Imaging & BioInformatics Publications (Selected)

2023 Top of page.

Paulus, E., Burie, JC., Verbeek F.J. (2023)
Text Line Extraction Strategy for Palm Leaf Manuscripts.
Pattern Recognition Letters (DOI: 10.1016/j.patrec.2023.08.007)

Kurchaba, S., van Vliet, J., Verbeek, F.J., Veenman, C.J. (2023)
Anomalous NO2 emitting ship detection with TROPOMI satellite data and machine learning.
Remote Sensing of Environment. Volume 297, DOI: 10.1016/j.rse.2023.113761

Tang, A., Lv, L., Javanmardi, S., Wang, Y., Fan, J., Verbeek. F.J. Xiao, G. (2023)
Nanoparticle Image Synthesis and Modified BlendMask Instance Segmentation for Automated Phenotyping.
IEEE Transactionc on Medical Imaging. Vol. X, No. xx, 2023

Li, C., Yiu, WWC., Hu, W.,Cao L., Verbeek, FJ. (2023)
A Feature Weighted Tracking Method for 3D Neutrophils in Time-lapse Microscopy
Proc. 2022 IEEE Int. Conf. on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022, pp. 2196-2202, DOI: 10.1109/BIBM55620.2022.9995160.

Jahanbanifard M., Price, E., González, B.A., Raggi,L.A., Javanmardi, S., Lens, F., Gradendeel, B., Espinoza E., Verbeek F.J.(20203)
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
Int. Journal Mass Spectrometry (April 2023); DOI: 10.1016/j.ijms.2023.117050

Li, J., He, J., Long, J., Wang, C., Kers, J., Verbeek, F.J. (2023)
Foreground Extraction in Histo-Pathological Image by Combining Mathematical Morphology Operations and U-Net.
In Proceedings of the 16th Int. Joint Conf. on Biomedical Engineering Systems and Technologies - Volume 2: BIOIMAGING, pgs 146-153. DOI:10.5220/0011803500003414

2022 Top of page.

Chen Li, C., Polling M.,Cao L., Gravendeel B., Verbeek FJ.(2022)
Analysis of Automatic Image Classification Methods for Urticaceae Pollen Classification.
Necurocomputing (accepted Nov. 2022)

Kurchaba S., van Vliet J.,Verbeek FJ., Meulman JJ., Veenman CJ.(2022)
Supervised segmentation of NO2 plumes from individual ships using TROPOMI satellite data.
Remote Sensing (accepted Nov. 2022).

Javanmardi, S., Latif, AF.,Sadeghi, MT., Jahanbanifard, M., Bonsangue, M., Verbeek, FJ.(2022)
Caps Captioning: A Modern Image Captioning Approach Based on Improved Capsule Network.
Sensors 2022, 22(21), 8376; https://doi.org/10.3390/s22218376

Wang, X., Du, Y., Verberne S., Verbeek, FJ. (2022)
Improving Weakly Supervised Phrase Grounding via Visual Representation Contextualization with Contrastive Learning.
Applied Intelligence (Accepted October 2022, In press)

Cao, L., Schoenmaker, L.,Schwach, V, Ten Den. SA.,Passier, R., Verbeek, FJ.(2022)
Automated sarcomere structure analysis for studying cardiotoxicity in human pluripotent stem cell-derived cardiomyocytes.
Microscopy and Microanalysis (Accepted October 2022)

Wang, X., Du, Y., Verberne S., Verbeek, FJ. (2022)
Fine-Grained Label Learning in Object Detection with Weak Supervision of Captions.
Mutimedia Tools and Applications (Accepted july 2022)

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, Volume 73, 2022, 102164, ISSN 0141-9382,https://doi.org/10.1016/j.displa.2022.102164.

Duan, F., Rietveld, K.F.D., Lamers, G.E.M., Verbeek,F.J.(2022)
Real-Time Interactive Visualization of 3D Models from Bioimaging in a Holographic Pyramid.
Proceedings 4th International Conference on Advances in Computer Vision, Image and Virtualization (CVIV 2022)
Suzhou China, 2022 (Accepted)

Xue Wang (2022)
Multi Modal Representation Learning and Cross-Modal Semantic Matching.
PhD Thesis, Leiden University (June 2022)

Antonios Somarakis (2022)
Visual Analytics for Spatially Resolved Omics Data at Single Cell Resolution:
Methods & Applications.
PhD Thesis, Leiden University (January 2022)

2021 Top of page.

Miraei Ashtiani, S-H, Javanmardi, S., Jahanbanifard, M.m , Martynenko, A., Verbeek, FJ.(2021)
Detection of Mulberry Ripeness Stages Using Deep Learning Models.
IEEE Access 9, 100380-100394

Paulus, E., Burie, JC., Verbeek, FJ. (2021)
Binarization Strategy using Multiple Convolutional Autoencoder Network for Old Sundanese Manuscript Images.
Proceedings ICDAR 2021, Lausanne (September 2021), Springer LNCS Vol 129117.

Elmahdy, MS., Beljaards, L., Yousefi, S., Sokooti, H., Verbeek, FJ., van der Heide, UA., Staring, M.(2021)
Joint Registration and Segmentation via Multi-Task Learning for Adaptive Radiotherapy of Prostate Cancer
IEEE Access, June 2021, Doi 10.1109/ACCESS.2021.3091011

Mast, D., de Vries, S.I., Broekens, J.D., Verbeek, F.J. (2021)
The Participant Journey Map: Understanding the Design of Interactive Augmented Play Spaces
Frontiers in Computer Science 3, 45

Polling, M., Li, C., Cao, L., Verbeek, F.J., de Weger, L., Belmonte, J., De Linares, C., Willemse, J., de Boer, H., Gravendeel, B. (2021)
Neural networks for increased accuracy of allergenic pollen monitoring.
Scientific Reports 11 (1), 1-10.

Pierson, J., Robinson, SC, Boddington, P., Chazerand, P., Kerr, A., Milan, S., Verbeek, FJ., Kutterer C., Nerantzi, E., Aconstantinesei IC (2021)
AI4People 2020: AI in Media and Technology Sector: Opportunities, Risks, Requirements and Recommendations
Atomium European Institute for Science, Media and Democracy.

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 2021, Vol. 22, Art#178

Javanmardi, S., Miraei Ashtiani, S-H, Verbeek, FJ., Martynenko, A. (2021)
Computer-vision classification of corn seed varieties using deep convolutional neural network.
Journal of Stored Products Research, Vol 92 (May 2021) doi.org/10.1016/j.jspr.2021.101800

Stork. L, Weber, W., van der Herik, H.J., Plaat, ,A., Verbeek, F.J., Wolstencroft K.J. (2021)
Large-scale zero-shot learning in the wild: Classifying zoological illustrations
Ecological Informatics Vol 62, (May 2021) doi.org/10.1016/j.ecoinf.2021.101222

Hu, W., van Steijn, L., Li, C., Verbeek, FJ., Cao, L., Merks, RMH., Spaink, HP (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 (February 2021) doi.org/10.3389/fcell.2021.624571.

Verbeek. FJ, Cao, L.(2021)
L-systems from 3D-imaging of phenotypes of arborized structures.
In: A Moasaic of Computational Topics: from Classical to Novel (Eds. M ter Beek et al.), pp 327–345,
DOI 10.3233/STAL200004



Wanbin Hu (2021)
The Function of Toll-like receptor 2 in Infection and Inflammation.
PhD Thesis, Leiden University (December 2021)

L. van Steijn (2021)
Insights from modeling metabolism and amoboid cell motility in the immune system.
PhD Thesis, Leiden University (July 2021)

L. Stork (2021)
Knowledge Extraction from Archives of Natural History Collections.
PhD Thesis, Leiden University (July 2021)


2020 Top of page.

Tang, X., Spaink, HAJ, van WIjk, RC., Verbeek, FJ.(2020)
Segmentation-driven Optimization for Iterative Reconstruction in Optical Projection Tomography: An Exploration.
IEEE Transactions on Computational Imaging (Accepted October 2020)

Cao, L., van der Meer, A., Passier, R., Verbeek, F.J.(2020)
High Throughput Image Analysis for Cardiotoxicity Study using Human Pluripotent Stem Cell-Derived Cardiomyocytes.
Cell Immunology Journal (Accepted September 2020)

Jahanbanifard, M., Beckers, V., Koch, G., Beeckman, H., Gravendeel, B., Verbeek, FJ, Baas, P., Priester, C., Lens F.,(2020)
Description of wood anatomical characters of Diospyros and its close relatives (Ebenaceae).
IAWA Journal 2020, pp 1-43.

Zammit, A., Helwerda, L.S, Oltshoorn, R., Verbeek, F.J., Gultyaev A.P. (2020)
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions.
BioInformatics, 1-7, 2020, https://doi.org/10.1093/bioinformatics/btaa759

van Wijk, R.C., Hu, W., Dijkema S.H., van den Berg, DJ., Liu, J., Bahi, R., Verbeek, F.J., Simonsson, U.S.H., Spaink H.P., van der Graaf, P.H., Krekels E.H.J.(2020)
Anti-tuberculosis effect of isoniazid scales accurately from zebrafish to humans.
British Journal of Pharmacology (2020), Accepted.

Verbeek. FJ, Cao, L.(2020)
L-systems from 3D-imaging of phenotypes of arborized structures.
Fundamenta Informaticae 175 (2020) pp 327–345, DOI 10.3233/FI-2020-1940.

Duan, F., Rietveld, KFD, Verbeek, FJ. (2020)
Interactive visualization of complex three-dimensional models: case study in zebrafish.
Proceedings IHCI 2020. Accepted.

Duan, F., Lamers, GEM, Rietveld, KFD, Verbeek, FJ. (2020)
Interactive visualization of 3D biological model in holographic pyramid.
Proceedings ESCS 2020.

Lens, F., Liang, C., Guo, Y., Tang, X., Jahanbanifard, M., Correa da Silva Soares, F., Ceccantini, G., Verbeek, F.J. (2020)
Computer assisted timber identification based on features extracted from microscopic wood sections.
IAWA Journal (July 2020), DOI 10.1163-22941932-bja10029

Martorelli, I., Helwerda L.S., Kerkvliet, J., Gomes, S.I.F., Nuytinck, J., van der Werff, C.R.A., Ramackers, G.J.,
Gultyaev, A.P., Merckx, V.S.F.T., Verbeek F.J. (2020)
Fungal meta-barcoding data integration framework for the MycoDiversity DataBase (MDDB)
Journal of Integrative BioInformatics (2020) Vol 17,#1, pp 1-26. DOI 10.1515/jib-2019-0046

Beljaards L., Elmahdym, M., Verbeek., F.J., Staring, M. (2020)
A Cross-Stitch Architecture for Joint Registration and Segmentation in Adaptive Radiotherapy.
Proceedings Medical Imaging and Deep Learning (MIDL 2020),
Proceedings Marchine Learning Research; PMLR 121:62-74

Guo, Y., Verbeek, F.J., Yang, G. (2020)
Probabilistic Inference for Camera Calibration in Light Microscopy under Circular Motion.
Proceedings International Symposium on BioMedical Imaging (ISBI),
Iowa Arpil 2020, IEEE Proc. DOI 10.1109/ISBI45749.2020.9098432

Cao, L., van der Meer, A., Verbeek, F.J., Passier, R. (2020)
Automated image analysis system for studying cardiotoxicity in human pluripotent stem cell-Derived cardiomyocytes.
BMC BioInformatics 2020; Vol 21, Art# 187.


X. Tang (2020)
Computational Optimization of Optical Projection Tomography for 3D Image Analysis.
PhD Thesis, Leiden University (June 2020)


2019 Top of page.

Stork,L., Weber, A., van den Herik, H.J., Plaat, A., Verbeek, F.J. Wolstencroft K. (2019)
Automated Semantic Annotation of Species Names in Handwritten Texts
In: Proceedings ECIR 2019.

van Steijn, L., 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, zeb.2018.1712–15. http://doi.org/10.1089/zeb.2018.1712

Dekker, L., Peeperkorn, M., Liu D., Verbeek, F.J. (2019)
An alternative Interaction Paradigm for DNA-Sequence Data.
Proceedings of the IADIS International Conference Interfaces and Human Computer Interaction 2019 part of MCCSIS 2019) (eds. Katherine Blashki and Yingcai Xiao); pp. 343-347

Papagiannis, A., Liu D., Zammit, A., Gultyaev A.P., Verbeek, F.J. (2019)
Interacting with RNA secondary structure through sonification.
Proceedings of the IADIS International Conference Interfaces and Human Computer Interaction 2019 part of MCCSIS 2019) (eds. Katherine Blashki and Yingcai Xiao); pp. 43-49

2018 Top of page.

van Rooijen, A., Bouma H., Verbeek, FJ. (2018)
Fast and accurate person re-identification with Xception Conv-Net and C2F
In: Proceedings CIARP 2018; Madrid 2018, LNCS Vol. 11401, pp 611-619 Spinger.

Guo, Y., Xiong, Z., Verbeek FJ. (2018)
An efficient and robust hybrid method for segmentation of zebrafish objects from bright-field microscope images.
Machine Vision and Applications, https://doi.org/10.1007/s00138-018-0934-y

van Vreumingen, D., Tewari, T., Verbeek, FJ., van Ruitenbeek JM (2018)
Towards controlled single-molecule manipulation using real-time molecular dynamics simulation: a GPU implementation.
Micromachines, 2018, 9(6), 270; https://doi.org/10.3390/mi9060270

Rafael V Carvalho, Fons J Verbeek, Clarimar J. Coelho (2018)
Bio-Modelling using Petri Nets: a Computational Approach.
In: Theoretical and Applied Aspects of Systems Biology (Eds. Fabricio Alves Barbosa da Silva, Nicolas Carels, Floriano Paes Silva Junior). Springer, 2018.

Stork L., Weber, A,. Gasso Miracle, E., Verbeek, FJ., Plaat, A., van den Herik, HJ., Wolstencroft, K.(2018)
Semantic Annotation of Natural History Collections.
Journal of Web Semantics 59, 100462

Stork L., Weber, A,. van den Herik, HJ., Plaat, A., Verbeek, FJ., Wolstencroft, K. (2018)
From Historical Handwritten Manuscripts to Linked Data..
In: Proc. TPDL 2018 - 22nd Int.Conf.on Theory and Practice of Digital Libraries.
LNCS Vol, Springer (In Press)

Tang, X., Lamers, GEM., Verbeek, FJ. (2018)
3D Image Quality Improvement for Optical Projection Tomography via Point Spread Function Modelling
In: Proc. Imaging and Applied Optics 2018 (3D, AO, AIO, COSI, DH, IS, LACSEA, LS&C, MATH, pcAOP)
OSA Technical Digest (Optical Society of America, 2018), paper 3W5G.5.



H. Schraffenberger (2018)
Arguable augmented Reality, relationships between the virtual and the real.
PhD Thesis, Leiden University (November 2018)


2017 Top of page.

Helwerda,L., Niessink,F., Verbeek, FJ. (2017)
Conceptual process models and quantitative analysis of classification problems in Scrum software development practices.
In: Proc. 9th Int. Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management (IC3K KDIR), Madeira

Guo Y., van Wijk R.C., Krekels E.H.J., Spaink, H.P., van der Graaf P.H., Verbeek F.J. (2017)
Multi-modal 3D reconstruction and measurements of zebrafish larvae and its organs using axial-view microscopy.
In: Proc. IEEE International Conference on Image Processing (ICIP), 2017 pp.

