Fons Verbeek
Professor of Computational Bio-imaging
- Name
- Prof.dr.ir. F.J. Verbeek
- Telephone
- +31 71 527 5773
- f.j.verbeek@liacs.leidenuniv.nl
- ORCID iD
- 0000-0003-2445-8158
Fons Verbeek has a background in Computer Science and Biology; he has a PhD in Applied Physics. His research topic is Image Analysis with a focus on microscopy imaging. His research stretches from feature extraction and segmentation to classification strategies in the domain of the life-sciences.
More information about Fons Verbeek
PhD Candidates
News
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Video series: Why Latin America matters -
Computers help wood anatomists with wood identification -
New database brings structure to global fungal diversity -
Measuring sulfur with satellites -
LIACS part of AI-driven VR-film -
Govert Brinkmann runner-up for KNVI Thesis Award for Informatics -
Leiden: The scene of the Zebrafish Disease Models conference 2018 -
Fons Verbeek on computational bio-imaging at SleutelstadFM -
Magnifying the minute -
Leiden builds stronger bonds with China and South Korea -
Leiden University and ICTU start research on software development -
NWO grant for super fast analysis of disease progression -
Publication gets press attention
See also
Former PhD candidates
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Mounia Belmamoune -
Douwe Joost Broekens
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Fuyu Cai
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Lu Cao
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Joelia Borisovna Dmitrieva
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Yuanhao Guo
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Wanbin Hu
-
Amalia Kallergi
-
Solomiia Kurchaba
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Enrique Larios Vargas
-
Danyi Liu
-
Wouter Mensink
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Alexander Evgenievich Nezhinsky
-
Hanna Schraffenberger
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Leonie van Steijn
-
Lise Stork
-
Xiaoqin Tang
-
Mohamed Tleis
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Rafael Viana de Carvalho
-
Xue Wang
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Monique C.M. Welten
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Yanju Zhang
Fons Verbeek has a background in Computer Science and Biology; he has a PhD in Applied Physics. His research topic is Image Analysis with a focus on microscopy imaging. His research stretches from feature extraction and segmentation to classification strategies in the domain of the life-sciences.
Visualization of research data is much addressed in his research projects. In the master program he teaches a course on Image Processing and Analysis. In additon, in his research he is using modelling techniques applied to biomedical data to gain further understanding on cohesion in biomolecular processes.
Imaging & Visualization typically require Human interaction. Therefore, in research project the subject of Human Computer Interaction is often addressed. In the Media Technology programme and the CS bachelor he is involved in teaching the Human Computer Interaction course and engaged in supervising students in their research.
For more information check the research group website of Imaging & BioInformatics for projects at the Leiden Institute of Advanced Computer Science he works on.
See for more information my Personal website
Professor of Computational Bio-imaging
- Science
- Leiden Inst of Advanced Computer Science
- Li C., Polling M., Cao L., Gravendeel B. & Verbeek F.J. (2023), Analysis of automatic image classification methods for Urticaceae pollen classification, Neurocomputing 522: 181-193.
- Wang X., Du Y., Verberne S. & Verbeek F.J. (2023), Fine-grained label learning in object detection with weak supervision of captions, Multimedia Tools and Applications 82(5): 6557-6579.
- Kurchaba S., Vliet J. van, Verbeek F.J. & Veenman C.J. (2023), Anomalous NO2 emitting ship detection with TROPOMI satellite data and machine learning, Remote Sensing of Environment 297: 113761.
- Mast D., Broekens D.J., Vries S. de & Verbeek F.J. (2023), Participation patterns of interactive playful museum exhibits: evaluating the participant journey map through situated observations. Byrne D., Martelaro N., Boucher A., Chatting D., Fdili Alaoui S., Fox S., Nicenboim I. & MacArthur C. (Eds.), Proceedings of the ACM designing interactive systems conference. ACM Designing Interactive Systems Conference 10 July 2023 - 14 July 2023: Association for Computing Machinery. 1861-1885.
- Cao L., Schoenmaker L., Den S.A. ten, Passier R., Schwach V. & Verbeek F.J. (2023), Automated sarcomere structure analysis for studying cardiotoxicity in human pluripotent stem cell-derived cardiomyocytes, Microscopy and Microanalysis 29(1): 254-264.
- Jahanbanifard M., Price E., González Benito A., Raggi L.A., Javanmardi S., Lens F., Gravendeel B., Espinoza E. & Verbeek F.J. (2023), A novel method to analyse DART TOFMS spectra based on Convolutional Neural Networks: a case study on methanol extracts of wool fibres from endangered camelids, International Journal of Mass Spectrometry 489: 117050.
- Wang X., Du Y., Verberne S. & Verbeek F.J. (2022), Improving weakly supervised phrase grounding via visual representation contextualization with contrastive learning, Applied Intelligence 53(11): 14690-14702.
- Brinkmann G.G., Rietveld K.F.D., Verbeek F.J. & Takes F.W. (2022), Real-time interactive visualization of large networks on a tiled display system, Displays 73: 102164.
- Javanmardi S., Latif A.M., Sadeghi M.T., Jahanbanifard M., Bonsangue M.M. & Verbeek F.J. (2022), Caps captioning: a modern image captioning approach based on improved capsule network, Sensors 22(21): 8376.
- Kurchaba S., Vliet J. van, Verbeek F.J., Meulman J.J. & Veenman C.J. (2022), Supervised segmentation of NO2 plumes from individual ships using TROPOMI satellite data, Remote Sensing 14(22): 5809.
- Ashtiani S.H.M, Javanmardi S., Jahanbanifard M. , Martynenko A. & Verbeek F.J. (2021), Detection of mulberry ripeness stages using deep learning models, IEEE Access 9: 100380-100394.
- Hu W., Steijn L. van, Li C., Verbeek F.J., Cao L., Merks R.M.H. & Spaink H.P. (2021), A novel function of TLR2 and MyD88 in the regulation of leukocyte cell migration behavior during wounding in zebrafish larvae, Frontiers in Cell and Developmental Biology 9: 624571.
- Polling M., Li C., Cao L., Verbeek F.J., Weger L.A. de, Belmonte J., De Linares C., Willemse J.J., Boer H. de & Gravendeel B. (2021), Neural networks for increased accuracy of allergenic pollen monitoring, Scientific Reports 11: 11357.
- Javanmardi S., Ashtiani S.H.M. & Verbeek F.J. Martynenko A. (2021), Computer-vision classification of corn seed varieties using deep convolutional neural network, Journal of Stored Products Research 92: 101800.
- Paulus E., Burie J-C. & Verbeek F.J. (2021), Binarization strategy using multiple convolutional autoencoder network for old Sundanese manuscript images. Barney Smith E.H. & Pal U. (Eds.), Document Analysis and Recognition – ICDAR 2021 Workshops, Proceeding, Part 2. International Conference on Document Analysis and Recognition 5 September 2021 - 10 September 2021 no. 12916. Cham: Springer. 142-157.
- Mast D., Vries S.I. de, Broekens D.J. & Verbeek F.J. (2021), The participant journey map: understanding the design of interactive augmented play spaces, Frontiers in Computer Science 3: 674132.
- Chen Y., Verbeek F.J. & Wolstencroft K.J. (2021), Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations, BMC Bioinformatics 22(1): 178.
- Stork L., Weber A., Herik H.J. van den, Plaat A., Verbeek F.J. & Wolstencroft K.J. (2021), Large-scale zero-shot learning in the wild: classifying zoological illustrations, Ecological Informatics 62: 101222.
- Elmahdy M.S., Beljaards L., Yousefi S., Sokooti H., Verbeek F.J., Heiden U.A. van der & Staring M. (2021), Joint registration and segmentation via multi-task learning for adaptive radiotherapy of prostate cancer, IEEE Access 9: 95551-95568.
- Verbeek F.J. & Cao L. (2021), L-systems from 3D-imaging of phenotypes of arborized structures. In: Beek M.H. ter, Koutny M. & Rozenberg G. (Eds.), A Moasaic of Computational Topics: from Classical to Novel: IOS Press. 327-345.
- Pierson J., Robinson S.C., Boddington P., Chazerand P., Kerr A., Milan S., Verbeek F.J., Kutterer C., Nerantzi E. & Aconstantinesei I.C. (2021), AI4People 2020: AI in media and technology sector: opportunities, risks, requirements and recommendations. Brussels: Atomium - European Institute for Science, Media and Democracy (EISMD).
- Kurchaba S., Vliet J. van, Meulman J.J., Verbeek F.J. & Veenman C.J. (2021), Improving evaluation of NO2 emission from ships using spatial association on TROPOMI satellite data. Meng X., Wang F., Lu C.T., Huang Y., Shekhar S. & Xie X. (Eds.), Proceedings of the 29th International Conference on Advances in Geographic Information Systems. SIGSPATIAL '21: 29th International Conference on Advances in Geographic Information Systems 2 November 2021 - 5 November 2021. New York, U.S.A.: ACM. 454-457.
- Tang X., Spaink H.A.J., Wijk R.C. van & Verbeek F.J. (2020), Segmentation-driven optimization for iterative reconstruction in optical projection tomography: an exploration, IEEE Transactions on Computational Imaging 6: 1537-1547.
- Cao L. Meer A.D. van der Verbeek F.J. Passier R. (2020), Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes, BMC Bioinformatics 21: 187.
- Cao L. & Verbeek F.J. (2020), L-systems from 3D-imaging of phenotypes of arborized structures, Fundamenta Informaticae 175(1-4): 327-345.
- Lens F.P., Liang C., Guo Y., Tang X., Jahanbanifard M., Soares Correa da Silva F., Ceccantini. G. & Verbeek F.J. (2020), Computer-assisted timber identification based on features extracted from microscopic wood sections, IAWA Journal 41(4): 660-680.
- Wijk R.C. van, Hu W.B., Dijkema S.M., Berg D. van den, Liu J., Bahi R., Verbeek F.J., Simonsson U.S.H., Spaink H.P., Graaf P.H. van der & Krekels E.H.J. (2020), Anti-tuberculosis effect of isoniazid scales accurately from zebrafish to humans, British Journal of Pharmacology 177(24): 5518-5533.
- Jahanbanifard M., Beckers V.M.H., Koch G., Beeckman H., Gravendeel B., Verbeek F.J., Baas P., Priester C. & Lens F.P. (2020), Description and evolution of wood anatomical characters in the ebony wood genus Diospyros and its close relatives (Ebenaceae): a first step towards combatting illegal logging, IAWA Journal 41(4): 577-619.
- Martorelli I., Helwerda L.S., Kerkvliet J., Gomes S.I.F., Nuytinck J., Werff C.R.A. van der, Ramackers G.J., Goultiaev A.P., Merckx V.S.F.T. & Verbeek F.J. (2020), Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB), Journal Integrative Bioinformatics 17(1): 20190046.
- Zammit A., Helwerda L.S., Olsthoorn R.C.L., Verbeek F.J. & Goultiaev A.P. (2020), A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions, Bioinformatics 37(7): 956-962.
- Mast D., Vries S. de, Broekens D.J. & Verbeek F.J. (2020), The importance of the peak-end rule for repeated visits to Augmented Play Spaces. PERSUASIVE 2020 - 15th International conference on Persuasive Technology, Aalborg. 20 April 2020 - 23 April 2020. [conference poster].
- Steijn L. van, Verbeek F.J., Spaink H.P. & Merks R.M.H. (2019), Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio, Zebrafish 16(4): 348-362.
- Jahanbanifard M., Gravendeel B., Lens F.P., Verbeek F.J. & (2019), Ebony wood identification to battle illegal trade. Hogeweg L. & Pieterse S. (Eds.), Biodiversity Information Science and Standards. Biodiversity Next 2019 20 October 2019 - 25 October 2019. Biodiversity Information Science and Standards no. 3: Pensoft Publishers. e37084.
- Stork L., Weber A., Gassó Miracle E., Verbeek F.J., Plaat A., Herik H.J. van den & Wolstencroft K.J. (2019), Semantic annotation of natural history collections, Journal of Web Semantics 59: 100462.
- Vreumingen D. van, Tewari S., Verbeek F.J. & Ruitenbeek J.M. van (2018), Towards controlled single-molecule manipulation using "real-time" molecular dynamics simulation: A GPU implementation, Micromachines 9(6): 270.
- Stork L., Weber A., Herik H.J. van den, Plaat A., Verbeek F.J. & Wolstencroft K.J. (2018), From handwritten manuscripts to linked data. Méndez E., Crestani F., Ribeiro C., David G. & Lopes J. (Eds.), Digital libraries for open knowledge. International Conference on Theory and Practice of Digital Libraries (TPLD) 2018 10 September 2018 - 13 September 2018. Lecture Notes in Computer Science no. 11057. Cham: Springer. 330-334.
- Guo Y., Xiong Z. & Verbeek F.J. (2018), An efficient and robust hybrid method for segmentation of zebrafish objects from bright-field microscope images, Machine Vision and Applications 29(8): 1211-1225.
- Carvalho R.V., Verbeek F.J. & Coelho C.J. (2018), Bio-Modelling using Petri Nets: a Computational Approach. In: Alves Barbosa da Silva F., Carels N. & Paes Silva Junior F. (Eds.), Theoretical and Applied Aspects of Systems Biology. Computational BiologyCOBO no. 27. Cham: Springer. 3-26.
- Tang X., Lamers G.E.M. & Verbeek F.J. (2018), 3D Image quality improvement for optical projection tomography via point spread function modelling, Proceedings imaging and applied optics 2018 (3D, AO, AIO, COSI, DH, IS, LACSEA, LS&C, MATH, pcAOP). Imaging and Applied Optics 2018 25 June 2018 - 28 June 2018: OSA. 3W5G.5.
- Tang X., Zwaan D.M. van der, Zammit A., Rietveld K.F.D. & Verbeek F.J. (2017), Fast post-processing pipeline for optical projection tomography, IEEE Transactions on NanoBioscience 16(5): 367-374.
- Guo Y., Veneman W.J., Spaink H.P. & Verbeek F.J. (2017), Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging, Biomedical Optics Express 8(5): 2611-2634.
- Helwerda L.S., Niessink F. & Verbeek F.J. (2017), Conceptual process models and quantitative analysis of classification problems in Scrum software development practices. Fred A.L.N. & Filipe J.B.L. (Eds.), Proceedings of the 9th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management. IC3K 2017 : 9th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management 1 November 2017 - 3 November 2017 no. 1. Madeira, Portugal: Scitepress. 357-366.
- Guo Y., Wijk R.C. van, Krekels E.H.J., Spaink H.P., Graaf P.H. van der & Verbeek F.J. (2017), Multi-modal 3D reconstruction and measurements of zebrafish larvae and its organs using axial-view microscopy, 2017 IEEE International conference on image processing (ICIP). IEEE International Conference on Image Processing 2017 17 September 2017 - 20 September 2017: IEEE Xplore. 2194-2198.
- Guo Y., Zhang Y. & Verbeek F.J. (2017), A two-phase 3D reconstruction approach for light microscopy axial-view imaging, IEEE Journal of Selected Topics in Signal Processing 11(7): 1034-1046.
- Guo Y., Veneman W., Spaink H.P. & Verbeek F.J. (2017), 3D reconstruction and measurements of zebrafish larvae from High-throughput axial-view in vivo imaging, Biomedical Optics Express 8(5): 2611-2634.
- Alkemade R., Verbeek F.J. & Lukosch S. (2017), On the efficiency of a VR hand gesture based interface for 3D object manipulations in conceptual design, International Journal of Human-Computer Interaction 33(11): 882-901.
- Xiong Z. & Verbeek F.J. (2016), Segmentation of zebrafish larvae inhomogeneous 3D images using the level-set method, Proceedings IS&T international symposium on electronic imaging: visualization and data analysis. Visualization and Data Analysis Conference 14 February 2016 - 18 February 2016: Society for Imaging Science and Technology. VDA-480.1-VDA-480.9.
- Teernstra L., Putten P.W.H. van der, Noordegraaf-Eelens L. & Verbeek F.J. (2016), The morality machine: tracking moral values in tweets. Boström H., Knobbe A., Soares C. & Papapetrou P. (Eds.), Advances in intelligent data analysis XV. The 15th International Symposium on Intelligent Data Analysis 13 October 2016 - 15 October 2016. Lecture Notes in Computer Science no. 9897. Cham: Springer International Publishing. 26-37.
- Bertens L.M.F., Kleijn J., Hille S., Heiner M., Koutny M. & Verbeek F.J. (2016), Modeling Biological Gradient Formation: Combining Partial Differential Equations and Petri Nets, Natural computing 154(4): 665-675.
- Cai F., Wang H., Tang X., Emmerich M.T.M. & Verbeek F.J. (2016), Fuzzy Criteria in Multi-objective Feature Selection for Unsupervised Learning, Procedia Computer Science 102: 51-58.
- Fokkelman M., Balcioglu H.E., Klip J.E., Yan K., Verbeek F.J., Danen E.H.J. & Water B. van de (2016), Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour, Scientific Reports 6: 31707.
- Tang X., Hoff V.M., Hoogenboom J., Guo Y., Cai F., Lamers G.E.M. & Verbeek F.J. (2016), Fluorescence and bright-field 3D image fusion based on sinogram unification for optical projection tomography. Tian T., Jiang Q., Liu Y., Burrage K., Son J., Wang Y., Hu X., Morishita S., Zhu Q. & Wang G. (Eds.), Proceedings 2016 IEEE international conference on bioinformatics and biomedicine Dec 15-18, 2016 Shenzhen, China. The IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016) 15 December 2016 - 18 December 2016. Danvers: Institute of Electrical and Electronics Engineers(IEEE). 403-410.
- Gómez Maureira M.A. & Verbeek F.J. (2016), The impact of co-located play on social presence and game experience in a VR game, Proceedings of the First International Joint Conference of DiGRA and FDG. 1st International Joint Conference of DiGRA and FDG 1 August 2016 - 6 August 2016. Digital Games Research Association and Society for the Advancement of the Science of Digital Games no. 13: Digital Games Research Association and Society for the Advancement of the Science of Digital Games.
- Schomaker L., Weber A., Thijssen M., Heerlien M., Plaat A., Nijssen S.G.R., Verbeek F.J., Lew M.S.K., Gasso Micacle E., Wolstencroft K., Suyver E., Verheij B., Wiering M., Dekker M., Kok J., Roberts L. & Herik H.J. van den (2016), Making Sense of Illustrated Handwritten Archives, Digital Humanities 2016 Conference Abstracts. Digital Humanities 2016 11 July 2016 - 16 July 2016. Krakow: Jagiellonian University and Pedagogical University. 674-676.
- Cao L., Graauw M. de, Yan K., Winkel L. & Verbeek F.J. (2016), Hierarchical classification strategy for Phenotype extraction from epidermal growth factor receptor endocytosis screening, BMC Bioinformatics 17: 196.
- Larios Vargas E., Xia Z., Slob J. & Verbeek F.J. (2016), A semantic-based metadata validation for an automated High-Throughput Screening workflow: case study in CytomicsDB. Ortuno F. & Rojas I. (Eds.), Bioinformatics and biomedical engineering: 4th international conference, IWBBIO 2016, Granada, Spain, April 20-22, 2016, proceedings. 4th International Work-Conference on Bioinformatics and Biomedical Engineering 20 April 2016 - 11 April 2016 no. 9656. Heidelberg: Springer International Publishing. 557-572.
- Cai F. & Verbeek F.J. (2016), Rough Fuzzy C-Means and particle swarm optimization hybridized method for information clustering problem, Journal of Communications 11(12): 1106-1113.
- Viana de Carvalho R., Heuvel J. van den, Kleijn H.C.M. & Verbeek F.J. (2015), Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response, 3(2): 150-176.
- Tleis M. & Verbeek F.J. (2015), Machine learning approach to discriminate Saccharomyces cerevisiae yeast cells using sophisticated image features, Journal Integrative Bioinformatics 12(3): 276.
- Guo Y., Veneman W.J., Spaink H.P. & Verbeek F.J. (2015), Silhouette-based 3D model for zebrafish high-throughput imaging. Jennane R. (Ed.), 2015 International conference on image processing theory, tools and applications (IPTA). International Conference on Image Processing Theory, Tools and Applications (IPTA 2015) 10 November 2015 - 13 November 2015: IEEE. 403-408.
- Cai F. & Verbeek F.J. (2015), Dam-based rolling ball with fuzzy-rough constraints, a new background subtraction algorithm for image analysis in microscopy. Jennane R. (Ed.), Proceedings international conference on image processing theory, tools and applications (IPTA 2015). International Conference on Image Processing Theory, Tools and Applications (IPTA 2015) 10 November 2015 - 13 November 2015 no. CFP1562F-CDR: IEEE. 298-303.
- Tleis M. & Verbeek F.J. (2015), Contour expansion algorithm preprocessed by Hough transform and circular shortest path for ovoid objects. Jennane R. (Ed.), Proceedings international conference on image processing theory, tools and applications (IPTA 2015). International Conference on Image Processing Theory, Tools and Applications (IPTA 2015) 10 November 2015 - 13 November 2015 no. CFP1562F-CDR: IEEE. 149-154.
- Benard E.L., Racz P.I., Rougeot J.Y.Y., Nezhinsky A.E., Verbeek F.J., Spaink H.P. & Meijer A.H. (2015), Macrophage-expressed perforins Mpeg1 and Mpeg1.2 have an anti-bacterial function in zebrafish, Journal of Innate Immunity 7(2): 136-152.
- Di Z., Klop M.J.D., Rogkoti V.M., Le Dèvèdec S.E., Water B. van de, Verbeek F.J., Price L.S. & Meerman J.H.N. (2014), Ultra High Content Image Analysis and Phenotype Profiling of 3D Cultured Micro-Tissues, PLoS ONE 9(10): e109688.
- Bomer N., Hollander W. den, Ramos Y.F., Bos S.D., Breggen R. van der, Lakenberg N., Pepers B.A., Eeden A.E. van, Darvishan A., Tobi E.W., Duijnisveld B.J., Akker E.B. van den, Heijmans B.T., Roon-Mom W.M. van, Verbeek F.J., Osch G.J. van, Nelissen G.J., Slagboom R.G. & Meulenbelt P.E. (2014), Underlying molecular mechanisms of DIO2 susceptibility in symptomatic osteoarthritis, Annals of the Rheumatic Diseases 74: 1571-1579.
- Lamers M.H., Putten P.W.H. van der & Verbeek F.J. (2014), Observations on Tinkering in Scientific Education. In: Cheok A.D., Nijholt A. & Romão T. (Eds.), Entertaining the Whole World. Human-Computer Interaction Series. London: Springer-Verlag. 137-145.
- Gomez-Maureira M., Teunisse C., Schaffenberger H.K. & Verbeek F.J. (2014), Illuminating shadows: introducing shadow interaction in spatial augmented reality. Leeuwen J.P. van, Stappers P.J., Lamer M.H. & Thissen M.J.M.R. (Eds.), Creating the difference: proceedings of the Chi Sparks 2014 conference. EventChi Sparks 2014: Creating the Difference 3 April 2014 - 3 April 2014: CHI Nederland. 11-18.
- Coelho Camargo J. & Verbeek F.J. (2014), Pointing task evaluation of gestural interface interface interaction in 3D environment. Leeuwen J.P. van, Stappers P.J., Lamers M.H. & Thissen M.J.M.R. (Eds.), Ceating the difference: proceedings of the Chi Sparks 2014 Conference. Chi Sparks 2014 3 April 2014 - 3 April 2014. IADIS International Journal on WWW/Internet: Chi Nederland. 113-130.
- Tleis M. & Verbeek F.J. (2014), Extracting contours of oval-shaped objects by Hough Transform and minimal path algorithms. Falco C.M., Chang C. & Jiang X. (Eds.), Proceedings of SPIE Vol. 9159 . Sixth International Conference on Digital Image Processing 5 April 2014 - 6 April 2014: SPIE. 915903.
- Coelho Camargo J. & Verbeek F.J. (2014), The Leap Motion Controller in a 3D Virtual Environment: explorations and evaluations of pointing tasks. Blashki K. & Xiao Y. (Eds.), Proceedings International Conference on Interfaces and Human Computer Interaction (HCI 2014). IADIS International Conference Interfaces and Human Computer Interaction 15 July 2014 - 19 July 2014: IADIS - International Association for Development of the Information Society. 3-11.
- Viana de Carvalho R., Kleijn H.C.M. & Verbeek F.J. (2014), A multi-scale extensive Petri net model of the bacterial-macrophage interaction. Heiner M. (Ed.), Proceedings of the 5th international workshop on biological processes & Petri Nets. 5th International Workshop on Biological Processes & Petri Nets 23 June 2014 - 23 June 2014 no. 1159: CEUR . 15-29.
- Slob J. & Verbeek F.J. (2014), Imaging ontology, contributing to "reasonable" semantics for biomedical repositories. Bodenreider O., Oliveira J.L. & Rinaldi F. (Eds.), Proceedings of the 6th international symposium on semantic mining in biomedicine (SMBM 2014). International Symposium on Semantic Mining in Biomedicine 6 October 2014 - 7 October 2014: University of Aveiro. 33-37.
- Larios Vargas E., Zhang Y., Cao L. & Verbeek F.J. (2014), CytomicsDB: a metadata-based storage and retrieval approach for high-throughput screening experiments. Comin M., Käll L., Marchiori E., Ngom A. & Rajapakse J. (Eds.), Pattern recognition in bioinformatics: PRIB 2014. APR International Conference on Pattern Recognition in Bioinformatics PRIB 2014 21 August 2014 - 23 August 2014. Lecture Notes in Computer Science no. 8626. Cham: Springer. 72-84.
- Graauw M. de, Cao L., Winkel L., Miltenburg M.H.A.M. van, Dévédec S.E. le, Klop M., Yan K., Pont C.M., Rogkoti V.M., Tijsma A., Chaudhuri A., Lalai R.A., Price L.S., Verbeek F.J. & Water B. van de (2014), Annexin A2 depletion delays EGFR endocytic trafficking via cofilin activation and enhances EGFR signaling and metastasis formation, Oncogene 33(20): 2610-2619.
- Laroche F.J.F., Tulotta C., Lamers G.E.M., Stougaard J., Blaise M., Verbeek F.J., Yang P., Bustos M., Meijer A.H. & Spaink H.P. (2013), The embryonic expression patterns of zebrafish genes encoding LysM-domains, Gene Expression Patterns 13(7): 212-224.
- Cao L. & Verbeek F.J. (2013), Analytical evaluation of algorithms for point cloud surface reconstruction using shape features, Journal of Electronic Imaging 22(4): 043008.
- Fitzsimons C.P., Hooijdonk L.W.A. van, Schouten M., Zalachoras I., Brinks V., Zheng T., Schouten T.G., Saaltink D.J., Dijkmans T., Steindler D.A., Verhaagen J., Verbeek F.J., Lucassen P.J., Kloet E.R. de, Meijer O.C., Karst H., Joels M., Oitzl M.S. & Vreugdenhil E. (2013), Knockdown of the glucocorticoid receptor alters functional integration of newborn neurons in the adult hippocampus and impairs fear-motivated behavior, Molecular Psychiatry 18(9): 993-1005.
- Kallergi A. & Verbeek F.J. (2013), Playfull Interfaces for Scientific Image data. In: Blashki K. & Isaias P. (Eds.), Emerging Research and Trends in Interactivity and the Human-Computer Interface: IGI Global. 471-489.
- Lamers Maarten H., Verbeek F.J. & Putten P.W.H. van der (2013), Tinkering in Scientific Education. Reidsma D., Katayose H. & Nijholt A. (Eds.), Advances in Computer Entertainment. no. Lecture Notes in Computer Science 8253: Springer-Verlag. 568-571.
- Tleis M., Anemaet I.G., Heusden G.P.H. van & Verbeek F.J. (2013), Image analysis platform for yeast biologists, 2013 2nd international conference on advances in biomedical engineering. 2013 2nd International Conference on Advances in Biomedical Engineering 11 September 2013 - 13 September 2013: IEEE. 105-108.
- Bertens L.M.F., Kleijn J., Hille S.C., Koutny M., Heiner M. & Verbeek F.J. (2013), Modeling biological gradient formation: combining partial differential equations and Petri nets. Newcastle: University of Newcastle-upon-Tyne, UK.
- Damiano L., Le Devedec S.E., Di Stefano P., Repetto D., Lalai R.A., Truong H., Xiong J.L., Danen E.H., Yan K., Verbeek F.J., De Luca E., Attanasio F., Buccione R., Turco E., Water B. van de & Defilippi P. (2012), p140Cap suppresses the invasive properties of highly metastatic MTLn3-EGFR cells via impaired cortactin phosphorylation, Oncogene 31(5): 624-633.
- Viana de Carvalho R., Kleijn H.C.M., Meijer A.H. & Verbeek F.J. (2012), Modeling innate immune response to early mycobacterium infection, Computational and Mathematical Methods in Medicine 2012: 790482.
- Bono B. de, Kasteleyn P., Potikanond Dome, Kokash N., Verbeek F.J. & Grenon P. (2012), Tissue Motifs and Multi-scale Transport Physiology, Workshop of Ontologies in Biomedicine and Life Sciences. .
- Potikanond D. & Verbeek F.J. (2012), Visualization and analysis of 3D gene expression patterns in zebrafish using web services. Wong P.C., Kao D.L., Hao M.C., Chen C., Kosara R., Livingston M.A.,Park J. & Roberts I. (Eds.), Proceedings Volume 8294, Visualization and Data Analysis 2012. IS&T/SPIE Electronic Imaging, 2012 22 January 2012 - 26 January 2012. Proceedings of SPIE - International Society for Optical Engineering no. 8294: SPIE. 829412.
- Tleis M. & Verbeek F.J. (2012), Yeast-Cell Features Extraction Plugin, Proceedings ImageJ Conference 2012. .
- Kok J.N., Lamprecht A.-L., Verbeek F.J. & Wilkinson M.D. (2012), Bioscientific data processing and modeling. Margaria T. & Steffen B. (Eds.), Leveraging applications of formal methods, verification and validation: applications and case studies. ISoLA 2012. International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISoLA 2012 15 October 2012 - 18 October 2012. Lecture Notes in Computer Science no. 7610. Berlin, Heidelberg: Springer. 7-11.
- Sanchez-Faddeev H., Emmerich Michael T.M., Verbeek F.J., Henry A.H., Grimshaw S., Spaink H.P., Vlijmen H.W.T. van & Bender A. (2012), Using multiobjective optimization and energy minimization to design an isoform-selective ligand of the 14-3-3 Protein. Margaria T. & Steffen B. (Eds.), Leveraging applications of formal methods, verification and validation. applications and case studies (ISoLA 2012). International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISoLA 2012 15 October 2012 - 18 October 2012. Lecture Notes in Computer Science no. 7610. Berlin, Heidelberg: Springer. 12-24.
- Cao L. & Verbeek F.J. (2012), Evaluation of algorithms for point cloud surface reconstruction through the analysis of shape parameters. Baskurt A.M. & Sitnik R. (Eds.), Three-Dimensional Image Processing (3DIP) and Applications II. IS&T/SPIE Electronic Imaging, 2012 22 January 2012 - 26 January 2012. Proceedings of SPIE: SPIE. 82900G.
- Carvalho R.V., Davids W., Meijer A.H. & Verbeek F.J. (2012), Spatio-temporal Modeling and Simulation of Mycobacterium Pathogenesis Using Petri Nets. Hart E., Timmis J., Mitchell P., Nakamo T. & Dabiri F. (Eds.), Bio-Inspired Models of Networks, Information, and Computing Systems. BIONETICS 2011. . 6th International ICST Conference, BIONETICS 2011 5 December 2011 - 6 December 2011. Lecture Notes of the Institute of Computer Sciences, Social Informatics and Telecommunications Engineering no. 103. Berlin, Heidelberg: Springer. 236-241.
- Nezhinsky A.E. & Verbeek F.J. (2012), Efficient and robust shape retrieval from deformable templates. Margaria T. & Steffen B. (Eds.), Leveraging applications of formal methods, verification and validation: applications and case studies (ISoLA 2012). International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISoLA 2012 15 October 2012 - 18 October 2012. Lecture Notes in Computer Science no. 7610: Springer. 42-55.
- Yan K. & Verbeek F.J. (2012), Segmentation for high-throughput image analysis: watershed masked clustering. Margaria T. & Steffen B. (Eds.), Leveraging applications of formal methods, verification and validation: applications and case studies (ISoLA 2012). International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISoLA 2012 15 October 2012 - 18 October 2012. Lecture Notes in Computer Science no. 7610. Berlin/Heidelberg: Springer. 25-41.
- Kallergi A. & Verbeek F.J. (2012), Storytelling as playful exploration of biological image data: reviewing a candidate interaction paradigm. Blashki K. (Ed.), Proceedings of the IADIS International Conference Interfaces and Human Computer Interaction. IADIS International Conference Interfaces and Human Computer Interaction 21 July 2012 - 23 July 2012: IADIS - International Association for Development of the Information Society . 35-42.
- Nezhinsky A., Stoop E.J., Sar A.M. van der & Verbeek F.J. (2012), Numerical analysis of image based high-throughput zebrafish infection screens: matching meaning with data. Schier J., Correia C.M.B.A., Fred A.L.N. & Gamboa H. (Eds.), BIOINFORMATICS 2012: proceedings of the international conference on bioinformatics models, methods and algorithms. BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms 1 February 2012 - 4 February 2012: SciTePress. 257-262.
- Heijer G.J. den, Putten P.W.H. van der, Benard E.L., Meijer A.H. & Verbeek F.J. (2012), Explorations in Texture Based Classification for Bacterial Infection in Zebrafish. Baets B. de, Manderick B., Rademaker M. & Waegeman W. (Eds.), BeneLearn 2012 : proceedings of the 21st Belgian-Dutch conference on machine learning. 21st Belgian-Dutch conference on Machine Learning (BeneLearn 2012) 24 May 2012 - 25 May 2012 13-18.
- Larios E., Zhang Yanju, Yan K., Di Z., Le Dévédec S., Groffen F. & Verbeek F.J. (2012), Automation in cytomics: a modern RDBMS based platform for image analysis and management in high-throughput screening experiments. He J., Liu X., Krupinski E.A. & Xu G. (Eds.), Health Information Science. HIS 2012. HIS 2012: Health Information Science 8 April 2012 - 10 April 2012. Berlin, Heidelberg: Springer. 76-87.
- Nezhinsky A., Stoop E.J., Vasylevska A.A., Sar A.M. van der & Verbeek F.J. (2012), Spatial Analysis of Bacterial Infection Patterns in Zebrafish. De Baets B., Manderick B., Rademaker M. & Waegeman W. (Eds.), Proceedings 21th Annual Belgian-Dutch Conference on Machine Learning. 21st Belgian-Dutch conference on Machine Learning (BeneLearn 2012) 24 May 2012 - 25 May 2012.
- Le Dévédec S.E., Geverts B., Bont H.J.G.M. de, Yan K., Verbeek F.J., Houtsmuller A.B. & Water B. van de (2012), The residence time of focal adhesion kinase (FAK) and paxillin at focal adhesions in renal epithelial cells is determined by adhesion size, strength and life cycle status, Journal of Cell Science 125(19): 4498-4506.
- Di Z., Herpers B.H.A., Fredriksson L., Yan K., Water B. van de, Verbeek F.J. & Meerman J.H.N. (2012), Automated analysis of NF-κB nuclear translocation kinetics in high-throughput screening, PLoS ONE 7(12): e52337.
- Bertens L.M.F., Kleijn J. & Verbeek F.J. (2012), Biomodelling and Petri Nets, Eureka magazine : 6-8.
- Qin Y., Stokman G., Yan K., Ramaiahgari S.C., Verbeek F.J., Graauw M. de, Water B. van de & Price L.S. (2012), cAMP signalling protects proximal tubular epithelial cells from cisplatin-induced apoptosis via activation of Epac, British Journal of Pharmacology 165(4b): 1137-1150.
- Bertens L.M.F., Slob J. & Verbeek F.J. (2011), A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology, Journal Integrative Bioinformatics 8(2): 167.
- Herik H.J. van den, Lamers M.H. & Verbeek F.J. (2011), Understanding the artificial, International Journal of Social Robotics 3(2): 107-109.
- Boer F. & Verbeek F.J. (2011), Seeing through virtual windows, Proceedings CHI-sparks CHI-NL. Chi Sparks 2011 23 June 2011 - 23 June 2011.
- Cao L., Yan K., Winkel L., Graauw M. de & Verbeek F.J. (2011), Pattern recognition in high-content cytomics screens for target discovery: case studies in endocytosis. Loog M., Wessels L., Reinders M.J.T. & Ridder D. (Eds.), Pattern recognition in bioinformatics. IAPR International Conference on Pattern Recognition in Bioinformatics PRIB 2011 2 November 2011 - 4 November 2011. Lecture Notes in Computer Science no. 7036. Berlin/Heidelberg: Springer. 330-342.
- Potikanond D. & Verbeek F.J. (2011), 3D Visual Integration of Spatio-Temporal Gene Expression Patterns on Digital Atlas of Zebrafish Embryo using Web Services, ACEEE International Journal on Information Technology 1(3): 56-62.
- Dmitrieva J. & Verbeek F.J. (2011), Modular Approach for a new Ontology. Kutz O. & Schneider T. (Eds.), Proceedings Fifth International Workshop WoMO 2011. Fifth International Workshop (WoMO 2011) 8 August 2011 - 12 August 2011. Frontiers in Artificial Intelligence and Applications no. 230. Amsterdam: IOS Press. 40-54.
- Vries A. de, Oskam O. & Verbeek F.J. (2011), 3-Dimengination: playing a puzzle with texture and projections, Proceedings CHI-NL. .
- Yan K., Larios E., LeDevedec S., Water B. van de & Verbeek F.J. (2011), Automation in Cytomics: Systematic Solution for Image Analysis and Management in High Throughput Sequences, Proceedings IEEE Conference Engineering and Technology (CET 2011). 195-198.
