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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
}

Ariadna E Morales, Yan Liang, William R Thomas, Evgeny Leushkin, Francisco X Castellanos, Denis M Larkin, Tom Brown, Bastian Fromm, Suzanne J Hand, Zixia Huang, Graham M Hughes, Matthew F Jones, Burton K Lim, Meike Mai, Eugene W Myers, Martin Pippel, Sébastien J Puechmaille, Nancy B Simmons, Linelle Abueg, Nadav Ahituv, Zahran A AlAbdulsalam, Ine Alvarez van Tussenbroek, Dineilys V Aparicio, Lina M Arcila Hernández, Alexander Ben Hamadou, Petr Benda, Mark L Blaxter, Alex V Borisenko, Jorge Brocca, Nair Cabezón, Lucia Carbone, Jose I Carvajal, Wharton O Y Chan, Paul Davis, Dina K N Dechmann, Annette Denzinger, Judith L Eger, Seth J Eiseb, David Enard, Mark D Engstrom, Nicole M Foley, Giulio Formenti, Jackson Fuller, Ismael Galván, Akshamal M Gamage, Neil J Gemmell, Joanne E Gillum, Alejandro Gonzales-Irribarren, Mailyn A Gonzalez, Steven M Goodman, Jonathan Gray, Carola Greve, Michael W Guernsey, Edgar G Gutiérrez, Yelena Guttman, Michael Hackenberg, Elena Hilario, Leon Hilgers, Thomas W Horsley, Melissa R de Waal, Deirdre M Jafferally, Erich D Jarvis, Sahieda A Joemratie, Mirjam Knörnschild, Jenna E Kohles, Dimitrios-Georgios Kontopoulos, Bon-Kyoung Koo, M Elise Lauterbur, Michael Letko, Harris A Lewin, Shenglin Liu, Darrell K Lizamore, Brian D Lloyd, Livia Loureiro, M Cristina MacSwiney G, Yury V Malovichko, Kirsty McCaffrey, Dominik W Melville, Magdalena Meyer, William O Mgoola, Matthieu Muffato, Vincent J Munster, William J Murphy, Martina Nagy, Nicolas Nesi, Kimberly A Nevonen, Haris Nicolaou, Evans E Nkrumah, Zacharias Norman, Brian P O'Toole, Sarah H Olson, Alain Ondzie, Bismark A Opoku, Jorge Ortega, William S Pearman, Francy J Perez-Llanos, Kendra L Phelps, Myrtani Pieri, Sarahjane Power, Maksym Prylutskyi, Paola Pulido-Santacruz, Guoying Qi, Bernal Rodríguez-Herrera, Danny Rojas, Indranee Roopsind, Stephen J Rossiter, Constance Scharff, Tilman Schell, Stephanie N Seifert, Fernando Simal, Pipat Soisook, Simone Sommer, Andrew Spalton, Emma L Stone, Peter H Sudmant, Sam Talbot, Robert M Timm, Laura Uelze, Nathan S Upham, Marek Uvizl, Peter Vallo, Juan M Vazquez, Lin-Fa Wang, Linet C Watson, Daniel Whitby, Sylke Winkler, York Winter, Laurel R Yohe, Monika Zavodna, Ning Zhang, Huabin Zhao, David A Ray#, Sonja Vernes#, Liliana M Dávalos#, Michael Hiller#, Emma Teeling#
Reference genomes and fossils revise bat family phylogeny and biogeography.
Nature, 658(8134) 141-152 (2026)
Open Access PubMed Source   

Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate1. However, the evolutionary history of bats and the understanding of these adaptations remain unresolved. We analysed chromosome-level, long-read genome assemblies from 103 bat species, including 42 new assemblies, representing all 21 bat families. This dataset, expanded in scope and assembly quality, yielded a new bat phylogeny. We placed Myzopodidae as the earliest branch within Vespertilionoidea, and resolved yangochiropteran relationships, identifying Emballonuroidea and Vespertilionoidea as sister groups. Our analysis revealed a mosaic evolutionary history across bats and explained why previous phylogenetic studies were misled. Chromosomal ancestral-state reconstructions supported 26 ancestral bat chromosomes. We integrated a morphological dataset of 699 characters for 65 species, including 44 pre-Quaternary fossils and representatives of most living bat families, with neutrally evolving genomic sites. Fossilized birth-death and dispersal-extinction cladogenesis analyses showed that bats, and thus powered flight, probably originated in Europe in the late Palaeocene, refuting African and North American origins. Placement of the fossil †Vielasia in the oldest 'Eochiroptera' clade indicates that laryngeal echolocation predates crown-bat diversification. Total evidence dating, including the fossil taxa, significantly reduced unrepresented basal branch lengths compared with molecular-only divergence estimates. By integrating comprehensive genomic and morphological datasets, analysed using innovative methods, we resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats.
