
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
See also
Former PhD candidates
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Mounia Belmamoune
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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
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Amalia Kallergi
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Enrique Larios Vargas
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Wouter Mensink
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Alexander Evgenievich Nezhinsky
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Hanna Schraffenberger
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Leonie van Steijn
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Lise Stork
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Xiaoqin Tang
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Mohamed Tleis
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Rafael Viana de Carvalho
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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
- 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.
- Paulus E., Burie J-C. & Verbeek F.J. (2021), Binarization strategy using multiple convolutional autoencoder network for old Sundanese manuscript images. In: Barney Smith E.H. & Pal U. (Eds.) Document Analysis and Recognition – ICDAR 2021 Workshops, Proceeding, Part 2. no. 12916 Cham: Springer. 142-157.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- Cao L. & Verbeek F.J. (2020), L-systems from 3D-imaging of phenotypes of arborized structures, Fundamenta Informaticae 175(1-4): 327-345.
- Zammit A., Helwerda L., Olsthoorn R.C.L., Verbeek F.J. & Gultyaev A.P. (2020), A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions, Bioinformatics 37(7): 956-962.
- 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.
- Martorelli I., Helwerda L.S., Kerkvliet J., Gomes S.I.F., Nuytinck J., Werff C.R.A. van der, Ramackers G.J., Gultyaev 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).
- 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.
- 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 20 4 2020-23 4 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. In: Hogeweg L. & Pieterse S. (Eds.) Biodiversity Information Science and Standards.: Pensoft. 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.
- Tang X., Lamers G.E.M. & Verbeek F.J. (2018), 3D Image Quality Improvement for Optical Projection Tomography via Point Spread Function Modelling. In: Proceedings Imaging and Applied Optics 2018 (3D, AO, AIO, COSI, DH, IS, LACSEA, LS&C, MATH, pcAOP).: OSA. 3W5G.5.
- 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. (Ed.) Theoretical and Applied Aspects of Systems Biology. Computational BiologyCOBO no. 27 Cham: Springer. 3-26.
- Stork L., Weber A., Herik H.J. van den, Plaat A., Verbeek F.J. & Wolstencroft K.J. (2018), From Handwritten Manuscripts to Linked Data. In: Méndez E., Crestani F., Ribeiro C., David G., Lopes J. (Eds.) Digital Libraries for Open Knowledge. no. Lecture Notes in Computer Science, volume 11057 Cham: Springer. 330-334.
- 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.
- 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., 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.
- 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.
- Helwerda L.S., Niessink F. & Verbeek F.J. (2017), Conceptual process models and quantitative analysis of classification problems in Scrum software development practices. In: Fred A.L.N., Filipe J.B.L. (Ed.) Proceedings of the 9th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management. 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. In: 2017 IEEE International Conference on Image Processing (ICIP).: IEEE Xplore. 2194-2198.
- 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.
- 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.
- Tang X., Hoff V.M., Hoogenboom J., Guo Y., Cai.F., Lamers G. & Verbeek F. (2016), Fluorescence and bright-field 3D image fusion based on sinogram unification for optical projection tomography. In: 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. Danvers: Institute of Electrical and Electronics Engineers(IEEE). 403-410.
- 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.
- 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. In: Ortuno F., Rojas I. (Eds.) Bioinformatics and Biomedical Engineering: 4th International Conference, IWBBIO 2016, Granada, Spain, April 20-22, 2016, Proceedings. no. 9656 Heidelberg: Springer International Publishing. 557-572.
- Cai F., Hao Wang, Tang X., Emmerich Michael T.M. & Verbeek F.J. (2016), Fuzzy Criteria in Multi-objective Feature Selection for Unsupervised Learning, Procedia Computer Science 102: 51-58.
- 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.
- 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. In: Digital Humanities 2016 Conference Abstracts. Krakow: Jagiellonian University and Pedagogical University. 674-676.
- 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. & 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.
- Xiong Z. & Verbeek F.J. (2016), Segmentation of Zebrafish Larvae Inhomogeneous 3D Images Using the Level-Set Method. In: Visualization and Data Analysis 2016.: Society for Imaging Science and Technology.
- Gómez Maureira M.A. & Verbeek F.J. (2016), The Impact of Co-Located Play on Social Presence and Game Experience in a VR Game. In: Proceedings of the First International Joint Conference of DiGRA and FDG. no. 13: Digital Games Research Association and Society for the Advancement of the Science of Digital Games.
- Teernstra L., Putten P.W.H. van der, Noordegraaf-Eelens L. & Verbeek F.J. (2016), The Morality Machine: Tracking Moral Values in Tweets. In: Boström H., Knobbe A., Soares C., Papapetrou P. (Eds.) Advances in Intelligent Data Analysis XV. IDA 2016. no. 9897 Cham: Spinger. 26-37.
- Teernstra L., Putten P.W.H. van der, Noordegraaf-Eelens L. & Verbeek F.J. (2016), The Morality Machine: Tracking Moral Values in Tweets. In: Boström H., Knobbe A., Soares C., Papapetrou P. (Eds.) Advances in Intelligent Data Analysis XV. no. 9897 Cham: Springer International Publishing. 26-37.
- 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, Computation 3(2): 150-176.
- Tleis M. & Verbeek F.J. (2015), Contour Expansion Algorithm Preprocessed by Hough Transform and Circular Shortest Path for Ovoid Objects. In: Jennane R. (Ed.) Proceedings International Conference on Image Processing Theory, Tools and Applications (IPTA 2015). no. CFP1562F-CDR: IEEE. 149-154.
- Cai F. & Verbeek F.J. (2015), Dam-based Rolling Ball with Fuzzy-Rough Constraints, a New Background Subtraction Algorithm for Image Analysis in Microscopy. In: Jennane R. (Ed.) Proceedings International Conference on Image Processing Theory, Tools and Applications (IPTA 2015). no. CFP1562F-CDR: IEEE. 298-303.
- 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.
- Coelho Camargo J. & Verbeek F.J. (2015), Pointing task evaluation of gestural interface interface interaction in 3D environment. In: 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. IADIS International Journal on WWW/Internet: Chi Nederland , the Dutch association promoting Human - Computer Interaction in The Netherlands . 78-85.
- Guo Y., Veneman W., Spaink H.P. & Verbeek F.J. (2015), Silhouette-based 3D Model for Zebrafish High-throughput Imaging. In: 2015 International Conference on Image Processing Theory, Tools and Applications (IPTA).: IEEE. 403-408.
- 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.
- Viana de Carvalho R., Kleijn J. & Verbeek F.J. (2014), A multi-scale extensive Petri net model of the bacterial-macrophage interaction. In: Proceedings BioPPN 2014. no. CEUR Workshop Proceedings: CEUR Workshop Proceedings, vol. 1159. 15-29.
- Larios Vargas E., Zhang Y., Cao L. & Verbeek F.J. (2014), CytomicsDB: A Metadata-Based Storage and Retrieval Approach for High-Throughput Screening Experiments. In: Comin M. et al (Ed.) Proceedings PRIB 2014. no. LNBI 8626: Springer International PUblisher Switzerland. 72-84.
- Tleis M. & Verbeek F.J. (2014), Extracting contours of oval-shaped objects by Hough Transform and minimal path algorithms. In: Falco C.M. (Ed.) Proceedings Sixth International Conference on Digital Image Processing (ICDIP 2014)..
- Gomez-Maureira M., Teunisse C., Schaffenberger H.K. & Verbeek F.J. (2014), Illuminating Shadows: Introducing Shadow Interaction in Spatial Augmented Reality. In: Proceedings CHI-NL.. 11-18.
- Slob J. & Verbeek F.J. (2014), Imaging Ontology, contributing to "reasonable" semantics for biomedical repositories. In: Bodenreider, Olivier; Oliveira, José Luis; Rinaldi, Fabio (Eds.) Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014).. 33-37.
- Benard E.L., Racz P.I., Rougeot J., Nezhinsky A.E., Verbeek F.J., Spaink H.P. & Meijer A.H. (2014), Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish, Journal of Innate Immunity .
- Maarten H. Lamers, 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.
- Camargo Coelho J. & Verbeek F.J. (2014), Pointing Task Evaluation of Gestural Interface Interaction in 3D Virtual Environment. In: Proceedings CHI-NL.. 78-85.
- Coelho Camargo J. & Verbeek F.J. (2014), The Leap Motion Controller in a 3D Virtual Environment: explorations and evaluations of pointing tasks. In: Proceedings International Conference on Interfaces and Human Computer Interaction (HCI 2014)..
- 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 (April).
- Cao L. & Verbeek F.J. (2013), Analytical evaluation of algorithms for point cloud surface reconstruction using shape features, Journal of Electronic Imaging 22(4): paper number 043008.
- Tleis M., Anemaet G., van Heusden P. & Verbeek F.J. (2013), Image analysis platform for yeast biologists. In: Proceedings Second International Conference on Advances in Biomedical Engineering.: 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: University of Newcastle-upon-Tyne, UK.
- Kallergi A. & Verbeek F.J. (2013), Playfull Interfaces for Scientific Image data. In: Emerging Research and Trends in Interactivity and the Human-Computer Interface.: IGI Global. 471-489.
- 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.
- Maarten H. Lamers, Verbeek F.J. & Putten P.W.H. van der (2013), Tinkering in Scientific Education. In: Reidsma D., Katayose H., Nijholt A. (Eds.) Advances in Computer Entertainment. no. Lecture Notes in Computer Science 8253: Springer-Verlag. 568-571.
- 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., Van de Water B. & Defilippi P. (2012), p140Cap suppresses the invasive properties of highly metastatic MTLn3-EGFR cells via impaired cortactin phosphorylation, Oncogene 31(5): 624-633.
- Larios E., Zhang Yanju, Yan K., Di Z., LeDevedec 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. In: Proceedings of 1st Int. Conf. on Health Information Science.: Springer. 76-87.
- Bertens L.M.F., Kleijn J. & Verbeek F.J. (2012), Biomodelling and Petri Nets, Eureka magazine : 6-8.
- Kok J.N., Lamprecht A-L., Verbeek F.J. & Wilkinson M.D. (2012), Bioscientific Data Processing and Modeling. In: Margaria T., Steffen B. (Eds.) Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies (ISoLA 2012)).: Springer. 7-11.
- Nezhinsky A. & Verbeek F.J. (2012), Efficient and Robust Shape Retrieval from Deformable Templates. In: Margaria T., Steffen B. (Eds.) Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies (ISoLA 2012).: Springer. 42-55.
- Cao L. & Verbeek F.J. (2012), Evaluation of algorithms for point cloud surface reconstruction through the analysis of shape parameters. In: Baskurt A.M., Sitnik R. (Eds.) Three-Dimensional Image Processing (3DIP) and Applications II. Proceedings of SPIE. 82900G.
- Heijer G.J. Den, Putten P.W.H. van der, Benard E.L., Meijer Annemarie & Verbeek F.J. (2012), Explorations in Texture Based Classification for Bacterial Infection in Zebrafish. In: Proceedings BENELEARN 2012.. 13-18.
- Carvalho R.V., Kleijn J., Meijer A.H. & Verbeek F.J. (2012), Modeling innate immune response to early mycobacterium infection, Computational and Mathematical Methods in Medicine 2012: 1-12.
- 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.
- Nezhinsky A., Stoop E.J., Sar A.M. van der & Verbeek F.J. (2012), Numerical Analysis of Image Based High-Througput Zebrafish Infection Screens: /Matching Meaning with Data/. In: BIOINFORMATICS 2012, Proceedings of the Int. Conf. on Bioinformatics Models, Methods and Algorithms.. 257-262.
- Yan Kuan & Verbeek F.J. (2012), Segmentation for High-Throughput Image Analysis: Watershed Masked Clustering. In: Margaria T., Steffen B. (Eds.) Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies (ISoLA 2012).: Springer. 25-41.
- 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. In: Proceedings 21th Annual Belgian-Dutch Conference on Machine Learning..
- Carvalho R.V., Davids W., Meijer A.H. & Verbeek F.J. (2012), Spatio-Temporal Modeling and Simulation of Mycobacterium Pathogenesis using Petri Nets. In: Proceedings Bionetics. York: Springer.
- Viana de Carvalho R., Meijer A.H. & Verbeek F.J. (2012), Spatio-Temporal Modeling and Simulation of Mycobacterium Pathogenesis Using Petri Nets. In: Emma Hart, Jon Timmis, Paul Mitchell, Takadash Nakamo, Foad Dabiri (Ed.) Bio-Inspired Models of Networks, Information, and Computing Systems. no. 1867-8211: Springer Berlin Heidelberg. 236-241.
- Kallergi A. & Verbeek F.J. (2012), Storytelling as playful exploration of biological image data: Reviewing a candidate interaction paradigm. In: Proceedings of the IADIS International Conference Interfaces and Human Computer Interaction.. 35-42.
- Bono B. de, Kasteleyn P., Potikanond Dome, Kokash N., Verbeek F.J. & Grenon P. (2012), Tissue Motifs and Multi-scale Transport Physiology. In: Workshop of Ontologies in Biomedicine and Life Sciences..
- Sanchez-Faddeev H., Michael T. M.Emmerich, 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. In: Margaria T., Steffen B. (Eds.) Leveraging Applications of Formal Methods, Verification and Validation. Applications and Case Studies (ISoLA 2012).: Springer. 12-24.
- Potikanond Dome & Verbeek F.J. (2012), Visualization and analysis of 3D gene expression patterns in zebrafish using web services. In: Wong P.C. (Ed.) Visualization and Data Analysis 2012. Proceedings of SPIE. 829412.
- Tleis M. & Verbeek F.J. (2012), Yeast-Cell Features Extraction Plugin. In: Proceedings ImageJ Conference 2012..
- Vries A. de, Oskam O. & Verbeek F.J. (2011), 3-Dimengination: playing a puzzle with texture and projections. In: Proceedings CHI-NL..
- Potikanond Dome & Verbeek F.J. (2011), 3D Visual Integration of Spatio-Temporal Gene Expression Patterns on Digital Atlas of Zebrafish Embryo using Web Services. In: Proceedings International Conference Advances in Communication and Information Technology (CIT 2011).. 56-62.
- 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).
- 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), Atlasing and Standardization in the Mouse Brain, PloS Biology 7(2).
- 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. In: Proceedings IEEE Conference Engineering and Technology (CET 2011).. 195-198.
- Qin Y., Stokman G., Yan K., Ramaiahgari S., Verbeek F.J., Graauw M. de, Water B. van de & Price L. (2011), Cyclic AMP signalling protects proximal tubular epithelial cells from cisplatin-induced apoptosis via activation of Epac, British Journal of Pharmacology 165(4b): 1150.
- Nezhinsky A., Martorelli I. & Verbeek F.J. (2011), Detection of Developmental Stage in Zebrafish Embryos in a high throughput processing environment. In: Proceedings 20th Annual Belgian-Dutch Conference on Machine Learning..
- Hawrylycz M., Baldock R.A., Burger A., Hashikawa T., Johnson G.A., Martone M., Ng L., Lau C., Larson 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 Biology 7: e1001065.
- Maarten H. Lamers & Verbeek F.J. (Eds.) (2011), Human-Robot Personal Relationships (HRPR 2010). Heidelberg Berlin: Springer.
- Zhang Yanju, 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).
- Dmitrieva J. & Verbeek F.J. (2011), Modular Approach for a new Ontology. In: Proceedings Fifth International Workshop WoMO 2011. Frontiers in Artificial Intelligence and Applications.
- Cao L., Yan K., Winkel Leah, Graauw M. de & Verbeek F.J. (2011), Pattern Recognition in High-Content Cytomics Screens for Target Discovery - Case Studies in Endocytosis. In: Pattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011.. 330-342.
- Boer F. & Verbeek F.J. (2011), Seeing through virtual windows. In: Proceedings CHI-sparks CHI-NL..
- Carvalho R.V., Davids W., Meijer A.H. & Verbeek F.J. (2011), Spatio-temporal Modeling and Simulation of Mycobacterium Pathogenesis Using Petri Nets. In: Proceedings BIONETICS 2011. Lecture Notes of the Institute of Computer Sciences, Social Informatics and Telecommunications Engineering: Springer. 236-241.
- Herik H.J. van den, Maarten H. Lamers & Verbeek F.J. (2011), Special issue Understanding the Artificial. Heidelberg: Springer.
- Kallergi A. & Verbeek F.J. (2011), The games Flickrites play: aninvestigation of Flickr-based gaming activity with special focus on opportunities for exploratory interaction. In: Proceedings of the IADIS International Conference Game and Entertainment Technologies 2011.. 35-42.
- Herik H.J. van den, Lamers Maarten H. & Verbeek F.J. (2011), Understanding the Artificial, International Journal of Social Robotics 3(2): 107-109.
- 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 : 526-536.
- Bertens L.M.F., Richardson M.K. & Verbeek F.J. (2010), Analysis of cardiac development in the turtle Emys orbicularis (Testudines: Emidydae) using 3D computer modeling and reconstruction based on serial sections, Anatomical Record 293(7): 1101-1114.
- LeDevedec S., Yan K., Bont H. de, Ghotra V.P., Truong H., Danen E.H., Verbeek F.J. & Water B. van de (2010), A Systems Microscopy Approach to Understand Cancer Cell Migration and Metastasis, Journal Cellular and Molecular Life Sciences 2010 67(19): 3219-3240.
- Zhang Yanju & Verbeek F.J. (2010), Comparison and Integration of Target Prediction Algorithms for microRNA Studies, Journal of Integrative BioInformatics 7(3:127): 1-12.
- Nezhinsky A., Kruisselbrink J.W. & Verbeek F.J. (2010), Convex Shape Retrieval from Edge Maps by the use of an Evolutionary Algorithm. In: A. Fred J. Filipe H. Gamboa (Ed.) Proceedings 1st International Conference on Bioinformatics, Valencia, Spain.. 221-225.
- Dmitrieva J. & Verbeek F.J. (2010), Creating a new Ontology: a Modular Approach. In: Proceedings SWAT4LS (2010)..
- Dmitrieva J. & Verbeek F.J. (2010), Different Geometries in Ontology Visualization. In: Jinah Park Ming C. Hao Pak C. Wong (Ed.) Visualization and Data Analysis Proceedings SPIE EI 2010.. 12 pages.
- Bathoorn R., Welten M., Richardson M. K., Siebes Arno & Verbeek F.J. (2010), Frequent Episode Mining to support Pattern Analysis in Developmental Biology. In: 5th IAPR Conference on Pattern Recognition in BioInformatics (PRIB 2010). Lecture Notes in Bioinformatics: Springer. 253-263.
- 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. In: A.D. Sappa (Ed.) Proceedings 11th IASTED International Conference on Computer Graphics and Imaging (CGIM 2010)},.. track 679-014.
- Belmamoune M., Potikanond Dome & 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): 1-10.
- Bertens L.M.F., Kleijn H.C.M., Koutny M. & Verbeek F.J. (2010), Modelling Gradients Using Petri Nets: Universiteit Leiden.
- Bertens L.M.F., Kleijn J., Koutny M. & Verbeek F.J. (2010), Modelling Gradients Using Petri Nets. In: Proceedings International Workshop on Biological Processes & Petri Nets (BioPPN) Braga, Portugal, June 21 2010.. 55-69.
