Sanne Abeln

42 papers Journal 35Unranked 6
YearRankTypeTitle / Venue / Authors
2026 J jnl
Bridging the gap between Performance and Interpretability: An Explainable Disentangled Multimodal Framework for Cancer Survival Prediction.
CoRR
Aniek Eijpe, Soufyan Lakbir, Melis Erdal Cesur, Sara Pires de Oliveira, Angelos Chatzimparmpas, Sanne Abeln, Wilson Silva
2026 J jnl
PLM-eXplain: divide and conquer the protein embedding space.
Bioinform.
Jan van Eck, Dea Gogishvili, Wilson Silva, Sanne Abeln
2025 J jnl
Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data.
PLoS Comput. Biol.
Katharina Waury, Stefan Lelieveld, Sanne Abeln, Henk-Jan van den Ham
2025 — conf
Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction.
MICCAI (14)
Aniek Eijpe, Soufyan Lakbir, Melis Erdal Cesur, Sara Pires de Oliveira, Sanne Abeln, Wilson Silva
2025 J jnl
Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction.
CoRR
Aniek Eijpe, Soufyan Lakbir, Melis Erdal Cesur, Sara Pires de Oliveira, Sanne Abeln, Wilson Silva
2025 J jnl
Exploring Molecular Odor Taxonomies for Structure-based Odor Predictions using Machine Learning.
CoRR
Akshay Sajan, Stijn Sluis, Reza Haydarlou, Sanne Abeln, Pasquale Lisena, Raphaël Troncy, Caro Verbeek, Inger Leemans, Halima Mouhib
2025 J jnl
PLM-eXplain: Divide and Conquer the Protein Embedding Space.
CoRR
Jan van Eck, Dea Gogishvili, Wilson Silva, Sanne Abeln
2024 J jnl
CIBRA identifies genomic alterations with a system-wide impact on tumor biology.
Bioinform.
Soufyan Lakbir, Caterina Buranelli, Gerrit A. Meijer, Jaap Heringa, Remond J. A. Fijneman, Sanne Abeln
2024 J jnl
PatchProt: Hydrophobic patch prediction using protein foundation models.
CoRR
Dea Gogishvili, Emmanuel Minois-Genin, Jan van Eck, Sanne Abeln
2022 J jnl
INFLECT: an R-package for cytometry cluster evaluation using marker modality.
BMC Bioinform.
Jan Verhoeff, Sanne Abeln, Juan J. Garcia-Vallejo
2022 J jnl
Methods included.
Commun. ACM
Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojsa Tijanic, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilovic, Carole A. Goble, The Cwl Community
2022 J jnl
PIPENN: protein interface prediction from sequence with an ensemble of neural nets.
Bioinform.
Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou
2021 J jnl
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language.
CoRR
Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojsa Tijanic, Hervé Ménager, Stian Soiland-Reyes, Carole A. Goble
2021 J jnl
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes.
Bioinform.
Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2020 J jnl
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth.
PLoS Comput. Biol.
Juami Hermine Mariama van Gils, Erik van Dijk, Alessia Peduzzo, Alexander Hofmann, Nicola Vettore, Marie P. Schützmann, Georg Groth, Halima Mouhib, Daniel E. Otzen, Alexander K. Buell, Sanne Abeln
2019 — ch.
Protein Three-Dimensional Structure Prediction.
Encyclopedia of Bioinformatics and Computational Biology (2)
Sanne Abeln, K. Anton Feenstra, Jaap Heringa
2019 J jnl
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions.
Bioinform.
Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2019 J jnl
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit.
Bioinform.
Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa
2018 J jnl
Motif-Aware PRALINE: Improving the alignment of motif regions.
PLoS Comput. Biol.
Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
2018 J jnl
Training for translation between disciplines: a philosophy for life and data sciences curricula.
Bioinform.
K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa
2017 J jnl
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data.
F1000Research
Chao Zhang, Jochem Bijlard, Christine Staiger, Serena A. Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia D. Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino da Silva Santos, Jeroen Beliën, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond J. A. Fijneman, J. Dylan Spalding, Sanne Abeln
2016 J jnl
BioASF: a framework for automatically generating executable pathway models specified in BioPAX.
Bioinform.
Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2016 J jnl
ECCB 2016: The 15th European Conference on Computational Biology.
Bioinform.
Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder
2016 J jnl
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes.
F1000Research
Evert van den Broek, Stef van Lieshout, Christian Rausch, Bauke Ylstra, Mark A. van de Wiel, Gerrit A. Meijer, Remond J. A. Fijneman, Sanne Abeln
2016 J jnl
Integration of EGA secure data access into Galaxy.
F1000Research
Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia D. Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J. A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln
2016 — conf
SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences.
SWAT4LS
Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa
2016 J jnl
metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinform.
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
2015 — conf
Explaining disease using big data: How valid is your pathway?
HPCS
Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
2015 J jnl
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.
PLoS Comput. Biol.
Predrag Kukic, Arvind Kannan, Maurits J. J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo
2015 J jnl
NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.
Nucleic Acids Res.
Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt
2015 — conf
SCRY: Enabling Quantitative Reasoning in SPARQL Queries.
SWAT4LS
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
2015 J jnl
The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures.
PLoS Comput. Biol.
Erik van Dijk, Arlo Hoogeveen, Sanne Abeln
2015 — conf
To SCRY Linked Data: Extending SPARQL the Easy Way.
Diversity++@ISWC
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
2014 J jnl
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.
Bioinform.
Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
2014 J jnl
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.
Bioinform.
Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt
2013 J jnl
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds.
Briefings Bioinform.
Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa
2013 J jnl
Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies.
PLoS Comput. Biol.
Hannah Edwards, Sanne Abeln, Charlotte M. Deane
2012 J jnl
Comparing clustering and pre-processing in taxonomy analysis.
Bioinform.
Marc J. Bonder, Sanne Abeln, Egija Zaura, Bernd W. Brandt
2008 J jnl
Disordered Flanks Prevent Peptide Aggregation.
PLoS Comput. Biol.
Sanne Abeln, Daan Frenkel
2007 J jnl
Linking evolution of protein structures through fragments.
BMC Syst. Biol.
Sanne Abeln, Charlotte M. Deane
2007 J jnl
Using Phylogeny to Improve Genome-Wide Distant Homology Recognition.
PLoS Comput. Biol.
Sanne Abeln, Carlo Teubner, Charlotte M. Deane
2005 — conf
How old is your fold?
ISMB (Supplement of Bioinformatics)
Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane