Research Output 1996 2020

2020

Facilities that make the PDB data collection more powerful

Lange, J., Baakman, C., Pistorius, A., Krieger, E., Hooft, R., Joosten, R. P. & Vriend, G., 1 Jan 2020, In : Protein Science. 29, 1, p. 330-344 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Databases
Computational Biology
Proteins
Bioinformatics
Software
2019

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S. J., Montalban-Lopez, M., De Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B. & Kuipers, O. P., 10 Jan 2019, In : BMC Evolutionary Biology. 19, 1, p. 1-15 15 p., 15.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
strength (mechanics)
glucose
mutation
chemostat
fitness

Addendum: The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Jan Aalbersberg, I., 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., Goble, C., Grethe, J. S., Heringa, J., Hoen, P. A. C. T., 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., Jan Velterop, V., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 19 Mar 2019, In : Scientific Data. 6, p. 1-1 1 p., 6.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A framework for exhaustive modelling of genetic interaction pattern using Petri nets

Jacobsen, A., Ivanova, O., Amini, S., Heringa, J., Kemmeren, P. & Feenstra, K. A., 17 Dec 2019, In : Bioinformatics.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Petri nets
Petri Nets
Genes
Phenotype
Biological Phenomena

Diversity of SpaP in genetic and salivary agglutinin mediated adherence among Streptococcus mutans strains

Yang, J., Deng, D., Brandt, B. W., Nazmi, K., Wu, Y., Crielaard, W. & Ligtenberg, A. J. M., 1 Dec 2019, In : Scientific Reports. 9, 1, 19943.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Streptococcus mutans
Agglutinins
Genotype
Nonsense Codon
Tooth

Erratum: Author Correction: Evaluating FAIR maturity through a scalable, automated, community-governed framework (Scientific data (2019) 6 1 (174))

Wilkinson, M. D., Dumontier, M., Sansone, S. A., Bonino da Silva Santos, L. O., Prieto, M., Batista, D., McQuilton, P., Kuhn, T., Rocca-Serra, P., Crosas, M. & Schultes, E., 21 Oct 2019, In : Scientific Data. 6, 1, p. 230 1 p.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Open Access
maturity
amendment
community
Amendments
Maturity

Evaluating FAIR maturity through a scalable, automated, community-governed framework

Wilkinson, M. D., Dumontier, M., Sansone, S. A., Bonino da Silva Santos, L. O., Prieto, M., Batista, D., McQuilton, P., Kuhn, T., Rocca-Serra, P., Crosas, M. & Schultes, E., 20 Sep 2019, In : Scientific Data. 6, 1, p. 1-12 12 p., 174.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Acceptance tests
maturity
Resources
Application programs
resources

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
Peer Review
Facilitative Glucose Transport Proteins
Sampling
Mutation
Glucose Transporter Type 1

Long-term impact of oral surgery with or without amoxicillin on the oral microbiome-A prospective cohort study

Menon, R. K., Gomez, A., Brandt, B. W., Leung, Y. Y., Gopinath, D., Watt, R. M., Crielaard, W., Nelson, K. E. & Botelho, M. G., 1 Dec 2019, In : Scientific Reports. 9, 1, 18761.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Oral Surgery
Microbiota
Amoxicillin
Cohort Studies
Prospective Studies

Reasoning about cell dynamics using network models

Jacobsen, A., 2019, 182 p.

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

Open Access
File

RUNX2/CBFB modulates the response to MEK inhibitors through activation of receptor tyrosine kinases in KRAS-mutant colorectal cancer

Šuštić, T., Bosdriesz, E., van Wageningen, S., Wessels, L. F. A. & Bernards, R., 19 Dec 2019, In : Translational oncology. 13, 2, p. 201-211 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Mitogen-Activated Protein Kinase Kinases
Receptor Protein-Tyrosine Kinases
Colorectal Neoplasms
Colonic Neoplasms
Non-Receptor Type 11 Protein Tyrosine Phosphatase

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
Web Server
Proteins
Protein
Prediction
Interaction
computer vision
data analysis

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

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Information Storage and Retrieval
Head and Neck Neoplasms
Netherlands
Neck
Head
2018