- Kallergi A. & Verbeek F.J. (2010), Onto-Frogger: The Making Of. In: Blandford A., Guliksen J., Hvannberg E.T., Larusdottir M.K., Law E.L.-C., vVilhjalmsson H.H. (Eds.) Proceedings of the 6th Nordic Conference on Human-Computer Interaction. Reykjavik, Iceland: ACM Conference Proceedings Series. 691-694.
- Nezhinsky A. & Verbeek F.J. (2010), Pattern recognition for high throughput zebrafish imaging using genetic algorithm optimization. In: 5th IAPR Conference on Pattern Recognition in BioInformatics (PRIB 2010). Lecture Notes in Bioinformatics: Springer. 302-312.
- Zhang Y., Bruin de J.S. & Verbeek F.J. (2010), Specificity Enhancement in microRNA Target Prediction through Knowledge Discovery. In: V. Kordic (Ed.) Machine Learning..
- Giannoulis S. & Verbeek F.J. (2010), The happiness cube paradigm; eliciting relaxation and happiness through sound, video, light and odor. In: LABS: Leonardo Abstract Service..
- 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. (2010), The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain. In: Nature Preceedings..
- Slob J., Kallergi A., Dmitrieva J. & Verbeek F.J. (2010), Towards Metadata Patterns in Image Databases. In: 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. In: A. Lugmayr H. Fransila O. Sorama, T. Aaltonen (Eds.) Proceedings of the 14th International Academic MindTrek Conference: Envisioning Future Media Environments. Tampere, Finland: ACM Digital Library. 143-146.
- Brittijn S.A., Duivesteijn S.J., Belmamoune M., Bertens L.M.F., Bitter W., De Bruijn J.D., Champagne D.L., Cuppen E., Flik G., Van den Broucke-Grauls C.M., Janssen R., De Jong I.E.M., De Kloet E.R., Kros A., Meijer A., Metz J.R., Van der Sar A.M., 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, International Journal of Developmental Biology 53(5-6): 835-850.
- 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. In: Proceedings VISAPP 2009.. 281-287.
- 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, Tavassoli, Backendorf (Eds.) Proteins Killing Tumour Cells. Kerala, India: ResearchSignPost. 291-315.
- Dmitrieva J. & Verbeek F.J. (2009), Integration of Information from different ontologies. In: Marshall Burger Romano, Splendiani (Eds.) Proceedings Workshop on Semantic Web Applications and Tools for Life Sciences. CEUR Workshops proceedings Amsterdam.
- Roel G., Gent Y.J., Peterson-Maduro J., Verbeek F.J. & Destree O. (2009), Lef1 plays a role in patterning the mesoderm and ectoderm in Xenopus tropicals, International Journal of Developmental Biology 53: 81-89.
- Van Hooidonk L.W.A., 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.
- Dmitrieva J. & Verbeek F.J. (2009), Multi-view Ontology Visualisation. In: Proceedings 11th International Protege Conference..
- Dmitrieva J. & Verbeek F.J. (2009), Node-Link and Containment Methods in Ontology Visualization. In: Proceedings OWLED 2009..
- Slob J., Kallergi A. & Verbeek F.J. (2009), Observations on Semantic Annotation of Micrscope Images for Life Sciences. In: Marshall Burger Romano, Splendiani (Eds.) Proceedings Workshop on Semantic Web Applications and tools for Life Science. CEUR Workshops proceedings Amsterdam.
- Kallergi A. & Verbeek F.J. (2009), Onto-Frogger: Playing with Semantic Structure. In: Marshall Burger Romano, Splendiani (Eds.) Proceedings Workshop on Semantic Web Applications and Tools of Life Science. CEUR Workshops proceedings Amsterdam: CEUR-Workshop Porceedings.
- Verbeek F.J., Lenior D. & Steen M. van (Eds.) (2009), Proceedings CHI-NL 2009. Leiden: CHI-NL.
- Papakonstantinou C., Panagiotou I. & Verbeek F.J. (2009), Tag Based Meta-Search for Browsing the Web: The TicTag Application. In: Verbeek Lenior Steen (Ed.) Proceedings CHI-NL.. 93-101.
