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Agnes Backhausz, Christian Kuehn, Sjoerd van der Niet, Giulio Zucal
Spectral theory of dense hypergraph limits.
DISCRETE MATHEMATICS, 350(1) Art. No. 115362 (2027)
Open Access Source   

In this work, we develop a spectral theory for hypergraph limits. We prove the convergence of the spectra of adjacency and Laplacian matrices for hypergraph sequences converging in the 1-cut metric. On the other hand, we give examples of matrix operators associated with hypergraphs whose spectra are not continuous with respect to the 1-cut metric. Furthermore, we show that these operators are continuous with respect to other cut norms
@article{Backhausz9288,
author={Agnes Backhausz, Christian Kuehn, Sjoerd van der Niet, Giulio Zucal},
title={Spectral theory of dense hypergraph limits.},
journal ={DISCRETE MATHEMATICS},
volume={350},
issue ={1},
pages={null--null},
year=2027
}

Balazs Boros, Gheorghe Craciun, Oskar Henriksson, Jiaxin Jin, Diego Rojas La Luz
A flux-based approach for analyzing the disguised toric locus of reaction networks.
Advances in Applied Mathematics , 182 Art. No. 103160 (2027)
Open Access Source Full Text   

Dynamical systems with polynomial right-hand sides are very important in various applications, e.g., in biochemistry and population dynamics. The mathematical study of these dynamical systems is challenging due to the possibility of multistability, oscillations, and chaotic dynamics. One important tool for this study is the concept of reaction systems, which are dynamical systems generated by reaction networks for some choices of parameter values. Among these, disguised toric systems are remarkably stable: they have a unique attracting fixed point, and cannot give rise to oscillations or chaotic dynamics. The computation of the set of parameter values for which a network gives rise to disguised toric systems (i.e., the disguised toric locus of the network) is an important but difficult task. We introduce new ideas based on network fluxes for studying the disguised toric locus. We prove, under mild assumptions, that the disguised toric locus of any network G is a contractible manifold with boundary, and introduce an associated graph Gmax that characterizes its interior. These theoretical tools allow us, for the first time, to compute the full disguised toric locus for many networks of interest.
@article{Boros9313,
author={Balazs Boros, Gheorghe Craciun, Oskar Henriksson, Jiaxin Jin, Diego Rojas La Luz},
title={A flux-based approach for analyzing the disguised toric locus of reaction networks.},
journal ={Advances in Applied Mathematics },
volume={182},
pages={null--null},
year=2027
}

Anne Schwager*, Jonas Neipel*, Yahor Savich*, Douglas Diehl, Frank Jülicher#, Anthony Hyman#, Stephan W. Grill#
In vitro binding energies capture Klf4 occupancy across the human genome.
Proc Natl Acad Sci U.S.A., 123(44) Art. No. e2538133123 (2026)
Open Access PubMed Source   

Transcription factors (TFs) regulate gene expression by binding to specific genomic loci determined by DNA sequence. Their sequence specificity is commonly summarized by a consensus binding motif. However, eukaryotic genomes contain billions of low-affinity DNA sequences to which TFs associate with a sequence-dependent binding energy. We currently lack insight into how the genomic sequence defines this spectrum of binding energies and the resulting pattern of TF localization. Here, we set out to obtain a quantitative understanding of sequence-dependent TF binding to both motif and nonmotif sequences. We achieve this by first pursuing accurate measurements of physical binding energies of human TF Krüppel-like factor 4 (Klf4) to a library of short DNA sequences in a fluorescence-anisotropy-based bulk competitive binding assay. Second, we show that the highly nonlinear sequence dependence of Klf4 binding energies can be captured by combining a linear model of binding energies with an Ising model of the coupled recognition of nucleotides by a TF. In this model, nucleotide-TF interfaces collectively switch between two states, weak binding and strong nucleotide-specific binding, and the states of neighboring interfaces are coupled with [Formula: see text]. We find that this statistical mechanics model parameterized by our in vitro measurements captures Klf4 binding patterns on an individual long DNA molecule stretched in the optical tweezer, and is predictive for Klf4 occupancy across the entire human genome without additional fit parameters.
@article{Schwager9317,
author={Anne Schwager, Jonas Neipel, Yahor Savich, Douglas Diehl, Frank Jülicher, Anthony Hyman, Stephan W. Grill},
title={In vitro binding energies capture Klf4 occupancy across the human genome.},
journal ={Proceedings of the National Academy of Sciences of the United States of America},
volume={123},
issue ={44},
pages={null--null},
year=2026
}