- Kallergi A. & Verbeek F.J. (2011), The games Flickrites play: aninvestigation of Flickr-based gaming activity with special focus on opportunities for exploratory interaction. Blashki K. (Ed.), Proceedings of the IADIS International Conference Game and Entertainment Technologies 2011. IADIS International Conference Interfaces and Human Computer Interaction 20 July 2011 - 26 July 2011: IADIS - International Association for Development of the Information Society. 35-42.
- Nezhinsky A.E., Martorelli I. & Verbeek F.J. (2011), Detection of developmental stage in zebrafish embryos in a high throughput processing environment. Putten P. van der, Veenman C., Vanschoren J., Israel M. & Blockeel H. (Eds.), Proceedings 20th annual Belgian-Dutch conference on machine learning. 2011 Belgian-Dutch Conference on Machine Learning 20 May 2011 - 20 May 2011 97-98.
- Lamers M.H. & Verbeek F.J. (Eds.) (2011), Human-Robot Personal Relationships (HRPR 2010). Lecture Notes of the Institute of Computer Sciences, Social Informatics and Telecommunications Engineering no. 59. Heidelberg Berlin: Springer.
- Stoop E.J., Schipper T., Rosendahl Huber S.K., Nezhinsky A., Verbeek F.J., Gurcha S.S., Besra G.S., Vandenbroucke-Grauls C.M., Bitter W. & Sar A.M. van der (2011), Zebrafish embryo screen for mycobacterial genes involved in the initiation of granuloma formation reveals a newly ientified ESX-1 component, Disease Models & Mechanisms 4(4): 526-536.
- Zhang Y., Stupka E., Henkel C.V., Jansen H.J., Spaink H.P. & Verbeek F.J. (2011), Identification of common carp innate immune genes with whole-genome sequencing and RNA-seq data, Journal of Integrative BioInformatics 8(2): 169.
- Hawrylycz M., Baldock R.A., Burger A., Hashikawa T., Johnson G.A., Martone M., Ng L., Lau C., Larsen S.D., Nissanov J., Puelles L., Ruffins S., Verbeek F.J., Zaslavsky I. & Boline J. (2011), Digital atlasing and standardization in the mouse brain, PLoS Computational Biology 7(2): e1001065.
- Belmamoune M., Potikanond D. & Verbeek F.J. (2010), Mining and analysing spatio-temporal patterns of gene expression in an integrative database framework, Journal of Integrative BioInformatics 7(3): 128.
- Le Dévédec S.E., Yan K., Bont H.J.G.M. de, Ghotra V.P., Truong H., Danen E.H., Verbeek F.J. & Water B. van de (2010), Systems microscopy approaches to understand cancer cell migration and metastasis, Cellular and Molecular Life Sciences 67(19): 3219-3240.
- Slob J., Kallergi A., Dmitrieva J. & Verbeek F.J. (2010), Towards Metadata Patterns in Image Databases, Supplementary Proceedings of Pattern Recognition in Bioinformatics, 5th IAPR International Conference, (PRIB2010). .
- Kallergi A. & Verbeek F.J. (2010), Video games for collection exploration: games for and out of data repositories. Lugmayr A., Fransila H., Sorama O. & Aaltonen T. (Eds.), MindTrek '10: Proceedings of the 14th International Academic MindTrek Conference: Envisioning Future Media Environments. MindTrek '10: Academic MindTrek 2010 6 October 2010 - 6 October 2010. New York, U.S.A.: ACM Digital Library. 143-146.
- Dmitrieva J. & Verbeek F.J. (2010), Creating a new ontology: a modular approach. Burger A., Marshall M.S., Romano P., Paschke A. & Splendiani A. (Eds.), Proceedings of the workshop on semantic web applications and tools for life sciences. SWAT4LS-2010 10 December 2010 - 10 December 2010 no. 698: CEUR-WS.org. 1-4.
- Nezhinsky A.E. & Verbeek F.J. (2010), Pattern recognition for high throughput zebrafish imaging using genetic algorithm optimization. Dijkstra T.M.H., Tsivtsivadze E., Marchiori E. & Heskes T. (Eds.), Pattern recognition in bioinformatics. IAPR International Conference on Pattern Recognition in Bioinformatics PRIB 2010 22 September 2010 - 24 September 2010. Lecture Notes in Computer Science no. 6282. Berlin/Heidelberg: Springer. 302-312.
- Zhang Y., Bruin J.S. de & Verbeek F.J. (2010), Specificity enhancement in microRNA target prediction through knowledge discovery. In: Zhang Y. (Ed.), Machine Learning 391-410.
- Kallergi A. & Verbeek F.J. (2010), Onto-Frogger: the making of. Blandford A., Guliksen J., Hvannberg E.T., Larusdottir M.K., Law E.L.-C. & Vilhjalmsson H.H. (Eds.), Proceedings of the 6th Nordic conference on human-computer interaction: extending boundaries. NordiCHI '10: 6th Nordic Conference on Human-Computer Interaction 16 October 2010 - 20 October 2010. New York: Association for Computing Machinery. 691-694.
- Bertens L.M.F., Kleijn J., Koutny M. & Verbeek F.J. (2010), Modelling gradients using petri nets. Donatelli S., Kleijn H.C.M., Machado R.J. & Fernandez J.M. (Eds.), Proceedings of the workshops of the 31st international conference on application and theory of petri nets and other models of concurrency (PETRI NETS 2010). RAPNeC-2010 Recent Advances in Petri Nets and Concurrency 21 June 2010 - 22 June 2010. CEUR Workshop Proceedings no. 827: CEUR-WS. 39-53.
- Yan K., Bertens L.M.F. & Verbeek F.J. (2010), Image Registraton and Realignment using Evolutionary Algorithms with High resolution 3D model from Human Liver. Sappa A.D. (Ed.), Proceedings 11th IASTED International Conference on Computer Graphics and Imaging (CGIM 2010)},. 11th IASTED International Conference on Computer Graphics and Imaging (CGIM 2010)}, 17 February 2010 - 19 February 2010: Acta Press. 679-014.
- Bathoorn R., Welten M., Richardson M.K., Siebes A. & Verbeek F.J. (2010), Frequent episode mining to support pattern analysis in developmental biology. Dijkstra T.M.H., Tsivtsivadze E., Marchiori E. & Heskes T. (Eds.), 5th IAPR conference on pattern recognition in bioinformatics (PRIB 2010). IAPR International Conference on Pattern Recognition in Bioinformatics PRIB 2010 22 September 2010 - 24 September 2010. Lecture Notes in Computer Science. Berlin/Heidelberg: Springer. 253-263.
- Nezhinsky A., Kruisselbrink J.W. & Verbeek F.J. (2010), Convex shape retrieval from edge maps by the use of an evolutionary algorithm. Fred A., Filipe J. & Gamboa H. (Eds.), Bioinformatics 2010: proceedings of the first international conference on bioinformatics. First International Conference on Bioinformatics 20 January 2010 - 23 January 2010: INSTICC. 221-225.
- Dmitrieva J. & Verbeek F.J. (2010), Different Geometries in Ontology Visualization. Park J., Hao M.C., Wong P.C. & Chen C. (Eds.), Proc. SPIE 7530, Visualization and Data Analysis 2010. IS&T/SPIE Electronic Imaging 17 January 2010 - 21 January 2010: SPIE. 12 pages.
- Bertens L.M.F., Kleijn H.C.M., Koutny M. & Verbeek F.J. (2010), Modelling Gradients Using Petri Nets. Leiden: Universiteit Leiden.
- Bertens L.M.F., Richardson M.K. & Verbeek F.J. (2010), Analysis of cardiac development in the turtle Emys orbicularis (Testudines: Emidydae) using 3-D computer modeling from histological sections, The Anatomical Record 293(7): 1101-1114.
- Zhang Y. & Verbeek F.J. (2010), Comparison and integration of target prediction algorithms for microRNA studies, Journal of Integrative BioInformatics 7(3): 127.
- Hawrylycz M., Boline J., Burger A., Hashikawa T., Johnson G.A., Martone M., Ng L., Nissanov J., Puelles L., Ruffins S., Verbeek F.J. & Zaslavsky I. (2009), The INCF Digital Atlasing Program: report on Digital Atlasing Standards in the rodent brain, Nature Precedings : .
- Kallergi A., Bei Y., Kok P., Dijkstra J., Abrahams J.P. & Verbeek F.J. (2009), Cyttron: A Virtualized Microscope supporting image integration and knowledge discovery. In: Noteborn M.H.M., Tavassoli M. & Backendorf C. (Eds.), Proteins Killing Tumour Cells. Kerala, India: ResearchSignPost. 291-315.
- Dmitrieva J. & Verbeek F.J. (2009), Node-link and containment methods in ontology visualization. Hoekstra R. & Patel-Schneider P.F. (Eds.), Proceedings of the 6th international workshop on OWL: experiences and directions (OWLED 2009). 6th International Workshop on OWL: Experiences and Directions (OWLED 2009) 23 October 2009 - 24 October 2009. CEUR Workshop Proceedings no. 529: CEUR-WS.
- Giannoulis S. & Verbeek F.J. (2009), The happiness cube paradigm; eliciting emotions of happiness through sound, video, light and odor. Assessment of affective state with non invasive techniques. Reichardt D. (Ed.), Proceedings of 4th International Workshop on Emotion and Computing: Current Research and Future impact. 4th International Workshop on Emotion and Computing: Current Research and Future impact 15 September 2009 - 15 September 2009 7-14.
- Kallergi A., Bei Y. & Verbeek F.J. (2009), The ontology viewer: facilitating image annotation with ontology terms in the CSIDx imaging database. Handschuh S., Heath T. & Thai V. (Eds.), Proceedings of the IUI'09 Workshop on visual interfaces to the social and the semantic web. IUI'09 Workshop on Visual Interfaces to the Social and the Semantic Web 8 February 2009 - 8 February 2009 no. 443: CEUR-WS.org.
- Yan K., Le Devedec S., Water B. van de & Verbeek F.J. (2009), Cell Tracking and Data Analisys of in vitro Tumour Cells from Time--Lapse Image Sequences. Ranchordas A. & Araujo H. (Eds.), Proceedings of the Fourth International Conference on Computer Vision Theory and Applications, VISAPP. Fourth International Conference on Computer Vision Theory and Applications 5 February 2009 - 8 February 2009 no. Volume 1. Portugal: Scitepress. 281-286.
- Dmitrieva J. & Verbeek F.J. (2009), Multi-view ontology visualisation, Proceedings 11th international protege conference. 11th International Protégé Conference 23 June 2009 - 26 June 2009.
- Slob J., Kallergi A. & Verbeek F.J. (2009), Observations on semantic annotation of micrscope images for life sciences. Marshall M., Scott, Burger A., Romano P. & Splendiani A. (Eds.), Proceedings of the workshop on semantic web applications and tools for life sciences. SWAT4LS-2009 Semantic Web Applications and Tools for Life Sciences 20 November 2009 - 20 November 2009. CEUR Workshop Proceedings no. 559: CEUR-WS.
- Dmitrieva J. & Verbeek F.J. (2009), Integration of Information from different ontologies. Marshall M.S., Burger A., Romano P. & Splendiani A. (Eds.), Proceedings of the workshop on semantic web applications and tools for life sciences. SWAT4LS-2009 Semantic Web Applications and Tools for Life Sciences 20 November 2009 - 20 November 2009. CEUR Workshop proceedings no. 559: CEUR-WS.
- Papakonstantinou C., Panagiotou I. & Verbeek F.J. (2009), The TicTag application: towards tag-based meta-search-for browsing the web, Proceedings HCI 2009 People and Computers XXIII - Celebrating people and technology. People and Computers XXIII Celebrating People and Technology (HCI) 1 September 2009 - 5 September 2009. Cambridge, UK: British Computer Society, UK. 354-361.
- Kallergi A. & Verbeek F.J. (2009), Onto-frogger: playing with semantic structure. Marshall M.S., Burger A., Romano P. & Splendiani A. (Eds.), Proceedings workshop on semantic web applications and tools of life science. SWAT4LS-2009 Semantic Web Applications and Tools for Life Sciences 20 November 2009 - 20 November 2009. CEUR Workshop Proceedings no. 559: CEUR-WS.
- Verbeek F.J., Lenior D. & Steen M. van (Eds.) (2009), Proceedings CHI-NL 2009. Leiden: CHI-NL.
- Bertens L.M.F., Jansen H.J., Kleijn J., Koutny M. & Verbeek F.J. (2009), Using Petri Nets in Higher Level Development Biology: a case study on the AP axis development in Xenopus laevis. Extended abstract. Leiden: LIACS.
- Hooijdonk L.W.A. van, Ichwan M., Dijkmans T.F., Schouten T.G., Verbeek F.J., Vreugdenhil E. & Fitzsimons C.P. (2009), Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression, BMC Neuroscience 10(2): 2.
- Brittijn S.A., Duivesteijn S.J., Belmamoune M., Bertens L.M.F., Bitter W., Bruijn J.D. de, Champagne D.L., Cuppen E., Flik G., Broucke-Grauls C.M. van den, Janssen R., Jong I.E.M. de, Kloet E.R. de, Kros A., Meijer A., Metz J.R., Sar A.M. van der, Schaaf M.J., Schulte-Merker S., Spaink H.P., Tak P.P., Verbeek F.J., Vervoordeldonk M.J., Vonk F., Witte F., Yuan H. & Richardson M.K. (2009), Zebrafish development and regeneration: new tools for biomedical research, The International Journal of Developmental Biology 53(5-6): 835-850.
- Zhang Y., Woltering J.M. & Verbeek F.J. (2008), Screen of MicroRNA Targets in Zebrafish Using Heterogeneous Data Sources: A Case Study for Dre-miR-10 and Dre-miR-196, International Journal of Mathematical, Physical and Engineering Sciences 2(1): 10-17.
- Roël G., Gent Y.J., Peterson-Maduro J., Verbeek F.J. & Destrée O. (2008), Lef1 plays a role in patterning the mesoderm and ectoderm in Xenopus tropicalis, The International Journal of Developmental Biology 53(1): 81-89.
- Zhang Y., Bruin J.S. de & Verbeek F.J. (2008), miRNA Target Prediction through mining of miRNA Relationships, 2008 8th IEEE international conference on bioinformatics and bioengineering. 8th IEEE International Conference on BioInformatics and BioEngineering 8 October 2008 - 10 October 2008: IEEE.
- Dmitrieva J. & Verbeek F.J. (2008), Information Visualization from Ontology, FOIS 2008 : 5th international conference on formal ontology in information systems. FOIS 2008 : 5th international conference on formal ontology in information systems 22 April 2008 - 24 April 2008. FOIS: Formal Ontology in Information Systems .
- Umanski D., Kosters W.A., Verbeek F.J. & Schiller N.O. (2008), Integrating computer games in speech therapy for children who stutter. Berkling K., Giuliani D. & Potamianos A. (Eds.), The 1st Workshop on Child, Computer and Interaction, {WOCCI} 2008. 1st Workshop on Child, Computer and Interaction, WOCCI 2008 23 October 2008 - 23 October 2008: ISCA. 17-17.
- Belmamoune M. & Verbeek F.J. (2008), Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database, Journal of Integrative BioInformatics 5(2): 92.
- Belmamoune M. & Verbeek F.J. (2007), Developmental anatomy ontology of zebrafish: an integrative semantic framework, Journal Integrative Bioinformatics 4(3): 65.
- Zhang Y., Woltering J.M. & Verbeek F.J. (2007), Screen of MicroRNA Targets in Zebrafish Using Heterogeneous Data Sources: A Case Study for Dre-miR-10 and Dre-miR-196, Proceedings WASET, Bangkok. .
- Broekens D.J., Kosters W.A. & Verbeek F.J. (2007), On affect and self-adaptation: potential benefits of valence-controlled action-selection. Mira J. & Alvarez J.R. (Eds.), Bio-inspired modeling of cognitive tasks. International Work-Conference on the Interplay Between Natural and Artificial Computation IWINAC 2007: Bio-inspired Modeling of Cognitive Tasks 18 June 2007 - 21 June 2007. Lecture Notes in Computer Science no. 4527. Berlin/Heidelberg: Springer. 357-366.
- Putten P.W.H. van der, Bertens L.M.F., Liu J., Hagen F., Boekhout T. & Verbeek F.J. (2007), Classification of yeast cells from image features to evaluate pathogen conditions. Hanjalic A., Schettini R. & Sebe N. (Eds.), Proc. SPIE 6506: Multimedia content access: algorithms and systems. MultiMedia Content Access: Algorithms & Systems. SPIE Proceedings no. 6506: SPIE.
- Bei Y., Dmitrieva J., Belmamoune M. & Verbeek F.J. (2007), Ontology Driven Image Search Engine. Hanjalic A., Schettini R. & Sebe N. (Eds.), Multimedia Content Access: Algorithms and Systems. Electronic Imaging 2007 28 January 2007 - 1 February 2007. Proceedings of SPIE no. 6506: SPIE. 65060G.
- Broekens D.J., Kosters W.A. & Verbeek F.J. (2007), Affect, anticipation, and adaptation: affect-controlled selection of anticipatory simulation in artificial adaptive agents, Adaptive Behavior 15(4): 397-422.
- Braakman N., Matysik J., Duinen S.G. van, Verbeek F.J., Schlebs R., Groot H.J.M. de & Alia A. (2006), Longitudinal assessment of Alzheimer's beta-amyloid plaquedevelopment in transgenic mice monitored by in vivo magnetic resonance microimaging, Journal of Magnetic Resonance Imaging 24(3): 530-536.
- Welten M.C.M., Haan S.B. de, Boogert N. van den, Noordermeer J.N., Lamers G.E.M., Spaink H.P., Meijer A.H. & Verbeek F.J. (2006), ZebraFISH: fluorescent in situ hybridization protocol and three-dimensional imaging of gene expression patterns, Zebrafish 3(4): 465-474.
- Diks S.H., Bink R.J., Water S. van de, Joore J., Verbeek F.J., Hertog J. den, Peppelenbosch M.P. & Zivkovic D. (2006), The novel gene, asb11: a regulator of the size of the neural progenitor compartment, Journal of Cell Biology 174(4): 581-592.
- Belmamoune M., Lindoorn L. & Verbeek F.J. (2006), 3D-VisQuS: A 3D Visual Query System integrating semantic and geometric models. In: Guerrero-Bote Vicente P. (Ed.), Current Research in Information Sciences and Technologies 401-405.
- Belmamoune M. & Verbeek F.J. (2006), Heterogeneous Information Systems: bridging the gap of time and space. Management and retrieval of spatio-temporal Gene Expression data. In: Guerrero-Bote & Vicente P. (Eds.), Current Research in Information Sciences and Technologies 53-58.
- Mubarak Q., Dmitrieva J., Vermeulen T., Zhou Y., Groenewegen L.P.J., Basmagi S., Beek R. van & Verbeek F.J. (2006), BioTune, a component based repository of BioInformatics teaching modules. Méndez-Vilas A. (Ed.), Current developments in technology-assisted education . Current Developments in Technology-Assisted Education: FormaTex.
- Liu J., Putten P.W.H. van der, Hagen F., Chen X., Boekhout T. & Verbeek F.J. (2006), Detecting virulent cells of Cryptococcus neoformans yeast: clustering experiments. Tang Y., Wang P., Lorette G. & So Yeung D. (Eds.), Proceedings of the 18th international conference on pattern recognition ICPR2006. 18th International Conference on Pattern Recognition (ICPR'06) 20 August 2006 - 20 August 2006 no. 4: IEEE. 1112-1115.
- Bei Y., Belmamoune M. & Verbeek F.J. (2006), Ontology and image semantics in multimodal imaging: submission and retrieval. Santini S., Schettini R. & Gevers T. (Eds.), Proceedings Volume 6061, Internet Imaging VII; 60610C (2006). Electronic Imaging 2006 15 January 2006 - 19 January 2006: SPIE. C1-C12.
- Kabli S., Alia A., Spaink H.P., Verbeek F.J. & Groot H.J.M. de (2006), Magnetic resonance microscopy of the adult zebrafish, Zebrafish 3(4): 431-439.
- Meuleman W., Welten M.C.M. & Verbeek F.J. (2006), Construction of correlation networks with explicit time-slices using time-lagged, variable interval standard and partial correlation coefficients. Berthold M.R., Glen R.C. & Fischer I. (Eds.), Computational life sciences II. International Symposium on Computational Life Science CompLife 2006 27 September 2006 - 29 September 2006 no. 4216. Berlin/Heidelberg: Springer. 236-246.
- Jonge H.W. de, Bakker M.A.G. de, Verbeek F.J. & Weijs W.A. (2005), Embedding of large specimens in glycol methacrylate: prerequisites for multi-signal detection and high-resolution imaging, Microscopy Research and Technique 66(1): 25-30.
- Broekens D.J. & Verbeek F.J. (2005), Simulation, emotion and information processing: computational investigations of the regulative role of pleasure in adaptive behavior modeling natural action selection, Proceedings of the workshop on modeling natural action selection. : AISB Press. 166-173.
- Meijer A.H., Verbeek F.J., Salas-Vidal E., Corredor-Adamez M., Bussman J., Sar A.M. van der, Otto G.W., Geisler R. & Spaink H.P. (2005), Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection, Molecular Immunology 42(10): 1185-1203.
- Corredor-Adamez M., Welten H.P., Spaink H.P., Jeffery J.E., Schoon R.T., Bakker M.A.G., Bagowski C.P., Meijer A.H., Verbeek F.J. & Richardson M.K. (2005), Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, Evolution and Development 7(5): 362-375.
- Welten M.C.M., Verbeek F.J., Meijer A.H. & Richardson M.K. (2005), Gene expression and digit homology in the chicken embryo wing, Evolution and Development 7(1): 18-28.
- Richardson M.K. & Verbeek F.J. (2003), New directions in comparative embryology and the nature of developmental characters, Animal Biology 53(3): 303-311.
- Qayyum S.R., Webb S., Anderson R.H., Verbeek F.J., Brown N.A. & Richardson M.K. (2001), Septation and valvar formation in the outflow tract of the embryonic chick heart, The Anatomical Record 264(3): 273-283.
- Verbeek F.J. & Huijsmans D.P. (1998), A graphical database for 3D reconstruction supporting (4) different geometrical representations. In: Wong S.T.C. (Ed.), Medical image databases. The Springer International Series in Engineering and Computer Science no. 465. Boston, MA: Springer. 116-138.
- Verbeek F.J., Huijsmans D.P., Baeten R.J.A.M., Schoutsen N.J.C. & Lamers W.H. (1995), Design and implementation of a database and program for 3D reconstruction from serial sections: a data-driven approach, Microscopy Research and Technique 30(6): 496-512.
- Board Member