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Items: 1 to 50 of 52

1.

Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio.

van Steijn L, Verbeek FJ, Spaink HP, Merks RMH.

Zebrafish. 2019 Aug;16(4):348-362. doi: 10.1089/zeb.2018.1712. Epub 2019 Jun 19.

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.

The embryonic expression patterns of zebrafish genes encoding LysM-domains.

Laroche FJ, Tulotta C, Lamers GE, Meijer AH, Yang P, Verbeek FJ, Blaise M, Stougaard J, Spaink HP.

Gene Expr Patterns. 2013 Oct;13(7):212-24. doi: 10.1016/j.gep.2013.02.007. Epub 2013 Apr 6.

PMID:
23567754
13.

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.

14.

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.

15.

Knockdown of the glucocorticoid receptor alters functional integration of newborn neurons in the adult hippocampus and impairs fear-motivated behavior.

Fitzsimons CP, van Hooijdonk LW, Schouten M, Zalachoras I, Brinks V, Zheng T, Schouten TG, Saaltink DJ, Dijkmans T, Steindler DA, Verhaagen J, Verbeek FJ, Lucassen PJ, de Kloet ER, Meijer OC, Karst H, Joels M, Oitzl MS, Vreugdenhil E.

Mol Psychiatry. 2013 Sep;18(9):993-1005. doi: 10.1038/mp.2012.123. Epub 2012 Aug 28.

PMID:
22925833
16.

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.

17.

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
18.

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
19.

p140Cap suppresses the invasive properties of highly metastatic MTLn3-EGFR cells via impaired cortactin phosphorylation.

Damiano L, Le Dévédec SE, Di Stefano P, Repetto D, Lalai R, Truong H, Xiong JL, Danen EH, Yan K, Verbeek FJ, De Luca E, Attanasio F, Buccione R, Turco E, van de Water B, Defilippi P.

Oncogene. 2012 Feb 2;31(5):624-33. doi: 10.1038/onc.2011.257. Epub 2011 Jul 4.

PMID:
21725361
20.

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.

21.

Analysis of cardiac development in the turtle Emys orbicularis (Testudines: Emidydae) using 3-D computer modeling from histological sections.

Bertens LM, Richardson MK, Verbeek FJ.

Anat Rec (Hoboken). 2010 Jul;293(7):1101-14. doi: 10.1002/ar.21162.

22.

Comparison and integration of target prediction algorithms for microRNA studies.

Zhang Y, Verbeek FJ.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-127.

PMID:
20375447
23.

Mining and analysing spatio-temporal patterns of gene expression in an integrative database framework.

Belmamoune M, Potikanond D, Verbeek FJ.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-128.

PMID:
20375442
24.

Zebrafish development and regeneration: new tools for biomedical research.

Brittijn SA, Duivesteijn SJ, Belmamoune M, Bertens LF, Bitter W, de Bruijn JD, Champagne DL, Cuppen E, Flik G, Vandenbroucke-Grauls CM, Janssen RA, de Jong IM, de Kloet ER, Kros A, Meijer AH, Metz JR, van der Sar AM, Schaaf MJ, Schulte-Merker S, Spaink HP, Tak PP, Verbeek FJ, Vervoordeldonk MJ, Vonk FJ, Witte F, Yuan H, Richardson MK.

Int J Dev Biol. 2009;53(5-6):835-50. doi: 10.1387/ijdb.082615sb. Review.

25.

Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression.

van Hooijdonk LW, Ichwan M, Dijkmans TF, Schouten TG, de Backer MW, Adan RA, Verbeek FJ, Vreugdenhil E, Fitzsimons CP.

BMC Neurosci. 2009 Jan 13;10:2. doi: 10.1186/1471-2202-10-2.

26.

Lef1 plays a role in patterning the mesoderm and ectoderm in Xenopus tropicalis.

Roël G, Gent YY, Peterson-Maduro J, Verbeek FJ, Destrée O.

Int J Dev Biol. 2009;53(1):81-9. doi: 10.1387/ijdb.072395gr.

27.

ZebraFISH: fluorescent in situ hybridization protocol and three-dimensional imaging of gene expression patterns.

Welten MC, de Haan SB, van den Boogert N, Noordermeer JN, Lamers GE, Spaink HP, Meijer AH, Verbeek FJ.

Zebrafish. 2006;3(4):465-76. doi: 10.1089/zeb.2006.3.465.

PMID:
18377226
28.

Magnetic resonance microscopy of the adult zebrafish.

Kabli S, Alia A, Spaink HP, Verbeek FJ, De Groot HJ.

Zebrafish. 2006;3(4):431-9. doi: 10.1089/zeb.2006.3.431.

PMID:
18377223
29.

Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database.

Belmamoune M, Verbeek FJ.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-92.

PMID:
20134060
30.

The novel gene asb11: a regulator of the size of the neural progenitor compartment.

Diks SH, Bink RJ, van de Water S, Joore J, van Rooijen C, Verbeek FJ, den Hertog J, Peppelenbosch MP, Zivkovic D.

J Cell Biol. 2006 Aug 14;174(4):581-92. Epub 2006 Aug 7.

31.

Genomic annotation and transcriptome analysis of the zebrafish (Danio rerio) hox complex with description of a novel member, hox b 13a.

