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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
JOURNAL OF PHYSICS-COMPLEXITY, 7(2) Art. No. 022501 (2026)
Source  

@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
}

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
}

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, Art. No. doi: 10.1021/jacs.6c01205 (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={},
pages={1--1},
year=2026
}

Marcus Renner, M Oleś, Nagarajan Paramasivam, Christoph E Heilig, Annika Schneider, Caroline Modugno, Catherine Herremans, J Hüllein, Barbara Hutter, Cihan Erkut, Andreas Mock, Eva Krieghoff-Henning, Cecilia B Jensen, Amirhossein Sakhteman, Matthew The, Tony Prinz, Panna Lajer, A Baude-Müller, Katja Beck, Bettina Beuthien-Baumann, Leonidas Apostolidis, Sebastian Bauer, Melanie Boerries, Christian H Brandts, D T Rieke, Thomas Kindler, Frederick Klauschen, Klaus Schulze-Osthoff, Richard F Schlenk, Guy Berchem, M Allgäuer, Gunhild Mechtersheimer, A Stenzinger, Daniel B Lipka, Matthias Schlesner, Bernhard Kuster, Arne Jahn, Evelin Schröck, C Heining, M-V Teleanu, P Horak, Simon Kreutzfeldt, D Hübschmann, Wolfgang Hartmann, Hanno Glimm, Stefan Fröhling
Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor.
Nat Commun, 17(1) Art. No. 3397 (2026)
Open Access PubMed Source   

Desmoplastic small round cell tumor (DSRCT) is an ultra-rare sarcoma with limited treatment options. Here, we show that comprehensive molecular profiling informs diagnosis and individualized therapy in this disease. We report the results of whole-genome/exome, transcriptome, and DNA methylome analyses performed in 30 refractory DSRCT patients, complemented by (phospho)proteomic profiling in nine, within a nationwide precision oncology program. In eight patients (27%), DSRCT was diagnosed only after molecular profiling. Although DSRCTs have "quiet" genomes, 28 patients (93%) received 107 molecular-based management recommendations, including assessment of clinical trial eligibility in 17 (57%). Most recommendations are informed by overexpression of tyrosine kinases, SSTR3/5, and CLDN6, detected in 45%, 33%, and 20% of cases, respectively. Thirteen patients (46%) received recommended therapies, yielding disease control in eight (62%), including three long-lasting responses to pazopanib and trastuzumab deruxtecan, the latter administered based on ERBB2 overexpression in the absence of aberrant ERBB2 kinase activation. These findings demonstrate that multi-omics profiling provides clinically actionable insights for DSRCT management.
@article{Renner9203,
author={Marcus Renner, M Oleś, Nagarajan Paramasivam, Christoph E Heilig, Annika Schneider, Caroline Modugno, Catherine Herremans, J Hüllein, Barbara Hutter, Cihan Erkut, Andreas Mock, Eva Krieghoff-Henning, Cecilia B Jensen, Amirhossein Sakhteman, Matthew The, Tony Prinz, Panna Lajer, A Baude-Müller, Katja Beck, Bettina Beuthien-Baumann, Leonidas Apostolidis, Sebastian Bauer, Melanie Boerries, Christian H Brandts, D T Rieke, Thomas Kindler, Frederick Klauschen, Klaus Schulze-Osthoff, Richard F Schlenk, Guy Berchem, M Allgäuer, Gunhild Mechtersheimer, A Stenzinger, Daniel B Lipka, Matthias Schlesner, Bernhard Kuster, Arne Jahn, Evelin Schröck, C Heining, M-V Teleanu, P Horak, Simon Kreutzfeldt, D Hübschmann, Wolfgang Hartmann, Hanno Glimm, Stefan Fröhling},
title={Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor.},
journal ={Nature communications},
volume={17},
issue ={1},
pages={null--null},
year=2026
}

Wen Yu, Yanrun Zhou, Leshan Yang, Xiao Yan, Samuel N Smukowski, Yuefeng Ma, Jiali Fan, Young Ah Goo, Anthony Hyman#, Yifan Dai#
Origins of the Intrinsic Redox Activity of Biomolecular Condensates.
J Am Chem Soc, 148(13) 14443-14452 (2026)
Open Access PubMed Source   

How inherent redox activity arises in biomolecular condensates remains unclear. Unlike interfacial systems, such as water microdroplets, where water oxidation underpins redox chemistry, condensates comprise biomolecules that can potentially furnish alternative electron-transfer routes. Here, using electron paramagnetic resonance, electrochemical potentiometry, mass spectrometry, and confocal microscopy assays, we discovered that orthogonal to water oxidation, microenvironment-dependent spontaneous tyrosine oxidation encodes an alternative redox pathway. Through proton-coupled electron transfer, self-induced tyrosine autoxidation in condensates drives the formation of reactive carbon and oxygen species, providing a pathway in parallel to hydroxide oxidation for hydrogen peroxide formation in condensates. This self-induced redox pathway modulates nonequilibrium condensate behaviors, including responses to external chemical perturbations and evolution of the condensate interior microenvironment. By correlating condensate biomolecular composition with inherent redox activities, our work establishes a conceptual framework suggesting that condensate-dependent electron transfer can be critical to define the functions of condensates and deliver a new redox mechanism for cell biology.
@article{Yu9185,
author={Wen Yu, Yanrun Zhou, Leshan Yang, Xiao Yan, Samuel N Smukowski, Yuefeng Ma, Jiali Fan, Young Ah Goo, Anthony Hyman, Yifan Dai},
title={Origins of the Intrinsic Redox Activity of Biomolecular Condensates.},
journal ={Journal of the American Chemical Society},
volume={148},
issue ={13},
pages={14443--14452},
year=2026
}

Stefan Golfier, Veikko Geyer, Leon Lettermann, Ulrich S Schwarz#, Nicole Poulsen#, Stefan Diez#
Dynamic switching of cell-substrate contact sites allows gliding diatoms to modulate the curvature of their paths.
Proc Natl Acad Sci U.S.A., 123(14) Art. No. e2506122123 (2026)
Open Access PubMed Source   

The directed motility of unicellular organisms is critical for their survival and ecological success, yet the mechanisms that enable rigid-walled diatoms to dynamically reorient and alter the shape of their trajectories remain poorly understood. Here, we investigate the gliding motility of Craspedostauros australis, a raphid pennate diatom that moves rapidly across submerged surfaces using an intracellular actomyosin motility complex and the secretion of adhesive extracellular polymeric substances (EPS) strands through slit-like openings termed raphes. Using high-precision single-cell tracking, scanning electron microscopy (SEM), interference reflection microscopy (IRM), and mathematical modeling, we reveal how diatoms achieve diverse path curvatures by dynamically modulating the location of raphe-substrate contact and switching between one- and two-raphe branch contact gliding. Our results indicate that local curvature variations along the raphes dictate trajectory shapes, with one-raphe branch contact gliding producing highly curved paths, while two-raphe branch contact gliding results in paths of lower curvature. IRM imaging further confirms that transitions between these gliding modes underlie abrupt changes in path curvature and cell reorientation. This dynamic raphe-switching mechanism is conserved across cell sizes and correctly predicts the increased path curvatures observed in smaller cells according to their more pronounced local raphe curvature. By quantitatively linking raphe geometry, cell-substrate attachment dynamics and motility patterns, our study provides insights into the motility mechanism that allows diatoms to adapt their movement to complex environments.
@article{Golfier9198,
author={Stefan Golfier, Veikko Geyer, Leon Lettermann, Ulrich S Schwarz, Nicole Poulsen, Stefan Diez},
title={Dynamic switching of cell-substrate contact sites allows gliding diatoms to modulate the curvature of their paths.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={123},
issue ={14},
pages={null--null},
year=2026
}

Yuheng Zhang, Qi Tian, Yang Yang, Hanyu Liu, Taha Kadir Yesin, Wei Lu, Jessy D Joseph, Biswajyoti Borah, Saravana Ramasamy, Maximina H Yun, Shukry J Habib, Junyu Chen#, Anjali P Kusumbe#
From repair to disease: lymphatic contributions to regeneration, cancer and ageing.
J Adv Res, Art. No. doi:10.1016/j.jare.2026.04.005 (2026)
PubMed Source   

The lymphatic vasculature maintains tissue fluid homeostasis, lipid transport, and immune surveillance. Beyond these classical roles, lymphatic vessels regulate tissue development and repair through lymphangiocrine signalling, whereby lymphatic endothelial cells (LECs) secrete mediators such as Reelin, R-spondin-3, and CCL21 that modulate stem cell niches, immune trafficking, and regeneration. Ageing-associated lymphatic dysfunction, driven by LEC senescence, impaired lymphangiogenesis, and lymph node stromal remodelling, leads to defective tissue repair, chronic low-grade inflammation, and increased susceptibility to diseases including cancer, cardiovascular disease, and neurodegeneration.
@article{Zhang9208,
author={Yuheng Zhang, Qi Tian, Yang Yang, Hanyu Liu, Taha Kadir Yesin, Wei Lu, Jessy D Joseph, Biswajyoti Borah, Saravana Ramasamy, Maximina H Yun, Shukry J Habib, Junyu Chen, Anjali P Kusumbe},
title={From repair to disease: lymphatic contributions to regeneration, cancer and ageing.},
journal ={Journal of advanced research},
volume={},
pages={1--1},
year=2026
}
* joint first authors, # joint corresponding authors