How old is your fold? - Henry F. Winstanley; Sanne Abeln; Charlotte M. Deane (ISMB (Supplement of Bioinformatics), 2005)

Linking evolution of protein structures through fragments. - Sanne Abeln; Charlotte M. Deane (BMC Syst. Biol., 2007)

Using Phylogeny to Improve Genome-Wide Distant Homology Recognition. - Sanne Abeln; Carlo Teubner; Charlotte M. Deane (PLoS Comput. Biol., 2007)

Disordered Flanks Prevent Peptide Aggregation. - Sanne Abeln; Daan Frenkel (PLoS Comput. Biol., 2008)

Comparing clustering and pre-processing in taxonomy analysis. - Marc J. Bonder; Sanne Abeln; Egija Zaura; Bernd W. Brandt (Bioinform., 2012)

Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. - Sanne Abeln; Douwe Molenaar; K. Anton Feenstra; Huub C. J. Hoefsloot; Bas Teusink; Jaap Heringa (Briefings Bioinform., 2013)

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies. - Hannah Edwards; Sanne Abeln; Charlotte M. Deane (PLoS Comput. Biol., 2013)

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. - Ali May; Sanne Abeln; Wim Crielaard; Jaap Heringa; Bernd W. Brandt (Bioinform., 2014)

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. - Ali May; René Pool; Erik van Dijk; Jochem Bijlard; Sanne Abeln; Jaap Heringa; K. Anton Feenstra (Bioinform., 2014)

Explaining disease using big data: How valid is your pathway? - Bas Stringer; Maurits J. J. Dijkstra; K. Anton Feenstra; Sanne Abeln; Jaap Heringa (HPCS, 2015)

To SCRY Linked Data: Extending SPARQL the Easy Way. - Bas Stringer; Albert Meroño-Peñuela; Antonis Loizou; Sanne Abeln; Jaap Heringa (Diversity++@ISWC, 2015)

SCRY: Enabling Quantitative Reasoning in SPARQL Queries. - Bas Stringer; Albert Meroño-Peñuela; Antonis Loizou; Sanne Abeln; Jaap Heringa (SWAT4LS, 2015)

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. - Ali May; Sanne Abeln; Mark J. Buijs; Jaap Heringa; Wim Crielaard; Bernd W. Brandt (Nucleic Acids Res., 2015)

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures. - Erik van Dijk; Arlo Hoogeveen; Sanne Abeln (PLoS Comput. Biol., 2015)

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations. - Predrag Kukic; Arvind Kannan; Maurits J. J. Dijkstra; Sanne Abeln; Carlo Camilloni; Michele Vendruscolo (PLoS Comput. Biol., 2015)

SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences. - Bas Stringer; Albert Meroño-Peñuela; Sanne Abeln; Frank van Harmelen; Jaap Heringa (SWAT4LS, 2016)

BioASF: a framework for automatically generating executable pathway models specified in BioPAX. - Reza Haydarlou; Annika Jacobsen; Nicola Bonzanni; K. Anton Feenstra; Sanne Abeln; Jaap Heringa (Bioinform., 2016)

ECCB 2016: The 15th European Conference on Computational Biology. - Jaap Heringa; Marcel J. T. Reinders; Sanne Abeln; Jeroen de Ridder (Bioinform., 2016)

metaModules identifies key functional subnetworks in microbiome-related disease. - Ali May; Bernd W. Brandt; Mohammed El-Kebir; Gunnar W. Klau; Egija Zaura; Wim Crielaard; Jaap Heringa; Sanne Abeln (Bioinform., 2016)

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. - 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 (F1000Research, 2016)

Integration of EGA secure data access into Galaxy. - 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; et al. (F1000Research, 2016)

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. - 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; et al. (F1000Research, 2017)

Training for translation between disciplines: a philosophy for life and data sciences curricula. - K. Anton Feenstra; Sanne Abeln; Johan A. Westerhuis; Filipe Brancos dos Santos; Douwe Molenaar; Bas Teusink; Huub C. J. Hoefsloot; Jaap Heringa (Bioinform., 2018)

Motif-Aware PRALINE: Improving the alignment of motif regions. - Maurits J. J. Dijkstra; Punto Bawono; Sanne Abeln; K. Anton Feenstra; Wan J. Fokkink; Jaap Heringa (PLoS Comput. Biol., 2018)

Dataset for the tutorial "pinpoint key pathways with Heinz". - Chao Zhang; Sanne Abeln (Zenodo, 2018)

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. - Maurits J. J. Dijkstra; Atze van der Ploeg; K. Anton Feenstra; Wan J. Fokkink; Sanne Abeln; Jaap Heringa (Bioinform., 2019)

SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. - Qingzhen Hou; Paul F. G. De Geest; Christian J. Griffioen; Sanne Abeln; Jaap Heringa; K. Anton Feenstra (Bioinform., 2019)

Protein Three-Dimensional Structure Prediction. - Sanne Abeln; K. Anton Feenstra; Jaap Heringa (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. - 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 (PLoS Comput. Biol., 2020)

SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. - Qingzhen Hou; Bas Stringer; Katharina Waury; Henriette Capel; Reza Haydarlou; Fuzhong Xue; Sanne Abeln; Jaap Heringa; K. Anton Feenstra (Bioinform., 2021)

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. - Michael R. Crusoe; Sanne Abeln; Alexandru Iosup; Peter Amstutz; John Chilton; Nebojsa Tijanic; Hervé Ménager; Stian Soiland-Reyes; Carole A. Goble (CoRR, 2021)

PIPENN: protein interface prediction from sequence with an ensemble of neural nets. - Bas Stringer; Hans de Ferrante; Sanne Abeln; Jaap Heringa; K. Anton Feenstra; Reza Haydarlou (Bioinform., 2022)

INFLECT: an R-package for cytometry cluster evaluation using marker modality. - Jan Verhoeff; Sanne Abeln; Juan J. Garcia-Vallejo (BMC Bioinform., 2022)

Methods included. - 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 (Commun. ACM, 2022)

CIBRA identifies genomic alterations with a system-wide impact on tumor biology. - Soufyan Lakbir; Caterina Buranelli; Gerrit A. Meijer; Jaap Heringa; Remond J. A. Fijneman; Sanne Abeln (Bioinform., 2024)

PatchProt: Hydrophobic patch prediction using protein foundation models. - Dea Gogishvili; Emmanuel Minois-Genin; Jan van Eck; Sanne Abeln (CoRR, 2024)

Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction. - Aniek Eijpe; Soufyan Lakbir; Melis Erdal Cesur; Sara P. Oliveira; Sanne Abeln; Wilson Silva (CoRR, 2025)

PLM-eXplain: Divide and Conquer the Protein Embedding Space. - Jan van Eck; Dea Gogishvili; Wilson Silva; Sanne Abeln (CoRR, 2025)