Research Output 2002 2019

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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
Multiple Sequence Alignment
Workflow
Sequence Alignment
Work Flow
Alignment

The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern

Amini, S., Jacobsen, A., Ivanova, O., Lijnzaad, P., Heringa, J., Holstege, F. C. P., Feenstra, K. A. & Kemmeren, P., 13 May 2019, In : PLoS Computational Biology. 15, 5, p. 1-27 27 p., e1007061.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Transcription factors
Transcription Factor
Gene expression
Gene Expression
gene expression

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.

Research output: Contribution to JournalArticleAcademic

thermodynamics
protein
heat capacity
meta-analysis
hydrophobicity
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
Viral Core Proteins
High-Throughput Nucleotide Sequencing
Chronic Hepatitis B
Hepatitis B e Antigens
Hepatitis B virus

Deep sequencing identifies hepatitis B virus core protein signatures in chronic hepatitis B patients

van der Ree, M. H., Jansen, L., Welkers, M. R. A., Reesink, H. W., Feenstra, K. A. & Kootstra, N. A., Oct 2018, In : Antiviral research. 158, p. 213-225 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Viral Core Proteins
High-Throughput Nucleotide Sequencing
Chronic Hepatitis B
Hepatitis B e Antigens
Hepatitis B virus
Sequence Alignment
sequence alignment
Alignment
Multiple Sequence Alignment
Benchmarking

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

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

Both intrinsic substrate preference and network context contribute to substrate selection of classical tyrosine phosphatases

Palma, A., Tinti, M., Paoluzi, S., Santonico, E., Brandt, B. W., Hooft Van Huijsduijnen, R., Masch, A., Heringa, J., Schutkowski, M., Castagnoli, L. & Cesareni, G., 24 Mar 2017, In : Journal of Biological Chemistry. 292, 12, p. 4942-4958 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Phosphoric Monoester Hydrolases
Tyrosine
Phosphopeptides
Protein Tyrosine Phosphatases
Substrates

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

Revelation of the Genetic Basis for Convergent Innovative Anal Fin Pigmentation Patterns in Cichlid Fishes

Gu, L., Zhang, C. & Xia, C., 20 Jul 2017, (Submitted) In : bioRxiv.

Research output: Contribution to JournalArticleAcademic

pigmentation
fins
fish
genes
convergent evolution

Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest

Hou, Q., De Geest, P. F. G., Vranken, W. F., Heringa, J. & Feenstra, K. A., 15 May 2017, In : Bioinformatics. 33, 10, p. 1479-1487 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Random Forest
Protein-protein Interaction
Proteins
Prediction
Predictors

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
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
Free energy
energy
Conformations
protein conformation
Benchmarking

CLUB-MARTINI: Selecting favourable interactions amongst available candidates, a coarse-grained simulation approach to scoring docking decoys

Hou, Q., Lensink, M. F., Heringa, J. & Feenstra, K. A., 11 May 2016, In : PLoS ONE. 11, 5, e0155251.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Free energy
energy
Conformations
protein conformation
Benchmarking

ConBind: Motif-aware cross-species alignment for the identification of functional transcription factor binding sites

Lelieveld, S. H., Schütte, J., Dijkstra, M. J. J., Bawono, P., Kinston, S. J., Göttgens, B., Heringa, J. & Bonzanni, N., 5 May 2016, In : Nucleic Acids Research. 44, 8, p. e72

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Sequence Alignment
Transcription Factors
Nucleotides
Binding Sites
Nucleic Acid Regulatory Sequences

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
Catenins
beta Catenin
Petri nets
Stabilization
Wnt Signaling Pathway

Construction and Experimental Validation of a Petri Net Model of Wnt/beta-Catenin Signaling

Jacobsen, A., Heijmans, N., Verkaar, F., Smit, M. J., Heringa, J., van Amerongen, R. & Feenstra, K. A., 2016, In : PLoS ONE. 11, 5, e0155743.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Catenins
beta Catenin
Petri nets
Stabilization
Wnt Signaling Pathway

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

HapCol: Accurate and memory-efficient haplotype assembly from long reads

Pirola, Y., Zaccaria, S., Dondi, R., Klau, G. W., Pisanti, N. & Bonizzoni, P., 1 Jun 2016, In : Bioinformatics. 32, 11, p. 1610-1617 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Haplotype
Nucleotides
Polymorphism
Haplotypes
Sequencing

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

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

Knijnenburg, T. A., Klau, G. W., Iorio, F., Garnett, M. J., McDermott, U., Shmulevich, I. & Wessels, L. F. A., 23 Nov 2016, In : Scientific Reports. 6, 36812.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Learning systems
Genes
Cells

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

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes

Bonizzoni, P., Dondi, R., Klau, G. W., Pirola, Y., Pisanti, N. & Zaccaria, S., 1 Sep 2016, In : Journal of Computational Biology. 23, 9, p. 718-736 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Polyploidy
Haplotype
Error correction
Error Correction
Diploidy

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

The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, IJ. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J-W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 othersGray, A. J. G., Groth, P. T., Goble, C., Grethe, J. S., Heringa, J., ’t Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 15 Mar 2016, In : Scientific Data. 3, 160018.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Reusability
Data Management
Information management
management
Reuse
2015

Automatic classification of protein structure using the maximum contact map overlap metric

Andonov, R., Djidjev, H., Klau, G. W., Boudic-Jamin, M. L. & Wohlers, I., 2015, In : Algorithms. 8, 4, p. 850-869 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Protein Structure
Overlap
Contact
Proteins
Protein

CIDANE: Comprehensive isoform discovery and abundance estimation

Canzar, S., Andreotti, S., Weese, D., Reinert, K. & Klau, G. W., 2015, In : Lecture Notes in Computer Science. 9029, p. 60-61

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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

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

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment

El-Kebir, M., Heringa, J. & Klau, G. W., 2015, In : Algorithms. 8, 4, p. 1035-1051

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Quadratic Assignment
Alignment
Topology
Quadratic Assignment Problem
Molecular interactions

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

On the fixed parameter tractability and approximability of the minimum error correction problem

Bonizzoni, P., Dondi, R., Klau, G. W., Pirola, Y., Pisanti, N. & Zaccaria, S., 2015, In : Lecture Notes in Computer Science. p. 100-113

Research output: Contribution to JournalArticleAcademicpeer-review

On tree-constrained matchings and generalizations

Canzar, S., Elbassioni, K., Klau, G. W. & Mestre, J., 2015, In : Algorithmica. 71, 1, p. 98-119

Research output: Contribution to JournalArticleAcademicpeer-review

Bipartite Matching
Matching Problem
Bipartite Graph
Generalization

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

Use Case
Specificity
Monomers
Proteins
Protein-protein Interaction

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case

Hou, Q., Dutilh, B. E., Huynen, M. A., Heringa, J. & Feenstra, K. A., 8 Oct 2015, In : BMC Bioinformatics. 16, p. 325-325

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Use Case
Specificity
Monomers
Proteins
Protein-protein Interaction

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