[{"external_id":{"arxiv":["2410.04887"]},"page":"1905-1931","citation":{"chicago":"Jacot, Arthur, Peter Súkeník, Zihan Wang, and Marco Mondelli. “Wide Neural Networks Trained with Weight Decay Provably Exhibit Neural Collapse.” In <i>13th International Conference on Learning Representations</i>, 1905–31. ICLR, 2025.","ama":"Jacot A, Súkeník P, Wang Z, Mondelli M. Wide neural networks trained with weight decay provably exhibit neural collapse. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025:1905-1931.","ista":"Jacot A, Súkeník P, Wang Z, Mondelli M. 2025. Wide neural networks trained with weight decay provably exhibit neural collapse. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 1905–1931.","apa":"Jacot, A., Súkeník, P., Wang, Z., &#38; Mondelli, M. (2025). Wide neural networks trained with weight decay provably exhibit neural collapse. In <i>13th International Conference on Learning Representations</i> (pp. 1905–1931). Singapore, Singapore: ICLR.","mla":"Jacot, Arthur, et al. “Wide Neural Networks Trained with Weight Decay Provably Exhibit Neural Collapse.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025, pp. 1905–31.","ieee":"A. Jacot, P. Súkeník, Z. Wang, and M. Mondelli, “Wide neural networks trained with weight decay provably exhibit neural collapse,” in <i>13th International Conference on Learning Representations</i>, Singapore, Singapore, 2025, pp. 1905–1931.","short":"A. Jacot, P. Súkeník, Z. Wang, M. Mondelli, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 1905–1931."},"project":[{"_id":"911e6d1f-16d5-11f0-9cad-c5c68c6a1cdf","name":"Inference in High Dimensions: Light-speed Algorithms and Information Limits","grant_number":"101161364"}],"acknowledgement":"M. M. and P. S. are funded by the European Union (ERC, INF2, project number 101161364). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.","file":[{"access_level":"open_access","date_created":"2025-08-04T08:45:43Z","file_size":1337236,"creator":"dernst","content_type":"application/pdf","file_name":"2025_ICLR_Jacot.pdf","success":1,"date_updated":"2025-08-04T08:45:43Z","file_id":"20114","relation":"main_file","checksum":"59c48c173887139647cc9839c0801136"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"MaMo"}],"publication_status":"published","date_updated":"2025-08-04T08:47:00Z","date_published":"2025-04-01T00:00:00Z","has_accepted_license":"1","type":"conference","quality_controlled":"1","arxiv":1,"oa_version":"Published Version","date_created":"2025-07-20T22:02:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"corr_author":"1","OA_type":"diamond","abstract":[{"text":"Deep neural networks (DNNs) at convergence consistently represent the training data in the last layer via a geometric structure referred to as neural collapse. This empirical evidence has spurred a line of theoretical research aimed at proving the emergence of neural collapse, mostly focusing on the unconstrained features model. Here, the features of the penultimate layer are free variables, which makes the model data-agnostic and puts into question its ability to capture DNN training. Our work addresses the issue, moving away from unconstrained features and\r\nstudying DNNs that end with at least two linear layers. We first prove generic guarantees on neural collapse that assume (i) low training error and balancedness of linear layers (for within-class variability collapse), and (ii) bounded conditioning of the features before the linear part (for orthogonality of class-means, and their alignment with weight matrices). The balancedness refers to the fact that W⊤ℓ+1Wℓ+1 ≈ WℓW⊤ℓfor any pair of consecutive weight matrices of the linear part, and the bounded conditioning requires a well-behaved ratio between largest and smallest non-zero singular values of the features. We then show that such assumptions hold for gradient descent training with weight decay: (i) for networks with a wide first layer, we prove low training error and balancedness, and (ii) for solutions that are either nearly optimal or stable under large learning rates, we additionally prove the bounded conditioning. Taken together, our results are the first to show neural collapse in the end-to-end training of DNNs.","lang":"eng"}],"author":[{"last_name":"Jacot","first_name":"Arthur","full_name":"Jacot, Arthur"},{"last_name":"Súkeník","full_name":"Súkeník, Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","first_name":"Peter"},{"last_name":"Wang","first_name":"Zihan","full_name":"Wang, Zihan"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli"}],"publisher":"ICLR","OA_place":"publisher","file_date_updated":"2025-08-04T08:45:43Z","ddc":["000"],"day":"01","publication_identifier":{"isbn":["9798331320850"]},"year":"2025","_id":"20035","status":"public","month":"04","conference":{"name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28","location":"Singapore, Singapore","start_date":"2025-04-24"},"publication":"13th International Conference on Learning Representations","title":"Wide neural networks trained with weight decay provably exhibit neural collapse","scopus_import":"1","oa":1,"article_processing_charge":"No"},{"external_id":{"arxiv":["2408.11054"]},"page":"72303-72330","citation":{"ieee":"V. Pariza, M. Salehi, G. Burghouts, F. Locatello, and Y. M. Asano, “Near, far: Patch-ordering enhances vision foundation models’ scene understanding,” in <i>13th International Conference on Learning Representations</i>, Singapore, Singapore, 2025, pp. 72303–72330.","short":"V. Pariza, M. Salehi, G. Burghouts, F. Locatello, Y.M. Asano, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 72303–72330.","ista":"Pariza V, Salehi M, Burghouts G, Locatello F, Asano YM. 2025. Near, far: Patch-ordering enhances vision foundation models’ scene understanding. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 72303–72330.","ama":"Pariza V, Salehi M, Burghouts G, Locatello F, Asano YM. Near, far: Patch-ordering enhances vision foundation models’ scene understanding. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025:72303-72330.","apa":"Pariza, V., Salehi, M., Burghouts, G., Locatello, F., &#38; Asano, Y. M. (2025). Near, far: Patch-ordering enhances vision foundation models’ scene understanding. In <i>13th International Conference on Learning Representations</i> (pp. 72303–72330). Singapore, Singapore: ICLR.","mla":"Pariza, Valentinos, et al. “Near, Far: Patch-Ordering Enhances Vision Foundation Models’ Scene Understanding.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025, pp. 72303–30.","chicago":"Pariza, Valentinos, Mohammadreza Salehi, Gertjan Burghouts, Francesco Locatello, and Yuki M. Asano. “Near, Far: Patch-Ordering Enhances Vision Foundation Models’ Scene Understanding.” In <i>13th International Conference on Learning Representations</i>, 72303–30. ICLR, 2025."},"department":[{"_id":"FrLo"}],"publication_status":"published","date_updated":"2025-08-04T08:10:55Z","file":[{"date_updated":"2025-08-04T08:09:43Z","file_id":"20109","checksum":"ddbe981f3ad3f6cb6daf12c954822eb8","relation":"main_file","content_type":"application/pdf","file_name":"2025_ICLR_Pariza.pdf","success":1,"date_created":"2025-08-04T08:09:43Z","file_size":37788223,"creator":"dernst","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"arxiv":1,"quality_controlled":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-20T22:02:03Z","language":[{"iso":"eng"}],"date_published":"2025-04-01T00:00:00Z","has_accepted_license":"1","type":"conference","OA_type":"diamond","author":[{"full_name":"Pariza, Valentinos","first_name":"Valentinos","last_name":"Pariza"},{"last_name":"Salehi","full_name":"Salehi, Mohammadreza","first_name":"Mohammadreza"},{"last_name":"Burghouts","full_name":"Burghouts, Gertjan","first_name":"Gertjan"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello"},{"first_name":"Yuki M.","full_name":"Asano, Yuki M.","last_name":"Asano"}],"abstract":[{"lang":"eng","text":"We introduce NeCo: Patch Neighbor Consistency, a novel self-supervised training loss that enforces patch-level nearest neighbor consistency across a student and teacher model. Compared to contrastive approaches that only yield binary learning signals, i.e. \"attract\" and \"repel\", this approach benefits from the more fine-grained learning signal of sorting spatially dense features relative to reference patches. Our method leverages differentiable sorting applied on top of pretrained representations, such as DINOv2-registers to bootstrap the learning signal and further improve upon them. This dense post-pretraining leads to superior performance across various models and datasets, despite requiring only 19 hours on a single GPU. This method generates high-quality dense feature encoders and establishes several new state-of-the-art results such as +2.3 % and +4.2% for non-parametric in-context semantic segmentation on ADE20k and Pascal VOC, +1.6% and +4.8% for linear segmentation evaluations on COCO-Things and -Stuff and improvements in the 3D understanding of multi-view consistency on SPair-71k, by more than 1.5%."}],"day":"01","publication_identifier":{"isbn":["9798331320850"]},"publisher":"ICLR","OA_place":"publisher","file_date_updated":"2025-08-04T08:09:43Z","ddc":["000"],"title":"Near, far: Patch-ordering enhances vision foundation models' scene understanding","scopus_import":"1","oa":1,"article_processing_charge":"No","year":"2025","_id":"20036","month":"04","status":"public","conference":{"start_date":"2025-04-24","name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28","location":"Singapore, Singapore"},"publication":"13th International Conference on Learning Representations"},{"acknowledgement":"The authors would like to extend their gratitude to Lori Leu for her insightful comments on the\r\napplication of the Wasserstein distance metric. We also wish to thank Elias Frantar for his help in\r\nworking with the SparseGPT implementation and his advice for the project. Additionally, we would like to thank Tony Tong Wang and Thomas Athey for their valuable feedback and constructive discussions.\r\nThis work was supported by an NIH Brains CONNECTS U01 grant and AMD’s AI & HPC Fund.","external_id":{"arxiv":["2405.15756"]},"citation":{"ama":"Sawmya S, Kong L, Markov I, Alistarh D-A, Shavit N. Wasserstein distances, neuronal entanglement, and sparsity. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025:26244-26274.","ista":"Sawmya S, Kong L, Markov I, Alistarh D-A, Shavit N. 2025. Wasserstein distances, neuronal entanglement, and sparsity. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 26244–26274.","apa":"Sawmya, S., Kong, L., Markov, I., Alistarh, D.-A., &#38; Shavit, N. (2025). Wasserstein distances, neuronal entanglement, and sparsity. In <i>13th International Conference on Learning Representations</i> (pp. 26244–26274). Singapore, Singapore: ICLR.","mla":"Sawmya, Shashata, et al. “Wasserstein Distances, Neuronal Entanglement, and Sparsity.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025, pp. 26244–74.","ieee":"S. Sawmya, L. Kong, I. Markov, D.-A. Alistarh, and N. Shavit, “Wasserstein distances, neuronal entanglement, and sparsity,” in <i>13th International Conference on Learning Representations</i>, Singapore, Singapore, 2025, pp. 26244–26274.","short":"S. Sawmya, L. Kong, I. Markov, D.-A. Alistarh, N. Shavit, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 26244–26274.","chicago":"Sawmya, Shashata, Linghao Kong, Ilia Markov, Dan-Adrian Alistarh, and Nir Shavit. “Wasserstein Distances, Neuronal Entanglement, and Sparsity.” In <i>13th International Conference on Learning Representations</i>, 26244–74. ICLR, 2025."