Sanne Abeln

dr.

20052019
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Research Output 2005 2019

2019

Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using ConsDYN enhanced sampling

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

Research output: Contribution to JournalArticleAcademic

Open Access
Facilitative Glucose Transport Proteins
Sampling
Mutation
Glucose Transporter Type 1
Molecular dynamics

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

Hou, Q., De Geest, P., Griffioen, C. J., Abeln, S., Heringa, J. & Feenstra, K. A., 22 May 2019, In : Bioinformatics.

Research output: Contribution to JournalArticleAcademicpeer-review

Web Server
Proteins
Protein
Prediction
Interaction

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., 1 Aug 2019, In : Bioinformatics. p. 1-3 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Multiple Sequence Alignment
Workflow
Sequence Alignment
Work Flow
Alignment

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth

Dijk, E. V., Gils, J. H. M. V., Peduzzo, A., Hofmann, A., Groth, G., Mouhib, H., Otzen, D. E., Buell, A. K. & Abeln, S., 13 Jun 2019, In : arXiv.org. 25 p.

Research output: Contribution to JournalArticleAcademic

thermodynamics
protein
heat capacity
meta-analysis
hydrophobicity

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., 12 Sep 2019, In : Oral Oncology. 98, p. 8-12 5 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Information Storage and Retrieval
Head and Neck Neoplasms
Netherlands
Neck
Head
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
Aurora Kinase A
Colorectal Neoplasms
Cell Line
Protein Interaction Maps
Genes

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
Sequence Alignment
sequence alignment
Alignment
Multiple Sequence Alignment
Benchmarking

Preface to Introduction to Structural Bioinformatics

Feenstra, K. A. & Abeln, S., 29 Jan 2018, Introduction to Structural Bioinformatics.

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 JournalArticleAcademicpeer-review

Open Access
globules
folding
Molten materials
Hot Temperature
proteins

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
Aberrations
Chromosome Aberrations
Genes
Genome
DNA

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
Proteins

Making sense of our microbes as they become data in our computers

May, A., 2017, 94 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
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

Sequence Alignment
Sequence Analysis
Proteins
Nucleotides
Research Personnel

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
Model structures
Proteins
Concretes

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 othersMeijer, 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

The role of hydrophobicity in protein folding and aggregation

Dijk, E., 2017, 133 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File
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
Pathway
Research Personnel
Catenins
Biological Models
Wnt Signaling Pathway

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
biopolymer denaturation
hydrophobicity
proteins
solvation
specific heat

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
Microbiota
Gene expression
Gene Expression
Pathway
Mouth Diseases

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
Biofilms
Candida albicans
Transcriptome
Phenotype
Metabolic Networks and Pathways

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
Galaxies
Genes
Genome
Translational Medical Research
Workflow

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

protease
secretions
passengers
Hemoglobin
hemoglobin

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
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 JournalArticleAcademicpeer-review

polypeptides
Folding
Adsorption
folding
adsorption

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

Life sciences
Pathway
Health
Valid
Sector

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 JournalArticleAcademicpeer-review

Open Access
Chromosome Breakage
colorectal neoplasms
Colorectal Neoplasms
Genes
genes

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 JournalArticleAcademicpeer-review

Open Access
molecular dynamics
Force Field
Molecular Dynamics Simulation
Molecular dynamics
Fold

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 JournalArticleAcademicpeer-review

Open Access
Microbial Genetics
Genetic Markers
Sequence Analysis
High-Throughput Nucleotide Sequencing
Metagenomics

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 JournalArticleAcademicpeer-review

Open Access
Benchmarking
Sequence Alignment
sequence alignment
methodology
case studies

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Open Access
Protein Structure
protein structure
Temperature Dependence
Amino Acids
Amino acids

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 JournalArticleAcademicpeer-review

Open Access
File
Statistical tests
Application programming interfaces (API)
Interoperability
Testing
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 JournalArticleAcademicpeer-review

Open Access
Protein folding
protein folding
Protein Folding
amyloid
Amyloid

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 JournalArticleAcademicpeer-review

Atomistic Simulation
Free energy
Free Energy
Energy barriers
Proteins

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 JournalArticleAcademicpeer-review

Taxonomies
Taxonomy
Ribosomal DNA
Cluster Analysis
Preprocessing
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

Systems Biology
Bioinformatics
Computational Biology
Students
Teaching

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
Fold
fold
Proteins
Protein
protein

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
polypeptides
folding
assembly
self assembly
hydrophobicity
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

Taxonomies
Taxonomy
Cluster Analysis
Preprocessing
Clustering
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 JournalArticleAcademicpeer-review

Open Access
Proteins
Water
Amino Acids
Structural Models
Protein Folding

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 JournalErratumAcademic

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

2008

Disordered flanks prevent peptide aggregation

Abeln, S. & Frenkel, D., Dec 2008, In : PLoS Computational Biology. 4, 12, e1000241.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Peptides
peptide
Aggregation
Agglomeration
peptides
2007

Using phylogeny to improve genome-wide distant homology recognition

Abeln, S., Teubner, C. & Deane, C. M., 19 Jan 2007, In : PLoS Computational Biology. 3, 1, p. 0073-0083 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Phylogeny
homology
Homology
Genome
phylogeny
2005

Fold usage on genomes and protein fold evolution

Abeln, S. & Deane, C. M., 1 Sep 2005, In : Proteins. 60, 4, p. 690-700 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Genes
Genome
Proteins
Bacteria
Archaea

How old is your fold?

Winstanley, H. F., Abeln, S. & Deane, C. M., Jun 2005, In : Bioinformatics. 21, SUPPL. 1

Research output: Contribution to JournalArticleAcademicpeer-review

Fold
Proteins
Protein Structure
Phylogeny
Protein