Jiaxuan Peng, Jaime Agudo-Canalejo#, Monika Chodasiewicz#, Daniël Van Damme#, Vangelis Daskalakis#, Manuel González-Fuente, Rui Gao, Emmanouela Filippidi#, Hongwei Guo, Shengbo He#, Kai Huang#, Shuai Huang#, Geng-Jen Jang#, Min Jia#, Roland L Knorr#, Xuelei Lai#, Ruixi Li#, Qiyu Liang, Chen Liu, Xuyu Liu, Yuchuan Miao, Min Ouyang#, Xuebo Quan, Jorge Solis-Miranda, Lucia C Strader#, Suayib Üstün, Shuyu Wang, Wei Wang, Zhenyu Wang, Yifan Xiong, Cao Xu, Guoyong Xu, Hailong Ye, Chunzhao Zhao, Pan Zhu, Yu Zhu, Emilio Gutierrez-Beltran, Panagiotis N Moschou, Xiaofeng Fang
A practical guide to investigating biomolecular condensates: a comment from the plant community.
Sci China Life Sci, 69(11) 3786-3820 (2026)
Open Access PubMed Source   

Biomolecular condensates formed through phase separation have emerged as a central principle of cellular organization, enabling the dynamic regulation of gene expression, signaling, metabolism, and stress responses. While early conceptual advances in condensate biology have largely originated from animal and in vitro systems, plant cells present a unique set of biological and technical challenges, including rigid cell walls, turgor pressure, plastid autofluorescence, complex endomembrane organization, and acute environmental responsiveness. These distinctive features impede the direct transfer of existing methodologies and drive the development of heterogeneous experimental practices. In this community comment, we present a comprehensive methodological framework for studying biomolecular condensates in plants, spanning in silico prediction, in vitro reconstitution, molecular dynamics simulations, live-cell and super-resolution imaging, material property measurements, membrane-associated condensates, and synthetic condensate engineering. We highlight best practices, common pitfalls, and plant-specific considerations, emphasizing the need for orthogonal validation, quantitative interpretation, and physiological relevance. By consolidating current methodologies and articulating shared principles, this review aims to establish a foundation for rigorous, reproducible, and conceptually coherent research in condensate biology of plants and beyond, with emerging implications for crop genetic improvement and synthetic biology applications.
@article{Peng9290,
author={Jiaxuan Peng, Jaime Agudo-Canalejo, Monika Chodasiewicz, Daniël Van Damme, Vangelis Daskalakis, Manuel González-Fuente, Rui Gao, Emmanouela Filippidi, Hongwei Guo, Shengbo He, Kai Huang, Shuai Huang, Geng-Jen Jang, Min Jia, Roland L Knorr, Xuelei Lai, Ruixi Li, Qiyu Liang, Chen Liu, Xuyu Liu, Yuchuan Miao, Min Ouyang, Xuebo Quan, Jorge Solis-Miranda, Lucia C Strader, Suayib Üstün, Shuyu Wang, Wei Wang, Zhenyu Wang, Yifan Xiong, Cao Xu, Guoyong Xu, Hailong Ye, Chunzhao Zhao, Pan Zhu, Yu Zhu, Emilio Gutierrez-Beltran, Panagiotis N Moschou, Xiaofeng Fang},
title={A practical guide to investigating biomolecular condensates: a comment from the plant community.},
journal ={Science China. Life sciences},
volume={69},
issue ={11},
pages={3786--3820},
year=2026
}

