Output Cyttron I

A microfluidic cell observation platform, replacing Identifying relevant folding units in large molecular complexes
  • Patent application: A new microfluidic chip design allows for a side connection of many capillaries to one microfluidic chip resulting in a system that can be analysed under any type of light based microscope.
  • Patent application: Methods for immobilizing microvesicles, means and methods for detecting them, and uses thereof
  • Patent application: A cell cultivation receptacle and related apparatuses.
Characterizing protein structure and dynamics in crowded solutions
  • Protein Nanocrystallization, Dilyana Georgieva, Jan Pieter Abrahams, Maxim E. Kuil. Springer Series in Biophysics, J.L.R. Arrondo and A. Alonso, Advanced Techniques in Biophysics Springer-Verlag Berlin Heidelberg 2006.
  • Nano-dispensing by electrospray for biotechnology, Maxim E. Kuil, Jan Pieter Abrahams, Jan C. M. Marijnissen, Biotechnol. J. 2006, 1, 969–975
  • H. E. Lindfors, P. E. de Koning, J. W. Drijfhout, B. Venezia and M. Ubbink (2008) Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR J. Biomol. NMR 41, 157-167
  • Takahashi, S. Kuroiwa, H. E. Lindfors, L. A. Ndamba, Y. Hiruma, T. Yajima, N. Okishio,
    M. Ubbink and S. Hirota (2009) Modulation of protein-ligand interactions by photocleavage of a cyclic peptide using phosphatidylinositol 3-kinase SH3 domain as model system J. Peptide Sci. in press
  • H. E. Lindfors, J. W. Drijfhout, Y. Arendsen and M. Ubbink (2009) Dynamics in a high-affinity peptide-protein complex. Submitted
  • Thesis H.E. Lindfors; Src homology domain-mediated protein interactions, 2010.
Characterizing insoluble proteins and protein complexes by solid state NMR
  • van Gammeren, A.J., Buda, F., Hulsbergen, F.B., Kiihne, S., Hollander, J.G., Egorova-Zachernyuk, T.A., Fraser, N.J., Cogdell, R.J. and de Groot, H.J.M., Selective chemical shift assignment of B800 and B850 bacteriochlorophylls in uniformly [C-13,N-15]-labeled light-harvesting complexes by solid-state NMR spectroscopy at ultra-high magnetic field, Journal Of The American Chemical Society 127 (9) (2005) 3213-3219.
  • van Gammeren, A.J., Hulsbergen, F.B., Hollander, J.G. and de Groot, H.J.M., Residual backbone and side-chain C-13 and N-15 resonance assignments of the intrinsic transmembrane light-harvesting 2 protein complex by solid-state Magic Angle Spinning NMR spectroscopy, Journal Of Biomolecular Nmr 31 (4) (2005) 279-293.
  • Karawajczyk, A. and Buda, F., The metal bonding domain of the antitumor drug Fe(II)-bleomycin: a DFT investigation, Journal Of Biological Inorganic Chemistry 10 (1) (2005) 33-40.
  • Kiihne, S.R., Creemers, A.F.L., de Grip, W.J., Bovee-Geurts, P.H.M., Lugtenburg, J. and de Groot, H.J.M., Selective interface detection: Mapping binding site contacts in membrane proteins by NMR spectroscopy, Journal Of The American Chemical Society 127 (16) (2005) 5734-5735.
  • Kiihne, S.R., Creemers, A.F.L., Lugtenburg, J. and de Groot, H.J.M., Accurate CSA measurements from uniformly isotopically labeled biomolecules at high magnetic field, Journal Of Magnetic Resonance 172 (1) (2005) 1-8.
  • Ganapathy S, v. Gammeren AJ, Hulsbergen FB, de Groot HJM (2007) Probing secondary, tertiary and quaternary structure along with protein-cofactor interactions for a helical transmembrane protein complex through 1H spin diffusion with MAS NMR, J. of American Chemical Soc., 129, 1504-1505
  • Agrawal P, Hofmann MW, Meeuwenoord NJ, Filippov DV, Stalz H, Hulsbergen F, Langosh D, Overkleeft HS, de Groot HJM (2007) Solid Phase Synthesis and Purification of a Set of Uniformly 13C, 15N Labelled de novo Designed Membrane Fusogenic Peptides, Journal of Peptide Science, 13, 75-80
  • Agrawal P, Kiinhe SR, Hulsbergen F, Hofmann M, Langosh D, de GrootHJM. Solid State NMR Investigation of the Interaction between Biomimetic Lipid Bilayers and a de novo Designed Fusogenic Peptide, ChemBioChem in press
  • Cherepanov AV, Doroshenko EV, Matysik J, de Vries S, de Groot HJM (2008). Reply to Hengge: On the P-31 chemical shifts of the phosphorane compounds, Proceedings of the National Academy of Sciences of the United States of America, 105, 46, E85-E85
  • Cherepanov AV, Doroshenko EV, Matysik J, de Vries S, de Groot HJM (2008). The associative nature of adenylyl transfer catalyzed by T4 DNA ligase, Proceedings of the National Academy of Sciences of the United States of America, 105, 25, 8563-8568
  • Cherepanov AV, Doroshenko EV, Matysik J, de Vries S, de Groot HJM (2008). A view on phosphate ester photochemistry by time-resolved solid state NMR. Intramolecular redox reaction of caged ATP, Physical Chemistry Chemical Physics, 10, 45, 6820-6828
Simultaneous refinement X-ray structures & reciprocal space density modification
  • Skubak P, Ness SR, Pannu NS (2005) Acta Cryst D61, 1626-1635
  • Ness SR, Sikharulidze I, de Graaff RAG, Pannu NS (2005) CCP4 newsletter 42:5, Computer program for multivariate, reciprocal space density modification
  • Skubak, P. PhD thesis Leiden University
  • Paspaleva, K, Thomassen, E, Pannu, NS, Iwai, NS, Moolenaar, GF, Goosen, N, Abrahams, JP (2007) ‘Crystal structure of the DNA Repair Enzyme UV Damage Endonuclease’, Structure, 2007 Oct;15(10):1316-24
  • Involvement of a carboxylated lysine in UV damage endonuclease. Meulenbroek EM, Paspaleva K, Thomassen EA, Abrahams JP, Goosen N, Pannu NS. Protein Sci. 2009 Mar;18(3):549-58.
  • Crystal structure of chlorite dismutase, a detoxifying enzyme producing molecular oxygen. de Geus DC, Thomassen EA, Hagedoorn PL, Pannu NS, van Duijn E, Abrahams JP. J Mol Biol. 2009 Mar 20;387(1):192-206. Epub 2009 Jan 27.
Integrating single protein studies with low resolution studies of assemblies & single particle analysis
  • Plaisier JR, Jiang L, Abrahams JP. (2007). Cyclops: New modular software suite for Cryo-EM. Journal of Structural Biology 157, 19-27
  • D. Georgieva, M.E. Kuil, T. Oosterkamp, H.W. Zandbergen and J.P. Abrahams. Heterogeneous nucleation of 3D protein nano-crystals, Acta Crystallographica Section D, Volume 63, Issue 5, Page 564-570, May 2007.
  • Abrahams JP (2009) “The Strong Phase Object Approximation May Allow Extending Crystallographic Phases of Dynamical Electron Diffraction Patterns of 3D Protein Nano-Crystals”, Zeitschr. F. Kristallografie in the press
  • van Haren J, Draegestein K, Keijzer N, Abrahams JP, Grosveld F, Peeters PJ, Moechars D, Galjart N  (2009) “Mammalian Navigators are Microtubule Plus-End Tracking Proteins that can Reorganize the Cytoskeleton to Induce Neurite-Like Extensions” Cell Motility and the Cytoskeleton 66, 824-838
  • Jiang LH, Schaffitzel C, Bingel-Erlenmeyer R, Ban N, Korber P, Koning RI, de Geus DC, Plaisier JR, Abrahams JP (2009) “Recycling of Aborted Ribosomal 50S Subunit-Nascent Chain-tRNA Complexes by the Heat Shock Protein Hsp15” J. Mol. Biol. 386, 1357-1367
  • Jiang LH, Georgieva D, Zandbergen HW, Abrahams JP (2009) “ Unit-cell determination from randomly oriented electron-diffraction patterns” Acta Crystallogr. D65, 625-632
  • Zovko S, Abrahams JP, Koster AJ, Galjart N, Mommaas AM (2008)   Microtubule plus-end conformations and dynamics in the periphery of interphase mouse fibroblasts” Mol. Biol. Cell 19, 3138-3146
  • Thesis: L. Jiang (2009)  Image Processing and Computing in Structural Biology
Visualizing cell – and membrane surfaces
  • Stamouli, J.W.M. Frenken, T.H. Oosterkamp, R.J. Cogdell and T.J. Aartsma, The electron conduction of photosynthetic protein complexes embedded in a membrane, FEBS letters 560 (2004) 109-114
  • M. J. Rost, L. Crama, P Schakel, E. van Tol, G.B.E.M. van Velzen-Williams, C.F. Overgauw, H. ter Horst, H. Dekker, B. Okhuijsen, M. Seynen, A. Vijftigschild, Patrick Han, A.J. Katan, K. Schoots, R. Schumm, W. van Loo, T. Oosterkamp, J.W.M. Frenken;  Rev. Sci. Instr. 76, 053710-1 (2005) ” SPMs go video rate and beyond "
  • Thesis Dionne Klein, Leiden University (Nov 2004).