@article{Morales9308,
author={Ariadna E Morales, Yan Liang, William R Thomas, Evgeny Leushkin, Francisco X Castellanos, Denis M Larkin, Tom Brown, Bastian Fromm, Suzanne J Hand, Zixia Huang, Graham M Hughes, Matthew F Jones, Burton K Lim, Meike Mai, Eugene W Myers, Martin Pippel, Sébastien J Puechmaille, Nancy B Simmons, Linelle Abueg, Nadav Ahituv, Zahran A AlAbdulsalam, Ine Alvarez van Tussenbroek, Dineilys V Aparicio, Lina M Arcila Hernández, Alexander Ben Hamadou, Petr Benda, Mark L Blaxter, Alex V Borisenko, Jorge Brocca, Nair Cabezón, Lucia Carbone, Jose I Carvajal, Wharton O Y Chan, Paul Davis, Dina K N Dechmann, Annette Denzinger, Judith L Eger, Seth J Eiseb, David Enard, Mark D Engstrom, Nicole M Foley, Giulio Formenti, Jackson Fuller, Ismael Galván, Akshamal M Gamage, Neil J Gemmell, Joanne E Gillum, Alejandro Gonzales-Irribarren, Mailyn A Gonzalez, Steven M Goodman, Jonathan Gray, Carola Greve, Michael W Guernsey, Edgar G Gutiérrez, Yelena Guttman, Michael Hackenberg, Elena Hilario, Leon Hilgers, Thomas W Horsley, Melissa R de Waal, Deirdre M Jafferally, Erich D Jarvis, Sahieda A Joemratie, Mirjam Knörnschild, Jenna E Kohles, Dimitrios-Georgios Kontopoulos, Bon-Kyoung Koo, M Elise Lauterbur, Michael Letko, Harris A Lewin, Shenglin Liu, Darrell K Lizamore, Brian D Lloyd, Livia Loureiro, M Cristina MacSwiney G, Yury V Malovichko, Kirsty McCaffrey, Dominik W Melville, Magdalena Meyer, William O Mgoola, Matthieu Muffato, Vincent J Munster, William J Murphy, Martina Nagy, Nicolas Nesi, Kimberly A Nevonen, Haris Nicolaou, Evans E Nkrumah, Zacharias Norman, Brian P O'Toole, Sarah H Olson, Alain Ondzie, Bismark A Opoku, Jorge Ortega, William S Pearman, Francy J Perez-Llanos, Kendra L Phelps, Myrtani Pieri, Sarahjane Power, Maksym Prylutskyi, Paola Pulido-Santacruz, Guoying Qi, Bernal Rodríguez-Herrera, Danny Rojas, Indranee Roopsind, Stephen J Rossiter, Constance Scharff, Tilman Schell, Stephanie N Seifert, Fernando Simal, Pipat Soisook, Simone Sommer, Andrew Spalton, Emma L Stone, Peter H Sudmant, Sam Talbot, Robert M Timm, Laura Uelze, Nathan S Upham, Marek Uvizl, Peter Vallo, Juan M Vazquez, Lin-Fa Wang, Linet C Watson, Daniel Whitby, Sylke Winkler, York Winter, Laurel R Yohe, Monika Zavodna, Ning Zhang, Huabin Zhao, David A Ray, Sonja Vernes, Liliana M Dávalos, Michael Hiller, Emma Teeling},
title={Reference genomes and fossils revise bat family phylogeny and biogeography.},
journal ={Nature},
volume={658},
issue ={8134},
pages={141--152},
year=2026
}

Christopher D O Cooper*, Evgeny Tankhilevich*, Kim Remans*, Ahmed El Marjou, Aled M Edwards, Andrew Leach, Alan J Quigley, Anja Schutz, Anne Zemella, Ario de Marco, Åsa Sivertsson, Barbara Borgonovo, Ben Kemp, Bjørn Voldborg, Carlo Carolis, Carter Mitchell, Cecilia Wickstrand, Dafydd R Owen, David N. Drechsel, David Jones, Diego A Oyarzún, Dominic Esposito, Eric R Geertsma, Ewa Krupinska, Frank Bernhard, Frederico Ferreira-da-Silva, Hanna Tegel, Ian Hunt, Imre Berger, James Love, Jan Dohnalek, Jelena Thies, Jerome Basquin, Jesse Coker, Johannes Buyel, Joop van den Heuvel, Jurgen Haustraete, Katharina L Dürr, Kelvin Lau, Kristina Hedfalk, Kristof Bozovicar, Lihua Liu, Lisa Bamber, Luigi Angelo Scietti, Malin Bäckström, Maren Schubert, Mark Elvin, Martin Pelosse, Matthew Todd, Matthieu Schapira, Miroslava Alblova, Nicholas S Berrow, Nikolay Marinchev Dobrev, Oleg Brodsky, Ondřej Vaněk, Opher Gileadi, Pam Dossang, Paola Storici, Patrick H N Celie, Paul Wan, Peter A Loppnau, Rachel Harding, Ray Owens, Renaud Vincentelli, Richard Altman, Rick Davies, Rob Meijers, Robbert Kim, Ruth Saxl, Sabine Suppmann, Sameer Velankar, Sebastiano Pasqualato, Sergio Martinez Cuesta, Stephane Petres, Steven Harborne, Susanne Witt, Svend Kjaer, Tamar Unger, Timothy Craig, Tsafi Danieli, Ugis Sarkans, Wolfgang Knecht, Wolfgang Kuttenlochner, Yoav Peleg, Lovisa Holmberg Schiavone#, Nicola A Burgess-Brown#
"EXPERT" A Practical and Forward-Looking Guide to Capturing Protein Expression and Purification Metadata to develop Machine Learning Models.
