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

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

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

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 March 2025

High Prevalence of Chromosomal Rearrangements and LINE Retrotranspositions Detected in Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Tissue

Authors: Rubio-Alarcón, Carmen, Stelloo, Ellen, Vessies, Daan C.L., van 't Erve, Iris, Mekkes, Nienke J., Swennenhuis, Joost, Lakbir, Soufyan, van Bree, Elisabeth J., Tijssen, Marianne, Delis-van Diemen, Pien, Lanfermeijer, Mirthe, Linders, Theodora, van den Broek, Daan, Punt, Cornelis J.A., Heringa, Jaap, Meijer, Gerrit A., Abeln, Sanne, Feitsma, Harma, Fijneman, Remond J.A.

Source: In The Journal of Molecular Diagnostics December 2024 26(12):1065-1080

Structure determination

Authors: Mouhib, Halima, Stringer, Bas, van Ingen, Hugo, Gavaldá-García, Jose, Waury, Katharina, Abeln, Sanne, Feenstra, K. Anton

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2108.02706

How sticky are our proteins? Quantifying hydrophobicity of the human proteome

Authors: van Gils, Juami Hermine Mariama, Gogishvili, Dea, van Eck, Jan, Bouwmeester, Robbin, van Dijk, Erik, Abeln, Sanne

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2107.11837

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Authors: Crusoe, Michael R., Abeln, Sanne, Iosup, Alexandru, Amstutz, Peter, Chilton, John, Tijanić, Nebojša, Ménager, Hervé, Soiland-Reyes, Stian, Gavrilovic, Bogdan, Goble, Carole

Source: Commun. ACM 65 (2022) 54-63

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing

Access URL: http://arxiv.org/abs/2105.07028

Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias

Authors: Teunissen, Charlotte E., Kimble, Leighann, Bayoumy, Sherif, Bolsewig, Katharina, Burtscher, Felicia, Coppens, Salomé, Das, Shreyasee, Gogishvili, Dea, Fernandes Gomes, Bárbara, Gómez de San José, Nerea, Mavrina, Ekaterina, Meda, Francisco J., Mohaupt, Pablo, Mravinacová, Sára, Waury, Katharina, Wojdała, Anna Lidia, Abeln, Sanne, Chiasserini, Davide, Hirtz, Christophe, Gaetani, Lorenzo, Vermunt, Lisa, Bellomo, Giovanni, Halbgebauer, Steffen, Lehmann, Sylvain, Månberg, Anna, Nilsson, Peter, Otto, Markus, Vanmechelen, Eugeen, Verberk, Inge M.W., Willemse, Eline, Zetterberg, Henrik

Source: In Molecular & Cellular Proteomics October 2023 22(10)

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth

Authors: van Dijk, Erik, van Gils, Juami Hermine Mariama, Peduzzo, Alessia, Hofmann, Alexander, Groth, Georg, Mouhib, Halima, Otzen, Daniel E., Buell, Alexander K., Abeln, Sanne

Subject Terms: Condensed Matter - Soft Condensed Matter, Physics - Biological Physics, Quantitative Biology - Biomolecules, 92C05

Access URL: http://arxiv.org/abs/1906.05620