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| | === 2025 === |
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| | - Achterberg, T. & de Jong, A. (2025). ProPr54 web server: predicting σ54 promoters and regulon with a hybrid convolutional and recurrent deep neural network. //NAR Genomics and Bioinformatics//, //7//(1), lqae188 [ [[http://dx.doi.org/10.1093/nargab/lqae188|DOI]] | [[https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqae188/7944699|http]] ] |
| | - Aróstica, R., Nolte, D., Brown, A., et al. (2025). A software benchmark for cardiac elastodynamics. //Computer Methods in Applied Mechanics and Engineering//, //435//, 117485 [ [[http://dx.doi.org/10.1016/j.cma.2024.117485|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S0045782524007394|http]] ] |
| | - Bai, S., Yang, X., Koszorús, �., et al. (2025). Charge Radii of Neutron-Rich Scandium Isotopes and the Seniority Symmetry in the 0 f 7 / 2 Shell. //Physical Review Letters//, //134//(18), 182501 [ [[http://dx.doi.org/10.1103/PhysRevLett.134.182501|DOI]] | [[https://link.aps.org/doi/10.1103/PhysRevLett.134.182501|http]] ] |
| | - Barts, E., Tenzin, K., & Sławińska, J. (2025). Efficient spin accumulation carried by slow relaxons in chiral tellurium. //Nature Communications//, //16//(1), 4056 [ [[http://dx.doi.org/10.1038/s41467-025-59143-0|DOI]] | [[https://www.nature.com/articles/s41467-025-59143-0|http]] ] |
| | - Brait, N., Hackl, T., & Lequime, S. (2025). detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data. //Molecular Ecology Resources//, //25//(4), e14083 [ [[http://dx.doi.org/10.1111/1755-0998.14083|DOI]] | [[https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.14083|http]] ] |
| | - Bravo, H., Ben Chehida, Y., & Van Der Meij, S. E. T. (2025). SAMPLE: An R Package to Estimate Sampling Effort for Species' Occurrence Rates. //Ecology and Evolution//, //15//(4), e70998 [ [[http://dx.doi.org/10.1002/ece3.70998|DOI]] | [[https://onlinelibrary.wiley.com/doi/10.1002/ece3.70998|http]] ] |
| | - Bruegger, J., Cătană, D. I., Macovaz, V., et al. (2025). Large-Image Object Detection for Fine-Grained Recognition of Punches Patterns in Medieval Panel Painting. In P. Machado, C. Johnson, & I. Santos, editors, //Artificial Intelligence in Music, Sound, Art and Design//, volume 15611, pages 34--50. Springer Nature Switzerland, Cham. ISBN 978-3-031-90166-9 978-3-031-90167-6. Series Title: Lecture Notes in Computer Science [ [[http://dx.doi.org/10.1007/978-3-031-90167-6_3|DOI]] | [[https://link.springer.com/10.1007/978-3-031-90167-6_3|http]] ] |
| | - Brunner, F., Andric, P., & Maresca, F. (2025). An atomistic //K// -test framework for general grain boundaries and triclinic single crystals. //Modelling and Simulation in Materials Science and Engineering//, //33//(3), 035004 [ [[http://dx.doi.org/10.1088/1361-651X/adba03|DOI]] | [[https://iopscience.iop.org/article/10.1088/1361-651X/adba03|http]] ] |
| | - Chen, J., Sardjan, A. S., De Roo, C. M., et al. (2025). Generation of [(N4Py)Fe(IV)═O]<sup>2+</sup> through Heterolytic O–O Bond Cleavage in [(N4Py)Fe(II)(OOH)]<sup>+</sup>. //Inorganic Chemistry//, //64//(19), 9408--9417 [ [[http://dx.doi.org/10.1021/acs.inorgchem.4c05172|DOI]] | [[https://pubs.acs.org/doi/10.1021/acs.inorgchem.4c05172|http]] ] |