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, Vol 11, 7, pp 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

Tang, X., van der Zwaan, D.M., Zammit, A., Rietveld, K.D.F., Verbeek, F.J. (2017)
Fast Post-Processing Pipeline for Optical Projection Tomography.
IEEE Trans. Nanobioscience, vol. 16, no. 5, pp. 367-374

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. DOI 10.1080/10447318.2017.1296974

F. Cai (2017)
Fuzzy Systems and Unsupervised Computing. Exploration of Applications in Biology
PhD Thesis, Leiden University (December 2017)

Y. Guo (2017)
Shape Analysis For Phenotype Characterisation from High-Throughput Imaging.
PhD Thesis, Leiden University (October 2017)

2016 Top of page.

Tang, X., van't Hoff, M., Hoogenboom, J., Guo, Y., Cai, F., Lamers, GEM., Verbeek, FJ (2016)
Fluorescence and Bright-field 3D Image Fusion Based on Sinogram Unification for Optical Projection Tomography.
In: Proceedings IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2016), 403-410

Cai, F., Verbeek, FJ, (2016)
Rough Fuzzy C-means and Particle Swarm Optimization Hybridized Method for Information Clustering Problem
J. of communication 11(12): 1106-1113

Cai, F., Liu, S., ten. Dijke, P., Verbeek FJ. (2016)
Image Analysis and Pattern Extraction of Proteins Classes from One-Dimensional Gels Electrophoresis
Int. J. of Bioscience, Biochemistry and Bioinformatics (JBBB), In Press

Teernstra, L., van der Putten, P.W.H., 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.Proceedings IDA 2016, LNCS

Fokkelman, M., Balcioglu, H.E., Klip, J.E., Yan, K., Verbeek, F.J., Danen, E.J.H., van de Water B. (2016)
Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour
Scientific Reports 6, Article number: 31707 (2016), doi:10.1038/srep31707

Cai F., Wang H., Tang X., Emmerich M., Verbeek F.J. (2016)
Fuzzy criteria in multi-objective feature selection for unsupervised learning.
Procedia Computer Science - Elsevier, 102:51-58

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.

Schomaker, L., Weber, A., Thijssen, M., Heerlien, M., Plaat, A., Nijssen, S., Verbeek F.J.,
Lew, M.,Gasso Micacle, E., Wolstencroft K., Suyver, E., Verheij, B., Wiering M., Dekker M.,
Kok, J., Roberts L., van den Herik, J.(2016)
Making Sense of Illustrated Handwritten Archives
Digital Humanities Eds(Maciej Eder, Jan Rybicki), Krakow 2016, pp 674 - 676.

Cao L., de Graauw M. , Yan K., Winkel L., Verbeek F.J. (2016)
Hierarchical classification strategy for Phenotype extraction from epidermal growth factor receptor endocytosis screening
BMC BioInformatics, 2016, 17:196, DOI 10.1186/s12859-016-1053-2

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: Proceedings IWBIO 2016, Granada, Spain, Eds (Ortuño, F., Rojas, I)
Lecture Notes in BioInformatics, Spinger, Heidelberg, pp 557-572

Xiong, Z., Verbeek, F.J. (2016)
Segmentation of Zebrafish Larvae Inhomogeneous 3DImages Using the Level-Set Method.
In Proceedings SPIE Electronic Imaging 2016, San Fransisco CA, USA (In Press).



M. Tleis (2016)
Objective Analsyis and Phenotype Characterization for Image-Based Gene expression in Yeast Cells.
PhD Thesis, Leiden University (July 2016)


2015 Top of page.

Bertens, L.M.F, Kleijn, J., Hille, S.C., Heiner, M., Koutny, M., Verbeek, F.J. (2015)
Modeling biological gradient formation: combining partial differential equations and Petri nets.
Natural Computing pp 1-11, DOI 10.1007/s11047-015-9531-4

Guo, Y, Veneman W., Spaink, H.P., Verbeek F.J. (2015)
Silhouette-based 3D Model for Zebrafish High-throughput Imaging.
In Proceedings Int. Conf. Image Processing Theory, Tools and Applications (eds.),
November 2015 Orleans, France. pp 403-408

Tleis, M., Verbeek, F.J. (2015)
Contour Expansion Algorithm Preprocessed by Hough Transform and Circular Shortest Path for Ovoid Objects.
In Proceedings Int. Conf. Image Processing Theory, Tools and Applications (eds.),
November 2015 Orleans, France. (In Press)

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 Proceedings Int. Conf. Image Processing Theory, Tools and Applications (eds.),
November 2015 Orleans, France. (In Press)

Tleis, M., Verbeek, F.J. (2015)
Machine Learning approach to discriminate Saccharomyces cerevisiae yeast cells using sophisticated image features.
Journal of integrative bioinformatics 12(3), 276(2015)

Tleis, M., Verbeek, F.J. (2015)
Machine Learning approach to segment Saccharomyces cerevisiae yeast cells.
In Proceedings Int. Conf. on Advances in BioMedical Engineering 2015 (ICABME 2015),
September 2015 Beirut, Lebanon. (In Press)

Carvalho R.V.,van den Heuvel J., Kleijn H.M., Verbeek F.J.(2015)
Coupling of Petri Net Models of the Mycobacterial Infection Process and Innate Immune Response.
Computation 2015, 3(2), 150-176; doi:10.3390/computation3020150

Coelho Camargo J., Verbeek FJ. (2015)
Pointing task evaluation of gestural interface interaction in 3D environment.
IADIS International Journal on WWW/Internet, Vol. 12, No.1, pp 113-130.



E. Larios Vargas (2015)
Design and development of a comprehensive data management platform for Cytomics, CytomicsDB. PhD Thesis, Leiden University (November 2015)

Viana de Carvalho, R. (2015)
Computational Modeling of Mycobacterium Infection and Innate Immune Response in Zebrafish.
PhD Thesis, Leiden University (October 2015).



2014 Top of page.

Slob J. Verbeek FJ. (2014)
Imaging Ontology, contributing to "reasonable" semantics for biomedical repositories.
In: Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014).
Eds (Bodenreider, Olivier; Oliveira, José Luis; Rinaldi, Fabio), Aveiro; pp 33-37, 2014
Zurich Open Repository and Archive (http://dx.doi.org/10.5167/uzh-98982)

Erica L Benard, Peter I Racz, Julien Rougeot, Alexander E Nezhinsky, Fons J Verbeek, Herman P Spaink, Annemarie H Meijer (2014)
Macrophage-Expressed Perforins Mpeg1 and Mpeg1.2 Have an Anti-Bacterial Function in Zebrafish.
Journal of Innate Immunity (DOI: 10.1159/000366103)2014

Zi Di, Maarten J D Klop, Vasiliki-Maria Rogkoti, Sylvia E Le Dévédec, Bob van de Water, Fons J Verbeek, Leo S Price, John H N Meerman (2014)
Ultra High Content Image Anlysis and Phenotype Profiling of 3D Cultured Micro-Tissues.
PLoS ONE 01/2014; 9(10)

Coelho Camargo J., Verbeek FJ. (2014)
The Leap Motion Controller in a 3D Virtual Environment: explorations and evaluations of pointing tasks.
Proc. Int Conf. Interfaces and Human Computer Interaction (IHCI 2014), Lisbon Portugal

Larios E., Zhang, Y., Cao, L., Verbeek FJ. (2014)
CytomicsDB: A Metadata-Based Storage and Retrieval Approach for High–Throughput Screening Experiments/
In Proceedings PRIB 2014 (M. Comin et al. (Eds.)). Springer Int. Publ. Switzerland; LNBI 8626, pp. 72–84, 2014

Carvalho, Rafael V., Kleijn, J., Verbeek, FJ. (2014)
A multi–scale extensive Petri Net model of the bacterial–macrophage interaction.
5th International Workshop on Biological Processes & Petri Nets. CEUR Workshop Proceedings Vol. 1159. 2014.

Gomez-Maureira, M., Teunisse, C., Schraffenberger, H.K., Verbeek F.J. (2014)
Illuminating Shadows: Introducing Shadow Interaction in Spatial Augmented Reality.
Proc. CHI–NL, 3-4-2014 The Hague, The Netherlands, pp 11-18

Camargo Coelho, J., Verbeek, F.J. (2014)
Pointing Task Evaluation of Gestural Interface Interaction in 3D Virtual Environment.
Proc. CHI–NL, 3-4-2014 The Hague, The Netherlands, pp 78-85.