J Biol Chem, Art. No. doi: 10.1016/j.jbc.2026.113610 (2026)
Open Access PubMed Source   

As machine learning (ML) becomes increasingly important in protein engineering, synthetic biology, and bioprocess optimisation, the lack of consistent, complete, and standardised experimental reporting remains a major barrier to building effective models. EXPERT (EXpression and Purification Experimental Reporting Template) defines a structured framework for capturing protein expression and purification data across the community, to increase reproducibility across laboratories and support downstream ML applications. We propose here the essential data that should be recorded during expression and purification workflows by both novice and experienced protein production scientists. Its recommendations are informed by expert contributions from across academia and industry. The reporting requirements were distilled to a focused set of parameters deemed sufficient for workflow reproducibility and constructing robust ML models aimed at improving protein production. By deploying these guidelines, we hope to enable the collection of larger data sets to support future model building.
@article{Cooper9315,
author={Christopher D O Cooper, Evgeny Tankhilevich, Kim Remans, Ahmed El Marjou, Aled M Edwards, Andrew Leach, Alan J Quigley, Anja Schutz, Anne Zemella, Ario de Marco, Åsa Sivertsson, Barbara Borgonovo, Ben Kemp, Bjørn Voldborg, Carlo Carolis, Carter Mitchell, Cecilia Wickstrand, Dafydd R Owen, David N. Drechsel, David Jones, Diego A Oyarzún, Dominic Esposito, Eric R Geertsma, Ewa Krupinska, Frank Bernhard, Frederico Ferreira-da-Silva, Hanna Tegel, Ian Hunt, Imre Berger, James Love, Jan Dohnalek, Jelena Thies, Jerome Basquin, Jesse Coker, Johannes Buyel, Joop van den Heuvel, Jurgen Haustraete, Katharina L Dürr, Kelvin Lau, Kristina Hedfalk, Kristof Bozovicar, Lihua Liu, Lisa Bamber, Luigi Angelo Scietti, Malin Bäckström, Maren Schubert, Mark Elvin, Martin Pelosse, Matthew Todd, Matthieu Schapira, Miroslava Alblova, Nicholas S Berrow, Nikolay Marinchev Dobrev, Oleg Brodsky, Ondřej Vaněk, Opher Gileadi, Pam Dossang, Paola Storici, Patrick H N Celie, Paul Wan, Peter A Loppnau, Rachel Harding, Ray Owens, Renaud Vincentelli, Richard Altman, Rick Davies, Rob Meijers, Robbert Kim, Ruth Saxl, Sabine Suppmann, Sameer Velankar, Sebastiano Pasqualato, Sergio Martinez Cuesta, Stephane Petres, Steven Harborne, Susanne Witt, Svend Kjaer, Tamar Unger, Timothy Craig, Tsafi Danieli, Ugis Sarkans, Wolfgang Knecht, Wolfgang Kuttenlochner, Yoav Peleg, Lovisa Holmberg Schiavone, Nicola A Burgess-Brown},
title={"EXPERT" A Practical and Forward-Looking Guide to Capturing Protein Expression and Purification Metadata to develop Machine Learning Models.},
journal ={The Journal of biological chemistry},
volume={},
pages={null--null},
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, Art. No. doi: 10.1038/s41556-026-02068-7 (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={},
pages={1--1},
year=2026
}
* joint first authors, # joint corresponding authors