| | - Chen Ye, C., Kreminska, Y., Ye, J., & Sławińska, J. (2025). First-principles studies of fermiology in topological phases of bulk ZrTe 5. //Physical Review Materials//, //9//(5), 054204 [ [[http://dx.doi.org/10.1103/PhysRevMaterials.9.054204|DOI]] | [[https://link.aps.org/doi/10.1103/PhysRevMaterials.9.054204|http]] ] |
| | - Chik, H. Y. J., Sibma, A., Mannarelli, M.-E., et al. (2025). Heritability and age-dependent changes in genetic variation of telomere length in a wild house sparrow population. //Evolution Letters//, //9//(2), 209--220 [ [[http://dx.doi.org/10.1093/evlett/qrae055|DOI]] | [[https://academic.oup.com/evlett/article/9/2/209/7906351|http]] ] |
| | - Chu, H., De Vette, S. P., Neh, H., et al. (2025). Three-Dimensional Deep Learning Normal Tissue Complication Probability Model to Predict Late Xerostomia in Patients With Head and Neck Cancer. //International Journal of Radiation Oncology*Biology*Physics//, //121//(1), 269--280 [ [[http://dx.doi.org/10.1016/j.ijrobp.2024.07.2334|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S0360301624031729|http]] ] |
| | - Chu, H., Ferreira, R. J., Lokhorst, C., et al. (2025). Predicting pulmonary hemodynamics in pediatric pulmonary arterial hypertension using cardiac magnetic resonance imaging and machine learning: an exploratory pilot study. //The International Journal of Cardiovascular Imaging// [ [[http://dx.doi.org/10.1007/s10554-025-03434-6|DOI]] | [[https://link.springer.com/10.1007/s10554-025-03434-6|http]] ] |
| | - Cotteret, M., Greatorex, H., Renner, A., et al. (2025). Distributed representations enable robust multi-timescale symbolic computation in neuromorphic hardware. //Neuromorphic Computing and Engineering//, //5//(1), 014008 [ [[http://dx.doi.org/10.1088/2634-4386/ada851|DOI]] | [[https://iopscience.iop.org/article/10.1088/2634-4386/ada851|http]] ] |
| | - Cui, J., Olthof, M., Hasselman, F., & Lichtwarck-Aschoff, A. (2025). Examining the research methods of early warning signals in clinical psychology through a theoretical lens. //BMC Psychiatry//, //25//(1), 261 [ [[http://dx.doi.org/10.1186/s12888-025-06688-5|DOI]] | [[https://bmcpsychiatry.biomedcentral.com/articles/10.1186/s12888-025-06688-5|http]] ] |
| | - De Biase, A., Sijtsema, N. M., Van Dijk, L. V., et al. (2025). Uncertainty-aware deep learning for segmentation of primary tumor and pathologic lymph nodes in oropharyngeal cancer: Insights from a multi-center cohort. //Computerized Medical Imaging and Graphics//, //123//, 102535 [ [[http://dx.doi.org/10.1016/j.compmedimag.2025.102535|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S0895611125000448|http]] ] |
| | - Di Berto Mancini, M., De Roo, C. M., Sardjan, A. S., et al. (2025). A Transient, Highly Reactive Fe(IV)═O Species Revealed Through the Interference by O<sub>2</sub> in the Activation of Organic Peracids by [(N4Py)Fe(II)]<sup>2+</sup>. //ACS Catalysis//, //15//(9), 7482--7495 [ [[http://dx.doi.org/10.1021/acscatal.5c00706|DOI]] | [[https://pubs.acs.org/doi/10.1021/acscatal.5c00706|http]] ] |
