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  • Sanne Abeln
2019

Abstract 1738: Characterization of structural variants within MACROD2 in the pathogenesis of colorectal cancer

Fijneman, R. J. A., Mekkes, N., Broek, E. V. D., Stringer, B., Glas, R. A., Komor, M. A., Rausch, C., Lieshout, S. V., Cuppen, E., Smith, M. L., Sebra, R. P., Rowell, W. J., Ashby, M., Carvalho, B., Heringa, J., Meijer, G. A. & Abeln, S., 1 Jul 2019. 1 p.

Research output: Contribution to ConferencePaperAcademic

Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using consdyn enhanced sampling [version 1; peer review: 1 approved with reservations, 1 not approved]

Mouhib, H., Higuchi, A., Abeln, S., Yura, K. & Feenstra, K. A., 22 Mar 2019, In : F1000Research. 8, p. 1-14 14 p., 322.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions

Hou, Q., De Geest, P. F. G., Griffioen, C. J., Abeln, S., Heringa, J. & Feenstra, K. A., 1 Nov 2019, In : Bioinformatics. 35, 22, p. 4794-4796 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

Dijkstra, M. J. J., van der Ploeg, A. J., Feenstra, K. A., Fokkink, W. J., Abeln, S. & Heringa, J., 15 Dec 2019, In : Bioinformatics (Oxford, England). 35, 24, p. 5315-5317 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The potential use of big data in oncology

Willems, S. M., Abeln, S., Feenstra, K. A., de Bree, R., van der Poel, E. F., Baatenburg de Jong, R. J., Heringa, J. & van den Brekel, M. W. M., Nov 2019, In : Oral Oncology. 98, p. 8-12 5 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
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 JournalArticleAcademicpeer-review

Open Access

Motif-Aware PRALINE: Improving the alignment of motif regions: Improving the alignment of motif regions

Dijkstra, M., Bawono, P., Abeln, S., Feenstra, K. A., Fokkink, W. & Heringa, J., 1 Nov 2018, In : PLoS Computational Biology. 14, 11, p. 1-19 19 p., e1006547.

Research output: Contribution to JournalArticleAcademicpeer-review

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

Protein three-dimensional structure prediction

Abeln, S., Feenstra, K. A. & Heringa, J., 1 Jan 2018, Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics. Elsevier, Vol. 1-3. p. 497-511 15 p. (Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics; vol. 1-3).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademic

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademic

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademic

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access

Mechanical Unfolding of an Autotransporter Passenger Protein Reveals the Secretion Starting Point and Processive Transport Intermediates

Baclayon, M., van Ulsen, P., Mouhib, H., Hashemi Shabestari, M., Verzijden, T., Abeln, S., Roos, W. H. & Wuite, G. J. L., 2016, In : ACS Nano. 10, 6, p. 5710-5719

Research output: Contribution to JournalArticleAcademicpeer-review

SCRY: Extending SPARQL with custom data processing methods for the life sciences

Stringer, B., Meroño-peñuela, A., Abeln, S., van Harmelen, F. & Heringa, J., 2016, In : CEUR Workshop Proceedings. 1795, p. 1-10 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
2013

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C., Teusink, B. & Heringa, J., Sep 2013, In : Briefings in bioinformatics. 14, 5, p. 589-98 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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