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Items: 1 to 20 of 33

1.

Towards Controlled Single-Molecule Manipulation Using "Real-Time" Molecular Dynamics Simulation: A GPU Implementation.

van Vreumingen D, Tewari S, Verbeek F, van Ruitenbeek JM.

Micromachines (Basel). 2018 May 29;9(6). pii: E270. doi: 10.3390/mi9060270.

2.

An efficient and robust hybrid method for segmentation of zebrafish objects from bright-field microscope images.

Guo Y, Xiong Z, Verbeek FJ.

Mach Vis Appl. 2018;29(8):1211-1225. doi: 10.1007/s00138-018-0934-y. Epub 2018 May 10.

3.

Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging.

Guo Y, Veneman WJ, Spaink HP, Verbeek FJ.

Biomed Opt Express. 2017 Apr 26;8(5):2611-2634. doi: 10.1364/BOE.8.002611. eCollection 2017 May 1.

4.

Fast Post-Processing Pipeline for Optical Projection Tomography.

Tang X, van der Zwaan DM, Zammit A, Rietveld KFD, Verbeek FJ.

IEEE Trans Nanobioscience. 2017 Jul;16(5):367-374. doi: 10.1109/TNB.2017.2706967. Epub 2017 May 23.

PMID:
28541218
5.

Modeling biological gradient formation: combining partial differential equations and Petri nets.

Bertens LM, Kleijn J, Hille SC, Heiner M, Koutny M, Verbeek FJ.

Nat Comput. 2016;15(4):665-675. Epub 2015 Oct 31.

6.

Cellular adhesome screen identifies critical modulators of focal adhesion dynamics, cellular traction forces and cell migration behaviour.

Fokkelman M, Balcıoğlu HE, Klip JE, Yan K, Verbeek FJ, Danen EH, van de Water B.

Sci Rep. 2016 Aug 17;6:31707. doi: 10.1038/srep31707.

7.

Hierarchical classification strategy for Phenotype extraction from epidermal growth factor receptor endocytosis screening.

Cao L, Graauw Md, Yan K, Winkel L, Verbeek FJ.

BMC Bioinformatics. 2016 May 3;17(1):196. doi: 10.1186/s12859-016-1053-2.

8.

Machine Learning approach to discriminate Saccharomyces cerevisiae yeast cells using sophisticated image features.

Tleis MS, Verbeek FJ.

J Integr Bioinform. 2015 Oct 6;12(3):276. doi: 10.2390/biecoll-jib-2015-276.

PMID:
26673792
9.

Ultra high content image analysis and phenotype profiling of 3D cultured micro-tissues.

Di Z, Klop MJ, Rogkoti VM, Le Dévédec SE, van de Water B, Verbeek FJ, Price LS, Meerman JH.

PLoS One. 2014 Oct 7;9(10):e109688. doi: 10.1371/journal.pone.0109688. eCollection 2014.

10.

Macrophage-expressed perforins mpeg1 and mpeg1.2 have an anti-bacterial function in zebrafish.

Benard EL, Racz PI, Rougeot J, Nezhinsky AE, Verbeek FJ, Spaink HP, Meijer AH.

J Innate Immun. 2015;7(2):136-52. doi: 10.1159/000366103. Epub 2014 Sep 19.

11.

Underlying molecular mechanisms of DIO2 susceptibility in symptomatic osteoarthritis.

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.

Ann Rheum Dis. 2015 Aug;74(8):1571-9. doi: 10.1136/annrheumdis-2013-204739. Epub 2014 Apr 2.

12.

Modeling innate immune response to early Mycobacterium infection.

Carvalho RV, Kleijn J, Meijer AH, Verbeek FJ.

Comput Math Methods Med. 2012;2012:790482. doi: 10.1155/2012/790482. Epub 2012 Dec 9.

13.

Automated analysis of NF-κB nuclear translocation kinetics in high-throughput screening.

Di Z, Herpers B, Fredriksson L, Yan K, van de Water B, Verbeek FJ, Meerman JH.

PLoS One. 2012;7(12):e52337. doi: 10.1371/journal.pone.0052337. Epub 2012 Dec 27.

14.

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.

Le Dévédec SE, Geverts B, de Bont H, Yan K, Verbeek FJ, Houtsmuller AB, van de Water B.

J Cell Sci. 2012 Oct 1;125(Pt 19):4498-506. doi: 10.1242/jcs.104273. Epub 2012 Jul 5.

15.

Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.

Zhang Y, Stupka E, Henkel CV, Jansen HJ, Spaink HP, Verbeek FJ.

J Integr Bioinform. 2011 Sep 12;8(2):169. doi: 10.2390/biecoll-jib-2011-169.

PMID:
21908900
16.

A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology.

Bertens LM, Slob J, Verbeek FJ.

J Integr Bioinform. 2011 Sep 8;8(2):167. doi: 10.2390/biecoll-jib-2011-167.

PMID:
21900708
17.

cAMP signalling protects proximal tubular epithelial cells from cisplatin-induced apoptosis via activation of Epac.

Qin Y, Stokman G, Yan K, Ramaiahgari S, Verbeek F, de Graauw M, van de Water B, Price LS.

Br J Pharmacol. 2012 Feb;165(4b):1137-50. doi: 10.1111/j.1476-5381.2011.01594.x.

18.

Zebrafish embryo screen for mycobacterial genes involved in the initiation of granuloma formation reveals a newly identified ESX-1 component.

Stoop EJ, Schipper T, Rosendahl Huber SK, Nezhinsky AE, Verbeek FJ, Gurcha SS, Besra GS, Vandenbroucke-Grauls CM, Bitter W, van der Sar AM.

Dis Model Mech. 2011 Jul;4(4):526-36. doi: 10.1242/dmm.006676. Epub 2011 Mar 3.

19.

Digital atlasing and standardization in the mouse brain.

Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, Martone M, Ng L, Lau C, Larson SD, Nissanov J, Puelles L, Ruffins S, Verbeek F, Zaslavsky I, Boline J.

PLoS Comput Biol. 2011 Feb 3;7(2):e1001065. doi: 10.1371/journal.pcbi.1001065. No abstract available. Erratum in: PLoS Comput Biol. 2011 Feb;7(2). doi: 10.1371/annotation/22c5808a-56cf-46e5-ba1b-456e838a5428. Larsen, Stephen D [corrected to Larson, Stephen D].

20.

Systems microscopy approaches to understand cancer cell migration and metastasis.

Le Dévédec SE, Yan K, de Bont H, Ghotra V, Truong H, Danen EH, Verbeek F, van de Water B.

Cell Mol Life Sci. 2010 Oct;67(19):3219-40. doi: 10.1007/s00018-010-0419-2. Epub 2010 Jun 18. Review.

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