PLM-eXplain: Divide and Conquer the Protein Embedding Space

Authors: van Eck, Jan, Gogishvili, Dea, Silva, Wilson, Abeln, Sanne

Subject Terms: Quantitative Biology - Biomolecules, Computer Science - Artificial Intelligence, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2504.07156

Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction

Authors: Eijpe, Aniek, Lakbir, Soufyan, Cesur, Melis Erdal, Oliveira, Sara P., Abeln, Sanne, Silva, Wilson

Subject Terms: Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2503.16069

Conceptual design of BabyIAXO, the intermediate stage towards the International Axion Observatory

Authors: The IAXO collaboration, A. Abeln, K. Altenmüller, S. Arguedas Cuendis, E. Armengaud, D. Attié, S. Aune, S. Basso, L. Bergé, B. Biasuzzi, P. T. C. Borges De Sousa, P. Brun, N. Bykovskiy, D. Calvet, J. M. Carmona, J. F. Castel, S. Cebrián, V. Chernov, F. E. Christensen, M. M. Civitani, C. Cogollos, T. Dafní, A. Derbin, K. Desch, D. Díez, M. Dinter, B. Döbrich, I. Drachnev, A. Dudarev, L. Dumoulin, D. D. M. Ferreira, E. Ferrer-Ribas, I. Fleck, J. Galán, D. Gascón, L. Gastaldo, M. Giannotti, Y. Giomataris, A. Giuliani, S. Gninenko, J. Golm, N. Golubev, L. Hagge, J. Hahn, C. J. Hailey, D. Hengstler, P. L. Henriksen, T. Houdy, R. Iglesias-Marzoa, F. J. Iguaz, I. G. Irastorza, C. Iñiguez, K. Jakovčić, J. Kaminski, B. Kanoute, S. Karstensen, L. Kravchuk, B. Lakić, T. Lasserre, P. Laurent, O. Limousin, A. Lindner, M. Loidl, I. Lomskaya, G. López-Alegre, B. Lubsandorzhiev, K. Ludwig, G. Luzón, C. Malbrunot, C. Margalejo, A. Marin-Franch, S. Marnieros, F. Marutzky, J. Mauricio, Y. Menesguen, M. Mentink, S. Mertens, F. Mescia, J. Miralda-Escudé, H. Mirallas, J. P. Mols, V. Muratova, X. F. Navick, C. Nones, A. Notari, A. Nozik, L. Obis, C. Oriol, F. Orsini, A. Ortiz de Solórzano, S. Oster, H. P. Pais Da Silva, V. Pantuev, T. Papaevangelou, G. Pareschi, K. Perez, O. Pérez, E. Picatoste, M. J. Pivovaroff, D. V. Poda, J. Redondo, A. Ringwald, M. Rodrigues, F. Rueda-Teruel, S. Rueda-Teruel, E. Ruiz-Choliz, J. Ruz, E. O. Saemann, J. Salvado, T. Schiffer, S. Schmidt, U. Schneekloth, M. Schott, L. Segui, F. Tavecchio, H. H. J. ten Kate, I. Tkachev, S. Troitsky, D. Unger, E. Unzhakov, N. Ushakov, J. K. Vogel, D. Voronin, A. Weltman, U. Werthenbach, W. Wuensch, A. Yanes-Díaz

Source: Journal of High Energy Physics, Vol 2021, Iss 5, Pp 1-80 (2021)

Subject Terms: Beyond Standard Model, Dark matter, CP violation, Other experiments, Nuclear and particle physics. Atomic energy. Radioactivity, QC770-798

File Description: electronic resource

Relation: https://doaj.org/toc/1029-8479

Access URL: https://doaj.org/article/98cfe5d0dc02483aa3cc967ba9034aa0

Mimicking the Gas-Phase to Transport Odorants through the Nasal Mucus: Functional Insights into Odorant Binding Proteins

Authors: Paesani, Massimiliano, Goetzee, Arthur G., Abeln, Sanne, Mouhib, Halima

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2410.15141

PatchProt: Hydrophobic patch prediction using protein foundation models

Authors: Gogishvili, Dea, Minois-Genin, Emmanuel, van Eck, Jan, Abeln, Sanne

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Artificial Intelligence, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2405.15928

CIBRA identifies genomic alterations with a system-wide impact on tumor biology

Authors: Lakbir, Soufyan, Buranelli, Caterina, Meijer, Gerrit A., Heringa, Jaap, Fijneman, Remond J. A., Abeln, Sanne

Source: Bioinformatics, Volume 40, Issue Supplement 2, September 2024, Pages ii37-ii44

Subject Terms: Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2403.03829

MMC Array to Study X-ray Transitions in Muonic Atoms

Authors: Unger, Daniel, Abeln, Andreas, Cocolios, Thomas Elias, Eizenberg, Ofir, Enss, Christian, Fleischmann, Andreas, Gastaldo, Loredana, Godinho, César, Heines, Michael, Hengstler, Daniel, Indelicato, Paul, Jadhav, Ashish, Kreuzberger, Daniel, Kirch, Klaus, Knecht, Andreas, Machado, Jorge, Ohayon, Ben, Paul, Nancy, Pohl, Randolf, von Schoeler, Katharina, Vogiatzi, Stergiani Marina, Wauters, Frederik

