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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
}

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, 302(3) 370-381 (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={302},
issue ={3},
pages={370--381},
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
}

Matthijs Romeijnders, Michiel van Boven, Francesco Corman, Carl D. Modes, Phillip P A Staniczenko, Debabrata Panja
Event-based spatiotemporal networks for modelling emergent phenomena in complex systems.
Nat Commun, Art. No. doi: 10.1038/s41467-026-73917-0 (2026)
Open Access PubMed Source   

Complex systems display emergent phenomena that vary significantly across spatial and temporal scales. These variations originate from fine-grained system processes, yet arriving at macroscopic dynamics from micro-level data - particularly when large, high-resolution datasets are available - remains a persistent challenge. Here we develop event-based spatiotemporal networks, a computational modelling framework that encodes system processes as discrete events anchored in space and time. Event-based spatiotemporal networks offer a unified, flexible and efficient approach to generate emergent behaviour in complex systems across space and time from these events. We demonstrate the effectiveness of event-based spatiotemporal networks through two illustrative real-world applications. First, following a local outbreak of a novel respiratory pathogen in the Netherlands, spatiotemporal networks enable fine-grained tracking of transmission routes, infection patterns, superspreaders and superspreading events through space and time. Second, we use spatiotemporal networks to model propagation of delays in a public transportation system (Sihltal-Zürich-Uetliberg-bahn) around Zürich, Switzerland. We also discuss broader uses of event-based spatiotemporal networks in fields like developmental biology and community ecology, where focusing on events rather than static system states can improve data analysis, simulation, and collection strategies.
@article{Romeijnders9238,
author={Matthijs Romeijnders, Michiel van Boven, Francesco Corman, Carl D. Modes, Phillip P A Staniczenko, Debabrata Panja},
title={Event-based spatiotemporal networks for modelling emergent phenomena in complex systems.},
journal ={Nature communications},
volume={},
pages={1--1},
year=2026
}

Maria Fedorova#, Anne K Bendt, Justine Bertrand-Michel, Oliver Fiehn, Joanna Godzien, Laura Goracci, Florian Gruber, Xue Li Guan, Xianlin Han, Michal Holčapek, Julia Kuligowski, Peter J Meikle, Palina Nepachalovich, Valerie B O'Donnell, Matej Orešič, Sider Penkov, Snježana Petrović, Anton Potapov, Patricia Prabutzki, Laura Righetti, Tatjana Ruskovska, Andrej Shevchenko, Kai Simons, Corinne M Spickett, Olga Vvedenskaya, Jennifer Watts, Markus R Wenk, Michael Witting, Yu Xia, Baoru Yang, Maria Rosário Domingues#
A lipidomics roadmap: from basic research to societal challenges.
Nat Commun, 17(1) Art. No. 4778 (2026)
Open Access PubMed Source   

Lipidomics, a rapidly evolving discipline at the interface of biology and analytical chemistry, seeks to comprehensively characterize the lipid composition of biological systems. Driven by advances in mass spectrometry, chromatography and computational analysis, lipidomics has enabled the high-resolution mapping of lipid networks and their functional dynamics across molecular, cellular and organismal scales. In biomedical research, lipidomics is emerging as a powerful platform for biomarker discovery, enabling early diagnosis, prognosis, and therapeutic monitoring of cancer, metabolic, and neurodegenerative diseases. The field is also reshaping drug discovery by uncovering lipid-mediated pathways, identifying novel therapeutic targets, and refining assessments of drug efficacy and safety. Beyond medicine, lipidomic analyses are redefining food and nutrition science by elucidating how dietary lipids influence metabolic health and disease risk. In parallel, environmental and ecological lipidomics are emerging as powerful frameworks for assessing ecosystem health, tracking the impact of pollutants and exploring the biological consequences of climate change. Such approaches are also informing the discovery of sustainable lipid resources and the development of novel biotechnological and agricultural innovations. With its rapidly expanding analytical repertoire and cross-disciplinary relevance, lipidomics is poised to make substantial contributions to both fundamental biology and applied science. This Perspective aims to synthesise the current state of the field, delineate major analytical and conceptual challenges, and outline future directions for translating lipidomic knowledge into tangible societal and environmental benefits.
@article{Fedorova9237,
author={Maria Fedorova, Anne K Bendt, Justine Bertrand-Michel, Oliver Fiehn, Joanna Godzien, Laura Goracci, Florian Gruber, Xue Li Guan, Xianlin Han, Michal Holčapek, Julia Kuligowski, Peter J Meikle, Palina Nepachalovich, Valerie B O'Donnell, Matej Orešič, Sider Penkov, Snježana Petrović, Anton Potapov, Patricia Prabutzki, Laura Righetti, Tatjana Ruskovska, Andrej Shevchenko, Kai Simons, Corinne M Spickett, Olga Vvedenskaya, Jennifer Watts, Markus R Wenk, Michael Witting, Yu Xia, Baoru Yang, Maria Rosário Domingues},
title={A lipidomics roadmap: from basic research to societal challenges.},
journal ={Nature communications},
volume={17},
issue ={1},
pages={1--1},
year=2026
}

Pavel Barahtjan*, Juan M Iglesias-Artola*, Kristin Böhlig, Annett Lohmann, André Nadler
Bifunctional Monosaccharides Preferentially Localize to Nuclear Subcompartments.
Chembiochem, 27(10) Art. No. e70373 (2026)
Open Access PubMed Source   

Recent progress in glycan research has been driven by widespread implementations of metabolic oligosaccharide engineering. Complementing existing approaches, we here introduce bifunctional, UV-crosslinkable, and clickable N-acetylglucosamine and N-acetylgalactosamine analogues, which enable direct visualization of the intracellular probe distribution as well as distinguishing monomeric and macromolecule-bound fractions. Using this feature, we find that monomeric N-acetylmonosaccharides partition into RNA-rich nuclear compartments such as nuclear speckles and nucleoli. This suggests the existence of spatially separated N-acetylmonosaccharide pools within the nucleoplasm. Taken together, bifunctional N-acetylmonosaccharide probes are versatile discovery tools for probing intracellular localization of monosaccharides.
@article{Barahtjan9233,
author={Pavel Barahtjan, Juan M Iglesias-Artola, Kristin Böhlig, Annett Lohmann, André Nadler},
title={Bifunctional Monosaccharides Preferentially Localize to Nuclear Subcompartments.},
journal ={Chembiochem : a European journal of chemical biology},
volume={27},
issue ={10},
pages={1--1},
year=2026
}

Helen H Lin, Emily B Mobley, Eric Y Lin, Rana Amini, Petr Pospíšil, Shuo-Ting Yen, Otger Campàs, Ellen M Sletten
Counterion-Enhanced Brightness of Fluorous-Soluble Heptamethine Cyanine Dyes for Near- and Shortwave Infrared Fluorescence Imaging.
Chem Biomed Imaging, 4(5) 945-953 (2026)
Open Access PubMed Source   

Fluorescence imaging across the near-infrared (NIR, 700-1000 nm) and shortwave infrared (SWIR, 1000-2000 nm) regions offers significant advantages for biomedical applications. Over the past decade, we have advanced a unique class of fluorophores-deemed fluorofluorophores-that are soluble in the fluorous phase. The unique properties of the fluorous phase, including low polarizability and high oxygen content, render this medium challenging for fluorophore brightness and photostability. However, the low dielectric constant of perfluorocarbon solvents causes the counterion to play a significant role in the resulting photophysical properties, offering a nontraditional avenue for fluorophore optimization. Here, we demonstrate that counterion exchange provides a straightforward strategy to enhance the brightness of two fluorous-soluble heptamethine cyanine dyes for NIR and SWIR imaging. Exchanging a chloride counterion with bulkier fluorinated aryl borate counterions boosts the brightness up to 10-fold and photostability up to 60-fold in perfluorooctyl bromide. We showcase the utility of these bright, NIR fluorofluorophores for imaging perfluorocarbon nanoemulsion uptake in macrophage cells, visualizing droplet actuation for mechanobiology studies in zebrafish, and mapping vasculature using high-resolution SWIR detection in mice. Overall, this simple modification provides a practical approach to optimize fluorofluorophores for in vivo imaging without the need to redesign the entire fluorophore scaffold.
@article{Lin9174,
author={Helen H Lin, Emily B Mobley, Eric Y Lin, Rana Amini, Petr Pospíšil, Shuo-Ting Yen, Otger Campàs, Ellen M Sletten},
title={Counterion-Enhanced Brightness of Fluorous-Soluble Heptamethine Cyanine Dyes for Near- and Shortwave Infrared Fluorescence Imaging.},
journal ={Chemical & biomedical imaging},
volume={4},
issue ={5},
pages={945--953},
year=2026
}

Marcela Uliano-Silva*, Helena Beatriz da Conceição*, Rafael L V Mercuri, Sylke Winkler, Gabriela D A Guardia, Eugene W Myers, Shane A McCarthy, Alan Tracey, Alexander Suh, Mark L Blaxter, Pedro A F Galante, Camila J Mazzoni
Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution.
BMC Biol, Art. No. doi: 10.1186/s12915-026-02632-5 (2026)
Open Access PubMed Source   

Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialized mammalian clades, yet the genomic basis of their adaptations remains poorly understood. Here, we present chromosome-level genomes for the two-toed sloth (Choloepus didactylus) and the southern anteater (Tamandua tetradactyla) and investigate how retrotransposon-mediated gene duplications (retrocopies) have shaped genome evolution in these and other species in Xenarthra.
@article{Uliano-Silva9236,
author={Marcela Uliano-Silva, Helena Beatriz da Conceição, Rafael L V Mercuri, Sylke Winkler, Gabriela D A Guardia, Eugene W Myers, Shane A McCarthy, Alan Tracey, Alexander Suh, Mark L Blaxter, Pedro A F Galante, Camila J Mazzoni},
title={Elevated retrocopy burden and sloth-specific expansions illuminate mammalian genome evolution.},
journal ={BMC biology},
volume={},
pages={1--1},
year=2026
}

Elisenda Feliu, Paul Alexander Helminck, Oskar Henriksson, Yue Ren, Benjamin Schröter, Mate L Telek
Root bounds of vertical systems using tropical geometry.
ArXiv, Art. No. arXiv:2605.07645 (2026)
Open Access Full Text   

Sparse polynomial systems with vertical coefficient dependencies arise naturally when describing the critical points of optimization problems and, when augmented with linear forms, the steady states of chemical reaction networks. Moreover, any polynomial system is the specialization of such a parametrized system. We prove that the generic number of complex zeros of an augmented vertically parametrized system is the tropical intersection number of a tropical linear space and a classical linear space. In the special case when the matroid of the tropical linear space is cotransversal, we express this number as a mixed volume. We also obtain bounds on the maximal number of positive zeros, which is often the significant number in applications. We derive lower bounds from the number of intersections between positive tropicalizations, and when the positive zeros have toric structure, we provide upper bounds that are simpler and in some cases smaller than the generic root count. The resulting algorithms are implemented in Julia.
@article{Feliu9226,
author={Elisenda Feliu, Paul Alexander Helminck, Oskar Henriksson, Yue Ren, Benjamin Schröter, Mate L Telek},
title={Root bounds of vertical systems using tropical geometry.},
journal ={ArXiv},
volume={},
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
}
* joint first authors, # joint corresponding authors