Peer reviewed publications

2017

  • McGuire, R., Verhoeven, S., Vass, M., Vriend, G., de Esch, I.J.P., Lusher, S.J., Leurs, R., Ridder, L., Kooistra, A.J., Ritschel, T., de Graaf, C. (2017) 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. Journal of Chemical Information and Modeling 57, 115-121. doi:10.1021/acs.jcim.6b00686
  • Wilkinson, M.D., Verborgh, R., da Silva Santos, L.O.B., Clark, T., Swertz, M.A., Kelpin, F.D.L, Gray, A.J.G., Schultes, E.A., van Mulligen, E.M., Ciccarese, P., Kuzniar, A., Gavai, A., Thompson, M., Kaliyaperumal, R., Bolleman, J.T., Dumontier, M. (2017) Interoperability and FAIRness through a novel combination of Web technologies. PeerJ CompSci. 3, e110. doi:10.7717/peerj-cs.110
  • Kuzniar, A., Laffeber, C., Eppink, B., Bezstarosti, K., Dekkers, D., Woelders, H., Zwamborn, A.P.M., Demmers, J., Lebbink, J.H.G. and Kanaar, R. (2017) Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields. PLoS ONE 12(2), e0170762. doi:10.1371/journal.pone.017076
  • 2016

    • van Oosterom, P., Martinez-Rubi, O., Tijssen, T., and Gonçalves, R.: Realistic Benchmarks for Point Cloud Data Management Systems. Advances in 3D Geoinformation, editor Abdul-Rahman, A., edition number 1, series ISSN 1863-2246, pages 1-30, doi: 10.1007/978-3-319-25691-7, November 2016.
    • Souley Madougou, Ana Varbanescu, Cees de Laat, and Rob V. van Nieuwpoort: The Landscape of GPGPU Performance Modeling Tools. Parallel Computing, volume 56, number C, pages 18-33, doi: 10.1016/j.parco.2016.04.002, August 2016.
    • Van Nieuwpoort, R., Spreeuw, H. RFI2016 Towards Exascale Real-Time RFI Mitigation
    • da Silva Santos, L.B., Wilkinson, M.D., Kuzniar, A., Kaliyaperumal, R., Thompson, M., Dumontier, M., Burger, K. FAIR Data Points Supporting Big Data Interoperability. In: Zelm M, Doumeingts G, Mendonça JP, editors. Enterprise Interoperability in the Digitized and Networked Factory of the Future. London: ISTE; 2016. pp. 270-279.
    • Wilkinson, M.D., Dumontier M., Aalbersberg, I.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., Gray, A.J., Groth, P., Goble, C., Grethe, J.S., Heringa, J., 't Hoen, P.A., 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. (2016) The FAIR Guiding Principles for scientific data management and stewardship, Scientific Data, 3, doi: 10.1038/sdata.2016.18
    • Otten, M., Vlothuizen, W., Spreeuw, H., Varbanescu, A.: EuMW2016 Real-Time Processing of Multi-Channel SAR Data with GPUs.
    • Deppenmeier, Anna-Lena; Haarsma, Reindert J.; Hazeleger, Wilco. The Bjerknes feedback in the tropical Atlantic in CMIP5 models. CLIMATE DYNAMICS, Volume: 47, Issue: 7-8, Pages: 2691-2707, OCT. 2016
    • Van der Linden, Eveline C.; Bintanja, Richard; Hazeleger, Wilco; et al. Low-frequency variability of surface air temperature over the Barents Sea: causes and mechanisms. CLIMATE DYNAMICS, Volume: 47, Issue: 3-4, Pages: 1247-1262, AUG 2016
    • Krikken, Folmer; Schmeits, Maurice; Vlot, Willem; et al. Skill improvement of dynamical seasonal Arctic sea ice forecasts. GEOPHYSICAL RESEARCH LETTERS, Volume: 43, Issue: 10, Pages: 5124-5132, MAY 28 2016
    • Rasmijn, L. M.; van der Schrier, G.; Barkmeijer, J.; et al. Simulating the extreme 2013/2014 winter in a future climate. JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES, Volume: 121, Issue: 10, Pages: 5680-5698, MAY 27 2016
    • Chuwah, Clifford; van Noije, Twan; van Vuuren, Detlef P.; et al. Global and regional climate impacts of future aerosol mitigation in an RCP6.0-like scenario in EC-Earth. CLIMATIC CHANGE, Volume: 134, Issue: 1-2, Pages: 1-14, JAN. 2016
    • Ranguelova, E. A Salient Region Detector for Structured Images. AICCSA2016, Dec. 2016
    • Ridder, L. (2016). MAGMa-Based Mass Spectrum Annotation in CASMI 2014. Accepted for publication in Current Metabolomics. DOI: 10.2174/2213235X04666160620100844
    • van Esse, G. W., Colette, A., Guzzonato, F., van Esse, H. P., Boekschoten, M., Ridder, L., Vervoort, J., de Vries, S. C. (2016). Transcriptional analysis of serk1 and serk3 receptor-like kinase mutants. Plant Physiology, pp-01478. DOI: http://dx.doi.org/10.1104/pp.16.01478
    • JanssenDuijghuijsen, L. M., Keijer, J., Mensink, M., Lenaerts, K., Ridder, L., Nierkens, S., Kartaram, S.W., Verschuren, M.C., Pieters, R.H., Bas, R., Witkamp, R.F., Wichers, H.J., van Norren, K. (2016). Adaptation of exercise-induced stress in well-trained healthy young men. Experimental physiology. DOI: 10.1113/EP086025
    • Pelupessy, I. and van Werkhoven, B. and van Elteren, A. and Viebahn, J. and Candy, A. and Portegies Zwart, S. and Dijkstra, H. The Oceanographic Multipurpose Software Environment. Geoscientific Model Development Discussions 2016. http://www.geosci-model-dev-discuss.net/gmd-2016-178/ doi: 10.5194/gmd-2016-178
    • Hut, R.W. and Drost, N. and van Meersbergen, M. and Sutanudjaja, E. and Bierkens, M. and Giesen van de, N. eWaterCycle: a hyper-resolution global hydrological model for riverdischarge forecasts made from open source pre-existing components. Geoscientific Model Development Discussions 2016. http://www.geosci-model-dev-discuss.net/gmd-2016-225/ doi: 10.5194/gmd-2016-225
    • Brunnabend, S.-E. and Dijkstra, H. A. and Kliphuis, M. A. and Bal, H. E. and Seinstra, F. and van Werkhoven, B. and Maassen, J. and van Meersbergen, M. Changes in extreme regional sea level under global warming. Ocean Science Discussions 2016. http://www.ocean-sci-discuss.net/os-2016-57/ doi: 10.5194/os-2016-57
    • Ben van Werkhoven, Inti Pelupessy, Arjen van Elteren, Jan Viebahn, Adam Candy, Simon Portegies Zwart and Henk Dijkstra. OMUSE: Oceanographic Multipurpose Software Environment. Environmental Computing Workshop at IEEE eScience 2016.
    • Y. Tian, F. Ozcan, T. Zou, R. Goncalves, H. Pirahesh. Building a Hybrid Warehouse: Efficient Joins Between Data Stored in HDFS and Enterprise Warehouse. Transactions on Database Systems (TODS) 2016
    • R. Goncalves, M. Kersten, K. Kyzirakos. A Datascope for satellite data. Conference on Big Data from Space (BiDS) 2016.
    • Nourian P, Goncalves R, Zlatanova S, Arroyo Ohori K, Vu Vo A. Voxelization Algorithms for Geospatial Applications. MethodsX 2016.
    • Goncalves R, van Tilburg T, Kyzirakos K, Alvanaki F, Koutsourakis P, van Werkhoven B, van Hage W. A spatial column-store to triangulate The Netherlands on the fly. ACM SIGSpatial 2016.
    • Goncalves R, Zlatanova S, Kyzirakos K, Nourian P, Alvanaki F, van Hage W. A columnar architecture for modern risk management systems. ECW workshop IEEE eScience 2016.
    • JM van der Zwaan, M Marx, and J Kamps. Validating Cross-Perspective Topic Modeling for Extracting Political Parties' Positions from Parliamentary Proceedings. ECAI 2016: 22nd European Conference on Artificial Intelligence. Frontiers in Artificial Intelligence and Applications. Vol. 285. IOS Press, 2016. doi: 10.3233/978-1-61499-672-9-28.
    • JM van der Zwaan, M van Meersbergen, A Fokkens, S ter Braake, I Leemans, E Kuijpers, P Vossen, and I Maks. Storyteller: Visualizing Perspectives in Digital Humanities Projects, in: Proceedings of the 2nd IFIP International Workshop on Computational History and Data-driven Humanities, Dublin, Ireland, 2016. doi: 10.1007/978-3-319-46224-0_8
    • Afshar S, Seymour K, Kelly SB, Woodcock S, van Hees VT, Mathers JC. Changes in physical activity after bariatric surgery: using objective and self-reported measures. Surg Obes Relat Dis. 2016 Sep 13. pii: S1550-7289(16)30698-0. doi: 10.1016/j.soard.2016.09.012.
    • van Hees VT, Thaler-Kall K, Wolf KH, Brønd JC, Bonomi A, Schulze M, Vigl M, Morseth B, Hopstock LA, Gorzelniak L, Schulz H, Brage S, Horsch A. Challenges and Opportunities for Harmonizing Research Methodology: Raw Accelerometry. Methods Inf Med. 2016 Oct 7;55(6). doi: 10.3414/ME15-05-0013
    • Martinez-Rubi, O., de Kleijn, M., Verhoeven, S., Drost, N., Attema, J., van Meersbergen, M., van Nieuwpoort, R., de Hond, R., Dias, E., Svetachov, P., 2016: Using modular 3D digital earth applications based on point clouds for the study of complex sites. International Journal of Digital Earth. http://www.tandfonline.com/doi/abs/10.1080/17538947.2016.1205673. DOI: 10.1080/17538947.2016.1205673
    • Maassen J, van Werkhoven B, van Meersbergen M, Bal HE, Kliphuis M, Brunnabend SE, Dijkstra HA, van Malenstein G, de Vos M, Kuijpers S, Boele S, Wolfrat J, Hill N, Wallom D, Grimm C, Kranzlmuller D, Ganpathi D, Jha S, El Khamra, Y, Bryan FO, Kirtman B, Seinstra FJ. On the Complexities of Utilizing Large-Scale Lightpath-Connected Distributed Cyberinfrastructure. Accepted for publication in Concurrency and Computation: Practice and Experience, special issue on Negative Results in eScience.
    • de Kleijn M, de Hond R, Martinez-Rubi O. A 3D spatial data infrastructure for Mapping the via Appia. Digital Applications in Archaeology and Cultural Heritage. ISSN 2212-0548. http://dx.doi.org/10.1016/j.daach.2016.03.001
    • Souley Madougou, Ana Lucia Varbanescu, Cees de Laat, and Rob van Nieuwpoort: A Tool for Bottleneck Analysis and Performance Prediction for GPU-accelerated Applications. Accepted for publication in The Sixth International Workshop on Accelerators and Hybrid Exascale Systems (AsHES), in conjunction with the 30th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Chicago, IL, USA, May 2016.
    • Alessio Sclocco, Joeri van Leeuwen, Henri E. Bal, Rob V. van Nieuwpoort: Real-Time Dedispersion for Fast Radio Transient Surveys, using Auto Tuning on Many-Core Accelerators. Accepted for publication in Astronomy and Computing, 2016. ArXiv link: http://arxiv.org/abs/1601.01165. DOI: 10.1016/j.ascom.2016.01.001.
    • Krikken, F., W. Hazeleger, M. Schmeitz, W. Vlot and V. Guemas, 2016: Skill improvement of dynamical seasonal Arctic sea ice forecasts. Geoph. Res. Lett., DOI: 10.1002/2016GL068462.
    • Rasmijn, L.M., G. van der Schrier, J. Barkmeijer, A. Sterl and W. Hazeleger, 2016: Simulating the extreme 2013/14 winter in a future climate. J. Geoph. Res. Atmospheres DOI: 10.1002/2015JD024492.
    • Deppenmeier, A., R. Haarsma and W. Hazeleger, 2016: The simulated Bjerknes feedback in the tropical Atlantic. Clim Dyn, DOI 10.1007/s00382-016-2992-z.
    • Chuwah, C., T. van Noije, D.P. van Vuuren, P. Le Sager, and W. Hazeleger, 2016: Climate impacts of future aerosol mitigation in an RCP6.0-like scenario. Climatic Change, 134, 1-14.