},"page":"26244-26274","date_published":"2025-04-01T00:00:00Z","has_accepted_license":"1","type":"conference","quality_controlled":"1","arxiv":1,"oa_version":"Published Version","date_created":"2025-07-20T22:02:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_name":"2025_ICLR_Sawmya.pdf","success":1,"date_updated":"2025-08-04T08:14:09Z","file_id":"20110","relation":"main_file","checksum":"39a8fa7dbdd7029859e156f53f20f6bc","access_level":"open_access","date_created":"2025-08-04T08:14:09Z","file_size":5447177,"creator":"dernst"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","department":[{"_id":"DaAl"}],"date_updated":"2025-08-04T08:16:43Z","related_material":{"link":[{"relation":"software","url":"https://github.com/Shavit-Lab/Sparse-Expansion"}]},"abstract":[{"lang":"eng","text":"Disentangling polysemantic neurons is at the core of many current approaches to interpretability of large language models. Here we attempt to study how disentanglement can be used to understand performance, particularly under weight sparsity, a leading post-training optimization technique. We suggest a novel measure for estimating neuronal entanglement: the Wasserstein distance of a neuron's output distribution to a Gaussian. Moreover, we show the existence of a small number of highly entangled \"Wasserstein Neurons\" in each linear layer of an LLM, characterized by their highly non-Gaussian output distributions, their role in mapping similar inputs to dissimilar outputs, and their significant impact on model accuracy. To study these phenomena, we propose a new experimental framework for disentangling polysemantic neurons. Our framework separates each layer's inputs to create a mixture of experts where each neuron's output is computed by a mixture of neurons of lower Wasserstein distance, each better at maintaining accuracy when sparsified without retraining. We provide strong evidence that this is because the mixture of sparse experts is effectively disentangling the input-output relationship of individual neurons, in particular the difficult Wasserstein neurons."}],"author":[{"full_name":"Sawmya, Shashata","first_name":"Shashata","last_name":"Sawmya"},{"full_name":"Kong, Linghao","first_name":"Linghao","last_name":"Kong"},{"last_name":"Markov","id":"D0CF4148-C985-11E9-8066-0BDEE5697425","full_name":"Markov, Ilia","first_name":"Ilia"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X"},{"full_name":"Shavit, Nir","first_name":"Nir","last_name":"Shavit"}],"corr_author":"1","OA_type":"diamond","year":"2025","_id":"20037","status":"public","month":"04","conference":{"start_date":"2025-04-24","end_date":"2025-04-28","name":"ICLR: International Conference on Learning Representations","location":"Singapore, Singapore"},"publication":"13th International Conference on Learning Representations","title":"Wasserstein distances, neuronal entanglement, and sparsity","scopus_import":"1","oa":1,"article_processing_charge":"No","publisher":"ICLR","file_date_updated":"2025-08-04T08:14:09Z","OA_place":"publisher","ddc":["000"],"day":"01","publication_identifier":{"isbn":["9798331320850"]}},{"OA_type":"diamond","author":[{"last_name":"Jin","first_name":"Tian","full_name":"Jin, Tian"},{"last_name":"Humayun","full_name":"Humayun, Ahmed Imtiaz","first_name":"Ahmed Imtiaz"},{"full_name":"Evci, Utku","first_name":"Utku","last_name":"Evci"},{"last_name":"Subramanian","full_name":"Subramanian, Suvinay","first_name":"Suvinay"},{"first_name":"Amir","full_name":"Yazdanbakhsh, Amir","last_name":"Yazdanbakhsh"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dziugaite, Gintare Karolina","first_name":"Gintare Karolina","last_name":"Dziugaite"}],"abstract":[{"text":"Pruning eliminates unnecessary parameters in neural networks; it offers a promising solution to the growing computational demands of large language models (LLMs). While many focus on post-training pruning, sparse pre-training--which combines pruning and pre-training into a single phase--provides a simpler alternative. In this work, we present the first systematic exploration of optimal sparse pre-training configurations for LLMs through an examination of 80 unique pruning schedules across different sparsity levels and training durations. We find that initiating pruning at 25% of total training compute and concluding at 75% achieves near-optimal final evaluation loss. These findings provide valuable insights for efficient and effective sparse pre-training of LLMs. Furthermore, we propose a new scaling law that modifies the Chinchilla scaling law to use the average parameter count over pre-training. Through empirical and theoretical validation, we demonstrate that this modified scaling law accurately models evaluation loss for both sparsely and densely pre-trained LLMs, unifying scaling laws across pre-training paradigms. Our findings indicate that while sparse pre-training achieves the same final model quality as dense pre-training for equivalent compute budgets, it provides substantial benefits through reduced model size, enabling significant potential computational savings during inference.","lang":"eng"}],"day":"01","publication_identifier":{"isbn":["9798331320850"]},"publisher":"ICLR","OA_place":"publisher","file_date_updated":"2025-08-04T08:23:47Z","ddc":["000"],"title":"The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws","scopus_import":"1","oa":1,"article_processing_charge":"No","year":"2025","_id":"20038","month":"04","status":"public","conference":{"start_date":"2025-04-24","name":"ICLR: International Conference on Learning Representations","end_date":"2025-04-28","location":"Singapore, Singapore"},"publication":"13th International Conference on Learning Representations","external_id":{"arxiv":["2501.12486 "]},"citation":{"short":"T. Jin, A.I. Humayun, U. Evci, S. Subramanian, A. Yazdanbakhsh, D.-A. Alistarh, G.K. Dziugaite, in:, 13th International Conference on Learning Representations, ICLR, 2025, pp. 85165–85181.","ieee":"T. Jin <i>et al.</i>, “The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws,” in <i>13th International Conference on Learning Representations</i>, Singapore, Singapore, 2025, pp. 85165–85181.","mla":"Jin, Tian, et al. “The Journey Matters: Average Parameter Count over Pre-Training Unifies Sparse and Dense Scaling Laws.” <i>13th International Conference on Learning Representations</i>, ICLR, 2025, pp. 85165–81.","apa":"Jin, T., Humayun, A. I., Evci, U., Subramanian, S., Yazdanbakhsh, A., Alistarh, D.-A., &#38; Dziugaite, G. K. (2025). The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws. In <i>13th International Conference on Learning Representations</i> (pp. 85165–85181). Singapore, Singapore: ICLR.","ista":"Jin T, Humayun AI, Evci U, Subramanian S, Yazdanbakhsh A, Alistarh D-A, Dziugaite GK. 2025. The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws. 13th International Conference on Learning Representations. ICLR: International Conference on Learning Representations, 85165–85181.","ama":"Jin T, Humayun AI, Evci U, et al. The journey matters: Average parameter count over pre-training unifies sparse and dense scaling laws. In: <i>13th International Conference on Learning Representations</i>. ICLR; 2025:85165-85181.","chicago":"Jin, Tian, Ahmed Imtiaz Humayun, Utku Evci, Suvinay Subramanian, Amir Yazdanbakhsh, Dan-Adrian Alistarh, and Gintare Karolina Dziugaite. “The Journey Matters: Average Parameter Count over Pre-Training Unifies Sparse and Dense Scaling Laws.” In <i>13th International Conference on Learning Representations</i>, 85165–81. ICLR, 2025."},"page":"85165-85181","acknowledgement":"We are deeply grateful to Elias Frantar, Naveen Kumar, Sanjiv Kumar, Daniel\r\nM. Roy, and Clemens Schaefer for their valuable feedback and thoughtful review of this paper.\r\nWe also acknowledge the critical support provided by the Google CoreML Performance Team, and Google Research during this project. We further recognize the extended team at Google DeepMind, who enabled and supported this research direction.\r\nThis work was in part supported by the Sloan Foundation, the MIT-IBM Watson AI Lab, Apple, and SRC JUMP 2.0 (CoCoSys).","department":[{"_id":"DaAl"}],"publication_status":"published","date_updated":"2025-08-04T08:24:59Z","file":[{"date_created":"2025-08-04T08:23:47Z","creator":"dernst","file_size":704989,"access_level":"open_access","date_updated":"2025-08-04T08:23:47Z","relation":"main_file","checksum":"dbc27120e9aba67dffbd9e5d513a6803","file_id":"20111","file_name":"2025_ICLR_Jin.pdf","content_type":"application/pdf","success":1}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","arxiv":1,"date_created":"2025-07-20T22:02:03Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2025-04-01T00:00:00Z","has_accepted_license":"1","type":"conference"},{"abstract":[{"text":"Contractive coupling rates have been recently introduced by Conforti as a tool to establish convex Sobolev inequalities (including modified log-Sobolev and Poincaré inequality) for some classes of Markov chains. In this work, for most of the examples discussed by Conforti, we use contractive coupling rates to prove stronger inequalities, in the form of curvature lower bounds (in entropic and discrete Bakry–Émery sense) and geodesic convexity of some entropic functionals. In addition, we recall and give straightforward generalizations of some notions of coarse Ricci curvature, and we discuss some of their properties and relations with the concepts of couplings and coupling rates: as an application, we show exponential contraction of the p-Wasserstein distance for the heat flow in the aforementioned examples.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"17351","relation":"earlier_version"}]},"author":[{"last_name":"Pedrotti","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","full_name":"Pedrotti, Francesco","first_name":"Francesco"}],"OA_type":"green","isi":1,"corr_author":"1","publication":"The Annals of Applied Probability","month":"02","_id":"20040","status":"public","year":"2025","article_processing_charge":"No","oa":1,"scopus_import":"1","title":"Contractive coupling rates and curvature lower bounds for Markov chains","fulldoi":"https://doi.org/10.1214/24-aap2113","doi":"10.1214/24-aap2113","OA_place":"repository","publisher":"Institute of Mathematical Statistics","publication_identifier":{"issn":["1050-5164"]},"day":"01","volume":35,"acknowledgement":"The author warmly thanks Jan Maas for suggesting the project and for his guidance, and Melchior Wirth and Haonan Zhang for useful discussions. The author is also grateful to an anonymous reviewer for carefully reading the manuscript and providing many valuable suggestions. The author gratefully acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme\r\n(grant agreement No. 716117) and by the Austrian Science Fund (FWF), Project SFB F65.","project":[{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"citation":{"short":"F. Pedrotti, The Annals of Applied Probability 35 (2025) 196–250.","ieee":"F. Pedrotti, “Contractive coupling rates and curvature lower bounds for Markov chains,” <i>The Annals of Applied Probability</i>, vol. 35, no. 1. Institute of Mathematical Statistics, pp. 196–250, 2025.","apa":"Pedrotti, F. (2025). Contractive coupling rates and curvature lower bounds for Markov chains. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/24-aap2113\">https://doi.org/10.1214/24-aap2113</a>","mla":"Pedrotti, Francesco. “Contractive Coupling Rates and Curvature Lower Bounds for Markov Chains.” <i>The Annals of Applied Probability</i>, vol. 35, no. 1, Institute of Mathematical Statistics, 2025, pp. 196–250, doi:<a href=\"https://doi.org/10.1214/24-aap2113\">10.1214/24-aap2113</a>.","ama":"Pedrotti F. Contractive coupling rates and curvature lower bounds for Markov chains. <i>The Annals of Applied Probability</i>. 2025;35(1):196-250. doi:<a href=\"https://doi.org/10.1214/24-aap2113\">10.1214/24-aap2113</a>","ista":"Pedrotti F. 2025. Contractive coupling rates and curvature lower bounds for Markov chains. The Annals of Applied Probability. 35(1), 196–250.","chicago":"Pedrotti, Francesco. “Contractive Coupling Rates and Curvature Lower Bounds for Markov Chains.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/24-aap2113\">https://doi.org/10.1214/24-aap2113</a>."