  • Dionne C.G. Klein, Cordula M. Stroh, Henriette Jensenius, Maarten van Es, A.S.M. Kamruzzahan, Amalia Stamouli, Hermann J. Gruber, Tjerk H. oosterkamp, Peter Hinterdorfer, Covalent immobilization of single proteins on mica for molecular recognition force microscopy, ChemPhysChem 4 (2003) 1367
  • D. Georgieva, M.E. Kuil, T. Oosterkamp, H.W. Zandbergen and J.P. Abrahams. Heterogeneous nucleation of 3D protein nano-crystals, Acta Crystallographica Section D, Volume 63, Issue 5, Page 564-570, May 2007.
  • Erwin C. Heeres, Erik P. A. M. Bakkers, Aarnoud L. Roest, Monja Kaiser, Tjerk H. Oosterkamp and Niels de Jonge, 
  • Electron emission from individual semiconductor nanowires, NANO LETTERS 7 (2): 536-540 FEB 2007
  • W. Merlijn van Spengen and Tjerk H. Oosterkamp, A sensitive electronic capacitance measurement system to measure comb drive motion of surface micromachined MEMS devices, J. Micromech. Microeng. 17 (2007) 828-834.
  • A.J. Katan, T.H. Oosterkamp: J. Phys. Chem. C 112, 9769 (2008) “Measuring hydrophobic interactions with three-dimensional nanometer resolution” Thesis Allard Katan, Leiden University (Nov 2007)
  • Thesis Maarten van Es, Leiden University (Dec 2008)
Tomography of single cells
  • Wang L, Humbel BM, Roubos EW. 2005. High-pressure freezing followed by cryosubstitution as a tool for preserving high-quality ultrastructure and immunoreactivity in the Xenopus laevis pituitary gland. Brain Res Protoc 15, 155-163.
  • De Haard HJW, Bezemer S, Ledeboer AM, Müller WH, Boender PJ, Moineau S, Coppelmans M-C, Verkleij AJ, Frenken LGJ, Verrips CT. 2005. Llama antibodies against a lactococcal protein located at the tip of the phage tail prevent phage infection. J Bacteriol 187:4531-4541.
  • Geerts WJC, Koster AJ, Verkleij AJ, Humbel BM. 2006. Electron microscopy tomography and localization of proteins and macromolecular complexes in cells. In: Golemis E and Adams P, editors. Protein-protein interactions: a molecular cloning manual, 2nd edition, New York, Cold Spring Harbor Protocols., ISBN 0-87969-722-9, Chapter 36, pp. 715-739
  • Rodriguez D, Barcena M, Mobius W, Schleich S, Esteban M, Geerts WJC, Koster AJ, Gareth Griffiths G, Krijnse Locker J. 2006. A vaccinia virus lacking A10L: viral core proteins accumulate on structures derived from the endoplasmic reticulum, Cellular Microbiology, 8, 427-437
  • Schwarz H, Humbel BM. 2007. Correlative Light and Electron Microscopy using Immunolabeled Resin Sections In: Electron Microscopy: Methods and Protocols, Methods in Molecular Biology, Kuo J (ed), Vol 117, Humana Press, Totowa, 369:229-56.
  • Jiménez N, Humbel BM, van Donselaar E, Verkleij AJ, Burger KNJ. 2006. Aclar discs a versatile substrate for routine high-pressure freezing of mammalian monolayers. J Microsc, 221, 216-223.
  • Dagmar Zeuschner, Willie J.C. Geerts, Elly van Donselaar, Jan Slot, Bruno M Humbel, Abraham J. Koster, Judith Klumperman. 2006. Immuno-electron tomography reveals the existence of free COPII-coated vesicular and tubular transport carriers. Nature Cell Biology (2006) Vol. 8 Nr 4 pp 377 – 383.
  • Braet F, Wisse E, Bomans P, Frederik P, Geerts W, Koster AJ, Soon L and Ringer S. Contribution of High-Resolution Correlative Imaging Techniques in the Study of the Liver Sieve in Three-Dimensions. Micros. Res. And Techn. 70:230–242 (2007)
  • Koster AJ and Barcena M. Cryotomography: Low-dose Automated Tomography of Frozen-hydrated Specimens. Book chapter in Electron Tomography (Ed. J. Frank). In press (2006).
  • Lazaro-Dieguez F, Jimenez N, Barth H, Koster AJ, Renau-Piqueras J, Llopis, JL, Burger KN, Egea G. Actin filaments are involved in the maintenance of Golgi cisternae morphology and intra-Golgi pH. Cell Motil Cytoskeleton. 2006 Dec;63(12):778-91
  • Grabenbauer M, Geerts WJ, Fernadez-Rodriguez J, Hoenger A, Koster AJ, Nilsson T.  Correlative microscopy and electron tomography of GFP through photooxidation. Nat Methods. 2005 Nov;2(11):857-62.
  • Jack A. Valentijn, Linda F. van Driel, Karen A. Jansen, Karine M. Valentijn, Abraham J. Koster. Correlative Light and Electron Microscopy: Getting the Best of Two Worlds. Chapter in Biomedical Imaging, edited by Reinzer Salzer. Submitted (2007).
  • Lebbink MN, Geerts WJ, van der Krift TP, Bouwhuis M, Hertzberger LO, Verkleij AJ, Koster AJ.  Template matching as a tool for annotation of tomograms of stained biological structures. J Struct Biol. 158:327-335 (2007).
  • A.E. Yakushevska, M.N. Lebbink, W.J.C. Geerts,,L. Spek, E.G. van Donselaar, K.A. Jansen, B.M. Humbel, J.A. Post, A.J. Verkleij and A.J. Koster. STEM Tomography in cell biology 159: 381–391 (2007).
  • Cveta Tomova, Willie J.C. Geerts, Thomas Müller-Reichert, Rolf Entzeroth and Bruno M. Humbel. New comprehension of the apicoplast of Sarcocystis by transmission electron tomography Biology of the Cell (2006) Vol 98 (9), 535-545
  • Combined 3D structural analysis of the anammoxosome: a membrane-bounded intracytoplasmic compartment in anammox bacteria. Laura van Niftrik, Willie J. C. Geerts, Elly G. van Donselaar, Bruno M. Humbel, Alevtyna Yakushevska, Arie J. Verkleij, Mike S. M. Jetten and Marc Strous, J. Struc Biol, 2008 190:708-717.
  • Van Donselaar E, Posthuma G, Zeuschner D, Humbel BM, Slot JW. 2007. Immunogold labeling of cryo-sections from high-pressure frozen cells. Traffic: in press.
  • Laser microdissection of fungal septa as visualized by scanning electron microscopy. Kenneth G.A. van Driel, Teun Boekhout, Han A.B. Wösten, Arie J. Verkleij, Wally H. Müller, Fungal Genetics and Biology, 44:466-473 (2007).
  • Degradation of the hexose transporter Hxt5p in Saccharomyces cerevisiae. Van Suylekom D, van Donselaar E, Blanchetot C, Nguyen Do Ngoc L, Humbel BM, Boonstra J. 2007. Biol Cell 99:13-23.
  • Agronskaia AV, Valentijn JA, van Driel LF, Schneijdenberg CTWM, Humbel BM, van Bergen en Henegouwen PMP, Verkleij AJ, Koster AJ, Gerritsen HC. 2008. Integrated fluorescence and transmission electron microscopy. J Struct Biol 164:183-189.
  • De Winter DAM, Schneijdenberg CTWM, Lebbink MN, Lich B, Verkleij AJ, Drury MR, Humbel BM. 2009. Tomography of insulating biological and geological materials using focused ion beam (FIB) sectioning and low kV BSE imaging. J Microsc 233:372–383.
  • Desbois G, Urai JL, Burkhardt C, Drury MR, Hayles M, Humbel BM. 2008. Cryogenic vitrification and 3D serial sectioning using high cryo FIB SEM technology for brine-filled grain boundaries in Halite: first results. Geofluids 8:60-72.
  • Jiménez N, Vocking K, van Donselaar E, Humbel BM, Post JA, Verkleij AJ. 2009. Tannic acid-mediated osmium impregnation after freeze-substitution: A strategy to enhance membrane contrast for electron tomography. J Struct Biol 166:103-106.
  • Karreman MA, Agronskaia AV, Verkleij AJ, Cremers FFM, Gerritsen HC, Humbel BM. 2009. Discovery of a new RNA containing nuclear structure in UVC-induced apoptotic cells by integrated laser electron microscopy. Biol Cell 101:287-299.
  • Lebbink MN, van Donselaar E, Humbel BM, Hertzberger LO, Post JA, Verkleij AJ. 2009. Induced membrane domains as visualized by electron tomography and template matching. J Struct Biol: 166:156-161.
  • Schwarz H, Humbel BM. 2008. Correlative light and electron microscopy. In Handbook of Cryo-Preparation Methods for Electron Microscopy, Cavalier A, Spehner D, Humbel BM. (eds). CRC Press: Boca Raton; 527-555.
  • Studer D, Humbel BM, Chiquet M. 2008. Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution. Histochem Cell Biol 130:877-889.
  • van Dooren GG, Reiff SB, Tomova C, Meissner M, Humbel BM, Striepen B. 2009. A novel dynamin-related protein has been recruited for apicoplast fission in Toxoplasma gondii. Curr Biol 19:267–276.
  • Van Dooren GG, Tomova C, Agrawal S, Humbel BM, Striepen B. 2008. Toxoplasma gondii Tic20 is essential for apicoplast protein import. Proc Natl Acad Sci USA 105:13574-13579.
  • Van Driel KGA, Humbel BM, Verkleij AJ, Stalpers J, Müller WH, Boekhout T. 2009. Septal pore complex morphology in the Agaricomycotina (Basidiomycota) with emphasis on the Cantharellales and Hymenochaetales. Mycological Research:in press.
