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  • Sanne Abeln
2018

Aurora kinase A (AURKA) interaction with Wnt and Ras-MAPK signalling pathways in colorectal cancer

Jacobsen, A., Bosch, L. J. W., Martens-De Kemp, S. R., Carvalho, B., Sillars-Hardebol, A. H., Dobson, R. J., De Rinaldis, E., Meijer, G. A., Abeln, S., Heringa, J., Fijneman, R. J. A. & Feenstra, K. A., 14 May 2018, In : Scientific Reports. 8, 1, p. 7522 7522.

Research output: Contribution to JournalArticle

Open Access
Open Access

Preface to Introduction to Structural Bioinformatics

Feenstra, K. A. & Abeln, S., 30 Jan 2018, Introduction to Structural Bioinformatics. Amsterdam: Centre for Integrative Bioinformatics (IBIVU) and Department of Computer Science, Vrije Universiteit, p. 5-9 5 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

File

The characteristics of molten globule states and folding pathways strongly depend on the sequence of a protein

Dijkstra, M. J. J., Fokkink, W. J., Heringa, J., van Dijk, E. & Abeln, S., 17 Nov 2018, In : Molecular Physics. 116, 21-22, p. 3173-3180 8 p.

Research output: Contribution to JournalArticle

Open Access

Training for translation between disciplines: A philosophy for life and data sciences curricula

Anton Feenstra, K., Abeln, S., Westerhuis, J. A., Brancos Dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J. & Heringa, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i4-i12 9 p.

Research output: Contribution to JournalArticle

Open Access
2017

Detection of structural variants and recurrent breakpoint genes in colorectal adenoma-to-carcinoma progression

van den Broek, E., Dijkstra, M. J. J., Voorham, Q. J. M., Carvalho, B., van de Wiel, M. A., Abeln, S., Meijer, G. A. & Fijneman, R. J. A., Feb 2017, In : Cancer Research. 77

Research output: Contribution to JournalArticle

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes

Fijneman, R. J. A., van den Broek, E., van Lieshout, S., Rausch, C., Ylstra, B., van de Wiel, M. A., Meijer, G. A. & Abeln, S., 6 Jul 2017, In : F1000Research. 5, p. 1-8 8 p., 2340.

Research output: Contribution to JournalArticle

Open Access

Introduction to Protein Structure Prediction

Abeln, S., Heringa, J. & Feenstra, K. A., 1 Dec 2017, (Submitted) Introduction to Structural Bioinformatics.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

File

Multiple sequence alignment

Bawono, P., Dijkstra, M., Pirovano, W., Feenstra, A., Abeln, S. & Heringa, J., 2017, Methods in Molecular Biology: Volume I: Data, Sequence Analysis, and Evolution. Humana Press Inc, Vol. 1525. p. 167-189 23 p. (Methods in Molecular Biology; vol. 1525).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Strategies for protein structure model generation

Abeln, S., Heringa, J. & Feenstra, K. A., 1 Dec 2017, (Submitted) Introduction to Structural Bioinformatics.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

File

Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data [version 1; referees: awaiting peer review]

Zhang, C., Bijlard, J., Staiger, C., Scollen, S., van Enckevort, D., Hoogstrate, Y., Senf, A., Hiltemann, S., Repo, S., Pipping, W., Bierkens, M., Payralbe, S., Stringer, B., Heringa, J., Stubbs, A., Bonino Da Silva Santos, LO., Belien, J. A. M., Weistra, W., Azevedo, R. V. D. M., van Bochove, K. & 6 others, Meijer, G., Boiten, J-W., Rambla, J., Fijneman, R. J., Spalding, JD. & Abeln, S., 16 Aug 2017, In : F1000Research. 6, 1488

Research output: Contribution to JournalArticle

Open Access
2016

BioASF: A framework for automatically generating executable pathway models specified in BioPAX

Haydarlou, R., Jacobsen, A., Bonzanni, N., Feenstra, K. A., Abeln, S. & Heringa, J., 15 Jun 2016, In : Bioinformatics. 32, 12, p. 60-69

Research output: Contribution to JournalArticle

Open Access

Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation

van Dijk, E., Varilly, P., Knowles, T. P. J., Frenkel, D. & Abeln, S., 19 Feb 2016, In : Physical Review Letters. 116, 7, p. 078101

Research output: Contribution to JournalArticle

Open Access

ECCB 2016: The 15th European Conference on Computational Biology

Heringa, J., Reinders, M., Abeln, S. & de Ridder, J., 1 Sep 2016, In : Bioinformatics. 32, 17, p. 389-392

Research output: Contribution to JournalArticle

Open Access

Gene expression metaModules identifies key functional subnet- works in microbiome-related disease

May, A., Brandt, B. W., El-Kebir, M., Klau, G. W., Zaura, E., Crielaard, W., Heringa, J. & Abeln, S., 2016, In : Bioinformatics. 32, 11, p. 1678-1685

Research output: Contribution to JournalArticle

Open Access

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping

Rajendran, R., May, A., Sherry, L., Kean, R., Williams, C., Jones, B. L., Burgess, K. V., Heringa, J., Abeln, S., Brandt, B. W., Munro, C. A. & Ramage, G., 21 Oct 2016, In : Scientific Reports. 6, July, p. 1-11 11 p., 35436.