Tleis M., Fons J. Verbeek, F.J. (2014)
Extracting contours of oval-shaped objects by Hough Transform and minimal path algorithms.
Proc. 6th Int. Conf. on Digital Image Processing (ICDIP2014) (Ed. C.M. Falco).

Lamers M.H.,van der Putten P.H.W., Verbeek F.J. (2014)(br> Observations on Tinkering in Scientific Education.
In: A. Cheok (Ed.), Entertaining the Whole World. Springer London
Human–Computer Interaction Series 2014, pp 137-145

Bomer N, den Hollander W, Ramos YF, Bos SD, van der Breggen R, Lakenberg N, Pepers BA, van Eeden AE, Darvishan A, Tobi EW, Duijnisveld BJ, van den Akker EB, Heijmans BT, van Roon-Mom WM, Verbeek FJ, van Osch GJ, Nelissen RG, Slagboom PE, Meulenbelt I. (2014)
Underlying molecular mechanisms of DIO2 susceptibility in symptomatic osteoarthritis.
Annals of Rheumatic Diseases 2014 (Apr 2. doi: 10.1136/annrheumdis-2013-204739)



Cao L.
Biological Model Representation and Analysis.
PhD Thesis, Leiden University (November 2014)



2013 Top of page.

Lamers M.H., Verbeek F.J., van der Putten P.H.W.(2013)
Tinkering in Scientific Education.
In: D. Reidsma, H. Katayose, and A. Nijholt (Eds.), ACE 2013, LNCS 8253, pp 568-571. Springer, 2013

Cao L., Verbeek F.J. (2013)
Analytical evaluation of algorithms for point cloud surface reconstruction using shape features.
J. Electron. Imaging. 22 (4), 043008 (October 21, 2013); doi: 10.1117/1.JEI.22.4.043008

Tleis M., Anemaet G., van Heusden P., Verbeek F.J. (2013)
Image analysis platform for yeast biologists.
Proc. 2nd Int. Conf. Advances in Biomedical Engineering (ICABME), pp.105-108. IEEE, 2013.

Cao L., Verbeek F.J. (2013)
Nature inspired phenotype analysis with 3D model representation optimization.
In: Ajith Abraham, Pavel Krömer, Václav Snášel (Eds). IBICA 2013. LNCS Vol. 237, pp 165-174, Springer 2014

de Graauw M., Cao L., Winkel L., Martine H.A.M. van Miltenburg M.H.A.M, le Dévédec S.E., Klop M., Yan K., Pont C., Rogkoti V-M, Tijsma A., Chaudhuri A., Lalai R., Price L., Verbeek F.J., van de Water B. (2013)
Annexin A2 depletion delays EGFR endocytic trafficking via cofilin activation and enhances EGFR signaling and metastasis formation.
Oncogene, 2013 Jun 24. doi: 10.1038/onc.2013.21

Kallergi, A., Verbeek F.J (2013)
Playfull Interfaces for Scientific Image data
In: Emerging Research and Trends in Interactivity and the Human-Computer Interface (Eds.Katherine Blashki & Pedro Isaias)
IGI Global, Hershey PA, USA. pp. 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 Vol. 13, 2013, 212-224


Nezhinsky A.E.
Pattern Recognition in High-Throughput Zebrafish Imaging.
PhD Thesis, Leiden University (November 2013)

Yan K.
Image Analysis and Platform Development for Automated Phenotyping in Cytomics
PhD Thesis, Leiden University (November 2013)

Di Z.
Development of Automatic Image Analysis Methods for High-Throughput and High-Content Screening.
PhD Thesis, Leiden University (December 2013)



2012 Top of page.

Di, Z., Herpers, B., Fredriksson, L., Yan, K., van de Water, B., Verbeek F.J., Meerman, J. (2012)
Automated analysis of NF-B nuclear translocation kinetics in high-throughput screening
Plos ONE Vol 7, #12

Carvalho R., Kleijn H., Meijer, A.H., Verbeek F.J (2012)
Modeling Innate Immune Response to early Mycobacterium Infection
Computational and Mathematical Methods in Medicine.
Volume 2012 (2012), Article ID 790482, 12 pages

Yan K., Verbeek F.J. (2012)
Segmentation for High-Throughput Image Analysis: Watershed Masked Clustering
In: ISoLA 2012, Part II, LNCS 7610 (T. Margaria, B. Steffen, and M. Merten (Eds.)),
Springer Berlin-Heidelberg 2012, pp. 25-41

Nezhinsky A.E., Verbeek F.J. (2012)
Efficient and Robust Shape Retrieval from Deformable Templates
In: ISoLA 2012, Part II, LNCS 7610 (T. Margaria, B. Steffen, and M. Merten (Eds.)),
Springer Berlin-Heidelberg 2012, pp. 42-55

Sanchez-Faddeev H., Emmerich M.T.M., Verbeek F.J., Henry A.H., Grimshaw S., Spaink H.P., van Vlijmen H.W., Bender A. (2012)
Using Multiobjective Optimization and Energy Minimization to Design an Isoform-Selective Ligand of the 14-3-3 Protein
In: ISoLA 2012, Part II, LNCS 7610 (T. Margaria, B. Steffen, and M. Merten (Eds.)),
Springer Berlin-Heidelberg 2012, pp. 12-24

de Bono, B., Kasteleyn, P., Potikanond, D., Kokash, N., Verbeek, F.J., and Grenon, P (2012)
Tissue Motifs and Multi-scale Transport Physiology
Proceedings OBML Workshop, Dresden September 27-28, 2012. (In Press)

Fitzsimons,C.P.,van Hooijdonk,L.W.A., 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., de Kloet,E.R., Meijer,O.C., Karst,H., Joels,M., Oitzl,M.S., & Vreugdenhil,E. (2012)
Knockdown of the Glucocorticoid Receptor Alters Functional Integration of Newborn Neurons in the Adult Hippocampus and Impairs Fear-motivated Behavior
J. Molecular Psychiatry (Accepted)

Kallergi A., Verbeek F.J.(2012)
Storytelling as Playful Exploration of Biological Image Data: Reviewing a Candidate Interaction Paradigm.
Proceedings of the IADIS Int. Conf. Interfaces and Human Computer Interaction 2012 (In Press)
Lisbon, Portugal, July 2012.

Nezhinsky A.E., Stoop E., Vasylevska A.A., van der Sar A., Verbeek F.J.(2012)
Spatial Analysis of Bacterial Infection Patterns in Zebrafish
In: Proceedings 21th Annual Belgian-Dutch Conference on Machine Learning (In Press)
May 2012, Gent, Belgium

LeDévédec S.E., Geverts B., de Bont H., Yan K., Verbeek F.J., Houtsmuller A.B., van de Water B. (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 (In Press)

Larios E., Zhang Y., Yan K., Z. Di, LeDévédec 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(Eds. Jing He, Xiaohui Liu, Elizabeth A. Krupinski, Guandong Xu ). Beijing, China April 2012. Springer (Heidelberg-Berlin), LNCS Vol. 7231, 76-87

Nezhinsky, AE., Stoop, E., van der Sar A., Verbeek FJ. (2012)
Numerical Analysis of Image Based High-Througput Zebrafish Infection Screens: Matching Meaning with Data
In: BIOINFORMATICS 2012 (Eds. Jan Schier, Carlos Correia, Ana Fred and Hugo Gamboa),Proceedings of the Int. Conf. on Bioinformatics Models, Methods and Algorithms Vilamoura, Algarve, Portugal, 1 - 4 February, 2012
ISBN: 978-989-8425-90-4. 257 - 262

Cao, L., Verbeek FJ. (2012)
Evaluation of surface reconstruction from point clouds by shape parameters.
In: 3D Image Processing (3DIP) and Applications 2012 (Eds. A.M. Baskurt, R.Sitnik)
Proceedings SPIE Vol. 8290,(SPIE Bellingham, WA, 2012). 82900G

Potikanond, D., Verbeek, FJ.(2012)
Visualization and analysis of 3D gene expression patterns in zebrafish using web services
In: Visualization and Data Analysis 2012 (Eds.Pak Chung Wong, David L. Kao, Ming C. Hao, Chaomei Chen, Robert Kosara, Mark A. Livingston, Jinah Park, Ian Roberts), Proceedings of SPIE Vol. 8294 (SPIE, Bellingham, WA, 2012) 829412.


Bertens L.M.F. (2012)
Computerised Modelling for Developmental Biology - An exploration with case studies.
PhD Thesis, Leiden University.(September 2012)

Kallergi A. (2012)
Connecting the Dots, Playful Interactions with Scientic Image Data in Repositories
PhD Thesis, Leiden University.(December 2012)



2011 Top of page.

Carvalho, RV., Davids, W., Meijer, AH., Verbeek, FJ (2011)
Spatio-Temporal Modeling and Simulation of Mycobacterium Pathogenesis using Petri Nets.
Proceedings BioNetics, York 2011 (Eds. NN)LNCS, Springer. (in Press)

Potikanond, D., Verbeek FJ. (2011)
3D Visual Integration of Spatio-Temporal Gene Expression Patterns on Digital Atlas of Zebrafish Embryo using Web Services
Proceedings Int. Conf. Advances in Communication and Information Technology (CIT 2011). Amsterdam 2011,56-62

Yan, K., Larios, E., LeDevedec S. van de Water, B., Verbeek FJ (2011)
Automation in Cytomics: Systematic Solution for Image Analysis and Management in High Throughput Sequences.
Proceedings IEEE Conf. Engineering and Technology (CET 2011), Vol 7. Shanghai 2011, 195-198

Dmitrieva, J. and Verbeek, FJ (2011)
Modular Approach for a new Ontology.
Proceedings of the Fifth International Workshop,WoMO 2011 (Eds. Kutz, O., Schneider, T.)
Volume 230 of Frontiers in Artificial Intelligence and Applications,
IOS Press (ISBN 978-1-60750-798-7)

Bertens, LMF., Slob, J., Verbeek, FJ (2011)
A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology.
Journal of Integrative Bioinformatics, 8(2), 167, 2011.

Zhang, Y., Stupka, E., Henkel, C., Jansen, HJ., Spaink, HP., Verbeek FJ.(2011)
Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data.
Journal of Integrative Bioinformatics, 8(2), 169, 2011.

Cao L., Yan K., Winkel L., de Graauw M., Fons J. Verbeek, FJ (2011) Pattern Recognition in High-Content Cytomics Screens for Target Discovery: Case Studies in Endocytosis PRIB 2011, Delft. LNCS, Springer 330-342

Qin,Y., Stokman, G., Yan, K., Ramaiahgari, S., Verbeek, FJ,. de Graauw, M., van de Water, B., Price, L. (2011)
Cyclic AMP signalling protects proximal tubular epithelial cells from cisplatin-induced apoptosis via activation of Epac.
British Journal of Pharmacology Volume 165, Issue 4b, pages 1137–1150, (Published February 2012)

Kallergi A., Verbeek F.J. (2011)
The Games Flickrites Play: An Investigation of Flickr-Based Gaming Activity with Special Focus on Opportunities For Exploratory Interaction.
Proceedings of the IADIS Int. Conf. Game and Entertainment Technologies 2011, 35-42.

de Vries, A., Oskam, O., Verbeek, FJ., (2011)
3-Dimengination: playing a puzzle with texture and projections
Proceedings CHI-sparks, CHI-NL conf., June 23, 2011, Arnhem, The Netherlands.

de Boer, F., Verbeek F.J. (2011)
Seeing through virtual windows
Proceedings CHI-sparks, CHI-NL conf., June 23, 2011, Arnhem, The Netherlands.

Damiano L.,Le Dévédec SE.,Di Stefano P., Repetto D., Lalai R., Truong H., Xiong JL., Danen EH, Kuan Yan K., Verbeek FJ., Attanasio F., Buccione R., van de Water B., Defilippi P.(2011)
p140Cap suppresses the invasive properties of highly metastatic MTLn3-EGFR cells via paired cortactin phosphorylation.
Oncogene Vol.30, (online: 4 July 2011,doi:10.1038/onc.2011.257)

Nezhinsky, A., Martorelli, I., Verbeek, FJ. (2011)
Detection of Developmental Stage in Zebrafish Embryos in a High throughput Processing Environment
Proceedings 20th Annual Belgian-Dutch Conference on Machine Learning,
May 2011, the Hague, the Netherlands

Stoop EJ, Schipper T, Rosendahl Huber SK, Nezhinsky AE, Verbeek FJ, Gurcha SS, Besra GS, Vandenbroucke-Grauls CM, Bitter W, van der Sar AM. (2011)
Zebrafish embryo screen for mycobacterial genes involved in the initiation of granuloma formation reveals a newly identified ESX-1 component.
Disease Model Mechanisms 2011, 526–536. doi:10.1242/dmm.006676

Hawrylycz, M., Baldock RA., Burger A., Hashikawa T.,Johnson GA., Martone M., Ng L., Lau C.,
Larsen SD., Nissanov J., Puelles L., Ruffins S., Verbeek FJ,. Zaslavsky I., Boline J.(2011)
Atlasing and Standardization in the Mouse Brain
PLoS Computational Biology 7(2): e1001065. doi:10.1371/journal.pcbi.1001065


Maarten H. Lamers and Fons J. Verbeek (Eds.),
Human-Robot Personal Relationships (HRPR 2010),
Lecture Notes of the Institute for Computer Sciences,
Social Informatics and Telecommunications Engineering, LNICST Vol. 59, 2011.

H. Jaap van den Herik, Maarten H. Lamers and Fons J. Verbeek (Eds.),
Special issue Understanding the Artificial,
International Journal of Social Robotics Vol.3, No.2, 2011.


Zhang Y. (2011)
Heterogeneous Data Analayis for Annotation of MicroRNA and Novel Genome Assembly
PhD Thesis Leiden University, November 2011

Dmitrieva, JB. (2011)
Aspects of Ontology Visualization and Integration.
PhD Thesis Leiden University, September 2011

Stupka, E. (2011)
Fish genomes: a powerful tool to uncover new functional elements in vertebrates.
PhD Thesis Leiden University, May 2011


2010 Top of page.

Dmitrieva, J., Verbeek F.J. (2010)
Creating a new Ontology: a Modular Approach.
Proceedings SWAT4LS (2010)

Kallergi, A., Verbeek, F.J. (2010)
Onto-Frogger: The Making Of.
Proceedings of the 6th Nordic Conference on Human-Computer Interaction (Oct.16–20, 2010)
Eds. Blandford, A., Gulliksen, J., Hvannberg, E.T., Larusdottir M.K., L-C Law, E., Vilhjalmsson H.H.
ACM Conf.Proceedings Series, ISBN 978-1-60558-934-3. Reykjavik, Iceland; pp 691-694

Kallergi, A., Verbeek, F.J. (2010)
Video Games for Collection Exploration: Games for and out of Data Repositories.
Proceedings of the 14th International Academic MindTrek Conference:
Envisioning Future Media Environments
Eds. Lugmayr A., Franssila H., Sotamaa O., Safran C., Aaltonen T.
ACM Digital Library, ISBN: 978-1-4503-0011-7. Tampere, Finland; pp 143 -146

Nezhinsky A., Verbeek F.J. (2010)
Pattern recognition for high throughput zebrafish imaging using genetic algorithm optimization.
5th IAPR Conference on Pattern Recognition in BioInformatics (PRIB 2010).
Lecture Notes in BioInformatics 6282 (eds. Dijkstra T., Tsivtsivadze, E., Heskes, T., Marchiori E.)
Springer, (Berlin - Heidelberg) 301-312

Bathoorn R., Welten M., Richardson M., Siebes A., Verbeek, F.J. (2010)
Frequent Episode Mining to support Pattern Analysis in Developmental Biology.
5th IAPR Conference on Pattern Recognition in BioInformatics (PRIB 2010).
Lecture Notes in BioInformatics 6282 (eds. Dijkstra T., Tsivtsivadze, E., Heskes, T., Marchiori E.)
Springer, (Berlin - Heidelberg) 253-263

LeDévédec S., Yan K., de Bont H., Ghotra V., Truong H.,
Danen E., Verbeek F.J., vande Water B.(2010)
A Systems Microscopy Approach to Understand Cancer Cell Migration and Metastasis.
journal Cellular and Molecular Life Sciences 2010;67(19):3219-3240

Bertens,L.M.F.,Kleijn,J., Koutny, M., Verbeek, F.J. (2010)
Modeling Gradients with Petri Nets
Workshop on Biological Processes and Petri Nets (BioPPN) - Petri Nets 2010, Braga (In Press)

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, 1-10, 2010 [PDF]

Zhang, Y., Verbeek, F.J. (2010)
Comparison and Integration of Target Prediction Algorithms for microRNA Studies.
Journal of Integrative Bioinformatics, 7(3):127, 1-12, 2010 [PDF]

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, Vol. 293,7; 1101-1114

Yan, K., Bertens, L.F.M., Verbeek, F.J. (2010)
Image Registraton and Realignment using Evolutionary Algorithms with High resolution 3D model from Human Liver.
Proceedings CGIM 2010 (Eds. Sappa,A.D.) 11th IASTED International Conference on Computer Graphics and Imaging. Innsbruck, Austria, February 2010: 679-014.

Dmitrieva, J., Verbeek, F.J. (2010)
Different Geometries in Ontology Visualization.
Visualization and Data Analysis (Eds.Jinah Park, Ming C. Hao, Pak C. Wong, Chaomei Chen)
Proceedings SPIE EI 2010, Volume 7530, San Jose, USA, January 2010. 7530007 - 12 pages

Nezhinsky, A., Kruisselbrink, J., Verbeek, F.J. (2010)
Convex Shape Retrieval from Edge Maps by the use of an Evolutionary Algorithm
1st International Conference on Bioinformatics, Valencia, Spain
Proceedings Bioinformatics 2010 (Eds.Fred,A., Filipe,J., & Gamboa,H.): 221-225

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 Preceedings. Report, (doi:10.1038/npre.2009.4000.1.) 43 pages.

2009 Top of page.

Kallergi, A., Verbeek, F.J. (2009)
Onto-Frogger: Playing with Semantic Structure.
Proceedings Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS)
CEUR-Workshop Proceedings ISSN 1613-0073, [PDF]
Volume 559 (Eds. Marshall, S.M.,Burger A.,Romano P.,Paschke A.,Splendiani A.)
Amsterdam, The Netherlands, November 20, 2009

Slob, J., Kallergi, A., Verbeek, F.J. (2009)
Observations on Semantic Annotation of Microscope Images for Life Sciences
Proceedings Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS)
CEUR-Workshop Proceedings ISSN 1613-0073, [PDF]
Volume 559 (Eds. Marshall, S.M.,Burger A.,Romano P.,Paschke A.,Splendiani A.)
Amsterdam, The Netherlands, November 20, 2009

Dmitrieva, J., Verbeek, F.J. (2009)
Integration of information from different ontologies.
Proceedings Workshop on Semantic Web Applications and Tools for Life Sciences (SWAT4LS)
CEUR-Workshop Proceedings ISSN 1613-0073, [PDF]
Volume 559 (Eds. Marshall, S.M.,Burger A.,Romano P.,Paschke A.,Splendiani A.)
Amsterdam, The Netherlands, November 20, 2009

Dmitrieva, J., Verbeek, F.J. (2009)
Node-Link and Containment Methods in Ontology Visualization.
Proceedings OWLED 2009, Washington DC, USA (http://www.webont.org/owled/2009/).

Papakonstantinou, C., Ioannis Panagiotou, I., Verbeek, F.J. (2009)
Tag Based Meta-Search for Browsing the Web: The TicTag Application.
Proceedings HCI 2009, People and Computers XXIII – Celebrating people and technology.
British Computer Society, United Kingdom: 354 -361

Giannoulis, S., Verbeek, F.J. (2009)
The happiness cube paradigm; eliciting happiness through sound, video, light and odor. Assessment of affective state with non-invasive techniques.
In: 4th International Workshop on Emotion and Computing,
in conj. with 32nd Annual Conference on Artificial Intelligence (KI2009), Paderborn, Germany: 7–14,

Zhang, Y., de Bruin, J.S., Verbeek, F.J. (2009)
Specificity Enhancement in microRNA Target Prediction through Knowledge Discovery.
(In: Machine Learning. (Eds. V. Kordic), (ISBN 978-953-7) (In Press)

Sebastiaan A. Brittijn, Suzanne J. Duivesteijn, Mounia Belmamoune, Laura F.M.Bertens, Wilbert Bitter, Joost D. de Bruijn, Danielle L. Champagne, Edwin Cuppen, Gert Flik, Christina M. Vandenbroucke-Grauls, Richard A.J. Janssen, Ilse M.L. de Jong, Edo Ronald de Kloet, Alexander Kros, Annemarie H. Meijer, Juriaan R. Metz, Astrid M. van der Sar, Marcel J.M. Schaaf, Stefan Schulte-Merker, Herman P. Spaink, Paul P. Tak, Fons J. Verbeek, Margriet J. Vervoordeldonk, Freek J. Vonk, Frans Witte, Huipin Yuan and Michael K. Richardson (2009)
Zebrafish development and regeneration: new tools for biomedical research.
Int. J. Dev. Biol. (2009) 53: 835-850

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: Cell Death and Disease Series (Eds.Backendorf,Noteborn,Tavassoli):
Proteins Killing Tumour Cells, ResearchSignPost, Kerala India, 291-315

Papakonstantinou, C., Ioannis Panagiotou, I., Verbeek, F.J. (2009)
Tag Based Meta-Search for Browsing the Web: The TicTag Application.
Proceedings CHI-NL, (Eds.: Verbeek, Lenior, Steen), Leiden, The Netherlands, pg. 93-101.

Dmitrieva, J., Verbeek, F.J. (2009)
Multi-view Ontology Visualization.
Proceedings 11th International Protege Conference [PDF]

Kallergi, A., Bei, Y., Verbeek, FJ. (2009)
The Ontology Viewer: Facilitating Image Annotation with Ontology Terms in the CSIDx imaging Database.
Proceedings VISS-WS 2009, CEUR-WS Proceedings Vol. 443 (http://ceur-ws.org)

Yan, K., Le Devedec, S., van de Water, B., Verbeek, F.J. (2009)
Cell Tracking and Data Analisys of in vitro Tumour Cells from Time-Lapse Image Sequences.
Proceedings VISAPP 2009 Volume 1, 281-287.

Roël, G., Gent Y.J., Peterson-Maduro, J., Verbeek, F.J. & Destrée, O. (2009)
Lef1 plays a role in patterning the mesoderm and ectoderm in Xenopus tropicalis.
International Journal of Developmental Biology 53: 81-89

Lenneke W.A van Hooijdonk, Muhammad Ichwan, Thomas F. Dijkmans, Theo G. Schouten, Fons J. Verbeek, Erno Vreugdenhil, Carlos P. Fitzsimons (2009)
Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression.
BMC Neuroscience 10:2 (13 January 2009)


Belmamoune, M. (2009)
Spatio-Temporal Framwork for Inegrative Analysis of Zebrafish developmental Studies.
PhD Thesis, Leiden University. ISBN 978-90-9024866

2008 Top of page.

Dmitrieva, J., Verbeek F.J. (2008)
Information Visualization from Ontology
Proc. 5th international conference on formal ontology in information systems. FOIS 2008

Umanski, D., Kosters, W., Verbeek, F.J., Schiller, N.O. (2008).
Integrating computer games in speech therapy for children who stutter.
Proc. 1st Workshop Child, Computer and Interaction. Crete-Greece, October 2008 (In Press)

Zhang, Y., de Bruin, J.S., Verbeek, F.J. (2008)
miRNA Target Prediction through Mining of miRNA Relationships.
Proc. 8th IEEE Int. Conf. on BioInformatics and BioEngineering, 2008. BIBE 2008; 1 - 6.

Belmamoune M. and 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, 2008

Richardson et al., with Bertens, LFM., Belmamoune, M., Verbeek, FJ.(2008)
Zebrafish Developmental Patterning: New Tools for Medical Research
International Journal of Developmental Biology (Accepted)

Zhang, Yanju, 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, Vol. 2 (1), 10 - 17.

2007 Top of page.

Bei, Y., Dmitrieva, J., Belmamoune, M., Verbeek, F.J. (2007)
Ontology Driven Image Search Engine.
Proc. SPIE Vol. 6506, MultiMedia Content Access: Algorithms & Systems (Eds Hanjalic, A., Schettini, R., Sebe, N.), 65060G-1,65060G-10

van der Putten, P., Bertens, L.F.M., Liu, J., Hagen, F., Boekhout T., Verbeek F.J. (2007)
Classification of Yeast Cells from Image Features to Evaluate Pathogen Conditions.
Proc. SPIE Vol. 6506, MultiMedia Content Access: Algorithms & Systems, Vol. 6506 (Eds Hanjalic, A., Schettini, R., Sebe, N.), 65060I-1,65060I-14

Kabli, S., Spaink, H.P., de Groot, H.J.M., Verbeek, F.J., Alia, A. (2007)
In Vivo magnetic resonance microimaging in adult zebrafish.
Proceedings International Society for Magnetic Resonance in Medicine 2007; 15: 1347.

Broekens, J., Kosters, W., Verbeek, F.J. (2007)
On Affect and Self-Adaptation: Potential Benefits of Valence-Controlled Action-Selection.
Proceedings of the 2nd. International Work-Conference on the Interplay between Natural and Artificial Computation (IWINAC 2007, Murcia, Spain) Lecture Notes in Computer Science, LNCS 4527 (pp. 357-366) Springer-Verlag.

Dmitrieva, J., Bei, Y., Verbeek, F.J. (2007)
Ontological Context Visualization. Proceedings OWLED2007.

Belmamoune, M., & Verbeek, F.J. (2007)
Developmental Anatomy Ontology of Zebrafish: an Integrative semantic framework.
Journal of Integrative Bioinformatics 4(3), 2007.

Broekens, J., Kosters, W., Verbeek, F.J. (2007)
Affect, Anticipation, and Adaptation: Affect-Controlled Selection of Anticipatory Simulation in Artificial Adaptive Agents.
Adaptive Behavior, 15(4), 397-422

Zhang, Yanju, 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 VOLUME 26 DECEMBER 2007 , Bangkok 2007,258-265.


Welten, M.C.M. (2007)
Spatio-temporal gene expression analysis from 3D in situ hybridisation images.
PhD Thesis, Leiden University.

Broekens, J.D. (2007)
Affect and Learning: A Computational Analysis
PhD Thesis, Leiden University.

2006 Top of page.

Bei Y, Belmamoune M and Verbeek FJ. (2006)
Ontology and image semantics in multimodal imaging: submission and retrieval.
Proc. SPIE Internet Imaging VII, Vol. 6061, 60610C1-C12, 2006.

Welten, M.C.M, De Haan, S., van den Boogert, N., Noordermeer, J.N., Lamers, G., Spaink, H.P., Meijer, A.H., Verbeek, F.J. (2006)
ZebraFISH: Fluorescent in situ hybridization protocol and 3D images of gene expression patterns. Zebrafish, Vol 3. #4, pp 465 - 476.

Kabli, S., Alia, A., Spaink, H.P., Verbeek, F.J., de Groot, H.J.M. (2006)
Magnetic Resonance Microscopy of the Adult Zebrafish.
Zebrafish, Vol 3., #4, pp 431 - 439

Braakman, N., Matysik, J., van Duinen, S.G., Verbeek, F.J., Schliebs, R., de Groot, H.J.M., Alia, A.(2006)
Longitudinal Assessment of Alzheimers ß-Amyloid Plaque Development in Transgenic Mice Monitored by In Vivo Magnetic Resonance Microimaging.
Journal of Magnetic Resonance Imaging VOl 24., 530 - 536.

Diks, S.H. Bink, R.J., van de Water, S., Joore, J., Verbeek, F.J., den Hertog J., Peppelenbosch, M.P., Zivkovic, D. (2006)
The novel gene, asb11: a regulator of the size of the neural progenitor compartment
Journal of Cell Biology Vol. 174(4); pp 581-592

Meuleman, W., Welten, M.C., Verbeek, F.J. (2006)
Construction of correlation networks with explicit time-slices using time-lagged, variable interval standard and partial correlation coefficients.
Lecture Notes in Computer Science, Volume 4216, Computational Life Sciences II, pp 236-246.

Belmamoune, M. and Verbeek, F.J. (2006)
Heterogeneous Information Systems: bridging the gap of time and space. Management and retrieval of spatio-temporal Gene Expression data.
In: InSCit2006 (Ed. Vicente P. Guerrero-Bote), Volume I "Current Research in Information Sciences and Technologies. Multidisciplinary approaches to global information systems", pp 53-58.

Belmamoune, M., Lindoorn, L. and Verbeek, F.J. (2006)
3D-VisQuS: A 3D Visual Query System integrating semantic and geometric models.
In: InSCit2006 (Ed. Vicente P. Guerrero-Bote), Volume II "Current Research in Information Sciences and Technologies. Multidisciplinary approaches to global information systems", pp 401-405.

Broekens, Joost, Kosters, Walter A., Verbeek, Fons J. (2006) On Emotion, Anticipation and Adaptation: Investigating the Potential of Affect-Controlled Selection of Anticipatory Simulation in Artificial Adaptive Agents. Adaptive Behavior (Special Issue on Mechanisms for Action Selection) (Accepted)

Mubarak Q., Dmitrieva J., Vermeulen T., Zhou Y., Groenewegen L., Basmagi, S., van Beek R., Verbeek F.J.(2006)
BioTune, a component based repository of BioInformatics teaching modules.
Proceedings MICTE 2006 (Eds. Méndez-Vilas, A., Solano Martin, A., Mesa Gonzalez, JA., Mesa Gonzalez, J.) "Current Developments in Technology-Assisted Education" , Sevilla 2006, FormaText, pp. 1186 -1192

Liu, J., van der Putten, P., Hagen, F., Chen, X., Boekhout, T., and F.J. Verbeek F.J. (2006),
Detecting virulent cells of Cryptococcus neoformans yeast: clustering experiments,
Proceedings ICPR Volume 1 IEEE Computer Society 2006, 1112- 1115, Hongkong , China.

2005 Top of page.

de Jonge H.W., de Bakker M.A.G., Verbeek F.J., Weijs W.A. (2005)
Embedding of large specimens in air sensitive glycol methacrylate: Prerequisites for multi-signal detection and high-resolution imaging.
Microscopy Research and Techniques 2005 Jan 1;66(1):25-30.

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 & Development 2005 (#1):18-28

Meijer AH, Verbeek FJ, Salas-Vidal E, Corredor-Adamez M, Bussman J, van der Sar AM, Otto GW, Geisler R, Spaink HP (2005).
Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection.
Mol Immunol. 2005 Jun;42(10):1185-203.

Corredor-Adámez M., Welten, M.C.M. , Spaink, H.P., Jeffery, J.E. ,Schoon, R.T. ,de Bakker, M.A.G. Bagowski, C.P., Meijer, A.H. , Verbeek, F.J. and Richardson. M.K. (2005).
Genomic annotation and transcriptome analysis of the Danio rerio hox complex with description of a novel member, hoxb13a.
Evolution & Development 2005 (#5):362-375

Joost Broekens and Fons J. Verbeek (2005)
Simulation, Emotion and Information Processing: Computational Investigations of the Regulative Role of Pleasure in Adaptive Behavior Modeling Natural Action Selection.
Proceedings MNAS Workshop, Edinburgh, UK.

2003-2004 Top of page.

Verbeek,F.J., Rodrigues,D.D., Spaink H., Siebes A (2004) Data submission of 3D image sets to a bio-molecular database using active shape models and a 3D reference model for projection. In: Proceedings SPIE 5304, Internet Imaging V. 13-23.