| | - Dimastrogiovanni, E., Fasiello, M., Michelotti, M., & Özsoy, O. (2025). A universal constraint on axion non-Abelian dynamics during inflation. //Journal of Cosmology and Astroparticle Physics//, //2025//(03), 007 [ [[http://dx.doi.org/10.1088/1475-7516/2025/03/007|DOI]] | [[https://iopscience.iop.org/article/10.1088/1475-7516/2025/03/007|http]] ] |
| | - Driver, M. D. & Onck, P. R. (2025). Selective phase separation of transcription factors is driven by orthogonal molecular grammar. //Nature Communications//, //16//(1), 3087 [ [[http://dx.doi.org/10.1038/s41467-025-58445-7|DOI]] | [[https://www.nature.com/articles/s41467-025-58445-7|http]] ] |
| | - Duijnstee, D. R., Tromp, M., Browne, W. R., & Staykov, A. (2025). Mobility of thiolates on Au(111) surfaces. //Physical Chemistry Chemical Physics//, //27//(9), 4892--4904 [ [[http://dx.doi.org/10.1039/D4CP03709J|DOI]] | [[https://xlink.rsc.org/?DOI=D4CP03709J|http]] ] |
| | - Erven, J. A. M., Mattiangeli, V., Dreshaj, M., et al. (2025). Archaeogenomic insights into commensalism and regional variation in pig management in Neolithic northwest Europe. //Proceedings of the National Academy of Sciences//, //122//(12), e2410235122 [ [[http://dx.doi.org/10.1073/pnas.2410235122|DOI]] | [[https://pnas.org/doi/10.1073/pnas.2410235122|http]] ] |
| | - Espinoza Cangahuala, M. K., Krishnaswamy, S. R., Kuevda, A. V., Pshenichnikov, M. S., & Jansen, T. L. C. (2025). The first step of cyanine dye self-assembly: Dimerization. //The Journal of Chemical Physics//, //162//(5), 054311 [ [[http://dx.doi.org/10.1063/5.0237531|DOI]] | [[https://pubs.aip.org/jcp/article/162/5/054311/3333888/The-first-step-of-cyanine-dye-self-assembly|http]] ] |
| | - Fellert, M., Hein, R., Ryabchun, A., et al. (2025). A Multiresponsive Ferrocene‐Based Chiral Overcrowded Alkene Twisting Liquid Crystals. //Angewandte Chemie International Edition//, //64//(1), e202413047 [ [[http://dx.doi.org/10.1002/anie.202413047|DOI]] | [[https://onlinelibrary.wiley.com/doi/10.1002/anie.202413047|http]] ] |
| | - Ferrao, J. L., Mikaelson, L., Pepper, K., & Perez-Campanero, N. (2025). Self-Ablating Transformers: More Interpretability, Less Sparsity. In //ICLR 2025 Workshop on Building Trust in Language Models and Applications// [ [[https://openreview.net/forum?id=QcmEb490bK|http]] ] |
| | - Gulyaeva, A., Liu, L., Garmaeva, S., et al. (2025). Identification and characterization of //Faecalibacterium// prophages rich in diversity-generating retroelements. //Microbiology Spectrum//, //13//(2), e01066--24 [ [[http://dx.doi.org/10.1128/spectrum.01066-24|DOI]] | [[https://journals.asm.org/doi/10.1128/spectrum.01066-24|http]] ] |
| | - Happe, A., Meijer, K. J., Dajka, J., et al. (2025). Synthesis of Population Trends Reveals Seascape‐Wide Reorganisation of Biodiversity From Microalgae to Birds. //Global Change Biology//, //31//(6), e70298 [ [[http://dx.doi.org/10.1111/gcb.70298|DOI]] | [[https://onlinelibrary.wiley.com/doi/10.1111/gcb.70298|http]] ] |
| | - Hein, R., Gisbert, Y., & Feringa, B. L. (2025). Multi-State Redox and Light-Driven Switching of Pseudorotaxanation and Cation Shuttling. //Journal of the American Chemical Society//, //147//(16), 13649--13657 [ [[http://dx.doi.org/10.1021/jacs.5c00997|DOI]] | [[https://pubs.acs.org/doi/10.1021/jacs.5c00997|http]] ] |