Research output: Contribution to JournalArticle

Open Access

Integration of EGA secure data access into Galaxy

Hoogstrate, Y., Zhang, C., Senf, A., Bijlard, J., Hiltemann, S., van Enckevort, D., Repo, S., Heringa, J., Jenster, G., Fijneman, R. J. A., Boiten, J-W., Meijer, G. A., Stubbs, A., Rambla, J., Spalding, D. & Abeln, S., 2016, In : F1000Research. 5, 2841.

Research output: Contribution to JournalArticle

Open Access
2015

Competition between surface adsorption and folding of fibril-forming polypeptides

Ni, R., de Kleijn, M., Abeln, S., Cohen Stuart, M. A. & Bolhuis, P. G., 2015, In : Physical Review E.

Research output: Contribution to JournalArticle

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

Stringer, B., Dijkstra, M., Feenstra, A., Abeln, S. & Heringa, J., 2 Sep 2015, Proceedings of the 2015 International Conference on High Performance Computing and Simulation, HPCS 2015. Institute of Electrical and Electronics Engineers, Inc., p. 662-664 3 p. 7237114

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer

van den Broek, E., Dijkstra, M. J. J., Krijgsman, O., Sie, D. L. S., Haan, J. C., Traets, J. J. H., van de Wiel, M. A., Nagtegaal, I. D., Punt, C. J. A., Carvalho, B., Ylstra, B., Abeln, S., Meijer, G. A. & Fijneman, R. J. A., 2015, In : PLoS ONE. 10, 9, e0138141.

Research output: Contribution to JournalArticle

Open Access

Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

Ku, G. M., Kannan, A., Dijkstra, M. J. J., Abeln, S., Camilloni, C. & Vendruscolo, M., 2015, In : PLoS Computational Biology. 11, 10

Research output: Contribution to JournalArticle

Open Access

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL

May, A., Abeln, S., Buijs, M. J., Heringa, J., Crielaard, W. & Brandt, B. W., 2015, In : Nucleic Acids Research.

Research output: Contribution to JournalArticle

Open Access

Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

van der Velde, A., Bawono, P., Abeln, S. & Heringa, J., 2015, In : PLoS ONE. 10, 5

Research output: Contribution to JournalArticle

Open Access

SCRY: Enabling quantitative reasoning in SPARQL queries

Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S. & Heringa, J., 2015, In : CEUR Workshop Proceedings. 1546, p. 214-215 2 p.

Research output: Contribution to JournalArticle

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

van Dijk, E., Hoogeveen, A. & Abeln, S., 1 May 2015, In : PLoS Computational Biology. 11, 5, e1004277.

Research output: Contribution to JournalArticle

Open Access

To SCRY Linked Data: Extending SPARQL the Easy Way

Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S. & Heringa, J., 2015, In : CEUR Workshop Proceedings. 1501, p. 8-14 7 p.

Research output: Contribution to JournalArticle

Open Access
File
2014

A simple lattice model that captures protein folding, aggregation and amyloid formation

Abeln, S., Vendruscolo, M., Dobson, C. M. & Frenkel, D., 2014, In : PLoS ONE.

Research output: Contribution to JournalArticle

Open Access

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

May, A., Pool, R., van Dijk, E., Bijlard, J., Abeln, S., Heringa, J. & Feenstra, K. A., 1 Feb 2014, In : Bioinformatics. 30, 3, p. 326-34 9 p.

Research output: Contribution to JournalArticle

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.

May, A., Abeln, S., Crielaard, W., Heringa, J. & Brandt, B. W., 2014, In : Bioinformatics. 30, p. 1530-1538

Research output: Contribution to JournalArticle

2013

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

Edwards, H., Abeln, S. & Deane, C. M., 2013, In : PLoS Computational Biology. 9, 11, p. e1003325

Research output: Contribution to JournalArticle

Open Access
File

Interplay between Folding and Assembly of Fibril-Forming Polypeptides.

Ni, R., Abeln, S., Schor, M., Stuart, M. A. C. & Bolhuis, P. G., 2013, In : Physical Review Letters. 111, 5, p. 058101

Research output: Contribution to JournalArticle

File
2012

Comparing clustering and pre-processing in taxonomy analysis.

Bonder, M. J., Abeln, S., Zaura, E. & Brandt, B. W., 2012, In : Bioinformatics. 28, 22, p. 2891-2897

Research output: Contribution to JournalArticle

2011

Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins.

Abeln, S. & Frenkel, D., 2011, In : Biophysical Journal. 100, 3, p. 693

Research output: Contribution to JournalArticle

Open Access

Correction: Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins. Biophys. J. 100:693–700

Abeln, S. & Frenkel, D., 17 Aug 2011, In : Biophysical Journal. 101, 4, p. 1014-1014 1 p.

Research output: Contribution to JournalErratum

Open Access
2010

Multiple alignment of transmembrane protein sequences

Pirovano, W. A., Abeln, S., Feenstra, K. A. & Heringa, J., 2010, Structural Bioinformatics of Membrane Proteins. Frishman, D. (ed.). Vienna: Springer-Verlag, p. 103-122 400 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic