Research Output 1967 2020

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2020

On optimising cost and value in compute systems for radio astronomy

Chris Broekema, P., Allan, V. L., van Nieuwpoort, R. & Bal, H., Jan 2020, (Accepted/In press) In : Astronomy and Computing. 30

Research output: Contribution to JournalArticleAcademicpeer-review

User-centric pattern mining on knowledge graphs: An archaeological case study

Wilcke, W. X., de Boer, V., de Kleijn, M. T. M., van Harmelen, F. A. H. & Scholten, H. J., 2020, (Accepted/In press) In : Journal of Web Semantics.

Research output: Contribution to JournalArticleAcademicpeer-review

Pipelines
Association rules
Transparency
Data mining
Data structures

Using a systems-theoretic approach to analyze safety in radiation therapy-first steps and lessons learned

Silvis-Cividjian, N., Verbakel, W. F. A. R. & Admiraal, M., 2020, In : Safety Science. 122, p. 104519

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Radiotherapy
Hazards
Safety
Failure modes
process analysis
2019

A Boxology of Design Patterns for Hybrid Learning and Reasoning Systems

van Harmelen, F. & ten Teije, A., Jan 2019, In : JOURNAL OF WEB ENGINEERING. 18, 1-3, p. 97-123 27 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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 Formal Proof of the Expressiveness of Deep Learning

Bentkamp, A., Blanchette, J. C. & Klakow, D., Aug 2019, In : Journal of Automated Reasoning. 63, 2, p. 347-368

Research output: Contribution to JournalArticleAcademicpeer-review

Aggregation of linked data in the cultural heritage domain: A case study in the Europeana network

Freire, N., Voorburg, R., Cornelissen, R., de Valk, S., Meijers, E. & Isaac, A., Aug 2019, In : Information (Switzerland). 10, 8, p. 1-15 15 p., 252.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Agglomeration
Metadata
Data structures
Semantics
Digital libraries

A manifesto for energy-aware software

Fonseca, A., Kazman, R. & Lago, P., 1 Nov 2019, In : IEEE Software. 36, 6, p. 79-82 4 p., 8880037.

Research output: Contribution to JournalArticleAcademicpeer-review

Electric power utilization
Communication
Internet
Hardware

An adaptive temporal-causal network model for social networks based on the homophily and more-becomes-more principle

Beukel, S. V. D., Goos, S. H. & Treur, J., 4 Feb 2019, In : Neurocomputing. 338, p. 361-371 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Tobacco Use
Social Support
Alcohols
Tobacco
Datasets

Analysis of a Network’s Asymptotic Behaviour via its Structure Involving its Strongly Connected Components

Treur, J., 1 Oct 2019, In : Network Science.

Research output: Contribution to JournalArticleAcademicpeer-review

Tics
general conditions

Architecting with microservices: A systematic mapping study

Di Francesco, P., Lago, P. & Malavolta, I., 1 Apr 2019, In : Journal of Systems and Software. 150, 4, p. 77-97 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Are all citations worth the same? Valuing citations by the value of the citing items

Giuffrida, C., Abramo, G. & D'Angelo, C. A., May 2019, In : Journal of Informetrics. 13, 2, p. 500-514 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Values
operationalization
weighting
present
methodology

A tale of three systems: Case studies on the application of architectural tactics for cyber-foraging

Lewis, G., Lago, P., Echeverria, S. & Simoens, P., 1 Jul 2019, In : Future generations computer systems: FGCS. 96, p. 119-147 29 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Mobile devices
Demonstrations
Servers

Bioinformatics in the Netherlands: The value of a nationwide community

Van Gelder, C. W. G., Hooft, R. W. W., Van Rijswijk, M. N., Van Den Berg, L., Kok, R. G., Reinders, M., Mons, B. & Heringa, J., 22 Mar 2019, In : Briefings in bioinformatics. 20, 2, p. 375-383 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Bioinformatics
Computational Biology
Netherlands
Biological Science Disciplines
Research

Divide and congruence III: From decomposition of modal formulas to preservation of stability and divergence

Fokkink, W., van Glabbeek, R. & Luttik, B., 1 Oct 2019, In : Information and Computation. 268, p. 1-31 31 p., 104435.

