Ginestra Bianconi, Christian Bick, Magnus Botnan, Timoteo Carletti, Lucia Cavallaro, Andrea Civilini, Tina Eliassi-Rad, Xue Gong, Krystal Guo, Heather A Harrington, Jürgen Jost, P L Krapivsky, Pietro Liò, Ben D MacArthur, Carolina Mattsson, Pedro A M Mediano, Ana P Millan, Raffaella Mulas, Alice Patania, Giovanni Petri, Cerene Rathilal, Rubén J Sánchez-García, Martina Scolamiero, Michael T Schaub, Hanlin Sun, Yu Tian, Francesco Vaccarino, Kelin Xia
Hypergraphs and simplicial complexes in focus: a roadmap for future research in higher-order interactions.
J Phys Complex, 7(2) Art. No. 022501 (2026)
Open Access Source   

Higher-order interactions are increasingly being recognized as fundamental to our understanding of complex systems, networks, and the development of the next generation of AI algorithms. However, modeling higher-order interactions requires us to go beyond graphs and networks, which can only encode pairwise interactions, and so demands a new theory. Hypergraphs and simplicial complexes (also called higher-order networks), which arise as natural mathematical representations of higher-order complex systems, are therefore attracting increasing attention. The mathematics of higher-order networks is already providing important insights, yet many fundamental mathematical questions remain unsolved; for instance, in spectral graph theory, discrete topology, and higher-order network dynamics. This roadmap summarizes the scientific discussions that took place on these topics between pure mathematicians, theoretical physicists, computer and network scientists at the Newton Institute Satellite meeting on 'Hypergraphs: Theory and Applications'. We survey the current state-of-the-art in higher-order network research, and propose some trajectories for future research, including in areas such as extremal and spectral hypergraph theory, discrete topology, higher-order dynamics, higher-order machine learning, and applications in the brain and social sciences.
@article{Abiad9217,
author={Aida Abiad, Alex Arenas, Ágnes Backhausz, József Balogh, Christopher R S Banerji, Sergio Barbarossa, Ginestra Bianconi, Christian Bick, Magnus Botnan, Timoteo Carletti, Lucia Cavallaro, Andrea Civilini, Tina Eliassi-Rad, Xue Gong, Krystal Guo, Heather A Harrington, Jürgen Jost, P L Krapivsky, Pietro Liò, Ben D MacArthur, Carolina Mattsson, Pedro A M Mediano, Ana P Millan, Raffaella Mulas, Alice Patania, Giovanni Petri, Cerene Rathilal, Rubén J Sánchez-García, Martina Scolamiero, Michael T Schaub, Hanlin Sun, Yu Tian, Francesco Vaccarino, Kelin Xia},
title={Hypergraphs and simplicial complexes in focus: a roadmap for future research in higher-order interactions.},
journal ={Journal of physics: Complexity},
volume={7},
issue ={2},
pages={1--1},
year=2026
}

Janek Weißpflog, Christine Steinbach, Frank Simon, Michaela Yuan, Urska Repnik, Simona Schwarz
Synergistic iron ion and sulfate removal via chitosan-engineered yeast biosorbents.
Bioresour Technol, 449 Art. No. 134343 (2026)
PubMed Source   

The sustainable removal of iron ions (Fe2+/3+) and sulfate (SO42-) from contaminated water remains a major challenge, particularly in mining-affected regions such as Lusatia (Germany), where both contaminants frequently co-occur at elevated levels. Here, a dual-modification strategy based on chitosan (Cs)-modified yeast cells (Cs@YC) and chitin-glucan complexes (CGC), is presented to enhance biosorption performance. Dried Cs@YC showed improved adsorption capacities compared to unmodified YC, while the combined Cs-functionalized CGC (Cs@CGC) exhibited the highest uptake capacities, reaching 2.09 mmol g-1 for Fe2+/3+ and 0.79 mmol g-1 for SO42- at pH 6. Microscopic and spectroscopic analyses (SEM-EDX, TEM, AFM, XPS) showed that Cs surface functionalization combined with alkaline-induced CGC restructuring increases the density and accessibility of amino and hydroxyl groups and promotes controlled iron (oxyhydr)oxide nucleation and crystallization. Equilibrium modelling using Langmuir, Freundlich, and Sips isotherms demonstrated that Cs@YC provides high-affinity metal-binding sites with positively charged surface domains that facilitate electrostatic association and adsorption of SO42-. To the best of our knowledge, this is the first study to demonstrate the synergistic interaction between Cs modification and CGC-based structural tuning in yeast-derived biosorbents for dual Fe2+/3+/SO42- remediation. The results demonstrate that Cs@YC offers promising adsorption performance under controlled laboratory conditions, warranting further evaluation in real mining-affected waters containing competing ions and organic matter.
@article{Weißpflog9181,
author={Janek Weißpflog, Christine Steinbach, Frank Simon, Michaela Yuan, Urska Repnik, Simona Schwarz},
title={Synergistic iron ion and sulfate removal via chitosan-engineered yeast biosorbents.},
journal ={Bioresource technology},
volume={449},
pages={null--null},
year=2026
}