Richardson, M.K., Verbeek, F.J. (2003) New Directions in Comparative Embryology and the Nature of Developmental Characters. Animal Biology 53 303-311.

2001-2002 Top of page.

Verbeek, F.J., Boon, P.J., Sloetjes, H., van der Velde, R., de Vos, N. (2002). Visualization of complex data sets over Internet: 2D and 3D visualization of the 3D digital atlas of zebrafish development. Proceedings SPIE 4672, Internet Imaging III. 20-29

Verbeek, F.J., Boon, P.J. (2002) High Resolution 3D Reconstruction from serial sections. Microscope instrumentation, software design and its implementations. In: Proceedings SPIE 4621, Three Dimensional and Multi Dimensional Microscopy. Image Acquisition and Processing IX. 65-76

Voncken, F., Tjaden, J., Boxma, B., Akhmanova, A., Veenhuis, M., Huynen, M., Verbeek, F.J., Tielens, A.G.M., Haferkamp, I., Neuhaus, E., Vogels, G., & Hackstein. J.H.P. (2002) Multiple origins of hydrogenosomes: A mitochondrial-type ADP/ATP carrier in the hydrogenosomes of the anaerobic chytrid Neocallimastix sp. L2. Molecular Microbiology 264(3) 273-83.


Allen, S.P., Bogardi, J.-P., Barlow, A.J., Saaidia, A., Qayyum, S.R., Verbeek, F.J., Anderson, R.H., Francis West, P.H., Brown, N., and Richardson M.K. (2001). Misexpression of Noggin Leads to Septal Defects in the Outflow Tract of the Chick Heart. Developemental Biology 235, 98-109.

Qayyum, S.R., Webb, S., Brown, N., Anderson, R.H., Verbeek, F.J., and Richardson M.K. (2001). Septation and Valval Formation in the Outflow Tract of the Embryonic Chick Heart.
Anatomical Record. 264(3) 273-283

ten Berge, D., Brouwer, A., Korving, J., Reijnen, M.J., van Raaij, E.J., Verbeek, F.J., Gatfield, W., and Meijlink, F. (2001). Prx1 and Prx2 are upstream regulators of Sonic hedgehog, and control cell proliferation during mandibular arch morphogenesis. Development 128, 2929-2938.

van Raaij, E.J., ten Berge, D., Hage, W.J., Brouwer, A., Maintz, J.B.A., and Verbeek, F.J. (2001). Automated Topographical Cell Proliferation Analysis. Cytometry 45, 13-18.

1996-2000 Top of page.

Boon, P.J., Eminovic, N., de Vos, A., Buitendijk, B., van Raaij, E.J., Hage, W.J., and Verbeek, F.J. (2000)
A virtual lab-notebook for multi-dimensional microscope images. IEEE Comp.Soc.Press, Proceedings Information Visualisation 4, 187-191.

Verbeek, F.J., den Broeder, M.J., Boon, P.J., Buitendijk, B., Doerry, E., van Raaij, E.J., and Zivkovic, D. (2000)
A standard atlas of zebrafish embryonic development for projection of experimental data. Proceedings of SPIE 3964, 242-252.


van Raaij, E.J., Boon, P.J., Maintz, J.B.A., and Verbeek, F.J. (1999)
Composition of high resolution image mosaics for 3D reconstruction from serial sections. In Biomedical Image Registration. F. Pernus, S. Kovcic, H.S. Stiehl, and M.A. Viergever, eds. 262-271.

Verbeek, F.J., Lawson, K.A., and Bard, J.B.L. (1999)
Developmental BioInformatics: linking genetic data to virtual embryos. Int.J.Dev.Biol. 43, 761-771.

Verbeek, F.J. (1999)
Theory & Practice of 3D-reconstructions from serial sections. In Image Processing, A Practical Approach. R.A. Baldock and J. Graham, eds. (Oxford: Oxford University Press), pp. 153-195.


Nievelstein, R.A.J., Werf, v.d., Vermeij-Kiers, C., Verbeek, F.J., and Valk, J. (1998)
Normal and abnormal embryonic development of the anorectum in human embryos. Teratology 57, 70-78.

Verbeek, F.J. and Huijsmans, D.P. (1998)
A Graphical database for 3D reconstruction supporting 4 different Geometrical Representations. In Medical Image Databases. S.T.C. Wong, ed. (Boston: Kluwer Academic Publishers), pp. 117-144.


Baldock, R.A., Verbeek, F.J., and Vonesh, J.L. (1997).
3D reconstructions for graphical databases of gene-expression. Seminars in Cell & Developmental Biology 8, 499-507.

Griffini, P., Smorenburg, S.M., Verbeek, F.J., and van Noorden, C.J.F. (1997)
Three-Dimensional reconstruction of colon carcinoma metastasis in Liver. J.Microscopy 169, 375-382.

Lamers, W.H., Geerts, W.J., Jonker, A., Verbeek, F.J., Wagenaar, G.T., and Moorman, A.F. (1997)
Quantitative graphical description of portocentral gradients in hepatic gene expression by image analysis.
Hepatology 26, 398-406.



Verbeek, F.J. (1996). 3D reconstruction from serial sections, applications and limitations. Microscopy and Analysis 96-11, 33-35.

Roshani, H., Dabhoiwala, N.F., Verbeek, F.J., and Lamers, W.H. (1996). Functional Anatomy of the Human Uterovesical Junction. Anatomical Record 245, 645-651.


1992-1995 Top of page.

Verbeek, F.J. (1995). Three dimensional reconstruction from serial sections including deformation correction (Delft: Delft University of Technology).

Verbeek, F.J., Huijsmans, D.P., Baeten, R.W.A.M., Schoutsen, C.M., and Lamers, W.H. (1995). Design and implementation of a program for 3D-reconstruction from serial sections; a data-driven approach. Microscopy Research and Technique 30, 496-512.


Smith, A., Connell, M.G., Jackson, M., Verbeek, F.J., and Anderson, R.H. (1994).
Atrioventricular conduction system in hearts with muscular ventricular septal defects in the setting of complete transposition.
J.Thorac.Cardiovasc.Surg. 108, 9-16.

Wagenaar, G.T., Moorman, A.F.M., Chamuleau, R.A.F.M., Deutz, N.E.P., de Gier, C., de Boer, P.A.J., Verbeek, F.J., and Lamers, W.H. (1994).
Vascular branching pattern and zonation of gene-experession in the mammalian liver; a comparative study in rat, mouse, cynomolgus monkey, and pig.
Anatomical Record 239, 441-452.


Manders, E.M.M., Verbeek, F.J., and Aten, J.A. (1993). Measurement of co-localisation of objects in dual colour confocal images. J.Microscopy 169, 375-382.

Verbeek, F. J. and Mullikin, J. C. (1993) Extraction of Shape Features from the Vector Distance Transform. Proc. Int. Conf. Volume Image Processing., 149-151

Verbeek, F.J., de Groot, M.M., Huijsmans, D.P., Lamers, W.H., and Young, I.T. (1993). 3D BASE: A geometrical database system for the analysis and visualisation of 3D shapes obtained from parallel serial sections including three different geometrical representations. Computerised Medical Imaging and Graphics 17, 151-163.


Verbeek, F. J. Deformation correction using Euclidean contour distance maps. (1992)
IEEE Comp.Soc.Press, Proceedings 11th Int.Conf.on Pattern Recognition 3, 347-351.

Lamers, W.H., Wessels, A., Verbeek, F.J., Moorman, A.F.M., Viragh, S., Wenink, A.C.G., Gittenberger-de Groot, A.C., and Anderson, R.H. (1992).
New findings concerning ventricular septation in the human heart - their implications for maldevelopment. Circulation 86, 1194-1205.

Wessels, A., Vermeulen, J.L., Verbeek, F.J., Viragh, S., Kalman, F., Lamers, W.H., and Moorman, A.F. (1992).
Spatial distribution of "tissue-specific" antigens in the developing human heart and skeletal muscle. III. An immunohistochemical analysis of the distribution of the neural tissue antigen G1N2 in the embryonic heart; implications for the development of the atrioventricular conduction system. Anatomical Record 232, 97-111.


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