Publications by authors named "Sanne Abeln"

35Publications

The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth.

PLoS Comput Biol 2020 05 4;16(5):e1007767. Epub 2020 May 4.

Computer Science Department, Center for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1007767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7282669PMC
May 2020

The potential use of big data in oncology.

Oral Oncol 2019 11 12;98:8-12. Epub 2019 Sep 12.

Department of Head and Neck Oncology and Surgery, Netherlands Cancer Institute, Amsterdam, the Netherlands.

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http://dx.doi.org/10.1016/j.oraloncology.2019.09.003DOI Listing
November 2019

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

Bioinformatics 2019 12;35(24):5315-5317

Department of Computer Science, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954659PMC
December 2019

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

Bioinformatics 2019 11;35(22):4794-4796

IBIVU - Center for Integrative Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz428DOI Listing
November 2019

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

PLoS Comput Biol 2018 11 1;14(11):e1006547. Epub 2018 Nov 1.

Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.

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http://dx.plos.org/10.1371/journal.pcbi.1006547
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http://dx.doi.org/10.1371/journal.pcbi.1006547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6233922PMC
November 2018

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

Bioinformatics 2018 07;34(13):i4-i12

Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022589PMC
July 2018

Multiple Sequence Alignment.

Methods Mol Biol 2017 ;1525:167-189

Centre for Integrative Bioinformatics, Vrije Universiteit, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_8DOI Listing
January 2018

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping.

Sci Rep 2016 10 21;6:35436. Epub 2016 Oct 21.

School of Medicine, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, UK.

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http://dx.doi.org/10.1038/srep35436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073228PMC
October 2016

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

Bioinformatics 2016 09;32(17):i389-i392

University Medical Centre Utrecht, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw481DOI Listing
September 2016

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

Bioinformatics 2016 06;32(12):i60-i69

Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btw250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908334PMC
June 2016

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

ACS Nano 2016 06 3;10(6):5710-9. Epub 2016 Jun 3.

Physics of Living Systems & LaserLaB Amsterdam, Vrije Universiteit Amsterdam , 1081 HV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/acsnano.5b07072DOI Listing
June 2016

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

Phys Rev Lett 2016 Feb 16;116(7):078101. Epub 2016 Feb 16.

Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, Netherlands.

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http://dx.doi.org/10.1103/PhysRevLett.116.078101DOI Listing
February 2016

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

PLoS Comput Biol 2015 Oct 27;11(10):e1004435. Epub 2015 Oct 27.

Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624779PMC
October 2015

metaModules identifies key functional subnetworks in microbiome-related disease.

Bioinformatics 2016 06 5;32(11):1678-85. Epub 2015 Sep 5.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv526DOI Listing
June 2016

The hydrophobic temperature dependence of amino acids directly calculated from protein structures.

PLoS Comput Biol 2015 May 22;11(5):e1004277. Epub 2015 May 22.

Computer Science Department, Centre for Integrative Bioinformatics (IBIVU), VU University, Amsterdam, Netherlands.

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http://dx.plos.org/10.1371/journal.pcbi.1004277
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http://dx.doi.org/10.1371/journal.pcbi.1004277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441443PMC
May 2015

Quantifying the displacement of mismatches in multiple sequence alignment benchmarks.

PLoS One 2015 19;10(5):e0127431. Epub 2015 May 19.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands; Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127431PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438059PMC
April 2016

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

Nucleic Acids Res 2015 Jul 15;43(W1):W301-5. Epub 2015 Apr 15.

Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands

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http://dx.doi.org/10.1093/nar/gkv346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489229PMC
July 2015

Competition between surface adsorption and folding of fibril-forming polypeptides.

Phys Rev E Stat Nonlin Soft Matter Phys 2015 Feb 19;91(2):022711. Epub 2015 Feb 19.

Van 't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.

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http://dx.doi.org/10.1103/PhysRevE.91.022711DOI Listing
February 2015

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

Bioinformatics 2014 Jun 10;30(11):1530-8. Epub 2014 Feb 10.

Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands, Centre for Integrative Bioinformatics VU and AIMMS Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands and NBIC Netherlands Bioinformatics Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btu085DOI Listing
June 2014

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

PLoS One 2014 15;9(1):e85185. Epub 2014 Jan 15.

Deptartment of Chemistry, University of Cambridge, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085185PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893179PMC
December 2014

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

Bioinformatics 2014 Feb 22;30(3):326-34. Epub 2013 Nov 22.

Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Netherlands Bioinformatics Centre (NBIC), Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands and Department of Biological Psychology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/30/3/326.fu
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt675DOI Listing
February 2014

Exploring fold space preferences of new-born and ancient protein superfamilies.

PLoS Comput Biol 2013 14;9(11):e1003325. Epub 2013 Nov 14.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1003325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828129PMC
July 2014

Interplay between folding and assembly of fibril-forming polypeptides.

Phys Rev Lett 2013 Aug 29;111(5):058101. Epub 2013 Jul 29.

Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands.

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http://dx.doi.org/10.1103/PhysRevLett.111.058101DOI Listing
August 2013

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

Brief Bioinform 2013 Sep 19;14(5):589-98. Epub 2013 Apr 19.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands. Tel.: +31 20 59 87816; Fax: +31 20 59 87653;

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http://dx.doi.org/10.1093/bib/bbt023DOI Listing
September 2013

Comparing clustering and pre-processing in taxonomy analysis.

Bioinformatics 2012 Nov 8;28(22):2891-7. Epub 2012 Sep 8.

Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam-ACTA, University of Amsterdam and VU University Amsterdam, VU University Amsterdam, The Netherlands.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts552DOI Listing
November 2012

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

Biophys J 2011 Feb;100(3):693-700

Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1016/j.bpj.2010.11.088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030183PMC
February 2011

Disordered flanks prevent peptide aggregation.

PLoS Comput Biol 2008 Dec 19;4(12):e1000241. Epub 2008 Dec 19.

FOM Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands.

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https://dx.plos.org/10.1371/journal.pcbi.1000241
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http://dx.doi.org/10.1371/journal.pcbi.1000241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588114PMC
December 2008

Using phylogeny to improve genome-wide distant homology recognition.

PLoS Comput Biol 2007 Jan 20;3(1):e3. Epub 2006 Nov 20.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.0030003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779300PMC
January 2007

Fold usage on genomes and protein fold evolution.

Proteins 2005 Sep;60(4):690-700

Department of Statistics, University of Oxford, United Kingdom.

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http://dx.doi.org/10.1002/prot.20506DOI Listing
September 2005

How old is your fold?

Bioinformatics 2005 Jun;21 Suppl 1:i449-58

Department of Statistics 1 South Parks Road, Oxford OX1 3TG, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti1008DOI Listing
June 2005