    • J. Borgdorff, W. van Hage, L.J. Dijkstra, E. Mancini and M.H. Lees, 2016: Simulation-supported Urban Movement Analysis, Visually-supported Computational Movement Analysis 2016, http://viz.icaci.org/vcma2016/wp-content/uploads/2016/07/vcma_borgdorf-paper.pdf
    • Bos, Patrick and Wijfjes, Huub and Piscaer, Maaike and Voerman, Gerrit (2016): Quantifying “Pillarization”: Extracting Political History from Large Databases of Digitized Media Collections, CEUR Workshop Proceedings: The 3rd HistoInformatics Workshop [1632] pages 57 - 66
    • Martinez-Ortiz, C., Kenter, T., Wevers, M., Huijnen, P., Verheul, J., van Eijnatten J. (2016): Design and Implementation of ShiCo: Visualising Shifting Concepts over Time, CEUR Workshop Proceedings: The 3rd HistoInformatics Workshop [1632] pages 11 - 19
    • H. G. Ouwersloot, A. F. Moene, J. J. Attema, J. Vilà-Guerau de Arellano, 2016: Large-eddy simulation comparison of a neutral flow over canopy: sensitivities to physical and numerical conditions, and similarity to other representations, Boundary Layer Meteorology, DOI 10.1007/s10546-016-0182-5
    • Fransz P, Linc G, Lee CR, Aflitos SA, Lasky JR, Toomajian C, Ali H, Peters J, van Dam P, Ji X, Kuzak M, Gerats T, Schubert I, Schneeberger K, Colot V, Martienssen R, Koornneef M, Nordborg M, Juenger TE, de Jong H, Schranz ME. Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana. Plant J. 2016 Jul 20
    • van der Linden, E.C., R. Bintanja, W. Hazeleger and R.G. Graversen. Low-frequency variability of surface air temperature over the Barents Sea. Climate Dynamics, 47(3-4), 2016. DOI 10.1007/s00382-015-2899-0.
    • C. Meijer, S. Verhoeven, E. Ranguelova, C.J. Camphuysen, J. Shamoun-Baranes and W. Bouten (2016), Visually Supported Annotation of Bird Tracking data and Subsequent Classification of Behaviour using Machine Learning, Visually-supported Computational Movement Analysis 2016
    • Judy Shamoun-Baranes, Willem Bouten, E. Emiel van Loon, Christiaan Meijer, C. J. Camphuysen (2016), Flap or soar? How a flight generalist responds to its aerial environment, Philosophical Transactions Of The Royal Society B. DOI: 10.1098/rstb.2015.0395
    • D. Ceolin, P. Groth, V. Maccatrozzo, W. Fokkink, W. van Hage, A. Nottamkandath (2016) Combining User Reputation and Provenance Analysis for Trust Assessment, Journal of Data and Information Quality 7(1-2) DOI: 10.1145/2818382
    • W. van Hage, J. Maassen, R. van Nieuwpoort (2016), Lightning talk: Software Impact Measurement at the Netherlands eScience Center, 4th Workshop on Sustainable Software for Science: Practice and Experiences, http://wssspe.researchcomputing.org.uk/wp-content/uploads/2016/06/WSSSPE4_paper_4.pdf

    2015

    • Alvanaki F, Goncalves R, Ivanova M, Kersten M, Kyzirakos K. GIS navigation boosted by column stores. Proc. VLDB Endow. 8(12), 1956–1959 (2015).
    • Attema JJ, Heusinkveld BG, Ronda RJ, Steeneveld GJ, Holtslag AAM. Summer in the City: Forecasting and Mapping Human Thermal Comfort in Urban Areas. In: e-Science (e-Science), 2015 IEEE 11th International Conference on. , 243–248 (2015).
    • Bierkens MFP, Bell VA, Burek P, et al. Hyper-resolution global hydrological modelling: what is next? Everywhere and locally relevant. Hydrol Process. 29(2), 310–320 (2015).
    • Borgdorff J, Krishna H, Lees MH. SIM-CITY: An e-Science Framework for Urban Assisted Decision Support. Procedia Comput. Sci. 51, 2327–2336 (2015).
    • Broekema PC, van Nieuwpoort R V, Bal HE. The Square Kilometre Array Science Data Processor. Preliminary compute platform design. J. Instrum. 10(07), C07004 (2015).
    • Buitinck L, Van Amerongen J, Tan E, De Rijke M. Multi-emotion Detection in User-Generated Reviews. In: Advances in Information Retrieval. , 43–48 (2015).
    • Chuwah C, van Noije T, van Vuuren DP, Stehfest E, Hazeleger W. Global impacts of surface ozone changes on crop yields and land use. Atmos. Environ. 106, 11–23 (2015).
    • Corti S, Palmer T, Balmaseda M, et al. Impact of Initial Conditions versus External Forcing in Decadal Climate Predictions: A Sensitivity Experiment. J. Clim. 28(11), 4454–4470 (2015).
    • D’Agostino D, Seinstra FJ. A parallel isosurface extraction component for visualization pipelines executing on GPU clusters. J. Comput. Appl. Math. 273, 383–393 (2015).
    • Goncalves R, Ivanova M, Alvanaki F, Maassen J, Kyzirakos K, Martinez-Rubi O, Mühleisen H. A round table for multi-disciplinary research on Geospatial and Climate Data. In: e-Science (e-Science), 2015 IEEE 11th International Conference on. , 165–170 (2015).
    • van Haren R, Haarsma RJ, van Oldenborgh GJ, Hazeleger W. Resolution dependence of European precipitation in a state-of-the-art atmospheric general circulation model. J. Clim. 28(13), 5134–5149 (2015).
    • van Haren R, Haarsma RJ, de Vries H, van Oldenborgh GJ, Hazeleger W. Resolution dependence of circulation forced future central European summer drying. Environ. Res. Lett. 10(5), 55002 (2015).
    • Hazeleger W, van den Hurk BJJM, Min E, et al. Tales of future weather. Nat. Clim. Change 5(2), 107–113 (2015).
    • van Hees VT, Sabia S, Anderson KN, et al. A Novel, Open Access Method to Assess Sleep Duration Using a Wrist-Worn Accelerometer. PLoS One. 10(11), e0142533 (2015).
    • Hijma P, Nieuwpoort RV van, Jacobs CJH, and Bal HE. Stepwise-refinement for Performance: a methodology for many-core programming. Concurrency and Computation: Practice and Experience. 27(10), 4515–4554 (2015). DOI: 10.1002/cpe.3416.
    • Krikken F, Hazeleger W. Arctic Energy Budget in Relation to Sea Ice Variability on Monthly-to-Annual Time Scales. J. Clim. 28(16), 6335–6350 (2015).
    • Locati MD, Terpstra I, de Leeuw WC, et al. Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization. Nucleic Acids Res. , 1–10 (2015).
    • Lusher SJ, Ritschel T. Finding the right approach to big data-driven medicinal chemistry. Future Med. Chem. 7(10), 1213–1216 (2015).
    • Manola I, Selten FM, de Ruijter WPM, Hazeleger W. The ocean-atmosphere response to wind-induced thermocline changes in the tropical South Western Indian Ocean. Clim. Dyn. 45(3-4), 989–1007 (2015).
    • Martinez-Ortiz C, Koolen M, Buschenhenke F, Dalen-Oskam V, others. Beyond the Book: Linking Books to Wikipedia. In: e-Science (e-Science), 2015 IEEE 11th International Conference on. , 12–21 (2015).
    • Mihaleva V V, Ünlü FY, Vervoort J, Ridder L. Automated Annotation of Microbial and Human Flavonoid-Derived Metabolites. In: Metabonomics and Gut Microbiota in Nutrition and Disease. Springer, 109–124 (2015).
    • van Oosterom P, Martinez-Rubi O, Ivanova M, et al. Massive point cloud data management: Design, implementation and execution of a point cloud benchmark. Comput. Graph. , 1–34 (2015).
    • Rasmijn LM, van der Schrier G, Barkmeijer J, Sterl A, Hazeleger W. On the use of the forced sensitivity method in climate studies. Q. J. R. Meteorol. Soc. 141(688), 845–853 (2015).
    • Ronda RJ, Steeneveld GJ, Attema J, Heusinkveld BG, Holtslag AAM. Summer in the city-High Resolution Modelling and Validation of Urban Weather for Amsterdam. In: Proceedings of the 9th International Conference on Urban Climate/12th Symposium on the Urban Environment,. (2015).
    • Sclocco A, Bal HE, van Nieuwpoort R V. Finding Pulsars in Real-Time. In: e-Science (e-Science), 2015 IEEE 11th International Conference on. , 98–107 (2015).
