Sanne Abeln

According to our database, Sanne Abeln authored at least 33 papers between 2005 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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

INFLECT: an R-package for cytometry cluster evaluation using marker modality.

Jan Verhoeff, Sanne Abeln, Juan J. Garcia-Vallejo

BMC Bioinform., 2022

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

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

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

2020

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

2019

Protein Three-Dimensional Structure Prediction.

Sanne Abeln, K. Anton Feenstra, Jaap Heringa

Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 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

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

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

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

2017

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, 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

F1000Research, 2017

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, Andrew Stubbs, Jordi Rambla, J. Dylan Spalding, Sanne Abeln

F1000Research, 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

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

ECCB 2016: The 15th European Conference on Computational Biology.

Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder

Bioinform., 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

SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences.

Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa

Proceedings of the 9th International Conference Semantic Web Applications and Tools for Life Sciences, 2016

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

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures.

Erik van Dijk, Arlo Hoogeveen, Sanne Abeln

PLoS Comput. Biol., 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

SCRY: Enabling Quantitative Reasoning in SPARQL Queries.

Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

To SCRY Linked Data: Extending SPARQL the Easy Way.

Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa

Proceedings of the 1st International Diversity++ Workshop co-located with the 14th International Semantic Web Conference (ISWC 2015), 2015

Explaining disease using big data: How valid is your pathway?

Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa

Proceedings of the 2015 International Conference on High Performance Computing & Simulation, 2015

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

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

2013

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies.

Hannah Edwards, Sanne Abeln, Charlotte M. Deane

PLoS Comput. Biol., 2013

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

2012

Comparing clustering and pre-processing in taxonomy analysis.

Marc J. Bonder, Sanne Abeln, Egija Zaura, Bernd W. Brandt

Bioinform., 2012

2008

Disordered Flanks Prevent Peptide Aggregation.

Sanne Abeln, Daan Frenkel

PLoS Comput. Biol., 2008

2007

Using Phylogeny to Improve Genome-Wide Distant Homology Recognition.

Sanne Abeln, Carlo Teubner, Charlotte M. Deane

PLoS Comput. Biol., 2007

Linking evolution of protein structures through fragments.

Sanne Abeln, Charlotte M. Deane

BMC Syst. Biol., 2007

2005

How old is your fold?

Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005