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)
Identiï¬cation 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.

Yanju Zhang
Heterogeneous Data Analayis for Annotation of MicroRNA and Novel Genome Assembly
PhD Thesis Leiden University, November 2011

Julia B. Dmitrieva
Aspects of Ontology Visualization and Integration.
PhD Thesis Leiden University, September 2011

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