191 citations · 284 across the 23 of their papers we have counts for
25 papers
Bridging the gap between Performance and Interpretability: An Explainable Disentangled Multimodal Framework for Cancer Survival Prediction
Aniek Eijpe, Soufyan Lakbir, Melis Erdal Cesur +4
While multimodal survival prediction models are increasingly more accurate, their complexity often reduces interpretability, limiting insight into how different data sources influe…
Exploring Molecular Odor Taxonomies for Structure-based Odor Predictions using Machine Learning
Akshay Sajan, Stijn Sluis, Reza Haydarlou +6
One of the key challenges to predict odor from molecular structure is unarguably our limited understanding of the odor space and the complexity of the underlying structure-odor rel…
Explainable AI in Healthcare: to Explain, to Predict, or to Describe?
Alex Carriero, Anne de Hond, Bram Cappers +4
Explainable Artificial Intelligence (AI) methods are designed to provide information about how AI-based models make predictions. In healthcare, there is a widespread expectation th…
Beyond Olfaction: New Insights into Human Odorant Binding Proteins
Mifen Chen, Soufyan Lakbir, Mihyeon Jeon +3
Until today, the exact function of mammalian odorant binding proteins (OBPs) remains a topic of debate. Although their main established function lacks direct evidence in human olfa…
PLM-eXplain: Divide and Conquer the Protein Embedding Space
Jan van Eck, Dea Gogishvili, Wilson Silva +1
Protein language models (PLMs) have revolutionised computational biology through their ability to generate powerful sequence representations for diverse prediction tasks. However,…
Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction
Aniek Eijpe, Soufyan Lakbir, Melis Erdal Cesur +3
To improve the prediction of cancer survival using whole-slide images and transcriptomics data, it is crucial to capture both modality-shared and modality-specific information. How…
Mimicking the Gas-Phase to Transport Odorants through the Nasal Mucus: Functional Insights into Odorant Binding Proteins
Massimiliano Paesani, Arthur G. Goetzee, Sanne Abeln +1
Mammalian odorant binding proteins (OBPs) have long been suggested to transport hydrophobic odorant molecules through the aqueous environment of the nasal mucus. While the function…
PatchProt: Hydrophobic patch prediction using protein foundation models
Dea Gogishvili, Emmanuel Minois-Genin, Jan van Eck +1
Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the prog…
CIBRA identifies genomic alterations with a system-wide impact on tumor biology
Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer +3
Background: Genomic instability is a hallmark of cancer, leading to many somatic alterations. Identifying which alterations have a system-wide impact is a challenging task. Neverth…
Monte Carlo for Protein Structures
Juami H. M. van Gils, Maurits Dijkstra, Halima Mouhib +4
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Molecular Dynamics
Halima Mouhib, Juami H. M. van Gils, Jose Gavaldá-Garciá +6
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Thermodynamics of Protein Folding
Juami H. M. van Gils, Halima Mouhib, Erik van Dijk +5
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Introduction to Protein Folding
Juami H. M. van Gils, Erik van Dijk, Ali May +6
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Function Prediction
Bas Stringer, Annika Jacobsen, Qingzhen Hou +6
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Data Resources for Structural Bioinformatics
Jose Gavaldá-Garciá, Bas Stringer, Olga Ivanova +3
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Structure Alignment
Olga Ivanova, Jose Gavaldá-Garciá, Dea Gogishvili +4
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Introduction to Protein Structure
Annika Jacobsen, Erik van Dijk, Halima Mouhib +6
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Structural Property Prediction
Maurits Dijkstra, Punto Bawono, Isabel Houtkamp +8
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
Structure determination
Halima Mouhib, Bas Stringer, Hugo van Ingen +4
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book…
How sticky are our proteins? Quantifying hydrophobicity of the human proteome
Juami Hermine Mariama van Gils, Dea Gogishvili, Jan van Eck +3
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, prot…
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
Michael R. Crusoe, Sanne Abeln, Alexandru Iosup +7
Computational Workflows are widely used in data analysis, enabling innovation and decision-making. In many domains (bioinformatics, image analysis, & radio astronomy) the analysis…
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth
Erik van Dijk, Juami Hermine Mariama van Gils, Alessia Peduzzo +6
Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In cont…
Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation
Erik van Dijk, Patrick Varilly, Tuomas Knowles +2
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hyd…
The competition between surface adsorption and folding of fibril-forming polypeptides
Ran Ni, J. Mieke Kleijn, Sanne Abeln +2
Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systemat…