  • Van Niftrik L, Geerts WJC, van Donselaar EG, Humbel BM, Webb RI, Fuerst JA, Verkleij AJ, Jetten MSM, Strous M. 2008. Linking ultrastructure and function in four genera of anaerobic ammonium-oxidizing bacteria: cell plan, glycogen storage, and localization of cytochrome C proteins. J Bacteriol 190:708-717.
  • Van Niftrik L, Geerts WJC, van Donselaar EG, Humbel BM, Yakushevska A, Verkleij AJ, Jetten MSM, Strous M. 2008. Combined structural and chemical analysis of the anammoxosome: A membrane-bounded intracytoplasmic compartment in anammox bacteria. J Struct Biol 161:401-410.
  • ‘Handbook of Cryo-Preparation Methods for Electron Microscopy’. 2008. Cavalier A, Spehner D, Humbel BM (eds). CRC Press Inc, Boca Raton, USA.
  • Schwarz H, Humbel BM. 2007. Correlative Light and Electron Microscopy using Immunolabeled Resin Sections In: Electron Microscopy: Methods and Protocols, Methods in Molecular Biology, Kuo J (ed), Vol 369, Humana Press, Totowa, New York, 229-256.
  • Humbel BM. 2008. Freeze-Substitution. In: ‘Handbook for Cryo-Preparation Methods for Electron Microscopy’, Chapter 13. Cavalier A, Spehner D, Humbel BM (eds). CRC Press Inc, Boca Raton, USA, 319-341.
  • Stierhof YD, van Donselaar E, Schwarz H, Humbel BM. 2008. Cryo-Fixation, Freeze-Substitution, Rehydration and Tokuyasu Cryo-sectioning. In: ‘Handbook for Cryo-Preparation Methods for Electron Microscopy’, Chapter 14. Cavalier A, Spehner D, Humbel BM (eds). CRC Press Inc, Boca Raton, USA, 343-365.
  • Humbel BM, Stierhof YD. 2008. Cryo-sectioning according to Tokuyasu. In: ‘Handbook for Cryo-Preparation Methods for Electron Microscopy’, Chapter 19. Cavalier A, Spehner D, Humbel BM (eds). CRC Press Inc, Boca Raton, USA, 467-497.
  • Geerts WJC, Humbel BM, Verkleij AJ. 2008. 3-D Electron Tomography of Cells and Organelles. In: ‘Handbook for Cryo-Preparation Methods for Electron Microscopy’, Chapter 24. Cavalier A, Spehner D, Humbel BM (eds). CRC Press Inc, Boca Raton, USA, 617-649.
  • Mari, M., Bujny, M.V., Zeuschner, D., Geerts, W.J., Griffith, J., Petersen, C.M., Cullen, P.J., Klumperman, J. and Geuze, H.J. (2008) SNX1 defines an early endosomal recycling exit for sortilin and mannose 6-phosphate receptors. Traffic 9, 380-393.
  • Kosta, A., Luciani, M-F., Geerts, W.J.C. and Golstein, P. (2008) Marked mitochondrial alterations upon starvation without cell death, caspases or Bcl-2 family members. Biochim. Biophys. Acta 1783, 2013-2019.
  • Rinse Klooster, Quint le Duc, Michael R. Eman, C. Theo Verrips and Jan A. Post. Differential ER resident protein expression in HeLa cells during ER stress: Selection and application of KDEL specific VHH antibodies. J. Immunological Methods 342:1-12 (2009).
  • L.H.P. Hekking, M.N. Lebbink, D.A.M. de Winter, C.T.W.M. Schneijdenberg, C.M. Brand, B.M. Humbel, A.J. Verkleij and J.A. Post. FIB-SEM: an in-depth study of atherosclerotic tissue. J. Microscopy. 235: 336–347 (2009).
  • Groot, A. J., Khattabi, M. E., Sachs, N., van der Groep, P., et al., Reverse proteomic antibody screening identifies anti adhesive VHH targeting VLA-3. Mol Immunol 2009
  • Bárcena M, Oostergetel GT, Bartelink W, Faas FG, Verkleij A, Rottier PJ, Koster AJ, Bosch BJ. Cryo-electron tomography of mouse hepatitis virus: Insights into the structure of the coronavirion. Proc Natl Acad Sci U S A. 2009 Jan13;106(2):582-7.
  • Raz V, Vermolen BJ, Garini Y, Onderwater JJ, Mommaas-Kienhuis MA, Koster AJ,Young IT, Tanke H, Dirks RW. The nuclear lamina promotes telomere aggregation and centromere peripheral localization during senescence of human mesenchymal stem cells. J Cell Sci. 2008 Dec 15;121(Pt 24):4018-28.
  • Asp L, Kartberg F, Fernandez-Rodriguez J, Smedh M, Elsner M, Laporte F,Bárcena M, Jansen KA, Valentijn JA, Koster AJ, Bergeron JJ, Nilsson T. Early stages of Golgi vesicle and tubule formation require diacylglycerol. Mol Biol Cell. 2009 Feb;20(3):780-90.
