Sanne Abeln

Publication Activity (10 Years)

Years Active: 2005-2024
Publications (10 Years): 24

Top Topics

Protein Structure

Multiple Sequence Alignments

Data Processing

Top Venues

PLoS Comput. Biol.

Publications

Dea Gogishvili, Emmanuel Minois-Genin, Jan van Eck, Sanne Abeln
PatchProt: Hydrophobic patch prediction using protein foundation models. CoRR (2024)
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
Methods included. Commun. ACM 65 (6) (2022)
Jan Verhoeff, Sanne Abeln, Juan J. Garcia-Vallejo
INFLECT: an R-package for cytometry cluster evaluation using marker modality. BMC Bioinform. 23 (1) (2022)
Bas Stringer, Hans de Ferrante, Sanne Abeln, Jaap Heringa, K. Anton Feenstra, Reza Haydarlou
PIPENN: protein interface prediction from sequence with an ensemble of neural nets. Bioinform. 38 (8) (2022)
Qingzhen Hou, Bas Stringer, Katharina Waury, Henriette Capel, Reza Haydarlou, Fuzhong Xue, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes. Bioinform. 37 (20) (2021)
Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojsa Tijanic, Hervé Ménager, Stian Soiland-Reyes, Carole A. Goble
Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language. CoRR (2021)
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
The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth. PLoS Comput. Biol. 16 (5) (2020)
Qingzhen Hou, Paul F. G. De Geest, Christian J. Griffioen, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions. Bioinform. 35 (22) (2019)
Maurits J. J. Dijkstra, Atze van der Ploeg, K. Anton Feenstra, Wan J. Fokkink, Sanne Abeln, Jaap Heringa
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit. Bioinform. 35 (24) (2019)
K. Anton Feenstra, Sanne Abeln, Johan A. Westerhuis, Filipe Brancos dos Santos, Douwe Molenaar, Bas Teusink, Huub C. J. Hoefsloot, Jaap Heringa
Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinform. 34 (13) (2018)
Maurits J. J. Dijkstra, Punto Bawono, Sanne Abeln, K. Anton Feenstra, Wan J. Fokkink, Jaap Heringa
Motif-Aware PRALINE: Improving the alignment of motif regions. PLoS Comput. Biol. 14 (11) (2018)
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
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. F1000Research 6 (2017)
Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder
ECCB 2016: The 15th European Conference on Computational Biology. Bioinform. 32 (17) (2016)
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
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes. F1000Research 5 (2016)
Bas Stringer, Albert Meroño-Peñuela, Sanne Abeln, Frank van Harmelen, Jaap Heringa
SCRY: Extending SPARQL with Custom Data Processing Methods for the Life Sciences. SWAT4LS (2016)
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
Integration of EGA secure data access into Galaxy. F1000Research 5 (2016)
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
metaModules identifies key functional subnetworks in microbiome-related disease. Bioinform. 32 (11) (2016)
Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. Bioinform. 32 (12) (2016)
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
To SCRY Linked Data: Extending SPARQL the Easy Way. Diversity++@ISWC (2015)
Ali May, Sanne Abeln, Mark J. Buijs, Jaap Heringa, Wim Crielaard, Bernd W. Brandt
NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Erik van Dijk, Arlo Hoogeveen, Sanne Abeln
The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures. PLoS Comput. Biol. 11 (5) (2015)
Bas Stringer, Maurits J. J. Dijkstra, K. Anton Feenstra, Sanne Abeln, Jaap Heringa
Explaining disease using big data: How valid is your pathway? HPCS (2015)
Predrag Kukic, Arvind Kannan, Maurits J. J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo
Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations. PLoS Comput. Biol. 11 (10) (2015)
Bas Stringer, Albert Meroño-Peñuela, Antonis Loizou, Sanne Abeln, Jaap Heringa
SCRY: Enabling Quantitative Reasoning in SPARQL Queries. SWAT4LS (2015)
Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. Bioinform. 30 (3) (2014)
Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinform. 30 (11) (2014)
Hannah Edwards, Sanne Abeln, Charlotte M. Deane
Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies. PLoS Comput. Biol. 9 (11) (2013)
Sanne Abeln, Douwe Molenaar, K. Anton Feenstra, Huub C. J. Hoefsloot, Bas Teusink, Jaap Heringa
Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds. Briefings Bioinform. 14 (5) (2013)
Marc J. Bonder, Sanne Abeln, Egija Zaura, Bernd W. Brandt
Comparing clustering and pre-processing in taxonomy analysis. Bioinform. 28 (22) (2012)
Sanne Abeln, Daan Frenkel
Disordered Flanks Prevent Peptide Aggregation. PLoS Comput. Biol. 4 (12) (2008)
Sanne Abeln, Carlo Teubner, Charlotte M. Deane
Using Phylogeny to Improve Genome-Wide Distant Homology Recognition. PLoS Comput. Biol. 3 (1) (2007)
Sanne Abeln, Charlotte M. Deane
Linking evolution of protein structures through fragments. BMC Syst. Biol. 1 (S-1) (2007)
Henry F. Winstanley, Sanne Abeln, Charlotte M. Deane
How old is your fold? ISMB (Supplement of Bioinformatics) (2005)