- 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 nog invasive techniques. In: Proceedings of 4th International Workshop on Emotion and Computing: Current Research and Future impact.. 7-14.
- Kallergi A., Bei Y. & Verbeek F.J. (2009), The Ontology Viewer: Facilitating Image Annotation with Ontology Terms in the CSIDx Imaging Database. In: Proceedings VISS-WS 2009.: CEUR.
- Papakonstantinou C., Panagiotou I. & Verbeek F.J. (2009), The TicTag Application: Towards Tag-based Meta-search-for Browsing the Web. In: Proceedings HCI 2009 People and Computers XXIII - Celebrating people and technology. Cambridge, UK: British Computer Society, UK. 354-361.
- 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. onbekend: LIACS.
- 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).
- Dmitrieva J. & Verbeek F.J. (2008), Information Visualization from Ontology. In: Proc. 5th international conference on 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. In: Proc. 1st Workshop Child, Computer and Interaction..
- 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, International Journal of Developmental Biology .
- Hooijdonk L.W.A. van, Ichwan M., Dijkmans T.F., Schouten T.G., Verbeek F.J., Vreugdenhil E. & Fitzsimons C.P. (2008), Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression, BMC Neuroscience .
- Zhang Y., Bruin J.S. de & Verbeek F.J. (2008), miRNA Target Prediction through Mining of miRNA Relationships.. In: 8th International Conference on BioInformatics and BioEngineering..
- 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.
- 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.
- 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. In: Hanjalic, A., Schettini, R., Sebe, N. (Eds.) SPIE Vol. 6506.. 650601-14.
- Broekens D.J., Kosters W.A. & Verbeek F.J. (2007), On Affect and Self-Adaptation: Potential Benefits of Valence-Controlled Action-Selection. In: 2nd. International Work-Conference on the Interplay between Natural and Artificial Computation (IWINAC).: Springer. 357-366.
- Broekens D.J., Kosters W.A. & Verbeek F.J. (2007), On Affect, Anticipation and Adaptation: Investigating the Potential of Affect-Controlled Selection of Anticipatory Simulation in Artificial Adaptive Agents, Adaptive Behavior 15: 397-422.
- Bei Y., Dmitrieva J., Belmamoune M. & Verbeek F.J. (2007), Ontology Driven Image Search Engine. In: Hanjalic, A., Schettini, R., Sebe, N. (Eds.) MultiMedia Content Access: Algorithms & Systems. Proceedings of SPIE. 1-10.
- 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. In: Proceedings WASET, Bangkok..
- Belmamoune M., Lindoorn L. & Verbeek F.J. (2006), 3D-VisQuS: A 3D Visual Query System integrating semantic and geometric models. In: Vicente P. Guerrero-Bote (Ed.) Current Research in Information Sciences and Technologies.. 401-405.
- 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. In: Méndez-Vilas, A. (Eds.) Proceedings MICTE 2006.: FormaText.
- 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, 4216: 236-246.
- 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. In: International Conference on Pattern Recognition (ICPR). IEEE Computer Society. 1112-1115.
- 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: Vicente P. Guerrero-Bote (Ed.) Current Research in Information Sciences and Technologies.. 53-58.
- 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.
- 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.
- Bei Y., Belmamoune M. & Verbeek F.J. (2006), Ontology and image semantics in multimodal imaging: submission and retrieval. In: Proc. SPIE Internet Imaging VII.. C1-C12.
- 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.
- 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: 465-474.
- 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.
- 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 5: 362-375.
- 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.. In: 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: 1185-1203.
- Richardson M.K. & Verbeek F.J. (2003), New directions in comparative embryology and the nature of developmental characters, Animal biology 53: 303-311.
- Verbeek F.J. & Huijsmans D.P. (1998), Chapter 5: A graphical database for 3D reconstruction supporting 4 different geometrical representations.. In: Wong S.T.C. (Ed.) Medical Image Databases, Kluwer international series in engineering and computer sciences, Secs 465, aug. 1998, ISBN 0792382897.. 116-138.
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