  • Knoops K, Kikkert M, Worm SH, Zevenhoven-Dobbe JC, van der Meer Y, Koster AJ,  Mommaas AM, Snijder EJ. SARS-coronavirus replication is supported by a reticulovesicular network of modified endoplasmic reticulum. PLoS Biol. 2008 Sep  16;6(9):e226.
  • Zovko S, Abrahams JP, Koster AJ, Galjart N, Mommaas AM. Microtubule plus-end conformations and dynamics in the periphery of interphase mouse fibroblasts. Mol  Biol Cell. 2008 Jul;19(7):3138-46.
  • Auer M, Koster AJ, Ziese U, Bajaj C, Volkmann N, Wang da N, Hudspeth AJ. Three-dimensional architecture of hair-bundle linkages revealed by electron-microscopic tomography. J Assoc Res Otolaryngol. 2008 Jun;9(2):215-24.
  • van Driel LF, Knoops K, Koster AJ, Valentijn JA. Fluorescent labeling of resin-embedded sections for correlative electron microscopy using tomography-based contrast enhancement. J Struct Biol. 2008 Mar;161(3):372-83.
  • Koning RI, Zovko S, Bárcena M, Oostergetel GT, Koerten HK, Galjart N, KosterAJ, Mieke Mommaas A. Cryo electron tomography of vitrified fibroblasts: microtubule plus ends in situ. J Struct Biol. 2008 Mar;161(3):459-68.
  • Valentijn KM, Valentijn JA, Jansen KA, Koster AJ. A new look at Weibel-Palade body structure in endothelial cells using electron tomography. J Struct Biol. 2008 Mar;161(3):447-58.
  • Valentijn JA, van Weeren L, Ultee A, Koster AJ. Novel localization of Rab3D in rat intestinal goblet cells and Brunner's gland acinar cells suggests a role in early Golgi trafficking. Am J Physiol Gastrointest Liver Physiol. 2007 Jul;293(1):G165-77.
  • Nuria Jiménez, Karin Vocking, Elly van Donselaar, Bruno H. Humbel, Jan A. Post and Arie J. Verkleij. Tannic Acid-Mediated Osmium Impregnation After Freeze-Substitution: A Strategy to Enhance Membrane Contrast For Electron Tomography Of Non-Post-Stained Plastic Sections. J. Structural. Biol. 166: 103-106 (2009).
  • Misjaël N. Lebbink, Nuria Jiménez, Karin Vocking, Liesbeth H. Hekking, Arie J. Verkleij, Jan A. Post. Spiral coating of the endothelial caveolar membranes as revealed by electron tomography and template matching. Traffic.  Under revision.
  • Nuria Jiménez, Elly G. van Donselaar, D.A. Matthijs de Winter, Karin Vocking, Arie J. Verkleij and Jan A. Post. Correlative light and electron microscopy, by TEM and FIB-SEM, using gridded Aclar as substrate for cell monolayer culture. J. Microscopy. In press.
  • G. Hunt, W.J.C. Geerts, E. Korkmaz and F. Braet. Hepatic steatosis and congenital portosystemic shunts: a three-dimensional transmission electron microscopic view.Liver International (2009) Volume 29, Issue 6, pp: 884-885           
  • Filip Braet, James Riches, Willie Geerts, Kristina A. Jahn, Eddie Wisse, Peter Frederik. Structural and functional considerations on the 3-D organization of the fenestrated cytoplasm of liver sinusoidal endothelial cells"  Liver International (2009), Volume 29, Issue 4, pp: 603-613.
  • Ilse Hurbain, Willie J.C. Geerts, Thomas Boudier, Sergio Marco, Arie J.Verkleij, Michael S. Marks and Graça Raposo. Electron tomography of early melanosomes: Implications for melanogenesis and the generation of fibrillar amyloid sheets. PNAS (2008), 105:19726-19731
  • C.B.Tomova, B.M. Humbel, W.J.C. Geerts, R. Entzeroth, J.C.M. Holthuis & A.J. Verkleij Membrane contact sites between the apicoplast and the endoplasmic reticulum in Toxoplasma gondii revealed by electron tomography. Traffic (2009), doi: 10.1111/j.1600-0854.2009.00954.x
  • Laura van Niftrik, Willie J.C. Geerts, Elly van Donselaar, Bruno M. Humbel, Richard I. Webb, Harry R. Harhangi, Huub J.M. Op den Camp, John A. Fuerst, Arie J. Verkleij, Mike S.M. Jetten, Marc Strous. Electron tomography reveals division ring in anammox bacteria. Molecular Microbiology (2009), doi: 10.1111/j.1365-2958.2009.06841.x
  • Cédric Delevoye, Ilse Hurbain, Danièle Tenza, Jean-Baptiste Sibarita, Stéphanie Uzan-Gafsou , Hiroshi Ohno , Willie J.C. Geerts, Arie J. Verkleij, Jean  Salamero, Michael S. Marks and Graça Raposo. AP-1 and KIF13A coordinate endosomal sorting and positioning during melanosome biogenesis. J. of Cell Biology (2009), accepted for publication