},"page":"196 - 250","external_id":{"arxiv":["2308.00516"],"isi":["001434322900006"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2308.00516"}],"issue":"1","ec_funded":1,"type":"journal_article","date_published":"2025-02-01T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-21T07:49:15Z","quality_controlled":"1","intvolume":"        35","arxiv":1,"article_type":"original","date_updated":"2025-11-05T13:50:07Z","department":[{"_id":"JaMa"}],"publication_status":"published"},{"abstract":[{"text":"The Cover Feature shows how recessed microelectrodes were employed as a versatile binder-free platform to investigate the electrochemical performance of Prussian Blue analogues (PBA), a class of promising battery materials, concerning capacity in varying aqueous electrolytes. To corroborate the micro-electrochemical findings, both ex-situ and operando chemical characterizations were conducted, offering complementary insights into the structural and chemical evolution of the PBA material during electrochemical cycling. More information can be found in the Research Article by W. Schuhmann and co-workers (DOI: 10.1002/batt.202400743).","lang":"eng"}],"author":[{"full_name":"Jiyane, Nomnotho","first_name":"Nomnotho","last_name":"Jiyane"},{"last_name":"Santana Santos","full_name":"Santana Santos, Carla","first_name":"Carla"},{"first_name":"Igor","id":"fbae1d3b-8142-11ed-8927-a8cf34feb495","full_name":"Echevarria Poza, Igor","last_name":"Echevarria Poza"},{"first_name":"Mario","full_name":"Palacios Corella, Mario","id":"452e82c6-803f-11ed-ab7e-ca0439e73a5d","last_name":"Palacios Corella"},{"last_name":"Abdillah Mahbub","first_name":"Muhammad Adib","full_name":"Abdillah Mahbub, Muhammad Adib"},{"first_name":"Gimena","full_name":"Marin‐Tajadura, Gimena","last_name":"Marin‐Tajadura"},{"full_name":"Quast, Thomas","first_name":"Thomas","last_name":"Quast"},{"last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ventosa, Edgar","first_name":"Edgar","last_name":"Ventosa"},{"full_name":"Schuhmann, Wolfgang","first_name":"Wolfgang","last_name":"Schuhmann"}],"article_number":"e202580302","OA_type":"free access","_id":"20042","status":"public","month":"03","year":"2025","publication":"Batteries & Supercaps","title":"Cover Feature: Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application","article_processing_charge":"No","oa":1,"doi":"10.1002/batt.202580302","OA_place":"publisher","publisher":"Wiley","ddc":["530"],"fulldoi":"https://doi.org/10.1002/batt.202580302","day":"01","publication_identifier":{"eissn":["2566-6223"]},"volume":8,"main_file_link":[{"url":"https://doi.org/10.1002/batt.202580302","open_access":"1"}],"citation":{"ieee":"N. Jiyane <i>et al.</i>, <i>Cover Feature: Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application</i>, vol. 8, no. 3. Wiley, 2025.","short":"N. Jiyane, C. Santana Santos, I. Echevarria Poza, M. Palacios Corella, M.A. Abdillah Mahbub, G. Marin‐Tajadura, T. Quast, M. Ibáñez, E. Ventosa, W. Schuhmann, Cover Feature: Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application, Wiley, 2025.","ista":"Jiyane N, Santana Santos C, Echevarria Poza I, Palacios Corella M, Abdillah Mahbub MA, Marin‐Tajadura G, Quast T, Ibáñez M, Ventosa E, Schuhmann W. 2025. Cover Feature: Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application, Wiley,p.","ama":"Jiyane N, Santana Santos C, Echevarria Poza I, et al. <i>Cover Feature: Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application</i>. Vol 8. Wiley; 2025. doi:<a href=\"https://doi.org/10.1002/batt.202580302\">10.1002/batt.202580302</a>","apa":"Jiyane, N., Santana Santos, C., Echevarria Poza, I., Palacios Corella, M., Abdillah Mahbub, M. A., Marin‐Tajadura, G., … Schuhmann, W. (2025). <i>Cover Feature: Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application</i>. <i>Batteries &#38; Supercaps</i> (Vol. 8). Wiley. <a href=\"https://doi.org/10.1002/batt.202580302\">https://doi.org/10.1002/batt.202580302</a>","mla":"Jiyane, Nomnotho, et al. “Cover Feature: Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application.” <i>Batteries &#38; Supercaps</i>, vol. 8, no. 3, e202580302, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/batt.202580302\">10.1002/batt.202580302</a>.","chicago":"Jiyane, Nomnotho, Carla Santana Santos, Igor Echevarria Poza, Mario Palacios Corella, Muhammad Adib Abdillah Mahbub, Gimena Marin‐Tajadura, Thomas Quast, Maria Ibáñez, Edgar Ventosa, and Wolfgang Schuhmann. <i>Cover Feature: Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application</i>. <i>Batteries &#38; Supercaps</i>. Vol. 8. Wiley, 2025. <a href=\"https://doi.org/10.1002/batt.202580302\">https://doi.org/10.1002/batt.202580302</a>."},"issue":"3","date_published":"2025-03-01T00:00:00Z","type":"other_academic_publication","intvolume":"         8","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","date_created":"2025-07-21T07:52:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaIb"}],"publication_status":"published","date_updated":"2026-06-18T18:18:57Z"},{"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"day":"01","PlanS_conform":"1","fulldoi":"https://doi.org/10.1093/evolut/qpaf061","ddc":["570"],"publisher":"Oxford University Press","file_date_updated":"2025-07-22T10:04:57Z","OA_place":"publisher","doi":"10.1093/evolut/qpaf061","oa":1,"article_processing_charge":"Yes (in subscription journal)","title":"Predicting the prevalence of genetic trade-offs among adaptive substitutions","publication":"Evolution","year":"2025","_id":"20044","status":"public","month":"07","OA_type":"hybrid","isi":1,"author":[{"first_name":"Tim","full_name":"Connallon, Tim","last_name":"Connallon"},{"full_name":"Czuppon, Peter","first_name":"Peter","last_name":"Czuppon"},{"last_name":"Olito","full_name":"Olito, Colin","first_name":"Colin"},{"last_name":"Goedert","full_name":"Goedert, Debora","first_name":"Debora"},{"full_name":"Kokko, Hanna","first_name":"Hanna","last_name":"Kokko"},{"last_name":"Nava-Bolaños","first_name":"Angela","full_name":"Nava-Bolaños, Angela"},{"last_name":"Nilén","first_name":"Sofie","full_name":"Nilén, Sofie"},{"first_name":"Erik I","full_name":"Svensson, Erik I","last_name":"Svensson"},{"first_name":"Martyna","full_name":"Zwoinska, Martyna","last_name":"Zwoinska"},{"full_name":"Dutoit, Ludovic","first_name":"Ludovic","last_name":"Dutoit"},{"first_name":"Filip","full_name":"Ruzicka, Filip","id":"347955dd-57b0-11ee-9095-c28bdd368f4b","last_name":"Ruzicka"}],"abstract":[{"lang":"eng","text":"Genetic trade-offs—which occur when variants that are beneficial in some contexts of natural selection are harmful in others—can influence a wide range of evolutionary phenomena, from the maintenance of genetic variation to the evolution of aging and sex differences. An extensive body of evolutionary theory has focused on the consequences of such trade-offs, and recent analyses of Fisher’s geometric model have further quantified the expected proportion of new mutations that exhibit trade-offs. However, the theory remains silent regarding the prevalence of trade-offs among the variants that contribute to adaptation. Here, we extend Fisher’s geometric model to predict the prevalence of trade-offs among the adaptive mutations that become established or fixed in a population. We consider trade-offs between sexes, habitats, fitness components, and temporally fluctuating environments. In all 4 scenarios, trade-off alleles are consistently under-represented among established relative to new beneficial mutations—an effect that arises from the greater susceptibility of trade-off alleles to genetic drift. Adaptation during a population size decline exacerbates this deficit of trade-offs among established mutations, whereas population expansions dampen it. Consequently, threatened populations should primarily adapt using unconditionally beneficial alleles, while invasive populations are more prone to adaptation using variants that exhibit trade-offs."}],"date_updated":"2025-09-30T14:06:38Z","publication_status":"published","department":[{"_id":"BeVi"}],"file":[{"success":1,"file_name":"2025_Evolution_Connallon.pdf","content_type":"application/pdf","relation":"main_file","checksum":"68c4c996d0e8c9ee3d4fb61bca75b31a","file_id":"20068","date_updated":"2025-07-22T10:04:57Z","access_level":"open_access","creator":"dernst","file_size":8150623,"date_created":"2025-07-22T10:04:57Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_created":"2025-07-21T07:57:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        79","has_accepted_license":"1","type":"journal_article","date_published":"2025-07-01T00:00:00Z","issue":"7","ec_funded":1,"external_id":{"isi":["001477180800001"]},"citation":{"ista":"Connallon T, Czuppon P, Olito C, Goedert D, Kokko H, Nava-Bolaños A, Nilén S, Svensson EI, Zwoinska M, Dutoit L, Ruzicka F. 2025. Predicting the prevalence of genetic trade-offs among adaptive substitutions. Evolution. 79(7), 1243–1255.","ama":"Connallon T, Czuppon P, Olito C, et al. Predicting the prevalence of genetic trade-offs among adaptive substitutions. <i>Evolution</i>. 2025;79(7):1243-1255. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf061\">10.1093/evolut/qpaf061</a>","mla":"Connallon, Tim, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” <i>Evolution</i>, vol. 79, no. 7, Oxford University Press, 2025, pp. 1243–55, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf061\">10.1093/evolut/qpaf061</a>.","apa":"Connallon, T., Czuppon, P., Olito, C., Goedert, D., Kokko, H., Nava-Bolaños, A., … Ruzicka, F. (2025). Predicting the prevalence of genetic trade-offs among adaptive substitutions. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf061\">https://doi.org/10.1093/evolut/qpaf061</a>","ieee":"T. Connallon <i>et al.</i>, “Predicting the prevalence of genetic trade-offs among adaptive substitutions,” <i>Evolution</i>, vol. 79, no. 7. Oxford University Press, pp. 1243–1255, 2025.","short":"T. Connallon, P. Czuppon, C. Olito, D. Goedert, H. Kokko, A. Nava-Bolaños, S. Nilén, E.I. Svensson, M. Zwoinska, L. Dutoit, F. Ruzicka, Evolution 79 (2025) 1243–1255.","chicago":"Connallon, Tim, Peter Czuppon, Colin Olito, Debora Goedert, Hanna Kokko, Angela Nava-Bolaños, Sofie Nilén, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf061\">https://doi.org/10.1093/evolut/qpaf061</a>."},"page":"1243-1255","volume":79,"acknowledgement":"Support for this research came from the European Society of Evolutionary Biology (ESEB) through a “Special Topics Network” grant. Further financial support came from the European Research Council (ERC-2023-STG916 #101117517, to C.O.), the Swedish Research Council (#2022-03603, to C.O.; #2020‑03123, to E.I.S.), the Research Council of Norway (Norges forskningsråd #302619, to D.G.), the Alexander von Humboldt Foundation and the GenEvo graduate school (to H.K.), the Foundation for Zoological Research and the Birgitta Sintring Foundation (#S2024-0007, to M.K.Z.), a postdoctoral fellowship from the Consejo Nacional de Humanidades, Ciencias y Tecnología (to A.N.B.), and a H2020 Marie Skłodowska-Curie COFUND Action fellowship (#101034413, to F.R.). We wish to express our deepest gratitude to Lotte de Vries for extensive discussion of the project, rederiving some of our results, and providing comments on an earlier version of the manuscript, and to the European Society of Evolutionary Biology (ESEB) for a “Special Topics Network” grant that supported workshops that initiated this collaboration and facilitated many new ideas and friendships. We also thank two anonymous reviewers for their thoughtful comments and suggestions that helped us to substantially improve upon the original version of the article.","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}]},{"external_id":{"arxiv":["2305.06722"]},"citation":{"ista":"Falconi M, Lampart J, Leopold N, Mitrouskas DJ. 2025. Renormalized Bogoliubov theory for the Nelson model. Annales de l’Institut Henri Poincaré C.","ama":"Falconi M, Lampart J, Leopold N, Mitrouskas DJ. Renormalized Bogoliubov theory for the Nelson model. <i>Annales de l’Institut Henri Poincaré C</i>. 