    • Sclocco A, van Leeuwen J, Bal HE, van Nieuwpoort R V. A Real-Time Radio Transient Pipeline for ARTS. (2015).
    • Tian Y, Zou T, Ozcan F, Goncalves R, Pirahesh H. Joins for Hybrid Warehouses: Exploiting Massive Parallelism in Hadoop and Enterprise Data Warehouses. Proc. 18th International Conference on Extending Database Technology (EDBT) (2015).
    • Werkhoven B van, Hijma P. An integrated approach to porting large scientific applications to GPUs. In: e-Science (e-Science), 2015 IEEE 11th International Conference on. , 57–66 (2015).
    • Zwaan JM van der, Leemans I, Kuijpers E, and Maks I. HEEM, a Complex Model for Mining Emotions in Historical Text. In: e-Science (e-Science), 2015 IEEE 11th International Conference on. , 22–30 (2015).
    • Locati MD, Terpstra I, de Leeuw WC, Kuzak M, Rauwerda H, Ensink WA, van Leeuwen S, Nehrdich U, Spaink HP, Jonker MJ, Breit TM, Dekker RJ. Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization. Nucleic Acids Res. 2015 Aug 18;43(14):e89.

    2014

    • Lusher, S. J., McGuire, R., Van Schaik, R. C., Nicholson, C. D. & De Vlieg, J. Data-driven medicinal chemistry in the era of big data. Drug Discov. Today 19, 859–868 (2014).
    • Ridder, L., van der Hooft, J. J. J. & Verhoeven, S. Automatic Compound Annotation from Mass Spectrometry Data Using MAGMa. Mass Spectrom. 3, 7 (2014).
    • Ridder, L. et al. In silico prediction and automatic LC-MSn annotation of green tea metabolites in urine. Anal. Chem. 86, 4767–4774 (2014).
    • Van Werkhoven, B. et al. A distributed computing approach to improve the performance of the Parallel Ocean Program (v2. 1). Geosci. Model Dev. 7, 267–281 (2014).
    • Werkhoven, B. van, Maassen, J., Seinstra, F. J. & Bal, H. E. Performance models for CPU-GPU data transfers. in Clust. Cloud Grid Comput. (CCGrid), 2014 14th IEEE/ACM Int. Symp. 11–20 (2014).
    • Brunnabend, S.-E. et al. Changes in extreme regional sea surface height due to an abrupt weakening of the Atlantic MOC. Ocean Sci. Discuss. 11, 1213–1241 (2014).
    • Sclocco, A., Bal, H. E., Hessels, J., Leeuwen, J. van & Nieuwpoort, R. V. van. Auto-Tuning Dedispersion for Many-Core Accelerators. in Parallel Distrib. Process. Symp. 2014 IEEE 28th Int. 952–961 (2014).
    • Madougou, S., Varbanescu, A. L., de Laat, C. & van Nieuwpoort, R. An Empirical Evaluation of GPGPU Performance Models. in Euro-Par 2014 Parallel Process. Work. 165–176 (2014).
    • Steeneveld, G. J., Koopmans, S., Heusinkveld, B. G. & Theeuwes, N. E. Refreshing the role of open water surfaces on mitigating the maximum urban heat island effect. Landsc. Urban Plan. 121, 92–96 (2014).
    • Koopmans, S., Theeuwes, N. E., Steeneveld, G. J. & Holtslag, A. A. M. Modelling the influence of urbanization on the 20th century temperature record of weather station De Bilt (The Netherlands). Int. J. Climatol. (2014).
    • Van Werkhoven, B., Maassen, J., Bal, H. E. & Seinstra, F. J. Optimizing convolution operations on GPUs using adaptive tiling. Futur. Gener. Comput. Syst. 30, 14–26 (2014).

    2013

    • S.J. Lusher, P. Conti, W. Dokter, P.H. Hermkens, J. De Vlieg, Drug design approaches to manipulate the agonist-antagonist equilibrium in steroid receptors, in: Steroid Hormones, 2011: pp. 221–234.
    • J.J.J. van der Hooft, R.C.H. de Vos, V. Mihaleva, R.J. Bino, L. Ridder, N. de Roo, et al., Structural elucidation and quantification of phenolic conjugates present in human urine after tea intake., Analytical Chemistry. 84 (2012) 7263–71.