Richard Culliford, Charlie Mills, Daniel Chubb, Ben Kinnersley, Amit Sud, Alex J Cornish, Lisa Browning, Samuel E D Lawrence, Robert Bentham, Anna Frangou, Andreas J Gruber, Kevin Litchfield, David C Wedge, James Larkin, Samra Turajlic, Richard S Houlston
Contrasting Features of Papillary and Chromophobe Renal Cell Carcinoma Revealed by Whole-Genome Sequencing.
Mol Cancer Res, 24(5) 327-336 (2026)
Open Access PubMed Source   

The identification of cancer drivers is a cornerstone to the delivery of precision oncology. So far, sequencing of renal cell cancer (RCC) has largely been confined to the clear cell subtype of RCC. In contrast, sequencing analyses of the less common forms of RCC, papillary RCC (pRCC) and chromophobe RCC (ChRCC), have so far been limited. We analyzed whole-genome sequencing data on 164 tumor-normal pairs from the Genomics England 100,000 Genomes Project, providing a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genomic features, including mutational signatures, intratumor heterogeneity, and analysis of extrachromosomal DNA formation. Our research establishes correlations between genomic alterations and histologic diversification and the extent to which genetically-mediated immune escape contributes to the development of these RCC subtypes.
@article{Culliford9128,
author={Richard Culliford, Charlie Mills, Daniel Chubb, Ben Kinnersley, Amit Sud, Alex J Cornish, Lisa Browning, Samuel E D Lawrence, Robert Bentham, Anna Frangou, Andreas J Gruber, Kevin Litchfield, David C Wedge, James Larkin, Samra Turajlic, Richard S Houlston},
title={Contrasting Features of Papillary and Chromophobe Renal Cell Carcinoma Revealed by Whole-Genome Sequencing.},
journal ={Molecular cancer research : MCR},
volume={24},
issue ={5},
pages={327--336},
year=2026
}

Aswin Vinod Muthachikavil, Alexander von Appen, Thomas D Kühne
Computational Characterization of the Role of LEM2/LaminA Interactions on the Stability of BAF-Dimer Using Molecular Simulations.
Proteins, 94(5) 1104-1114 (2026)
Open Access PubMed Source   

The effect of the presence of the BAF-binding LEM-domain and LaminA Ig-fold on the stability of the BAF dimer was studied qualitatively using non-equilibrium pull simulations and quantitatively through the calculation of the potential of mean force profile along BAF-BAF separation distance. We find that hydrophobicity plays a significant role in stabilizing the BAF dimer when LEM-domain and LaminA are bound. The role of LEM-domain and LaminA in stabilizing the BAF dimer is explored by quantifying the strength of interaction between them, which are critical components of the nuclear lamina.
@article{Muthachikavil9104,
author={Aswin Vinod Muthachikavil, Alexander von Appen, Thomas D Kühne},
title={Computational Characterization of the Role of LEM2/LaminA Interactions on the Stability of BAF-Dimer Using Molecular Simulations.},
journal ={Proteins},
volume={94},
issue ={5},
pages={1104--1114},
year=2026
}

Anna Shevchenko, Archishman Ghosh, Andrea Schuhmann, Aliona Bogdanova, Henrik Thomas, Viditha Rao, Eric R Geertsma, T-Y Dora Tang#, Andrej Shevchenko#
Absolute quantification of fluorescent protein fusions by mass spectrometry.
Protein Sci, 35(5) Art. No. doi: 10.1002/pro.70556 (2026)
Open Access PubMed Source   

Fusions with fluorescent proteins (FPs) play a pivotal role in experimental biology because of their sensitive and spatially precise visualization by spectroscopy. However, observed fluorescence is not always proportional to their molar concentration. Only a fraction of the fusion protein that contains the mature fluorescence chromophore is detectable by spectroscopy and there is no accurate and generic method for estimating its molar abundance. We have developed a fluorescence-independent mass spectrometry-based method for absolute (molar) sub-femtomole quantification of FP-fusions that also estimates the fraction of fully matured chromophore. The method exploits an isotopically labeled 68 kDa recombinant protein standard expressed in E. coli and used without further purification. This chimeric protein contains multiple peptide proxies for six prototypical FPs (mCherry, mScarlet-I, mKate2, EGFP, mNeonGreen, and Dendra2) and two self-labelling (Halo- and SNAP-) tags and supports the quantification of proteins fused to any of 615 common FPs and tags. The method can be used broadly for the absolute quantification of fluorescent fusions in vivo and in vitro and is complementary to fluorescence measurements. We further combined mass spectrometry with fluorescence spectroscopy to study expression kinetics of FP fusions in cell-free systems. Molar concentrations of the expressed fusion, its fraction with mature chromophore, and of the fluorescing protein were integrated into a mathematical model to obtain kinetic rates of translation, chromophore maturation, and folding.
@article{Shevchenko9205,
author={Anna Shevchenko, Archishman Ghosh, Andrea Schuhmann, Aliona Bogdanova, Henrik Thomas, Viditha Rao, Eric R Geertsma, T-Y Dora Tang, Andrej Shevchenko},
title={Absolute quantification of fluorescent protein fusions by mass spectrometry.},
journal ={Protein science : a publication of the Protein Society},
volume={35},
issue ={5},
pages={1--1},
year=2026
}

Jan Peychl, Chiara Rossi, Nathalie Aulner, Audrey Salles, Nadia Halidi, Melinda Elaine Brunstein, Adeline Mallet, Karin Aumayr, Jean-Marc Verbavatz, Thomas Heuser, Rachel Santarella-Mellwig, Aurélien Dauphin, Eef Parthoens, Manuel Gunkel, Martin Fritsch, Sebastian T. Bundschuh, Rym Chaabouni, Agnes Uhereczky, Erin M Tranfield, Pablo Hernández Varas, Sebastian Munck, Core4Life Consortium
Stress and conflict management in core facilities-News from an imaging survey.
J Microsc, Art. No. doi: 10.1111/jmi.70102 (2026)
Open Access PubMed Source   

While conflict management is a well-known challenge for people working in the service sector, this topic remains largely unexplored in scientific imaging core facilities, despite frequent interactions with diverse users in environments with complex service demands. To address this gap, we conducted a survey to assess staff experiences, challenges, and the availability of institutional support. The 38-question survey, completed anonymously, covered three areas: (1) respondent background; (2) assessment of stress in core facilities and coping mechanisms and stress management resources; and (3) work environment challenges such as user interactions and overall work atmosphere. The results highlight the need for more awareness, targeted training, and organisational strategies to improve staff well-being and foster a collaborative work culture. By raising awareness and providing actionable insights, we aim to inform best practices for conflict de-escalation and, when necessary, conflict management in research infrastructure settings. While exemplified with scientific imaging facilities, we believe our survey results are easily transferable to other scientific cores and infrastructures with similar service and user interactions. In addition, the dataset is available to other researchers on figshare. Information concerning the data records, usage notes, code availability, and technical validation is presented.
@article{Peychl9221,
author={Jan Peychl, Chiara Rossi, Nathalie Aulner, Audrey Salles, Nadia Halidi, Melinda Elaine Brunstein, Adeline Mallet, Karin Aumayr, Jean-Marc Verbavatz, Thomas Heuser, Rachel Santarella-Mellwig, Aurélien Dauphin, Eef Parthoens, Manuel Gunkel, Martin Fritsch, Sebastian T. Bundschuh, Rym Chaabouni, Agnes Uhereczky, Erin M Tranfield, Pablo Hernández Varas, Sebastian Munck, Core4Life Consortium},
title={Stress and conflict management in core facilities-News from an imaging survey.},
journal ={Journal of microscopy},
volume={},
pages={1--1},
year=2026
}

Hiroyuki Uechi, Daxiao Sun, Yuki Saeki, Tetsuya Hiraiwa, Alf Honigmann, Anthony Hyman, Erina Kuranaga
A conserved motif tunes Sidekick condensate dynamics to control tricellular junction recruitment during epithelial remodeling.
Cell Rep, 45(5) Art. No. 117336 (2026)
Open Access PubMed Source   

The tricellular junction, where three or more cells contact, comprises specific proteins regulating epithelial morphogenesis and homeostasis. It remains elusive how these proteins are confined to tricellular junctions to function. We reveal that the intracellular domain of the adhesive transmembrane protein Sidekick forms condensates and contributes to its accumulation at tricellular junctions. Fly genetics and in vitro reconstitution indicate that condensation alone is not sufficient for targeting but promotes stable accumulation of Sidekick at physiological concentrations. We identify a conserved motif whose deletion increases condensate dynamics and leads to mislocalization of Sidekick during epithelial junction remodeling. Mislocalization is accompanied by disturbed recruitment of Sidekick-associating proteins involved in junction dynamics to tricellular junctions and leads to delay in junction formation. These findings suggest that condensates with relatively low internal dynamics stabilize Sidekick localization under tissue dynamics, which assists recruitment of junction dynamics-regulating proteins and ensures epithelial remodeling.
@article{Uechi9220,
author={Hiroyuki Uechi, Daxiao Sun, Yuki Saeki, Tetsuya Hiraiwa, Alf Honigmann, Anthony Hyman, Erina Kuranaga},
title={A conserved motif tunes Sidekick condensate dynamics to control tricellular junction recruitment during epithelial remodeling.},
journal ={Cell reports},
volume={45},
issue ={5},
pages={null--null},
year=2026
}

Dominik Sturm*, Hiba Bensalem*, Ivo F. Sbalzarini
Spatially Informed Autoencoders for Interpretable Visual Representation Learning.
In: International Conference on Learning Representations (ICLR) (2026), Appleton WI, ICLR (2026), 1-35
Open Access   Source Full Text   

We introduce spatially informed variational autoencoders (SI-VAE) as self-supervised deep-learning models that use stochastic point processes to predict spatial organization patterns from images. Existing approaches to learning visual representations based on variational autoencoders (VAE) struggle to capture spatial correlations between objects or events, focusing instead on pixel intensities. We address this limitation by incorporating a point-process likelihood, derived from the Papangelou conditional intensity, as a self-supervision target. This results in a hybrid model that learns statistically interpretable representations of spatial localization patterns and enables zero-shot conditional simulation directly from images. Experiments with synthetic images show that SI-VAE improve the classification accuracy of attractive, repulsive, and uncorrelated point patterns from 48% (VAE) to over 80% in the worst case and 90% in the best case, while generalizing to unseen data. We apply SI-VAE to a real-world microscopy data set, demonstrating its use for studying the spatial organization of proteins in human cells and for using the representations in downstream statistical analysis.
@proceedings{Sturm9155,
title = {Spatially Informed Autoencoders for Interpretable Visual Representation Learning.},
year = 2026,
editor = {Dominik Sturm, Hiba Bensalem, Ivo F. Sbalzarini},
volume = {International Conference on Learning Representations (ICLR)},
series = {},
publisher = {ICLR}
}

Clemens Kirschbaum#, Hjoerdis Mathilda Lennartz, Katelyn C Cook, Kristin Böhlig, Athanasios Papangelis, Carol V Robinson, André Nadler#
Bifunctional Lipid-Protein Cross-linking Efficiency and Reaction Products.
J Am Chem Soc, 148(15) 15349-15353 (2026)
Open Access PubMed Source   

Bifunctional diazirine lipids are versatile tools for mapping protein-lipid interactions and cellular localization by photo-cross-linking. Yet, the cross-linking efficiency of these probes has not been systematically evaluated. We use the lipid transfer protein STARD10, which binds phospholipids in a 1:1 stoichiometry within a hydrophobic pocket, to measure the upper limit of the photo-cross-linking efficiency of bifunctional lipid probes. We characterize reaction products using native and denaturing mass spectrometry. Our results show that approximately 5% of photoactivated lipids form covalent protein-lipid cross-links, while the majority follow intramolecular reaction trajectories, resulting in the formation of products featuring alkene, ketone and hydroxyl moieties. These findings provide essential context for the use of bifunctional probes to uncover the cell biology of lipids and highlight the need for continuous improvement to experimental workflows.
@article{Kirschbaum9202,
author={Clemens Kirschbaum, Hjoerdis Mathilda Lennartz, Katelyn C Cook, Kristin Böhlig, Athanasios Papangelis, Carol V Robinson, André Nadler},
title={Bifunctional Lipid-Protein Cross-linking Efficiency and Reaction Products.},
journal ={Journal of the American Chemical Society},
volume={148},
issue ={15},
pages={15349--15353},
year=2026
}

Julie Warin, Anne Grapin-Botton
Rethinking HNF1A-MODY: HNF1A at the crossroads of development and multiorgan metabolic disease.
Genes Dev, Art. No. doi: 10.1101/gad.353709.126 (2026)
Open Access PubMed Source   

In this issue of Genes & Development, Unger and colleagues (doi:10.1101/gad.353153.125) combined human pluripotent stem cell-derived in vitro models with targeted in vivo mouse models to reveal multiple developmental defects triggered by HNF1A mutations causing maturity-onset diabetes of the young. This work paints the picture of a disorder that starts well before diabetes manifests, highlighting its complexity arising from the diverse roles of HNF1A across distinct cell types, each potentially differentially impacted by different mutations.
@article{Warin9219,
author={Julie Warin, Anne Grapin-Botton},
title={Rethinking HNF1A-MODY: HNF1A at the crossroads of development and multiorgan metabolic disease.},
journal ={Genes & development},
volume={},
pages={1--1},
year=2026
}
* joint first authors, # joint corresponding authors