Subject Terms: Physics - Instrumentation and Detectors

Access URL: http://arxiv.org/abs/2311.12014

Towards Precision Muonic X-Ray Measurements of Charge Radii of Light Nuclei

Authors: Ohayon, Ben, Abeln, Andreas, Bara, Silvia, Cocolios, Thomas Elias, Eizenberg, Ofir, Fleischmann, Andreas, Gastaldo, Loredana, Godinho, César, Heines, Michael, Hengstler, Daniel, Hupin, Guillaume, Indelicato, Paul, Kirch, Klaus, Knecht, Andreas, Kreuzberger, Daniel, Machado, Jorge, Navratil, Petr, Paul, Nancy, Pohl, Randolf, Unger, Daniel, Vogiatzi, Stella, von Schoeler, Katharina, Wauters, Frederik

Source: Physics 2024, 6(1), 206-215

Subject Terms: Physics - Atomic Physics, Nuclear Experiment, Nuclear Theory

Access URL: http://arxiv.org/abs/2310.03846

Molecular Dynamics

Authors: Mouhib, Halima, van Gils, Juami H. M., Gavaldá-Garciá, Jose, Hou, Qingzhen, May, Ali, Rauh, Arriën Symon, Vreede, Jocelyne, Abeln, Sanne, Feenstra, K. Anton

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02176

Monte Carlo for Protein Structures

Authors: van Gils, Juami H. M., Dijkstra, Maurits, Mouhib, Halima, Rauh, Arriën Symon, Vreede, Jocelyne, Feenstra, K. Anton, Abeln, Sanne

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02177

Function Prediction

Authors: Stringer, Bas, Jacobsen, Annika, Hou, Qingzhen, de Ferrante, Hans, Ivanova, Olga, Waury, Katharina, Gavaldá-Garciá, Jose, Abeln, Sanne, Feenstra, K. Anton

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02173

Thermodynamics of Protein Folding

Authors: van Gils, Juami H. M., Mouhib, Halima, van Dijk, Erik, Dijkstra, Maurits, Houtkamp, Isabel, Goetzee, Arthur, Abeln, Sanne, Feenstra, K. Anton

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02175

Introduction to Protein Folding

Authors: van Gils, Juami H. M., van Dijk, Erik, May, Ali, Mouhib, Halima, Bijlard, Jochem, Jacobsen, Annika, Houtkamp, Isabel, Feenstra, K. Anton, Abeln, Sanne

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02174

Structural Property Prediction

Authors: Dijkstra, Maurits, Bawono, Punto, Houtkamp, Isabel, Gavaldá-Garciá, Jose, Okounev, Mascha, Bouwmeester, Robbin, Stringer, Bas, Heringa, Jaap, Abeln, Sanne, Feenstra, K. Anton, van Gils, Juami H. M.

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02172

Data Resources for Structural Bioinformatics

Authors: Gavaldá-Garciá, Jose, Stringer, Bas, Ivanova, Olga, Abeln, Sanne, Feenstra, K. Anton, Mouhib, Halima

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02171

Structure Alignment

Authors: Ivanova, Olga, Gavaldá-Garciá, Jose, Gogishvili, Dea, Houtkamp, Isabel, Bouwmeester, Robbin, Feenstra, K. Anton, Abeln, Sanne

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02170

Introduction to Protein Structure

Authors: Jacobsen, Annika, van Dijk, Erik, Mouhib, Halima, Stringer, Bas, Ivanova, Olga, Gavaldá-Garciá, Jose, Hoekstra, Laura, Feenstra, K. Anton, Abeln, Sanne

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2307.02169

Space Analogs and Behavioral Health Performance Research review and recommendations checklist from ESA Topical Team

Authors: Gabriel G. De la Torre, Gernot Groemer, Ana Diaz-Artiles, Nathalie Pattyn, Jeroen Van Cutsem, Michaela Musilova, Wieslaw Kopec, Stefan Schneider, Vera Abeln, Tricia Larose, Fabio Ferlazzo, Pierpaolo Zivi, Alexandra de Carvalho, Gro Mjeldheim Sandal, Leszek Orzechowski, Michel Nicolas, Rebecca Billette de Villemeur, Anne Pavy-Le Traon, Ines Antunes

Source: npj Microgravity, Vol 10, Iss 1, Pp 1-16 (2024)

Subject Terms: Biotechnology, TP248.13-248.65, Physiology, QP1-981

File Description: electronic resource

Relation: https://doaj.org/toc/2373-8065

Access URL: https://doaj.org/article/e9b22cb10d5c4d02affc0515eca509c7

Durability of right ventricular conduits in the Ross procedure

Authors: Abeln, Karen B. ^{a, ∗}, Froede, Lennart ^a, Giebels, Christian ^a, Schäfers, Hans-Joachim ^{a, b}

Source: In The Journal of Thoracic and Cardiovascular Surgery May 2025 169(5):1306-1314

FAIR data for optical tweezers experiments

Authors: Halma, Matthew T.J. ^{1, 2}, Kumar, Sowmiyaa ³, van Eck, Jan ³, Abeln, Sanne ³, Gates, Alexander ^{4, ∗}, Wuite, Gijs J.L. ^{1, 2, ∗∗}

Source: In Biophysical Journal 15 April 2025 124(8):1255-1272