| | - Huitema, I. R., Oskooei, A. R., Aktaş, M. S., & Riveni, M. (2025). Investigating Echo-Chambers in Decentralized Social Networks: A Mastodon Case Study. In H. Cherifi, M. Donduran, L. M. Rocha, C. Cherifi, & O. Varol, editors, //Complex Networks & Their Applications XIII//, volume 1188, pages 316--328. Springer Nature Switzerland, Cham. ISBN 978-3-031-82430-2 978-3-031-82431-9. Series Title: Studies in Computational Intelligence [ [[http://dx.doi.org/10.1007/978-3-031-82431-9_26|DOI]] | [[https://link.springer.com/10.1007/978-3-031-82431-9_26|http]] ] |
| | - Jansen, T. L. C. (2025). The Manhattan exciton size: A physically tractable delocalization measure. //The Journal of Chemical Physics//, //162//(7), 074113 [ [[http://dx.doi.org/10.1063/5.0253831|DOI]] | [[https://pubs.aip.org/jcp/article/162/7/074113/3336403/The-Manhattan-exciton-size-A-physically-tractable|http]] ] |
| | - Kolbe, M., Bintanja, R., Van Der Linden, E. C., & Cordero, R. R. (2025). Vertical structure and surface impact of atmospheric rivers reaching antarctic sea ice and land. //Atmospheric Research//, //315//, 107841 [ [[http://dx.doi.org/10.1016/j.atmosres.2024.107841|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S0169809524006239|http]] ] |
| | - Kolbe, M., Torres Alavez, J. A., Mottram, R., et al. (2025). Model performance and surface impacts of atmospheric river events in Antarctica. //Discover Atmosphere//, //3//(1), 4 [ [[http://dx.doi.org/10.1007/s44292-025-00026-w|DOI]] | [[https://link.springer.com/10.1007/s44292-025-00026-w|http]] ] |
| | - Kuevda, A. V., Espinoza Cangahuala, M. K., Hildner, R., Jansen, T. L. C., & Pshenichnikov, M. S. (2025). Linear Dichroism Microscopy Resolves Competing Structural Models of a Synthetic Light-Harvesting Complex. //Journal of the American Chemical Society//, //147//(7), 6171--6180 [ [[http://dx.doi.org/10.1021/jacs.4c17708|DOI]] | [[https://pubs.acs.org/doi/10.1021/jacs.4c17708|http]] ] |
| | - Kyuberis, A. A., Pašteka, L. F., Eliav, E., et al. (2025). Theoretical determination of the ionization potentials of ScF, YF, LaF, and AcF. //Physical Review A//, //111//(4), 042823 [ [[http://dx.doi.org/10.1103/PhysRevA.111.042823|DOI]] | [[https://link.aps.org/doi/10.1103/PhysRevA.111.042823|http]] ] |
| | - Lagendijk, D. G., Beentjes, K., Belting, H., et al. (2025). Arthropod taxa in faeces of chicks of Black-tailed Godwits and Northern Lapwings in Germany and the Netherlands revealed by DNA metabarcoding. //Wader Study//, //132//(1) [ [[http://dx.doi.org/10.18194/ws.00368|DOI]] | [[https://www.waderstudygroup.org/article/18883/|http]] ] |
| | - Lambert, J. W., Roeble, L., Pannetier, T., Etienne, R. S., & Valente, L. (2025). Using phylogenetic data for island biogeography analyses: The DAISIEprep package. //Molecular Phylogenetics and Evolution//, //206//, 108324 [ [[http://dx.doi.org/10.1016/j.ympev.2025.108324|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S1055790325000417|http]] ] |
| | - Ma, B., De Biase, A., Guo, J., et al. (2025). The prognostic value of pathologic lymph node imaging using deep learning-based outcome prediction in oropharyngeal cancer patients. //Physics and Imaging in Radiation Oncology//, //33//, 100733 [ [[http://dx.doi.org/10.1016/j.phro.2025.100733|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S2405631625000387|http]] ] |
| | - Ma, B., Guo, J., Dijk, L. V. V., et al. (2025). PET and CT based DenseNet outperforms advanced deep learning models for outcome prediction of oropharyngeal cancer. //Radiotherapy and Oncology//, //207//, 110852 [ [[http://dx.doi.org/10.1016/j.radonc.2025.110852|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S0167814025001471|http]] ] |
| | - Magini, J., Pisciotta, P., Hussein, M., et al. (2025). Integration of microdosimetry into treatment planning systems using look-up tables (LUT): A proof-of-concept. //Physica Medica//, //136//, 105031 [ [[http://dx.doi.org/10.1016/j.ejmp.2025.105031|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S1120179725001413|http]] ] |
| | - Mahajna, A., Geurkink, B., Gacesa, R., et al. (2025). Metatranscriptomes of activated sludge microbiomes from saline wastewater treatment plant. //Scientific Data//, //12//(1), 348 [ [[http://dx.doi.org/10.1038/s41597-025-04682-w|DOI]] | [[https://www.nature.com/articles/s41597-025-04682-w|http]] ] |
| | - Mohamed Yunus, R. A., Gürel, U., Guzik, A., et al. (2025). Glass Transition and Yielding of Ultrasoft Charged Spherical Micelles. //Macromolecules//, page acs.macromol.4c03215 [ [[http://dx.doi.org/10.1021/acs.macromol.4c03215|DOI]] | [[https://pubs.acs.org/doi/10.1021/acs.macromol.4c03215|http]] ] |
| | - Mol, F. N., Van Der Hoek, L., Ma, B., et al. (2025). MRI-Based Head and Neck Tumor Segmentation Using nnU-Net with 15-Fold Cross-Validation Ensemble. In K. A. Wahid, C. Dede, M. A. Naser, & C. D. Fuller, editors, //Head and Neck Tumor Segmentation for MR-Guided Applications//, volume 15273, pages 179--190. Springer Nature Switzerland, Cham. ISBN 978-3-031-83273-4 978-3-031-83274-1. Series Title: Lecture Notes in Computer Science [ [[http://dx.doi.org/10.1007/978-3-031-83274-1_13|DOI]] | [[https://link.springer.com/10.1007/978-3-031-83274-1_13|http]] ] |
| | - Ndung’u, S., Grobler, T., Wijnholds, S. J., & Azzopardi, G. (2025). Content-based image retrieval using COSFIRE descriptors with application to radio astronomy. //Monthly Notices of the Royal Astronomical Society//, //537//(4), 3286--3297 [ [[http://dx.doi.org/10.1093/mnras/staf230|DOI]] | [[https://academic.oup.com/mnras/article/537/4/3286/8003779|http]] ] |
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| | - van Noord, R., Esplà-Gomis, M., Chichirau, M., Ramírez-Sánchez, G., & Toral, A. (2025). Quality Beyond A Glance: Revealing Large Quality Differences Between Web-Crawled Parallel Corpora. In O. Rambow, L. Wanner, M. Apidianaki, H. Al-Khalifa, B. D. Eugenio, & S. Schockaert, editors, //Proceedings of the 31st International Conference on Computational Linguistics//, pages 1824--1838. Association for Computational Linguistics, Abu Dhabi, UAE [ [[https://aclanthology.org/2025.coling-main.124/|http]] ] |
| | - Ovalle, M., Doellerer, D., & Feringa, B. L. (2025). Azobenzene‐Oxindole Photochromic Dyads. //Angewandte Chemie//, page e202501872 [ [[http://dx.doi.org/10.1002/ange.202501872|DOI]] | [[https://onlinelibrary.wiley.com/doi/10.1002/ange.202501872|http]] ] |