2025. doi:<a href=\"https://doi.org/10.4171/aihpc/154\">10.4171/aihpc/154</a>","mla":"Falconi, Marco, et al. “Renormalized Bogoliubov Theory for the Nelson Model.” <i>Annales de l’Institut Henri Poincaré C</i>, EMS Press, 2025, doi:<a href=\"https://doi.org/10.4171/aihpc/154\">10.4171/aihpc/154</a>.","apa":"Falconi, M., Lampart, J., Leopold, N., &#38; Mitrouskas, D. J. (2025). Renormalized Bogoliubov theory for the Nelson model. <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press. <a href=\"https://doi.org/10.4171/aihpc/154\">https://doi.org/10.4171/aihpc/154</a>","ieee":"M. Falconi, J. Lampart, N. Leopold, and D. J. Mitrouskas, “Renormalized Bogoliubov theory for the Nelson model,” <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press, 2025.","short":"M. Falconi, J. Lampart, N. Leopold, D.J. Mitrouskas, Annales de l’Institut Henri Poincaré C (2025).","chicago":"Falconi, Marco, Jonas Lampart, Nikolai Leopold, and David Johannes Mitrouskas. “Renormalized Bogoliubov Theory for the Nelson Model.” <i>Annales de l’Institut Henri Poincaré C</i>. EMS Press, 2025. <a href=\"https://doi.org/10.4171/aihpc/154\">https://doi.org/10.4171/aihpc/154</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2305.06722"}],"date_updated":"2025-12-30T07:31:09Z","department":[{"_id":"RoSe"}],"publication_status":"epub_ahead","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-21T07:59:16Z","oa_version":"Preprint","language":[{"iso":"eng"}],"arxiv":1,"quality_controlled":"1","type":"journal_article","date_published":"2025-05-06T00:00:00Z","OA_type":"green","author":[{"first_name":"Marco","full_name":"Falconi, Marco","last_name":"Falconi"},{"last_name":"Lampart","first_name":"Jonas","full_name":"Lampart, Jonas"},{"full_name":"Leopold, Nikolai","first_name":"Nikolai","last_name":"Leopold"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"}],"abstract":[{"lang":"eng","text":"We consider the time evolution of the renormalized Nelson model, which describes N bosons linearly coupled to a quantized scalar field, in the mean-field limit of many particles N≫1 with coupling constant proportional to N^−1/2. First, we show that initial states exhibiting Bose–Einstein condensation for the particles and approximating a coherent state for the quantum field retain their structure under the many-body time evolution. Concretely, the dynamics of the reduced densities are approximated by solutions of two coupled PDEs, the Schrödinger–Klein–Gordon equations. Second, we construct a renormalized Bogoliubov evolution that describes the quantum fluctuations around the Schrödinger–Klein–Gordon equations. This evolution is used to extend the approximation of the evolved many-body state to the full norm topology. In summary, we provide a comprehensive analysis of the Nelson model that reveals the role of renormalization in the mean-field Bogoliubov theory."}],"publication_identifier":{"eissn":["1873-1430"],"issn":["0294-1449"]},"day":"06","fulldoi":"https://doi.org/10.4171/aihpc/154","publisher":"EMS Press","OA_place":"repository","doi":"10.4171/aihpc/154","oa":1,"article_processing_charge":"No","title":"Renormalized Bogoliubov theory for the Nelson model","publication":"Annales de l'Institut Henri Poincaré C","DOAJ_listed":"1","year":"2025","_id":"20045","status":"public","month":"05"},{"volume":30,"acknowledgement":"The authors thank Santiago Arenas-Velilla and Victor Pérez-Abreu for comments on an earlier draft of this manuscript and for contributing Appendix A. The authors also thank Yan Fyodorov for providing useful references.\r\nA. Campbell was partially supported by the European Research Council Grant No. 101020331. K. Luh was supported in part by the Ralph E. Powe Junior Faculty Enhancement Award and Simons Foundation Grant MP-TSM-00001988. S. O’Rourke has been supported in part by NSF CAREER grant DMS-2143142. ","project":[{"call_identifier":"H2020","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"external_id":{"arxiv":["2211.17175"],"isi":["001540927000024"]},"citation":{"chicago":"Campbell, Andrew J, Kyle Luh, Sean O’Rourke, Santiago Arenas-Velilla, and Victor Perez-Abreu. “Extreme Eigenvalues of Laplacian Random Matrices with Gaussian Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2025. <a href=\"https://doi.org/10.1214/25-ejp1366\">https://doi.org/10.1214/25-ejp1366</a>.","apa":"Campbell, A. J., Luh, K., O’Rourke, S., Arenas-Velilla, S., &#38; Perez-Abreu, V. (2025). Extreme eigenvalues of Laplacian random matrices with Gaussian entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/25-ejp1366\">https://doi.org/10.1214/25-ejp1366</a>","mla":"Campbell, Andrew J., et al. “Extreme Eigenvalues of Laplacian Random Matrices with Gaussian Entries.” <i>Electronic Journal of Probability</i>, vol. 30, Institute of Mathematical Statistics, 2025, pp. 1–52, doi:<a href=\"https://doi.org/10.1214/25-ejp1366\">10.1214/25-ejp1366</a>.","ista":"Campbell AJ, Luh K, O’Rourke S, Arenas-Velilla S, Perez-Abreu V. 2025. Extreme eigenvalues of Laplacian random matrices with Gaussian entries. Electronic Journal of Probability. 30, 1–52.","ama":"Campbell AJ, Luh K, O’Rourke S, Arenas-Velilla S, Perez-Abreu V. Extreme eigenvalues of Laplacian random matrices with Gaussian entries. <i>Electronic Journal of Probability</i>. 2025;30:1-52. doi:<a href=\"https://doi.org/10.1214/25-ejp1366\">10.1214/25-ejp1366</a>","short":"A.J. Campbell, K. Luh, S. O’Rourke, S. Arenas-Velilla, V. Perez-Abreu, Electronic Journal of Probability 30 (2025) 1–52.","ieee":"A. J. Campbell, K. Luh, S. O’Rourke, S. Arenas-Velilla, and V. Perez-Abreu, “Extreme eigenvalues of Laplacian random matrices with Gaussian entries,” <i>Electronic Journal of Probability</i>, vol. 30. Institute of Mathematical Statistics, pp. 1–52, 2025."},"page":"1-52","ec_funded":1,"has_accepted_license":"1","type":"journal_article","date_published":"2025-06-27T00:00:00Z","date_created":"2025-07-21T08:06:18Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"intvolume":"        30","file":[{"success":1,"content_type":"application/pdf","file_name":"2025_ElectronJourProbab_Campbell.pdf","file_id":"20069","checksum":"a7a9f2bb7a6295786c16d4c7bd612621","relation":"main_file","date_updated":"2025-07-23T08:35:53Z","access_level":"open_access","file_size":580591,"creator":"dernst","date_created":"2025-07-23T08:35:53Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","date_updated":"2025-09-30T14:07:19Z","publication_status":"published","department":[{"_id":"LaEr"}],"abstract":[{"text":"A Laplacian matrix is a real symmetric matrix whose row and column sums are zero. We investigate the limiting distribution of the largest eigenvalues of a Laplacian random matrix with Gaussian entries. Unlike many classical matrix ensembles, this random matrix model contains dependent entries. Our main results show that the extreme eigenvalues of this model exhibit Poisson statistics. In particular, after properly shifting and scaling, we show that the largest eigenvalue converges to the Gumbel distribution as the dimension of the matrix tends to infinity. While the largest diagonal entry is also shown to have Gumbel fluctuations, there is a rather surprising difference between its deterministic centering term and the centering term required for the largest eigenvalues.","lang":"eng"}],"author":[{"id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","full_name":"Campbell, Andrew J","first_name":"Andrew J","last_name":"Campbell"},{"last_name":"Luh","full_name":"Luh, Kyle","first_name":"Kyle"},{"last_name":"O’Rourke","full_name":"O’Rourke, Sean","first_name":"Sean"},{"last_name":"Arenas-Velilla","first_name":"Santiago","full_name":"Arenas-Velilla, Santiago"},{"last_name":"Perez-Abreu","first_name":"Victor","full_name":"Perez-Abreu, Victor"}],"OA_type":"gold","isi":1,"corr_author":"1","publication":"Electronic Journal of Probability","DOAJ_listed":"1","year":"2025","_id":"20046","status":"public","month":"06","oa":1,"article_processing_charge":"Yes","title":"Extreme eigenvalues of Laplacian random matrices with Gaussian entries","fulldoi":"https://doi.org/10.1214/25-ejp1366","ddc":["510"],"publisher":"Institute of Mathematical Statistics","doi":"10.1214/25-ejp1366","file_date_updated":"2025-07-23T08:35:53Z","OA_place":"publisher","publication_identifier":{"eissn":["1083-6489"]},"day":"27"},{"author":[{"first_name":"Tom-Lukas","full_name":"Breitkopf, Tom-Lukas","last_name":"Breitkopf"},{"last_name":"Dallot","first_name":"Julien","full_name":"Dallot, Julien"},{"last_name":"El-Hayek","id":"888a098e-fcac-11ee-aff7-d347be57b725","full_name":"El-Hayek, Antoine","first_name":"Antoine","orcid":"0000-0003-4268-7368"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"}],"abstract":[{"text":"This paper revisits a fundamental distributed computing problem in the population protocol model. Provided n agents each starting with an input color in [k], the relative majority problem asks to find the predominant color. In the population protocol model, at each time step, a scheduler selects two agents that first learn each other's states and then update their states based on what they learned.\r\nWe present the Circles protocol that solves the relative majority problem with k3 states. It is always-correct under weakly fair scheduling. Not only does it improve upon the best known upper bound of O(k7), but it also shows a strikingly simpler design inspired by energy minimization in chemical settings.","lang":"eng"}],"corr_author":"1","isi":1,"OA_type":"hybrid","title":"Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols","oa":1,"article_processing_charge":"No","year":"2025","_id":"20052","month":"06","status":"public","conference":{"start_date":"2025-06-16","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2025-06-20","location":"Huatulco, Mexico"},"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","day":"13","publication_identifier":{"isbn":["9798400718854"]},"publisher":"Association for Computing Machinery","doi":"10.1145/3732772.3733512","OA_place":"publisher","file_date_updated":"2025-08-05T07:32:01Z","ddc":["000"],"fulldoi":"https://doi.org/10.1145/3732772.3733512","project":[{"call_identifier":"H2020","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct, No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024 and the German Research Foundation (DFG), grant 470029389 (FlexNets). ","ec_funded":1,"external_id":{"isi":["001525534800069"]},"page":"549-552","citation":{"chicago":"Breitkopf, Tom-Lukas, Julien Dallot, Antoine El-Hayek, and Stefan Schmid. “Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number of States in Population Protocols.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, 549–52. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3732772.3733512\">https://doi.org/10.1145/3732772.3733512</a>.","mla":"Breitkopf, Tom-Lukas, et al. “Brief Announcement: Minimizing Energy Solves Relative Majority with a Cubic Number of States in Population Protocols.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2025, pp. 549–52, doi:<a href=\"https://doi.org/10.1145/3732772.3733512\">10.1145/3732772.3733512</a>.","apa":"Breitkopf, T.-L., Dallot, J., El-Hayek, A., &#38; Schmid, S. (2025). Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (pp. 549–552). Huatulco, Mexico: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3732772.3733512\">https://doi.org/10.1145/3732772.3733512</a>","ama":"Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2025:549-552. doi:<a href=\"https://doi.org/10.1145/3732772.3733512\">10.1145/3732772.3733512</a>","ista":"Breitkopf T-L, Dallot J, El-Hayek A, Schmid S. 2025. Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 549–552.","short":"T.-L. Breitkopf, J. Dallot, A. El-Hayek, S. Schmid, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 549–552.","ieee":"T.-L. Breitkopf, J. Dallot, A. El-Hayek, and S. Schmid, “Brief announcement: Minimizing energy solves relative majority with a cubic number of states in population protocols,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Huatulco, Mexico, 2025, pp. 549–552."