Theses:

  • M.N. Lebbink. Visualizing Membranes. 3D Electron microscopic imaging of cellular structure. 9th June 2009, Universiteit Utrecht.,
  • H. Friedrich. Quantitative electron tomography for nanstructured materials. 26th August 2009, Universiteit Utrecht.
  • C.B. Tomova. The three dimensional structure of the apicoplast.28th January 2009, Universiteit Utrecht.

 

Single molecule detection in live cells
  • Schmauder R, Alagaratnam S, Chan C, Schmidt T, Canters GW, Aartsma TJ  "Sensitive detection of the redox state of copper proteins using fluorescence ", J.Biol.Inorg.Chem. 13 (2005) 1.
  • Schmauder R, Librizzi F, Canters GW, Schmidt T, Aartsma TJ. "The Oxidation State of a Protein Observed Molecule-by-Molecule", Chem.Phys.Chem. 11 (2005) 1381.
  • Piet H.M. Lommerse, B. Ewa Snaar-Jagalska, Herman P. Spaink and Thomas Schmidt. "Single-Molecule Diffusion Measurements of H_Ras at the Plasma Membrane of Live Cells Reveal Microdomain Localization Upon Activation", J.Cell Sci. 118 (2005) 1799.
  • Laurent Holtzer, Tobias Meckel, and Thomas Schmidt. "Nanometric three-dimensional tracking of individual quantum dots in cells", Appl. Phys. Lett. 2007 90:053902.
  • Stefan Semrau and Thomas Schmidt. "Particle image correlation spectroscopy (PICS). Retrieving nanometer-scale correlations from high-density single-molecule position data", Biophys J. 2007 92:613.
  • Lommerse PH, Vastenhoud K, Pirinen NJ, Magee AI, Spaink HP, Schmidt T. "Single-molecule diffusion reveals similar mobility for the Lck, H-ras, and K-ras membrane anchor", Biophys J. 2006 91:1090-7.
  • W.J.A. Koopmans, T. Schmidt and S.J.T. van Noort. "Nucleosome immobilization strategies for single-pair FRET microscopy.", Chem. Phys. Chem. 2008, 9:2002-9.    
  • Florian Kulzer, Thomas Schmidt, Michel Orrit & Herman P. Spaink. "Photothermal Detection of Individual Gold Nanoparticles: Perspectives for High-Throughput Screening", Chem. Phys. Chem. 2008, 9:1761-6.    
  • S.F.Gabby Krens, Shuning He, Gerda E.M. Lamers, Annemarie H. Meijer, Jeroen Bakkers, Thomas Schmidt, Herman P. Spaink and B. Ewa Snaar-Jagalska. "Distinct functions for ERK1 and ERK2 in cell migration processes during zebrafish gastrulation.", Dev. Biol. 2008, 319:370-83.    
  • Sandra de Keijzer, Arnauld Serge, Freek van Hemert, Piet Lommerse, Gerda Lamers, Herman Spaink, Thomas Schmidt and Ewa Snaar-Jagalska. "A Spatially Restricted Increase in Receptor Mobility is Involved in Directional Sensing during Dictyostelium discoideum Chemotaxis", J. Cell Sci. 2008, 121:1750-7.    
  • Paige Shaklee, Timon Idema, Gerbrand Koster, Cees Storm, Thomas Schmidt and Marileen Dogterom. "Bidirectional membrane tube dynamics driven by nonprocessive motors;, Proc. Natl. Acad. Sci. 2008, 105:7993-7997.    
  • Stefan Semrau, Timon Idema, Laurent Holtzer, Thomas Schmidt and Cees Storm. "Accurate determination of elastic parameters for multi-component membranes.", Phys. Rev. Lett. 2008, 100:088101-4.    
  • Sandra de Keijzer and Thomas Schmidt. "Single-molecule imaging of cellular signaling in vivo.", in Single Molecules and Nanotechnology, Springer Series in Biophysics, R. Rigler & H. Vogel (Eds.) 2008, 12:107-129.
  • Stefan Semrau & Thomas Schmidt. "Membrane heterogeneity – from lipid domains to curvature effects.", Soft Matter 2009, 5 3174:3186.    
  • Marcel J.M. Schaaf, Wiepke J.A. Koopmans, Tobias Meckel, John van Noort, B. Ewa Snaar-Jagalska, Thomas Schmidt & Herman P. Spaink. "Single-molecule microscopy reveals membrane microdomain organization of cells in a living vertebrate.", Biophys. J. 2009, 97 1206:1214.    
  • Henriette Jensenius, Dionne C.G. Klein, Martin van Hecke, Tjerk H. Oosterkamp, Thomas Schmidt & Jens C. Jensenius. "Mannan-Binding Lectin: Structure, Oligomerization and Flexibility Studied by Atomic Force Microscopy.", J. Mol. Biol. 2009, 391 246:259.    
  • W.J.A. Koopmans, R. Buning, T. Schmidt and S.J.T. van Noort. "spFRET using Alternating Excitation and FCS reveals Progressive DNA Unwrapping in Nucleosomes.", Biophys. J. 2009 97 195:204.    
  • Laurent Holtzer & Thomas Schmidt. "Tracking of Individual Molecules in Cells and Tissue.", Single Particle Tracking and Single Molecule Energy Transfer, C. Bräuchle, D.C. Lamb, J. Michaelis (eds.), Wiley-VCH 2009 :-.    
  • Stefan Semrau, Timon Idema, Thomas Schmidt & Cornelis Strom. "Membrane mediated interactions measured using membrane domains", Biophys. J. 2009, 96 4906:4915.    
  • Thomas Schmidt & Gerhard Schütz. "Single Molecule Analysis of Biomembranes.", Handbook of Single-Molecule Biophysics, A. van Oijen & P. Hinterdorfer (eds.), Springer 2009 :-.    
  • Pedro Miguel Ribeiro Paulo, Alexander Gaiduk, Florian Kulzer,Gabby Krens, Herman Spaink, Thomas Schmidt, Michel Orrit. "Photothermal Correlation Spectroscopy of Gold Nanoparticles in Solution.", J. Phys. Chem. C 2009, 113 11451:11457.    