| | - Pramanik, R., Verstappen, R. W. C. P., & Onck, P. R. (2025). Emerging spatiotemporal patterns and collective swimming of magnetically actuated soft robots. //Nonlinear Dynamics// [ [[http://dx.doi.org/10.1007/s11071-025-11353-3|DOI]] | [[https://link.springer.com/10.1007/s11071-025-11353-3|http]] ] |
| | - Qin, T., Valente, L., & Etienne, R. S. (2025). Impact of evolutionary relatedness on species diversification and tree shape. //Journal of Theoretical Biology//, //598//, 111992 [ [[http://dx.doi.org/10.1016/j.jtbi.2024.111992|DOI]] | [[https://linkinghub.elsevier.com/retrieve/pii/S0022519324002777|http]] ] |
| | - Ryu, J., Trager, S. C., & Wilkinson, M. H. F. (2025). A Shared-Memory Parallel Alpha-Tree Algorithm for Extreme Dynamic Ranges. //IEEE Transactions on Image Processing//, //34//, 6629--6640 [ [[http://dx.doi.org/10.1109/TIP.2025.3616578|DOI]] | [[https://ieeexplore.ieee.org/document/11196007/|http]] ] |
| | - Shaheen, I., Brakman, S., Canello, J., & Garretsen, H. (2025). Firm interconnectedness and resilience: evidence from the Italian manufacturing. //Cambridge Journal of Regions, Economy and Society//, //18//(1), 211--226 [ [[http://dx.doi.org/10.1093/cjres/rsae034|DOI]] | [[https://academic.oup.com/cjres/article/18/1/211/7832401|http]] ] |
| | - Sloots, M., Franken, O., Meijer, K. J., et al. (2025). Marine Benthic Community Assembly Is Taxonomically Stochastic but Functionally Deterministic in a Dynamic Coastal Sea. //Ecology Letters//, //28//(10), e70228 [ [[http://dx.doi.org/10.1111/ele.70228|DOI]] | [[https://onlinelibrary.wiley.com/doi/10.1111/ele.70228|http]] ] |
| | - Stindt, C. N., Jo, T., Steen, J. D., Feringa, B. L., & Crespi, S. (2025). Computational Study on the Dynamics of a Bis(benzoxazole)-Based Overcrowded Alkene. //The Journal of Physical Chemistry A//, //129//(5), 1301--1309 [ [[http://dx.doi.org/10.1021/acs.jpca.4c06773|DOI]] | [[https://pubs.acs.org/doi/10.1021/acs.jpca.4c06773|http]] ] |
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| | - Tang, T., Snijders, T., & Flache, A. (2025). An Empirical and Simulation Investigation of Bounded Confidence and Negative Influence in Opinion Dynamics Using Stochastic Actor-Oriented Model. //Journal of Artificial Societies and Social Simulation//, //28//(1), 2 [ [[http://dx.doi.org/10.18564/jasss.5566|DOI]] | [[https://www.jasss.org/28/1/2.html|.html]] ] |
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| | - Wang, X. (2025). EGOFALLS: A Visual-Audio Dataset and Benchmark for Fall Detection Using Egocentric Cameras. In A. Antonacopoulos, S. Chaudhuri, R. Chellappa, C.-L. Liu, S. Bhattacharya, & U. Pal, editors, //Pattern Recognition//, volume 15302, pages 240--253. Springer Nature Switzerland, Cham. ISBN 978-3-031-78165-0 978-3-031-78166-7. Series Title: Lecture Notes in Computer Science [ [[http://dx.doi.org/10.1007/978-3-031-78166-7_16|DOI]] | [[https://link.springer.com/10.1007/978-3-031-78166-7_16|http]] ] |
| | - Zhong, K., Erić, V., Nguyen, H. L., et al. (2025). Application of the Time-Domain Multichromophoric Fluorescence Resonant Energy Transfer Method in the NISE Programme. //Journal of Chemical Theory and Computation//, //21//(1), 254--266 [ [[http://dx.doi.org/10.1021/acs.jctc.4c01135|DOI]] | [[https://pubs.acs.org/doi/10.1021/acs.jctc.4c01135|http]] ] |
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