},"quality_controlled":"1","oa_version":"Published Version","date_created":"2025-07-21T08:17:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_published":"2025-06-13T00:00:00Z","has_accepted_license":"1","type":"conference","department":[{"_id":"MoHe"}],"publication_status":"published","date_updated":"2026-02-16T11:46:37Z","file":[{"date_created":"2025-08-05T07:32:01Z","creator":"dernst","file_size":549706,"access_level":"open_access","date_updated":"2025-08-05T07:32:01Z","checksum":"e99679ffb28877b7cea4d54860302790","relation":"main_file","file_id":"20123","file_name":"2025_PODC_Breitkopf.pdf","content_type":"application/pdf","success":1}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-21T08:18:26Z","oa_version":"Published Version","language":[{"iso":"eng"}],"quality_controlled":"1","has_accepted_license":"1","type":"conference","date_published":"2025-06-13T00:00:00Z","date_updated":"2026-02-16T11:46:51Z","publication_status":"published","department":[{"_id":"KrCh"},{"_id":"KrPi"}],"file":[{"access_level":"open_access","creator":"dernst","file_size":783297,"date_created":"2025-08-05T07:15:31Z","success":1,"file_name":"2025_PODC_Chatterjee.pdf","content_type":"application/pdf","checksum":"cd628fe54d96e9fc6cc789bb8145422b","relation":"main_file","file_id":"20122","date_updated":"2025-08-05T07:15:31Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"acknowledgement":"This work was partially supported by MOE-T2EP20122-0014 (DataDriven Distributed Algorithms), German Research Foundation (DFG) project ReNO (SPP 2378) from 2023-2027, ERC CoG 863818 (ForMSMArt) and Austrian Science Fund (FWF) 10.55776/COE12.","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020"}],"ec_funded":1,"external_id":{"isi":["001525534800030"]},"citation":{"chicago":"Chatterjee, Krishnendu, Seth Gilbert, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.” In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, 241–51. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3732772.3733544\">https://doi.org/10.1145/3732772.3733544</a>.","ieee":"K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, and M. X. Yeo, “When is liquid democracy possible?: On the manipulation of variance,” in <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Huatulco, Mexico, 2025, pp. 241–251.","short":"K. Chatterjee, S. Gilbert, S. Schmid, J. Svoboda, M.X. Yeo, in:, Proceedings of the ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2025, pp. 241–251.","ista":"Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. 2025. When is liquid democracy possible?: On the manipulation of variance. Proceedings of the ACM Symposium on Principles of Distributed Computing. PODC: Symposium on Principles of Distributed Computing, 241–251.","ama":"Chatterjee K, Gilbert S, Schmid S, Svoboda J, Yeo MX. When is liquid democracy possible?: On the manipulation of variance. In: <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2025:241-251. doi:<a href=\"https://doi.org/10.1145/3732772.3733544\">10.1145/3732772.3733544</a>","mla":"Chatterjee, Krishnendu, et al. “When Is Liquid Democracy Possible?: On the Manipulation of Variance.” <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2025, pp. 241–51, doi:<a href=\"https://doi.org/10.1145/3732772.3733544\">10.1145/3732772.3733544</a>.","apa":"Chatterjee, K., Gilbert, S., Schmid, S., Svoboda, J., &#38; Yeo, M. X. (2025). When is liquid democracy possible?: On the manipulation of variance. In <i>Proceedings of the ACM Symposium on Principles of Distributed Computing</i> (pp. 241–251). Huatulco, Mexico: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3732772.3733544\">https://doi.org/10.1145/3732772.3733544</a>"},"page":"241-251","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2025/745"}],"oa":1,"article_processing_charge":"No","title":"When is liquid democracy possible?: On the manipulation of variance","conference":{"location":"Huatulco, Mexico","name":"PODC: Symposium on Principles of Distributed Computing","end_date":"2025-06-20","start_date":"2025-06-16"},"publication":"Proceedings of the ACM Symposium on Principles of Distributed Computing","year":"2025","month":"06","_id":"20053","status":"public","publication_identifier":{"isbn":["9798400718854"]},"day":"13","fulldoi":"https://doi.org/10.1145/3732772.3733544","ddc":["000"],"publisher":"Association for Computing Machinery","OA_place":"publisher","doi":"10.1145/3732772.3733544","file_date_updated":"2025-08-05T07:15:31Z","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"first_name":"Seth","full_name":"Gilbert, Seth","last_name":"Gilbert"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","first_name":"Jakub","last_name":"Svoboda"},{"orcid":"0009-0001-3676-4809","first_name":"Michelle X","full_name":"Yeo, Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo"}],"abstract":[{"lang":"eng","text":"Liquid democracy is a transitive vote delegation mechanism over voting graphs. It enables each voter to delegate their vote(s) to another better-informed voter, with the goal of collectively making a better decision. The question of whether liquid democracy outperforms direct voting has been previously studied in the context of local delegation mechanisms (where voters can only delegate to someone in their neighbourhood) and binary decision problems. It has previously been shown that it is impossible for local delegation mechanisms to outperform direct voting in general graphs. This raises the question: for which classes of graphs do local delegation mechanisms yield good results?\r\nIn this work, we analyse (1) properties of specific graphs and (2) properties of local delegation mechanisms on these graphs, determining where local delegation actually outperforms direct voting. We show that a critical graph property enabling liquid democracy is that the voting outcome of local delegation mechanisms preserves a sufficient amount of variance, thereby avoiding situations where delegation falls behind direct voting1. These insights allow us to prove our main results, namely that there exist local delegation mechanisms that perform no worse and in fact quantitatively better than direct voting in natural graph topologies like complete, random d-regular, and bounded degree graphs, lending a more nuanced perspective to previous impossibility results."}],"OA_type":"hybrid","isi":1,"corr_author":"1"},{"abstract":[{"lang":"eng","text":"Supercrystals represent three-dimensional orderings of colloidal nanocrystals (NCs), showcasing collective properties in photonics, phononics, and electronics applications.1,2 Recent studies have shown that such assemblies are directly produced during nanocrystal reactions.3–6 However, a fundamental understanding of in situ formed supercrystals that withstand typical NC purification processes remains underexplored, which is important for further use. Herein, we report the reaction precursor-mediated formation of stable PbTe supercrystals. Rationalizing the formation of these assemblies through small-angle x-ray scattering (SAXS) measurements, we unveil their formation mechanism. Our findings reveal that the supercrystal formation occurs in the presence of an excess of lead oleates in the crude solution. It should be noted that the formed supercrystals can be stabilized under specific conditions determined by the lead oleate cluster concentration, content of trioctylphosphine telluride (TOP-Te), NC size and the need of an annealing step at mild conditions. Furthermore, this approach allows for the continuous growth of a secondary phase within the supercrystal; for example in the case of PbTe supercrystals, a PbS shell can be grown on each PbTe NC constituent, resulting in core-shell PbTe-PbS supercrystals. Our work elucidates that reaction precursors play an important role in in situ SC formation and stabilization, implying the possibility of applying this knowledge to other NC reactions."}],"author":[{"last_name":"Lee","first_name":"Seungho","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Daniel","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta"},{"last_name":"Rayaroth Puthiyaveettil","id":"8aceb01b-8972-11ed-ae7b-d5fe53775add","full_name":"Rayaroth Puthiyaveettil, Aiswarya","first_name":"Aiswarya"},{"first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","last_name":"Ibáñez"}],"article_number":"173","corr_author":"1","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NMR"},{"_id":"LifeSc"}],"OA_type":"closed access","year":"2025","month":"03","_id":"20055","status":"public","conference":{"start_date":"2025-03-03","location":"Sevilla, Spain","end_date":"2025-03-07","name":"MATSUS: Materials for Sustainable Development Conference"},"publication":"Proceedings of the MATSUS Spring 2025 Conference","title":"Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case","article_processing_charge":"No","publisher":"Fundació de la comunitat valenciana SCITO","doi":"10.29363/nanoge.matsusspring.2025.173","fulldoi":"https://doi.org/10.29363/nanoge.matsusspring.2025.173","day":"15","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"acknowledgement":"ISTA and the Werner Siemens Foundation financially supported this work. The Scientific Service Units (SSU) of ISTA supported this research through resources provided by the Electron Microscopy Facility (EMF), NMR Facility and the Lab Support Facility (LSF).","citation":{"apa":"Lee, S., Balazs, D., Horta, S., Rayaroth Puthiyaveettil, A., &#38; Ibáñez, M. (2025). Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Sevilla, Spain: Fundació de la comunitat valenciana SCITO. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>","mla":"Lee, Seungho, et al. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” <i>Proceedings of the MATSUS Spring 2025 Conference</i>, 173, Fundació de la comunitat valenciana SCITO, 2025, doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>.","ista":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. 2025. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. Proceedings of the MATSUS Spring 2025 Conference. MATSUS: Materials for Sustainable Development Conference, 173.","ama":"Lee S, Balazs D, Horta S, Rayaroth Puthiyaveettil A, Ibáñez M. Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case. In: <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO; 2025. doi:<a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">10.29363/nanoge.matsusspring.2025.173</a>","short":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, M. Ibáñez, in:, Proceedings of the MATSUS Spring 2025 Conference, Fundació de la comunitat valenciana SCITO, 2025.","ieee":"S. Lee, D. Balazs, S. Horta, A. Rayaroth Puthiyaveettil, and M. Ibáñez, “Reaction precursor-mediated formation of stable supercrystals in colloidal nanocrystal synthesis: PbTe case,” in <i>Proceedings of the MATSUS Spring 2025 Conference</i>, Sevilla, Spain, 2025.","chicago":"Lee, Seungho, Daniel Balazs, Sharona Horta, Aiswarya Rayaroth Puthiyaveettil, and Maria Ibáñez. “Reaction Precursor-Mediated Formation of Stable Supercrystals in Colloidal Nanocrystal Synthesis: PbTe Case.” In <i>Proceedings of the MATSUS Spring 2025 Conference</i>. Fundació de la comunitat valenciana SCITO, 2025. <a href=\"https://doi.org/10.29363/nanoge.matsusspring.2025.173\">https://doi.org/10.29363/nanoge.matsusspring.2025.173</a>."},"date_published":"2025-03-15T00:00:00Z","type":"conference","quality_controlled":"1","date_created":"2025-07-21T08:33:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","language":[{"iso":"eng"}],"department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"publication_status":"published","date_updated":"2026-02-19T09:25:57Z"},{"volume":205,"acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"page":"E100-E117","citation":{"apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117.","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025.","chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>."},"external_id":{"isi":["001433250500001"],"pmid":["40179429"],"arxiv":["2205.02645"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2205.02645","open_access":"1"}],"issue":"4","type":"journal_article","date_published":"2025-04-01T00:00:00Z","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","date_created":"2025-07-21T08:37:27Z","intvolume":"       205","arxiv":1,"quality_controlled":"1","article_type":"original","date_updated":"2025-09-30T14:14:43Z","department":[{"_id":"EdHa"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics)."