Research output: Contribution to JournalArticleAcademicpeer-review

Preservation
Congruence
Divides
Divergence
Semantics

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

Evaluating named entity recognition tools for extracting social networks from novels

Dekker, N., Kuhn, T. & van Erp, M., 18 Apr 2019, In : PeerJ Computer Science. 2019, 4, p. 1-29 29 p., e189.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Processing

Evolving embodied intelligence from materials to machines

Eiben, A. E., Howard, D., Kennedy, D. F., Mouret, J-B., Valencia, P. & Winkler, D., Jan 2019, In : Nature Machine Intelligence. 1, 1, p. 12 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Robotics
Explosions
DNA
Robots
Proteins

Foundations for measuring IT-outsourcing success and failure

Delen, G. P. A. J., Peters, R. J., Verhoef, C. & van Vlijmen, S. F. M., 1 Oct 2019, In : Journal of Systems and Software. 156, p. 113-125 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Outsourcing

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk

Jansen, I. E., Savage, J. E., Watanabe, K., Bryois, J., Williams, D. M., Steinberg, S., Sealock, J., Karlsson, I. K., Hägg, S., Athanasiu, L., Voyle, N., Proitsi, P., Witoelar, A., Stringer, S., Aarsland, D., Almdahl, I. S., Andersen, F., Bergh, S., Bettella, F., Bjornsson, S. & 33 othersBrækhus, A., Bråthen, G., de Leeuw, C., Desikan, R. S., Djurovic, S., Dumitrescu, L., Fladby, T., Hohman, T. J., Jonsson, P. V., Kiddle, S. J., Rongve, A., Saltvedt, I., Sando, S. B., Selbæk, G., Shoai, M., Skene, N. G., Snaedal, J., Stordal, E., Ulstein, I. D., Wang, Y., White, L. R., Hardy, J., Hjerling-Leffler, J., Sullivan, P. F., van der Flier, W. M., Dobson, R., Davis, L. K., Stefansson, H., Stefansson, K., Pedersen, N. L., Ripke, S., Andreassen, O. A. & Posthuma, D., 1 Mar 2019, In : Nature Genetics. 51, 3, p. 404-413 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Meta-Analysis
Alzheimer Disease
Genome
Proxy
Genes

How enterprise architecture improves the quality of IT investment decisions

van den Berg, M., Slot, R., van Steenbergen, M., Faasse, P. & van Vliet, H., Jun 2019, In : Journal of Systems and Software. 152, p. 134-150 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Industry
Decision making

Identifying influence agents that promote physical activity through the simulation of social network interventions: Agent-based modeling study

Van Woudenberg, T. J., Simoski, B., Araújo, E. F. D. M., Bevelander, K. E., Burk, W. J., Smit, C. R., Buijs, L., Klein, M. & Buijzen, M., 5 Aug 2019, In : Journal of Medical Internet Research. 21, 8, 15 p., e12914.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Systems Analysis
Social Support
Exercise
Patient Selection
Health Behavior

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

Importance of parameter settings on the benefits of robot-to-robot learning in evolutionary robotics

Heinerman, J., Haasdijk, E. & Eiben, A. E., 4 Mar 2019, In : Frontiers Robotics AI. 6, MARCH, p. 1-11 11 p., 10.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Robot learning
Robotics
Robots

Kadaster knowledge graph: Beyond the fifth star of open data

Ronzhin, S., Folmer, E., Maria, P., Brattinga, M., Beek, W., Lemmens, R. & van't Veer, R., 9 Oct 2019, In : Information (Switzerland). 10, 10, p. 1-19 19 p., 310.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Urban planning
Stars
Lakes
Learning systems

L.E.J. Brouwer, fifty years later

van Dalen, D., Jongbloed, G., Klop, J. W. & van Mill, J., 11 Jan 2019, (Accepted/In press) In : Indagationes Mathematicae. p. 1-16 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Lamarckian Evolution of Simulated Modular Robots

Jelisavcic, M., Glette, K., Haasdijk, E. & Eiben, A. E., 18 Feb 2019, In : Frontiers in Robotics and AI. 6, 9

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Modular robots
Controllers
Robots
Robot learning
Brain

Learning on the job: Studying expertise in residential burglars using virtual environments*

Nee, C., van Gelder, J. L., Otte, M., Vernham, Z. & Meenaghan, A., Aug 2019, In : Criminology. 57, 3, p. 481-511 31 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Crime
expertise
Learning
Decision Making
offense

Leveraging European infrastructures to access 1 million human genomes by 2022

Saunders, G., Baudis, M., Becker, R., Beltran, S., Béroud, C., Birney, E., Brooksbank, C., Brunak, S., Van den Bulcke, M., Drysdale, R., Capella-Gutierrez, S., Flicek, P., Florindi, F., Goodhand, P., Gut, I., Heringa, J., Holub, P., Hooyberghs, J., Juty, N., Keane, T. M. & 21 othersKorbel, J. O., Lappalainen, I., Leskosek, B., Matthijs, G., Mayrhofer, M. T., Metspalu, A., Navarro, A., Newhouse, S., Nyrönen, T., Page, A., Persson, B., Palotie, A., Parkinson, H., Rambla, J., Salgado, D., Steinfelder, E., Swertz, M. A., Valencia, A., Varma, S., Blomberg, N. & Scollen, S., 1 Nov 2019, In : Nature Reviews Genetics. 20, 11, p. 693-701 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Human Genome
Precision Medicine
Information Dissemination
Genomics
Research