Elizabeth Eck*, Bruno Moretti*, Brandon H Schlomann*, Jordão Bragantini, Merlin Lange, Xiang Zhao, Shruthi VijayKumar, Guillaume Valentin, Cristina Loureiro, Pablo Perez Franco, Chloé Jollivet, Virginie Braman, Baldemar Motomochi, Loic Royer, Andrew C. Oates#, Hernan G Garcia#
Single-cell transcriptional dynamics in a living vertebrate.
Cell Syst, 17(10) Art. No. 101708 (2026)
PubMed Source   

The ability to follow transcription in individual cells with live imaging has revealed key dynamical mechanisms of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light-sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of the transcriptional dynamics of the segmentation clock. Our measurements reveal that smooth clock protein oscillations arise from discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.
@article{Eck9293,
author={Elizabeth Eck, Bruno Moretti, Brandon H Schlomann, Jordão Bragantini, Merlin Lange, Xiang Zhao, Shruthi VijayKumar, Guillaume Valentin, Cristina Loureiro, Pablo Perez Franco, Chloé Jollivet, Virginie Braman, Baldemar Motomochi, Loic Royer, Andrew C. Oates, Hernan G Garcia},
title={Single-cell transcriptional dynamics in a living vertebrate.},
journal ={Cell systems},
volume={17},
issue ={10},
pages={null--null},
year=2026
}

Theresa M Schütze, Annika Kolodziejczyk, Nora Ditzer, Silvia Vangelisti, Emanuele Capra, Jeong-Eun Lee, Ilaria Chiaradia, Vida Kufrin, Seiya Yamada, Jula Peters, Maximilian Krause, Christina Eugster Oegema, Razvan Derihaci, Cahit Birdir, Takashi Namba, Alexander A Wurm, Ulrich Martin, Pauline Wimberger, Katherine S. Long, Madeline Lancaster, Nereo Kalebic, Boyan Bonev, Mareike Albert
Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution.
Nat Commun, 17(1) Art. No. doi: 10.1038/s41467-026-78474-0 (2026)
Open Access PubMed Source   

As the seat of our cognition, the human neocortex is an object of immense fascination. Human neocortex expansion during evolution has been attributed to an increase in the proliferative capacity of neural progenitor cells during development, particularly basal radial glia. Despite their evolutionary relevance, the genomic changes driving human basal radial glia biology remain uncharacterised. We use comparative chromatin and transcriptional profiling of neural progenitor cells isolated from gorilla, chimpanzee and human cerebral organoids to identify cis-regulatory elements that have gained activity in humans. Focusing specifically on basal radial glia, we discover that morphoregulatory enhancer activity and gene expression signatures distinguish human basal radial glia from other great apes. Functional analysis of the morphoregulatory genes FAM107A and CNGA3 in human organoids reveals that these genes contribute to the morphological complexity of human basal radial glia. Taken together, our inter-species comparison of basal radial glia suggests that human-specific morphoregulatory signatures characterise neocortex evolution.
@article{Schütze9318,
author={Theresa M Schütze, Annika Kolodziejczyk, Nora Ditzer, Silvia Vangelisti, Emanuele Capra, Jeong-Eun Lee, Ilaria Chiaradia, Vida Kufrin, Seiya Yamada, Jula Peters, Maximilian Krause, Christina Eugster Oegema, Razvan Derihaci, Cahit Birdir, Takashi Namba, Alexander A Wurm, Ulrich Martin, Pauline Wimberger, Katherine S. Long, Madeline Lancaster, Nereo Kalebic, Boyan Bonev, Mareike Albert},
title={Human-specific morphoregulatory signatures in basal radial glia characterise neocortex evolution.},
journal ={Nature communications},
volume={17},
issue ={1},
pages={1--1},
year=2026
}