}],"related_material":{"record":[{"status":"public","id":"20121","relation":"software"}]},"pmid":1,"author":[{"last_name":"Nabeel","full_name":"Nabeel, Arshed","first_name":"Arshed"},{"full_name":"Karichannavar, Ashwin","first_name":"Ashwin","last_name":"Karichannavar"},{"first_name":"Shuaib","full_name":"Palathingal, Shuaib","last_name":"Palathingal"},{"last_name":"Jhawar","first_name":"Jitesh","full_name":"Jhawar, Jitesh"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner"},{"full_name":"Raj M, Danny","first_name":"Danny","last_name":"Raj M"},{"first_name":"Vishwesha","full_name":"Guttal, Vishwesha","last_name":"Guttal"}],"OA_type":"green","isi":1,"publication":"The American Naturalist","_id":"20056","month":"04","status":"public","year":"2025","article_processing_charge":"No","oa":1,"title":"Discovering stochastic dynamical equations from ecological time series data","fulldoi":"https://doi.org/10.1086/734083","OA_place":"repository","doi":"10.1086/734083","publisher":"University of Chicago Press","publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"day":"01"},{"title":"Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels","article_processing_charge":"Yes","oa":1,"_id":"20077","status":"public","month":"07","year":"2025","DOAJ_listed":"1","publication":"Biology","PlanS_conform":"1","day":"24","publication_identifier":{"issn":["2079-7737"]},"file_date_updated":"2025-07-31T09:11:09Z","OA_place":"publisher","doi":"10.3390/biology14080930","publisher":"MDPI","fulldoi":"https://doi.org/10.3390/biology14080930","ddc":["570"],"author":[{"last_name":"Rosani","first_name":"Umberto","full_name":"Rosani, Umberto"},{"full_name":"Altan, Nehir","first_name":"Nehir","last_name":"Altan"},{"last_name":"Venier","full_name":"Venier, Paola","first_name":"Paola"},{"last_name":"Bortoletto","full_name":"Bortoletto, Enrico","first_name":"Enrico"},{"last_name":"Volpi","full_name":"Volpi, Nicola","first_name":"Nicola"},{"orcid":"0000-0003-0893-7036","first_name":"Carrie A","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky"}],"abstract":[{"text":"Hyaluronic acid (HA) is a key extracellular matrix component of vertebrates, where it mediates cell adhesion, immune regulation, and tissue remodeling through its interaction with specific receptors. Although HA has been detected in a few invertebrate species, the lack of fundamental components of the molecular HA pathway poses relevant objections about its functional role in these species. Mining genomic and transcriptomic data, we considered the conservation of the gene locus encoding for the extracellular link protein (XLINK) in marine mussels as well as its expression patterns. Structural and phylogenetic analyses were undertaken to evaluate possible similarities with vertebrate orthologs and to infer the origin of this gene in invertebrates. Biochemical analysis was used to quantify HA in tissues of Mytilus galloprovincialis. As a result, we confirm that the mussel can produce HA (up to 1.02 ng/mg in mantle) and that its genome encodes two XLINK gene loci. These loci are conserved in Mytilidae species and show a complex evolutionary path. Mussel XLINK genes appeared to be expressed during developmental stages in three mussel species, ranking in the top 100 expressed genes in M. trossulus at 17 h post-fertilization. In conclusion, the presence of HA and an active gene with the potential to bind HA suggests that mussels have the potential to synthesize and use HA and are among the few invertebrates encoding this gene.","lang":"eng"}],"isi":1,"article_number":"930","OA_type":"gold","quality_controlled":"1","intvolume":"        14","language":[{"iso":"eng"}],"date_created":"2025-07-25T08:28:26Z","oa_version":"Published Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2025-07-24T00:00:00Z","type":"journal_article","has_accepted_license":"1","publication_status":"published","department":[{"_id":"CaBe"}],"date_updated":"2025-09-30T14:10:07Z","article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"date_created":"2025-07-31T09:11:09Z","creator":"dernst","file_size":1885781,"access_level":"open_access","date_updated":"2025-07-31T09:11:09Z","checksum":"f5e059e66803fa54249c1db029aef0f6","relation":"main_file","file_id":"20097","file_name":"2025_Biology_Rosani.pdf","content_type":"application/pdf","success":1}],"volume":14,"acknowledgement":"This research was funded by the Italian Ministry of University and Research (MIUR), grant ID: P2022JEEMT (Developing a tool for the study of haplotype diversity in Mytilus galloprovincialis (HAMIGA)).","issue":"8","citation":{"chicago":"Rosani, Umberto, Nehir Altan, Paola Venier, Enrico Bortoletto, Nicola Volpi, and Carrie Bernecky. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>. MDPI, 2025. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>.","ista":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. 2025. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. Biology. 14(8), 930.","ama":"Rosani U, Altan N, Venier P, Bortoletto E, Volpi N, Bernecky C. Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. 2025;14(8). doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>","apa":"Rosani, U., Altan, N., Venier, P., Bortoletto, E., Volpi, N., &#38; Bernecky, C. (2025). Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels. <i>Biology</i>. MDPI. <a href=\"https://doi.org/10.3390/biology14080930\">https://doi.org/10.3390/biology14080930</a>","mla":"Rosani, Umberto, et al. “Ancestral Origin and Functional Expression of a Hyaluronic Acid Pathway Complement in Mussels.” <i>Biology</i>, vol. 14, no. 8, 930, MDPI, 2025, doi:<a href=\"https://doi.org/10.3390/biology14080930\">10.3390/biology14080930</a>.","ieee":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, and C. Bernecky, “Ancestral origin and functional expression of a hyaluronic acid pathway complement in mussels,” <i>Biology</i>, vol. 14, no. 8. MDPI, 2025.","short":"U. Rosani, N. Altan, P. Venier, E. Bortoletto, N. Volpi, C. Bernecky, Biology 14 (2025)."},"external_id":{"isi":["001557922100001"]}},{"abstract":[{"lang":"eng","text":"Research question: Is LINC01638 involved in regulation of epithelial-to-mesenchymal transition (EMT) in endometriosis?\r\nDesign: A prospective patient cohort study was combined with functional experiments in the 12Z endometriosis epithelial cell line to investigate the role of LINC01638 in endometriosis. Eutopic endometrial samples were collected by curettage, and ectopic endometrial lesion samples were collected by laparoscopic surgery from 24 control patients and 41 patients with endometriosis. The phenotype of 12Z cells was assessed following LINC01638 knockdown using siRNA, performing proliferation, adhesion, migration and invasion assays, as well as assessing apoptosis and cell cycle changes with flow cytometry assays. In order to assess the relationship between LINC01638 and histone deacetylase class 1 enzyme (HDAC1), LINC01638 knockdown was combined with HDAC inhibition with the specific HDAC inhibitor romidepsin.\r\nResults: LINC01638 was up-regulated in the epithelial layer of endometriotic lesions, and LINC01638 knockdown in 12Z cells led to reduced proliferation, adhesion, migration and invasion. The reduction in proliferation was associated with increased p21 and p27 expression, and G1 phase arrest. Further analysis of LINC01638 control and knockdown cells revealed that a number of transcription factors associated with EMT are down-regulated in knockdown cells, along with the cytoskeleton regulatory gene RHOB, while HDAC1 was up-regulated. Chromatin immunoprecipitation analysis and HDAC1 inhibitory treatment combined with LINC01638 knockdown indicated that LINC01638 regulates RHOB expression via HDAC1-mediated promoter deacetylation. RHOB is up-regulated in the epithelial layer of endometriotic lesions compared with eutopic endometrium, supporting a role in the disease.\r\nConclusions: LINC01638 is an epigenetic regulator of the pathogenesis of endometriosis, promoting proliferation and EMT of endometriotic lesions."}],"author":[{"last_name":"Yotova","first_name":"Iveta","full_name":"Yotova, Iveta"},{"first_name":"Katharina","full_name":"Proestling, Katharina","last_name":"Proestling"},{"last_name":"Pauler","first_name":"Florian","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rainer","first_name":"Lisa","full_name":"Rainer, Lisa"},{"full_name":"Kaup, Leonie","first_name":"Leonie","last_name":"Kaup"},{"last_name":"Heine","full_name":"Heine, Jana","first_name":"Jana"},{"last_name":"Sandrieser","full_name":"Sandrieser, Lejla","first_name":"Lejla"},{"last_name":"Wenzl","first_name":"René","full_name":"Wenzl, René"},{"last_name":"Hudson","first_name":"Quanah J.","full_name":"Hudson, Quanah J."}],"pmid":1,"isi":1,"article_number":"104942","OA_type":"closed access","status":"public","_id":"20079","month":"07","year":"2025","publication":"Reproductive Biomedicine Online","scopus_import":"1","title":"LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression","article_processing_charge":"No","doi":"10.1016/j.rbmo.2025.104942","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.rbmo.2025.104942","day":"17","publication_identifier":{"issn":["1472-6483"],"eissn":["1472-6491"]},"acknowledgement":"The authors wish to thank all the participants and health professionals involved in this study. In addition, the authors wish to thank technical assistants Barbara Widmar, Matthias Witzmann-Stern and Isabella Haslinger for their work assisting with this study; and Simon Hippenmeyer for access to bioinformatic infrastructure and resources.\r\nOpen access funding was provided by the Medical University of Vienna.","volume":51,"citation":{"chicago":"Yotova, Iveta, Katharina Proestling, Florian Pauler, Lisa Rainer, Leonie Kaup, Jana Heine, Lejla Sandrieser, René Wenzl, and Quanah J. Hudson. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>.","ieee":"I. Yotova <i>et al.</i>, “LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression,” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3. Elsevier, 2025.","short":"I. Yotova, K. Proestling, F. Pauler, L. Rainer, L. Kaup, J. Heine, L. Sandrieser, R. Wenzl, Q.J. Hudson, Reproductive Biomedicine Online 51 (2025).","ama":"Yotova I, Proestling K, Pauler F, et al. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. 2025;51(3). doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>","ista":"Yotova I, Proestling K, Pauler F, Rainer L, Kaup L, Heine J, Sandrieser L, Wenzl R, Hudson QJ. 2025. LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. Reproductive Biomedicine Online. 51(3), 104942.","mla":"Yotova, Iveta, et al. “LINC01638 Promotes Epithelial-to-Mesenchymal Transition in Endometriosis Epithelial Cells by up-Regulating RHOB via HDAC1 Suppression.” <i>Reproductive Biomedicine Online</i>, vol. 51, no. 3, 104942, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">10.1016/j.rbmo.2025.104942</a>.","apa":"Yotova, I., Proestling, K., Pauler, F., Rainer, L., Kaup, L., Heine, J., … Hudson, Q. J. (2025). LINC01638 promotes epithelial-to-mesenchymal transition in endometriosis epithelial cells by up-regulating RHOB via HDAC1 suppression. <i>Reproductive Biomedicine Online</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.rbmo.2025.104942\">https://doi.org/10.1016/j.rbmo.2025.104942</a>"},"external_id":{"isi":["001549819000002"],"pmid":["40680553"]},"issue":"3","date_published":"2025-07-17T00:00:00Z","type":"journal_article","intvolume":"        51","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2025-07-27T22:01:25Z","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_type":"original","publication_status":"published","department":[{"_id":"SiHi"}],"date_updated":"2025-09-30T14:10:46Z"},{"publisher":"Frontiers Media","OA_place":"publisher","doi":"10.3389/fpls.2025.1612366","file_date_updated":"2025-07-31T07:28:54Z","ddc":["580"],"fulldoi":"https://doi.org/10.3389/fpls.2025.1612366","day":"04","PlanS_conform":"1","APC_amount":"3642,79 EUR","publication_identifier":{"eissn":["1664-462X"]},"year":"2025","month":"07","_id":"20080","status":"public","publication":"Frontiers in Plant Science","DOAJ_listed":"1","title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","scopus_import":"1","oa":1,"article_processing_charge":"Yes","article_number":"1612366","corr_author":"1","isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"OA_type":"gold","abstract":[{"lang":"eng","text":"Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction."}],"author":[{"last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"last_name":"Montesinos López","orcid":"0000-0001-9179-6099","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a","full_name":"Zarevski, Nikola","first_name":"Nikola","last_name":"Zarevski"},{"first_name":"Jan","full_name":"Pribyl, Jan","last_name":"Pribyl"},{"last_name":"Skládal","full_name":"Skládal, Petr","first_name":"Petr"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková"}],"pmid":1,"article_type":"original","file":[{"file_id":"20093","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","relation":"main_file","date_updated":"2025-07-31T07:28:54Z","success":1,"content_type":"application/pdf","file_name":"2025_FrontiersPlantSc_Gallemi.pdf","file_size":3665187,"creator":"dernst","date_created":"2025-07-31T07:28:54Z","access_level":"open_access"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication_status":"published","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"date_updated":"2026-05-20T07:53:03Z","date_published":"2025-07-04T00:00:00Z","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","intvolume":"        16","date_created":"2025-07-27T22:01:26Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"external_id":{"pmid":["40688689"],"isi":["001530690900001"]},"citation":{"ista":"Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.","ama":"Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. 2025;16. doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>","mla":"Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>, vol. 16, 1612366, Frontiers Media, 2025, doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>.","apa":"Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., &#38; Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>","ieee":"M. Gallemi <i>et al.</i>, “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” <i>Frontiers in Plant Science</i>, vol. 16. Frontiers Media, 2025.","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","chicago":"Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2025. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>."},"ec_funded":1,"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","name":"Hormonal cross-talk in plant organogenesis","grant_number":"207362","call_identifier":"FP7"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"acknowledgement":"The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method.","volume":16},{"external_id":{"isi":["001529134300001"],"pmid":["40664976"]},"page":"1258–1266","citation":{"chicago":"Dos Reis Rodrigues, Patricia, Mario Avellaneda Sarrió, Nikola Canigova, Florian R Gärtner, Kari Vaahtomeri, Michael Riedl, Ingrid de Vries, et al. “Migrating Immune Cells Globally Coordinate Protrusive Forces.” <i>Nature Immunology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41590-025-02211-w\">https://doi.org/10.1038/s41590-025-02211-w</a>.","short":"P. Dos Reis Rodrigues, M. Avellaneda Sarrió, N. Canigova, F.R. Gärtner, K. Vaahtomeri, M. Riedl, I. de Vries, J. Merrin, R. Hauschild, Y. Fukui, A. Juanes Garcia, M.K. Sixt, Nature Immunology 26 (2025) 1258–1266.","ieee":"P. Dos Reis Rodrigues <i>et al.</i>, “Migrating immune cells globally coordinate protrusive forces,” <i>Nature Immunology</i>, vol. 26. Springer Nature, pp. 1258–1266, 2025.","mla":"Dos Reis Rodrigues, Patricia, et al. “Migrating Immune Cells Globally Coordinate Protrusive Forces.” <i>Nature Immunology</i>, vol. 26, Springer Nature, 2025, pp. 1258–1266, doi:<a href=\"https://doi.org/10.1038/s41590-025-02211-w\">10.1038/s41590-025-02211-w</a>.","apa":"Dos Reis Rodrigues, P., Avellaneda Sarrió, M., Canigova, N., Gärtner, F. R., Vaahtomeri, K., Riedl, M., … Sixt, M. K. (2025). Migrating immune cells globally coordinate protrusive forces. <i>Nature Immunology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41590-025-02211-w\">https://doi.org/10.1038/s41590-025-02211-w</a>","ama":"Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, et al. Migrating immune cells globally coordinate protrusive forces. <i>Nature Immunology</i>. 2025;26:1258–1266. doi:<a href=\"https://doi.org/10.1038/s41590-025-02211-w\">10.1038/s41590-025-02211-w</a>","ista":"Dos Reis Rodrigues P, Avellaneda Sarrió M, Canigova N, Gärtner FR, Vaahtomeri K, Riedl M, de Vries I, Merrin J, Hauschild R, Fukui Y, Juanes Garcia A, Sixt MK. 2025. Migrating immune cells globally coordinate protrusive forces. Nature Immunology. 26, 1258–1266."},"project":[{"name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces","grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd"},{"_id":"c092d618-5a5b-11eb-8a69-f92e1e843fc8","name":"Bioelectric patrolling: the role of the local membrane potential in immune cell migration","grant_number":"944-2020"}],"volume":26,"acknowledgement":"This research was supported by the Scientific Service Units of ISTA through resources provided by the Imaging and Optics, Preclinical and Lab Support Facilities. In particular, we thank M. A. Symth and F. G. G. Leite, from the Virus Service Team, who helped generating the lentiviral particles used in this study. We thank all the members of the Sixt group for valuable discussions and feedback, in particular, I. Mayer, for helping with T cell isolation and Z. (P.) Li for providing the Actin–GFP DC line. We are also thankful to J. Mandl and C. Shen for their feedback during the writing of this manuscript. This work was supported by a European Research Council grant ERC-SyG 101071793 to M.S. M.J.A. was supported by an HFSP Postdoctoral Fellowship LTF 177 2021 and A.J.G. by a Lise Meitner Fellowship of the FWF (Austrian Science Fund). Y.F. was supported by the AMED-CREST (JP19gm1310005), the Medical Research Center Initiative for High Depth Omics and CURE:JPMXP1323015486 for MIB, Kyushu University. Open access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"date_updated":"2026-04-28T13:26:50Z","article_type":"letter_note","file":[{"date_created":"2025-07-31T08:00:33Z","file_size":13514646,"creator":"dernst","access_level":"open_access","date_updated":"2025-07-31T08:00:33Z","file_id":"20096","checksum":"0c725123dca7797c682609bff2c4c5ac","relation":"main_file","content_type":"application/pdf","file_name":"2025_NatureImmunology_ReisRodrigues.pdf","success":1}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","intvolume":"        26","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2025-07-27T22:01:26Z","oa_version":"Published Version","language":[{"iso":"eng"}],"date_published":"2025-08-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","corr_author":"1","isi":1,"OA_type":"hybrid","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"author":[{"id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","full_name":"Dos Reis Rodrigues, Patricia","first_name":"Patricia","orcid":"0000-0003-1681-508X","last_name":"Dos Reis Rodrigues"},{"last_name":"Avellaneda Sarrió","orcid":"0000-0001-6406-524X","first_name":"Mario","id":"DC4BA84C-56E6-11EA-AD5D-348C3DDC885E","full_name":"Avellaneda Sarrió, Mario"},{"full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","first_name":"Nikola","last_name":"Canigova"},{"orcid":"0000-0001-6120-3723","first_name":"Florian R","full_name":"Gärtner, Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner"},{"full_name":"Vaahtomeri, Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","orcid":"0000-0001-7829-3518","last_name":"Vaahtomeri"},{"first_name":"Michael","orcid":"0000-0003-4844-6311","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael","last_name":"Riedl"},{"last_name":"De Vries","first_name":"Ingrid","full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","last_name":"Merrin"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"full_name":"Fukui, Yoshinori","first_name":"Yoshinori","last_name":"Fukui"},{"last_name":"Juanes Garcia","orcid":"0000-0002-1009-9652","first_name":"Alba","full_name":"Juanes Garcia, Alba","id":"40F05888-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt"}],"pmid":1,"related_material":{"link":[{"url":"https://ista.ac.at/en/news/bench-pressing-cells/","description":"News on ISTA website","relation":"press_release"}],"record":[{"status":"public","relation":"dissertation_contains","id":"20149"}]},"abstract":[{"lang":"eng","text":"Efficient immune responses rely on the capacity of leukocytes to traverse diverse and complex tissues. To meet such changing environmental conditions, leukocytes usually adopt an ameboid configuration, using their forward-positioned nucleus as a probe to identify and follow the path of least resistance among pre-existing pores. We show that, in dense environments where even the largest pores preclude free passage, leukocytes position their nucleus behind the centrosome and organelles. The local compression imposed on the cell body by its surroundings triggers assembly of a central F-actin pool, located between cell front and nucleus. Central actin pushes outward to transiently dilate a path for organelles and nucleus. Pools of central and front actin are tightly coupled and experimental depletion of the central pool enhances actin accumulation and protrusion formation at the cell front. Although this shifted balance speeds up cells in permissive environments, migration in restrictive environments is impaired, as the unleashed leading edge dissociates from the trapped cell body. Our findings establish an actin regulatory loop that balances path dilation with advancement of the leading edge to maintain cellular coherence."}],"PlanS_conform":"1","day":"01","publication_identifier":{"eissn":["1529-2916"],"issn":["1529-2908"]},"publisher":"Springer Nature","doi":"10.1038/s41590-025-02211-w","file_date_updated":"2025-07-31T08:00:33Z","OA_place":"publisher","fulldoi":"https://doi.org/10.1038/s41590-025-02211-w","ddc":["570"],"title":"Migrating immune cells globally coordinate protrusive forces","scopus_import":"1","oa":1,"article_processing_charge":"Yes (via OA deal)","year":"2025","_id":"20082","status":"public","month":"08","publication":"Nature Immunology"},{"ec_funded":1,"issue":"3","citation":{"ama":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. 2025;4(3). doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>","ista":"Hwong Y-L, Byers E, Werning M, Quilcaille Y. 2025. Sustainable development key to limiting climate change-driven wildfire damages. Environmental Research: Climate. 4(3), 035005.","apa":"Hwong, Y.-L., Byers, E., Werning, M., &#38; Quilcaille, Y. (2025). Sustainable development key to limiting climate change-driven wildfire damages. <i>Environmental Research: Climate</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>","mla":"Hwong, Yi-Ling, et al. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>, vol. 4, no. 3, 035005, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/2752-5295/adec11\">10.1088/2752-5295/adec11</a>.","ieee":"Y.-L. Hwong, E. Byers, M. Werning, and Y. Quilcaille, “Sustainable development key to limiting climate change-driven wildfire damages,” <i>Environmental Research: Climate</i>, vol. 4, no. 3. IOP Publishing, 2025.","short":"Y.-L. Hwong, E. Byers, M. Werning, Y. Quilcaille, Environmental Research: Climate 4 (2025).","chicago":"Hwong, Yi-Ling, Edward Byers, Michaela Werning, and Yann Quilcaille. “Sustainable Development Key to Limiting Climate Change-Driven Wildfire Damages.” <i>Environmental Research: Climate</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/2752-5295/adec11\">https://doi.org/10.1088/2752-5295/adec11</a>."},"project":[{"call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"acknowledgement":"We thank Marina Andrijevic, Giacomo Falchetta, Samuel Lüthi, Caroline Muller, Carl Schleussner, and Adriano Vinca for providing useful ideas and feedback for this work. YLH is supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie Grant No. 101034413. EB, MW, and YQ are supported by the European Union’s Horizon Europe research and innovation programme under Grant Agreement No. 101081369 (SPARCCLE). We also thank the two anonymous reviewers for providing helpful feedback that greatly improved this manuscript.","volume":4,"publication_status":"published","department":[{"_id":"CaMu"}],"date_updated":"2025-08-04T07:46:33Z","article_type":"original","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"access_level":"open_access","creator":"dernst","file_size":2807041,"date_created":"2025-08-04T07:38:14Z","success":1,"file_name":"2025_EnvironResearchClimate_Hwong.pdf","content_type":"application/pdf","relation":"main_file","checksum":"ca679496767021e792b0378c48fdee8c","file_id":"20108","date_updated":"2025-08-04T07:38:14Z"}],"intvolume":"         4","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_created":"2025-07-31T14:03:16Z","date_published":"2025-07-15T00:00:00Z","type":"journal_article","has_accepted_license":"1","corr_author":"1","article_number":"035005","OA_type":"gold","author":[{"first_name":"Yi-Ling","orcid":"0000-0001-9281-3479","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","full_name":"Hwong, Yi-Ling","last_name":"Hwong"},{"first_name":"Edward","full_name":"Byers, Edward","last_name":"Byers"},{"last_name":"Werning","first_name":"Michaela","full_name":"Werning, Michaela"},{"first_name":"Yann","full_name":"Quilcaille, Yann","last_name":"Quilcaille"}],"related_material":{"record":[{"relation":"research_data","id":"20107","status":"public"}]},"abstract":[{"text":"Climate change is causing wildfires to become more frequent and intense. While predicting burned areas using bioclimatic and anthropogenic factors is an active research area, few studies have examined what drives the economic damages of wildfires. Our study aims to fill this gap by analyzing key factors influencing global economic wildfire damages and projecting future damages under three shared socioeconomic pathways (SSPs). We apply regression analyses to identify significant predictors of economic wildfire damages at country levels and use the fitted model to project future damages under SSP126, SSP245, and SSP370. Results show that the human vulnerability index (HVI), reflecting socioeconomic conditions, is the strongest predictor of historical wildfire damages, followed by water vapor pressure deficit during the fire season and population density around forested areas. We found high population density to be associated with lower damages. These findings contrast with studies of burned areas, where climate factors are more dominant. Our model projects that by 2070, average global economic wildfire damages will be three times higher under SSP370 than SSP126. Our model also shows that following SSP126 not only reduces wildfire damages but also lessens the inequalities in damage distribution across countries. This pathway’s dual focus on equitable socioeconomic progress and climate action potentially enhances a country’s resilience that helps mitigate wildfire damages. Our analyses also indicate that strong socioeconomic development can offset wildfire damages associated with climate hazards, although this is less certain under SSP370. SSP126’s integrated approach improves both socioeconomic conditions and limits global warming, providing substantial benefits to less developed countries while still reducing damages in developed nations, despite their already low HVI scores. Our work complements existing research on burned areas and underscores the importance of sustainable development and international collaboration in reducing the economic damages of wildfires.","lang":"eng"}],"day":"15","PlanS_conform":"1","publication_identifier":{"eissn":["2752-5295"]},"OA_place":"publisher","file_date_updated":"2025-08-04T07:38:14Z","doi":"10.1088/2752-5295/adec11","publisher":"IOP Publishing","ddc":["550"],"fulldoi":"https://doi.org/10.1088/2752-5295/adec11","scopus_import":"1","title":"Sustainable development key to limiting climate change-driven wildfire damages","article_processing_charge":"Yes","oa":1,"_id":"20098","month":"07","status":"public","year":"2025","publication":"Environmental Research: Climate","DOAJ_listed":"1"},{"year":"2025","status":"public","_id":"20100","month":"06","publication":"Computational and Structural Biotechnology Journal","DOAJ_listed":"1","title":"Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment","scopus_import":"1","oa":1,"article_processing_charge":"Yes","publisher":"Elsevier","doi":"10.1016/j.csbj.2025.07.039","OA_place":"publisher","file_date_updated":"2025-08-04T06:25:23Z","fulldoi":"https://doi.org/10.1016/j.csbj.2025.07.039","ddc":["000","570"],"day":"27","PlanS_conform":"1","publication_identifier":{"eissn":["2001-0370"]},"related_material":{"record":[{"id":"20103","relation":"software","status":"public"}],"link":[{"url":"https://github.com/sankethvedula/AFChimera","relation":"software"}]},"abstract":[{"text":"A key step in protein structure prediction involves the detection of co-evolving pairs of residues, a signal for spatial proximity. This information is gleaned from multiple sequence alignment and underscores Alphafold’s structure prediction for almost every known protein. A simple means to create proteins beyond those found in nature, is by unnaturally fusing together two known proteins or protein parts. Here we demonstrate that structured peptides are predicted with significantly reduced accuracy when added to the terminal ends of scaffold proteins. Appending the multiple sequence alignment for the individual peptide tags to that of the scaffold protein often restores prediction accuracy. This work suggests that this windowed multiple sequence alignment approach can be a useful tool for predicting the structure of fused, chimeric proteins.","lang":"eng"}],"author":[{"last_name":"Vedula","first_name":"Sanketh","full_name":"Vedula, Sanketh","id":"94f2fe44-70fa-11f0-b76b-92922c09452b"},{"last_name":"Bronstein","id":"58f3726e-7cba-11ef-ad8b-e6e8cb3904e6","full_name":"Bronstein, Alexander","first_name":"Alexander","orcid":"0000-0001-9699-8730"},{"full_name":"Marx, Ailie","first_name":"Ailie","last_name":"Marx"}],"isi":1,"OA_type":"gold","date_published":"2025-06-27T00:00:00Z","has_accepted_license":"1","type":"journal_article","intvolume":"        27","quality_controlled":"1","date_created":"2025-08-03T22:01:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","language":[{"iso":"eng"}],"article_type":"original","file":[{"access_level":"open_access","creator":"dernst","file_size":6609770,"date_created":"2025-08-04T06:25:23Z","success":1,"file_name":"2025_CompStrucBiotechJour_Vedula.pdf","content_type":"application/pdf","relation":"main_file","checksum":"78d01f30fc1dc11dd2bd1d7bb7ac8a62","file_id":"20104","date_updated":"2025-08-04T06:25:23Z"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"department":[{"_id":"AlBr"}],"publication_status":"published","date_updated":"2025-11-27T14:09:59Z","acknowledgement":"AM acknowledges the financial support of the Helmsley Fellowships Program for Sustainability and Health. AMB is supported by the Schmidt Chair in Artificial Intelligence.","volume":27,"external_id":{"isi":["001583543100001"]},"citation":{"ieee":"S. Vedula, A. M. Bronstein, and A. Marx, “Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment,” <i>Computational and Structural Biotechnology Journal</i>, vol. 27. Elsevier, pp. 3292–3298, 2025.","short":"S. Vedula, A.M. Bronstein, A. Marx, Computational and Structural Biotechnology Journal 27 (2025) 3292–3298.","ista":"Vedula S, Bronstein AM, Marx A. 2025. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. Computational and Structural Biotechnology Journal. 27, 3292–3298.","ama":"Vedula S, Bronstein AM, Marx A. Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. 2025;27:3292-3298. doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>","apa":"Vedula, S., Bronstein, A. M., &#38; Marx, A. (2025). Improving prediction accuracy in chimeric proteins with windowed multiple sequence alignment. <i>Computational and Structural Biotechnology Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>","mla":"Vedula, Sanketh, et al. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>, vol. 27, Elsevier, 2025, pp. 3292–98, doi:<a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">10.1016/j.csbj.2025.07.039</a>.","chicago":"Vedula, Sanketh, Alex M. Bronstein, and Ailie Marx. “Improving Prediction Accuracy in Chimeric Proteins with Windowed Multiple Sequence Alignment.” <i>Computational and Structural Biotechnology Journal</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.csbj.2025.07.039\">https://doi.org/10.1016/j.csbj.2025.07.039</a>."},"page":"3292-3298"},{"publication_status":"published","department":[{"_id":"NiBa"}],"date_updated":"2025-12-30T09:25:45Z","article_type":"original","file":[{"access_level":"open_access","date_created":"2025-12-30T09:25:17Z","creator":"dernst","file_size":2767745,"file_name":"2025_MolecEcology_Raffini.pdf","content_type":"application/pdf","success":1,"date_updated":"2025-12-30T09:25:17Z","checksum":"ec01edda64cfbc6cbc8adf300f719644","relation":"main_file","file_id":"20906"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"quality_controlled":"1","intvolume":"        34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-08-03T22:01:31Z","oa_version":"Published Version","language":[{"iso":"eng"}],"date_published":"2025-11-01T00:00:00Z","has_accepted_license":"1","type":"journal_article","issue":"21","external_id":{"isi":["001538172800001"]},"citation":{"ieee":"F. Raffini <i>et al.</i>, “Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail,” <i>Molecular Ecology</i>, vol. 34, no. 21. Wiley, 2025.","short":"F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram, J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).","ama":"Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. 2025;34(21). doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>","ista":"Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. Molecular Ecology. 34(21), e70025.","apa":"Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram, A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>","mla":"Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>, vol. 34, no. 21, e70025, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/mec.70025\">10.1111/mec.70025</a>.","chicago":"Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K. Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes at Two Different Points on the Speciation Continuum in a Marine Snail.” <i>Molecular Ecology</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/mec.70025\">https://doi.org/10.1111/mec.70025</a>."},"volume":34,"acknowledgement":"This study was supported by European Research Council grant 693030-BARRIERS to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021) to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU (ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’ and Norwegian Research Council RCN, project 315287 to AMW.","PlanS_conform":"1","day":"01","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"publisher":"Wiley","OA_place":"publisher","file_date_updated":"2025-12-30T09:25:17Z","doi":"10.1111/mec.70025","ddc":["570"],"fulldoi":"https://doi.org/10.1111/mec.70025","title":"Phenotypic divergence and genomic architecture between parallel ecotypes at two different points on the speciation continuum in a marine snail","scopus_import":"1","oa":1,"article_processing_charge":"Yes (in subscription journal)","year":"2025","month":"11","_id":"20102","status":"public","publication":"Molecular Ecology","article_number":"e70025","isi":1,"OA_type":"hybrid","author":[{"last_name":"Raffini","first_name":"Francesca","full_name":"Raffini, Francesca"},{"last_name":"De Jode","first_name":"Aurélien","full_name":"De Jode, Aurélien"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"last_name":"Zagrodzka","first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B."},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Galindo, Juan","first_name":"Juan","last_name":"Galindo"},{"last_name":"Rolán-Alvarez","full_name":"Rolán-Alvarez, Emilio","first_name":"Emilio"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"abstract":[{"lang":"eng","text":"Speciation is rarely observable directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially overlapping clusters in Spain suggesting a much stronger barrier to gene flow. The absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and country-specific chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems."}]}]