An Acquired Vulnerability of Drug-Resistant Melanoma with Therapeutic Potential

Wang, L., Leite de Oliveira, R., Huijberts, S., Bosdriesz, E., Pencheva, N., Brunen, D., Bosma, A., Song, J-Y., Zevenhoven, J., Los-de Vries, G. T., Horlings, H., Nuijen, B., Beijnen, J. H., Schellens, J. H. M. & Bernards, R., 31 May 2018, In : Cell. 173, 6, p. 1413-1425.e14

Research output: Contribution to JournalArticleAcademicpeer-review

Tumors
Melanoma
Mitogen-Activated Protein Kinase Kinases
Mitogen-Activated Protein Kinases
Reactive Oxygen Species

A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers

Šuštić, T., van Wageningen, S., Bosdriesz, E., Reid, R. J. D., Dittmar, J., Lieftink, C., Beijersbergen, R. L., Wessels, L. F. A., Rothstein, R. & Bernards, R., 27 Nov 2018, In : Genome Medicine. 10, 1, p. 90

Research output: Contribution to JournalArticleAcademicpeer-review

Unfolded Protein Response
Mitogen-Activated Protein Kinase Kinases
Colonic Neoplasms
Phosphotransferases
Yeasts

A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells

Ressa, A., Bosdriesz, E., de Ligt, J., Mainardi, S., Maddalo, G., Prahallad, A., Jager, M., de la Fonteijne, L., Fitzpatrick, M., Groten, S., Altelaar, A. F. M., Bernards, R., Cuppen, E., Wessels, L. & Heck, A. J. R., Oct 2018, In : Molecular and Cellular Proteomics. 17, 10, p. 1892-1908 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Colorectal Neoplasms
Cells
Molecular biology
Receptor Protein-Tyrosine Kinases
Pharmaceutical Preparations

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

Comparative Network Reconstruction using mixed integer programming

Bosdriesz, E., Prahallad, A., Klinger, B., Sieber, A., Bosma, A., Bernards, R., Blüthgen, N. & Wessels, L. F. A., 1 Sep 2018, In : Bioinformatics. 34, 17, p. i997-i1004

Research output: Contribution to JournalArticleAcademicpeer-review

Mixed Integer Programming
Integer programming
Boidae
Data Perturbation
Cell

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

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux

Bosdriesz, E., Wortel, M. T., Haanstra, J. R., Wagner, M. J., De La Torre Cortés, P. & Teusink, B., 3 Apr 2018, In : Scientific Reports. 8, 1, p. 1-9 9 p., 5576.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Facilitated Diffusion
Facilitative Glucose Transport Proteins
Glycolysis
Saccharomyces cerevisiae
Carrier Proteins

MAP3K1 and MAP2K4 mutations are associated with sensitivity to MEK inhibitors in multiple cancer models

Xue, Z., Vis, D. J., Bruna, A., Sustic, T., van Wageningen, S., Batra, A. S., Rueda, O. M., Bosdriesz, E., Caldas, C., Wessels, L. F. A. & Bernards, R., Jul 2018, In : Cell Research. 28, 7, p. 719-729 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Mitogen-Activated Protein Kinase Kinases
Mutation
Neoplasms
Mitogen-Activated Protein Kinases
Pharmaceutical Preparations

Modelling signalling networks from perturbation data

Dorel, M., Klinger, B., Gross, T., Sieber, A., Prahallad, A., Bosdriesz, E., Wessels, L. F. A. & Blüthgen, N., 1 Dec 2018, In : Bioinformatics. 34, 23, p. 4079-4086 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Data Perturbation
Modeling
Colonic Neoplasms
Steady-state Analysis
Mitogen-Activated Protein Kinases

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

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

Cloudy, increasingly FAIR; Revisiting the FAIR Data guiding principles for the European Open Science Cloud

Mons, B., Neylon, C., Velterop, J., Dumontier, M., Da Silva Santos, L. O. B. & Wilkinson, M. D., 1 Jan 2017, In : Information Services and Use. 37, 1, p. 49-56 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
interpretation
science
fairness
resources

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

Multi-Scale Investigation of Protein-Protein Interactions

Hou, Q., 2017, 139 p.

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

Open Access
File

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

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

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

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

Editorial

Heringa, J., Li, W. & Madura, J., 1 Oct 2016, In : Computational Biology and Chemistry. 64, p. vii-viii

Research output: Contribution to JournalEditorialAcademicpeer-review