Managing safety and mission completion via collective run-time adaptation

Bozhinoski, D., Garlan, D., Malavolta, I. & Pelliccione, P., May 2019, In : Journal of Systems Architecture. 95, p. 19-35 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Robots
Cameras
Sensors

Mathematical analysis of the emergence of communities based on coevolution of social contagion and bonding by homophily

Treur, J., 25 Jun 2019, In : Applied Network Science. 4, 1, p. 1-30 30 p., 39.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Contagion
Coevolution
Mathematical Analysis
Person
Network Structure

Metadata categorization for identifying search patterns in a digital library

Bogaard, T., Hollink, L., Wielemaker, J., van Ossenbruggen, J. & Hardman, L., 6 Mar 2019, In : Journal of Documentation. 75, 2, p. 270-286 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Digital libraries
Metadata
newspaper
user interface
inclusion

Mining inter-relationships in online scientific articles and its visualization: Natural language processing for systems biology modeling

Melethadathil, N., Nair, B., Diwakar, S. & Heringa, J., Feb 2019, In : International Journal of Online Engineering. 15, 2, p. 39-59 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Visualization
Medicine
Labels
Processing
Oncology

Modeling Higher-Order Adaptivity of a Network by Multilevel Network Reification

Treur, J., 2 Sep 2019, (Accepted/In press) In : Network Science.

Research output: Contribution to JournalArticleAcademicpeer-review

reification
Social sciences
Social Sciences
Network architecture
Object Attachment

PABO: Mitigating Congestion via Packet Bounce in Data Center Networks

Shi, X., Wang, L., Zhang, F., Zheng, K., Mühlhäuser, M. & Liu, Z., 1 May 2019, In : Computer Communications. 140-141, p. 1-14 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Switches
Topology
Flow control
Synchronization
Experiments

Projections for infinitary rewriting (extended version)

Lombardi, C., Ríos, A. & de Vrijer, R., 16 Aug 2019, In : Theoretical Computer Science. 781, p. 92-110 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Rewriting
Projection
Term Rewriting
Term
Contraction

Re-implementing a legacy system

Sneed, H. & Verhoef, C., 1 Sep 2019, In : Journal of Systems and Software. 155, p. 162-184 23 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Legacy systems

Reliable Restricted Process Theory

Ghassemi, F. & Fokkink, W., 14 Feb 2019, In : Fundamenta Informaticae. 165, 1, p. 1-41 41 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Communication
Network protocols
Network Protocols
Axiomatization
Multi-hop

Safety for mobile robotic system: A systematic mapping study from a software engineering perspective

Bozhinoski, D., Di Ruscio, D., Malavolta, I., Pelliccione, P. & Crnkovic, I., May 2019, In : Journal of Systems and Software. 151, p. 150-179 30 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Software engineering
Robotics
Robots

Scalable Fine-Grained Proofs for Formula Processing

Barbosa, H., Blanchette, J. C., Fleury, M. & Fontaine, P., 4 Jan 2019, In : Journal of Automated Reasoning. p. 1-26 26 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Surface mount technology
Data structures
Processing

Searching textual and model-based process descriptions based on a unified data format

Leopold, H., van der Aa, H., Pittke, F., Raffel, M., Mendling, J. & Reijers, H. A., 4 Apr 2019, In : Software and Systems Modeling. 18, 2, p. 1179-1194 16 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Model-based
Process Model
Repository
Business Process
Complement

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., 15 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

Stability in Software Engineering: Survey of the State-of-the-Art and Research Directions

Salama, M., Bahsoon, R. & Lago, P., 1 Jan 2019, In : IEEE Transactions on Software Engineering.

Research output: Contribution to JournalArticleAcademicpeer-review

Software engineering
Taxonomies

State of the art of cyber-physical systems security: An automatic control perspective

Zacchia Lun, Y., D'Innocenzo, A., Smarra, F., Malavolta, I. & Di Benedetto, M. D., Mar 2019, In : Journal of Systems and Software. 149, p. 174-216 43 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Industry
Cyber Physical System

Syllogistic logic with Most

Endrullis, J. & Moss, L. S., 1 Jun 2019, In : Mathematical Structures in Computer Science. 29, 6, p. 763-782 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Computability and decidability
Polynomials
Logic
Soundness
Decidability

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 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

Using Hidden Markov Models for the accurate linguistic analysis of process model activity labels

Leopold, H., van der Aa, H., Offenberg, J. & Reijers, H. A., 1 Jul 2019, In : Information Systems. 83, p. 30-39 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Hidden Markov models
Linguistics
Labels
Learning systems
Specifications