    • R. Lonsdale, S. Hoyle, D.T. Grey, L. Ridder, A.J. Mulholland, Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling., Biochemistry. 51 (2012) 1774–86.
    • P. Elfferich, M.E. van Royen, D.J. van de Wijngaart, J. Trapman, S.L.S. Drop, S.J. Lusher, E.L.T. van den Akker, et al., Variable Loss of Functional Activities of Androgen Receptor Mutants in Patients with Androgen Insensitivity Syndrome, Sexual Development. 7 (2013) 223–234.
    • W.W.M. Fleuren, E.J.M. Toonen, S. Verhoeven, R. Frijters, T. Hulsen, T. Rullmann, et al., Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining, BioData Mining. 6 (2013).
    • L. Ridder, J.J.J. Van Der Hooft, S. Verhoeven, R.C.H. De Vos, R.J. Bino, J. Vervoort, Automatic chemical structure annotation of an LC-MSn based metabolic profile from green tea., Analytical Chemistry. (2013).
    • L. Ridder, J.J.J. Van Der Hooft, S. Verhoeven, R.C.H. De Vos, R. Van Schaik, J. Vervoort, Substructure-based annotation of high-resolution multistage MS(n) spectral trees., Rapid Communications in Mass Spectrometry RCM. 26 (2012) 2461–71.
    • M. Ivanova, Y. Kargin, M. Kersten, S. Manegold, Y. Zhang, M. Datcu, et al., Data vaults: a database welcome to scientific file repositories, in: Proceedings of the 25th International Conference on Scientific and Statistical Database Management, ACM, 2013: p. 48.
    • M. Ivanova, M. Kersten, S. Manegold, Data vaults: a symbiosis between database technology and scientific file repositories, in: Scientific and Statistical Database Management, Springer, 2012: pp. 485–494.
    • N. Drost, J. Maassen, M.A.J. van Meersbergen, H.E. Bal, F. Pelupessy, S.P. Zwart, et al., Distributed Multi-Model/Multi-Kernel Simulations: A Case Study in Jungle Computing using eScience Infrastructure and High Speed Networks, In proceeding of: 8th IEEE International Conference on eScience 2012 - Collaborative Research using eScience Infrastructure and High Speed Networks (NECS 2012), At Chicago, IL, USA
    • F.I. Pelupessy, A. van Elteren, N. de Vries, S.L.W. McMillan, N. Drost, S.F. Zwart, The Astrophysical Multipurpose Software Environment, arXiv Preprint arXiv:1307.3016. (2013).
    • T. van Kessel, B. van Werkhoven, N. Drost, J. Maassen, H.E. Bal, F.J. Seinstra, User transparent data and task parallel multimedia computing with Pyxis-DT, Future Generation Computer Systems. (2013).
    • R. Aalmoes, R. Erkamp, Y. Cheung, R. van Nieuwpoort, Performance improvements for calculations of third party risk around airports, Library.witpress.com. (n.d.).
    • M.P. Van Haarlem, M.W. Wise, A.W. Gunst, G. Heald, J.P. Mckean, J.W.T. Hessels, et al., LOFAR : The LOw-Frequency ARray, (2013) Astronomy and Astrophysics, 1–56.
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    • T. Van Kessel, N. Drost, J. Maassen, H.E. Bal, F.J. Seinstra, A.J. Plaza, Towards a high-performance distributed cbir system for hyperspectral remote sensing data : a case study in jungle, (n.d.) 1–25.
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    • Brunnabend, S. E., Dijkstra, H. A., Kliphuis, M., van Werkhoven, B., Bal, H. E., Maassen, J., ... & Seinstra, F. J. (2013, April). Future high-resolution dynamic sea level changes. In EGU General Assembly Conference Abstracts (Vol. 15, p. 5437).
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    • B. van Werkhoven, J. Maassen, M. Kliphuis, H. A. Dijkstra, S. E. Brunnabend, M. van Meersbergen, F. J. Seinstra, and H. E. Bal. A distributed computing approach to improve the performance of the Parallel Ocean Program (v2.1), Geoscientific Model Development, 2014, 7:267-281
    • A. Overeem, J.C. R. Robinson, H. Leijnse, G.J. Steeneveld, B.K. P. Horn, R. Uijlenhoet, Crowdsourcing urban air temperatures from smartphone battery temperatures, Geophysical Research Letters. 40 (2013) 4081–408