Johannes Girstmair*, Tobias Pietzsch*, Vladimir Ulman, Stefan Hahmann, Matthias Arzt, Mette Handberg-Thorsager, Samuel Pantze, Ko Sugawara, Robert Haase, Shuichi Onami, Jean-Yves Tinevez#, Pavel Tomancak#
Mastodon: the command center for large-scale lineage-tracing microscopy datasets.
Development, Art. No. doi: 10.1242/dev.205569 (2026)
Open Access PubMed Source   

Understanding development in living organisms requires following the divisions, movements, and fates of cells. While advances in microscopy have enabled whole-embryo imaging at the cellular level, extracting and analyzing cell lineages from these massive datasets remains a significant computational challenge. We present Mastodon, a scalable, extensible software platform for manual, semi-automated, and automated cell tracking in large images. A purpose-built graph model supports responsive performance for datasets with millions of annotations, making Mastodon a scalable platform for cell lineage analysis. Built as a Fiji plugin, Mastodon enables interactive visualization, editing, and analysis of complex lineage trees, seamlessly integrated with the raw image data. Comprehension of cell lineages in complex three-dimensional geometries is facilitated by interoperability with the powerful open-source render engine Blender. In three distinct developmental contexts, we demonstrate how Mastodon will accelerate biological insights by providing user-friendly navigation and explorative analysis in complex lineage datasets.
@article{Girstmair9319,
author={Johannes Girstmair, Tobias Pietzsch, Vladimir Ulman, Stefan Hahmann, Matthias Arzt, Mette Handberg-Thorsager, Samuel Pantze, Ko Sugawara, Robert Haase, Shuichi Onami, Jean-Yves Tinevez, Pavel Tomancak},
title={Mastodon: the command center for large-scale lineage-tracing microscopy datasets.},
journal ={Development (Cambridge, England)},
volume={},
pages={1--1},
year=2026
}

Hjoerdis Mathilda Lennartz, Susana da Costa Nunes, Kristin Böhlig, Aditya Chhatre, Radek Šachl, Sascha M Kuhn, Lior Moneta, Pavel Barahtjan, Wan Yee Yau, Juan M Iglesias-Artola, Martin Hof, Lukáš Opálka, Carl D. Modes, Alf Honigmann#, André Nadler#
Quantification of lipid sorting during clathrin-mediated endocytosis.
Nat Cell Biol, 28(10) 2027-2035 (2026)
Open Access PubMed Source   

Clathrin-mediated endocytosis is a major transport route for proteins from the plasma membrane to the interior of the cell. While the recruitment of cargo proteins to clathrin-coated pits is well understood, it remains an open question whether lipids are also sorted by this process. Here, to address this question, we combined super-resolution stimulated emission depletion imaging of bifunctional lipid probes with mathematical modelling. Quantification of ten different lipid species revealed significant differences in pit partitioning, ranging from slight enrichment to moderate exclusion. We find that the lipid asymmetry in the plasma membrane is sufficient to explain the observed trend. Taken together, our findings imply that clathrin-mediated endocytosis has a minor selectivity for cytoplasmic leaflet lipids, but overall does not substantially contribute to lipid sorting compared with non-vesicular trafficking.
@article{Lennartz9314,
author={Hjoerdis Mathilda Lennartz, Susana da Costa Nunes, Kristin Böhlig, Aditya Chhatre, Radek Šachl, Sascha M Kuhn, Lior Moneta, Pavel Barahtjan, Wan Yee Yau, Juan M Iglesias-Artola, Martin Hof, Lukáš Opálka, Carl D. Modes, Alf Honigmann, André Nadler},
title={Quantification of lipid sorting during clathrin-mediated endocytosis.},
journal ={Nature cell biology},
volume={28},
issue ={10},
pages={2027--2035},
year=2026
}
* joint first authors, # joint corresponding authors