Corredor-Adámez M, Welten MC, Spaink HP, Jeffery JE, Schoon RT, de Bakker MA, Bagowski CP, Meijer AH, Verbeek FJ, Richardson MK.

Evol Dev. 2005 Sep-Oct;7(5):362-75.

PMID:
16174031
32.

Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection.

Meijer AH, Verbeek FJ, Salas-Vidal E, Corredor-Adámez M, Bussman J, van der Sar AM, Otto GW, Geisler R, Spaink HP.

Mol Immunol. 2005 Jun;42(10):1185-203. Epub 2005 Jan 12.

PMID:
15829308
33.

Embedding of large specimens in glycol methacrylate: prerequisites for multi-signal detection and high-resolution imaging.

De Jonge HW, De Bakker MA, Verbeek FJ, Weijs WA.

Microsc Res Tech. 2005 Jan 1;66(1):25-30.

PMID:
15816030
34.

Gene expression and digit homology in the chicken embryo wing.

Welten MC, Verbeek FJ, Meijer AH, Richardson MK.

Evol Dev. 2005 Jan-Feb;7(1):18-28.

PMID:
15642086
35.

Automated topographical cell proliferation analysis.

van Raaij EJ, ten Berge D, Hage W, Brouwer A, Meijlink F, Maintz JB, Verbeek FJ.

Cytometry. 2001 Sep 1;45(1):13-8.

36.

Septation and valvar formation in the outflow tract of the embryonic chick heart.

Qayyum SR, Webb S, Anderson RH, Verbeek FJ, Brown NA, Richardson MK.

Anat Rec. 2001 Nov 1;264(3):273-83.

37.

Misexpression of noggin leads to septal defects in the outflow tract of the chick heart.

Allen SP, Bogardi JP, Barlow AJ, Mir SA, Qayyum SR, Verbeek FJ, Anderson RH, Francis-West PH, Brown NA, Richardson MK.

Dev Biol. 2001 Jul 1;235(1):98-109.

38.

Developmental bioinformatics: linking genetic data to virtual embryos.

Verbeek FJ, Lawson KA, Bard JB.

Int J Dev Biol. 1999;43(7):761-71. Review.

39.

Anatomy of ureterovesical junction and distal ureter studied by endoluminal ultrasonography in vitro.

Roshani H, Dabhoiwala NF, Verbeek FJ, Kurth KH, Lamers WH.

J Urol. 1999 May;161(5):1614-9.

PMID:
10210428
40.

Normal and abnormal embryonic development of the anorectum in human embryos.

Nievelstein RA, van der Werff JF, Verbeek FJ, Valk J, Vermeij-Keers C.

Teratology. 1998 Feb;57(2):70-8.

PMID:
9562679
41.

3-D Reconstructions for graphical databases of gene expression

Baldock RA, Verbeek FJ, Vonesch JL.

Semin Cell Dev Biol. 1997 Oct;8(5):499-507.

PMID:
9441955
42.

Quantitative graphical description of portocentral gradients in hepatic gene expression by image analysis.

Lamers WH, Geerts WJ, Jonker A, Verbeek FJ, Wagenaar GT, Moorman AF.

Hepatology. 1997 Aug;26(2):398-406.

PMID:
9252151
43.

Three-dimensional reconstruction of colon carcinoma metastases in liver.

Griffini P, Smorenburg SM, Verbeek FJ, van Noorden CJ.

J Microsc. 1997 Jul;187(Pt 1):12-21.

44.

Endoluminal ultrasound of the urethra: a new modality for cross-sectional imaging of the urethra?

Messelink EJ, Dabhoiwala NF, Vrij V, Verbeek FJ, Kurth K.

Tech Urol. 1996 Fall;2(3):159-64.

PMID:
9118425
45.

Functional anatomy of the human ureterovesical junction.

Roshani H, Dabhoiwala NF, Verbeek FJ, Lamers WH.

Anat Rec. 1996 Aug;245(4):645-51.

46.

Design and implementation of a database and program for 3D reconstruction from serial sections: a data-driven approach.

Verbeek FJ, Huijsmans DP, Baeten RJ, Schoutsen NJ, Lamers WH.

Microsc Res Tech. 1995 Apr 15;30(6):496-512.

PMID:
7599361
47.

Vascular branching pattern and zonation of gene expression in the mammalian liver. A comparative study in rat, mouse, cynomolgus monkey, and pig.

Wagenaar GT, Moorman AF, Chamuleau RA, Deutz NE, De Gier C, De Boer PA, Verbeek FJ, Lamers WH.

Anat Rec. 1994 Aug;239(4):441-52.

PMID:
7978367
48.

Atrioventricular conduction system in hearts with muscular ventricular septal defects in the setting of complete transposition.

Smith A, Connell MG, Jackson M, Verbeek FJ, Anderson RH.

J Thorac Cardiovasc Surg. 1994 Jul;108(1):9-16.

PMID:
8028385
49.

The functional anatomy of the ureterovesical junction.

Thomson AS, Dabhoiwala NF, Verbeek FJ, Lamers WH.

Br J Urol. 1994 Mar;73(3):284-91.

PMID:
8162508
50.

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