Theses:

  • Sandra de Keijzer, Dynamics of a GPCR studied with single-molecule microscopy, April 2006
  • Gabby Kren, The function of mitogen activated protein kinases in zebrafish development, September 2007
  • Ralf Schmauder, Application of FCS and FRET in Protein Biochemistry and Biophysics, November 2005
  • Laurent Holtzer, Cargo dependent endosomal activity of Dpp mediates morphogen gradient formation, November 2009
  • Freek van Heemert, Single Molecule Microscopy on Receptor – G-protein signaling, Dec 2009

 

Integration of parameters of cellular processes on all relevant time and length scales
  • Tanke H.J., Dirks R.W., and Raap A.K. 2005. FISH and immunocytochemistry: towards visualizing single target molecules in living cells. Curr. Opin. Biotechnol. 16,49-54.
  • Meulmeester E., Maurice M..M., Boutell C., Teunisse A.F.A.S., Ovaa H., Abraham T.E., Dirks R.W., and Jochemsen A.G. 2005. Loss of Hausp-mediated deubiquitination contributes to DNA damage-induced destabilization of Hdmx and Hdm2. Mol. Cell 18,565-576.
  • Krouwels I.M., Wiesmeijer K., Abraham T.E., Molenaar C., Verwoerd N.P., Tanke H.J., and Dirks R.W. 2005. A glue for heterochromatin maintenance: stable SUV39H1 binding to heterochromatin is reinforced by the SET domain. J. Cell Biol. 170,537-549.
  • Kalayda G.V., Zhang G., Abraham T.E., Tanke H.J., and Reedijk J. 2005. Application of fluorescence microscopy for investigation of cellular distribution of dinuclear platinum anticancer drugs. J. Med. Chem. 48,5191-5202.
  • Dirks R.W., and Tanke H.J. 2006. Advances in fluorescent tracking of nucleic acids in living cells. BioTechniques 40, 489-496.
  • Dirks R.W. and Tanke H.J. 2006, Steryl molecules light-up RNAs. Chem. Biol. 13,559-560
  • Mair G.R., Braks J.A., Garver L.S., Wiegant J.C., Hall N., Dirks R.W., Khan S.M., Dimopoulos G., Janse C.J., and Waters A.P. 2006. Regulation of sexual development of Plasmodium by translational repression. Science 313,667-669.
  • Raz V., Carlotti F., Vermolen B.J., van der Sloos W.C., Kanna-Shanzer S., de Vries A.A, Hoeben R.C., Young I.I., Tnake H.J., Dirks R.W. 2006. Changes in lamina structure are followed by spatial reorganization of heterochromatic regions in caspase-8-activated human mesenchymal stem cells. J. Cell. Sci. 119, 4247-4256.
  • Shir O.M., Raz V., Dirks R.W., and Back T. 2007. Classification of cells fates with support vector machine learning. In: Proceedings EvoBIO 2007, LNCS 4447:258-269.
  • Wiesmeijer K., Krouwels I.M., Tanke H.J., and Dirks R.W. 2008. Chromatin movement visualized with photoactivatable GFP-labeled histone H4. Differentiation 76,83-90.
  • Vermolen B.J., Garini Y., Young I.T., Dirks R.W., and Raz V. 2008. Segmentation and analysis of the three-dimensional redistribution of nuclear components in human mesenchymal stem cells. Cytometry A 73,816-824.
  • Raz V., Vermolen B.J., Garini Y., Onderwater J.J., Mommaas-Kienhuis M.A., Koster A.J., Young I.T., Tanke H.J., and Dirks R.W. 2008. The nuclear lamina promotes telomere aggregation and centromere peripheral localization during senescence of human mesenchymal stem cells. J. Cell Sci. 121,4018-4028.
  • Dekker P, Maier AB, van Heemst D, de Koning-Treurniet C, Blom J, Dirks RW, Tanke HJ, and Westendorp RG. 2009. Stress-induced responses of human skin fibroblasts in vitro reflect human longevity. Aging Cell, in press.

 

Extending NSOM & Multimodal Imaging and Analysis

Publications 2003
Journals:

  • Rosanne A. Guijt-van Duijn, Rob Moerman, Arthur Kroon, Gijs W.K. van Dedem, L.R. van den Doel, L.J. van Vliet, I.T. Young, Frederic Laugere, Andre Bossche, and Pascalina Sarro, Miniaturized analytical assays in biotechnology, Biotechnology Advances, vol. 21, no. 5, 2003, 431-444.
  • I.T. Young, R. Moerman, L.R. van den Doel, V. Iordanov, A. Kroon, H.R.C.  Dietrich, G.W.K. van Dedem, A. Bossche, B.L. Gray, L. Sarro, P.W.  Verbeek, and L.J. van Vliet,  Monitoring enzymatic reactions in nanolitre wells, Journal of  Microscopy - Oxford, vol. 212, no. 3, 2003, 254-263.
  • Book Sections:
  • I.T. Young, Shading Correction: Compensation for Illumination and Sensor Inhomogeneities, in: J.P. Robinson, Z. Darzynkiewicz, P.N. Dean, et al. (eds.), Current Protocols in Cytometry, vol. 1, John Wiley & Sons, New York, 2000 (@2003), 2.11.1-2.11.12.

Publications 2004
Journals:

  • U. Huth, A. Wieschollek, Y. Garini, R. Schubert, and R. Peschka-Suss, Fourier transformed spectral bio-imaging for studying the intracellular fate of liposomes, Cytometry, vol. 57A, no. 1, 2004, 10-21.
  • Tony Chih Yuan Chuang, Sharareh Moshir, Y. Garini, Alice Ya-Chun Chuang, I.T, Young, B. Vermolen, R. van den Doel, Virginie Mougey, Mathilde Perrin, Martina Braun, Paul Donald Kerr, Thierry Fest, Petra Boukamp, and Sabine Mai, The three-dimensional organization of telomeres in the nucleus of mammalian cells, BMC Biology, vol. 2, 2004, 3 June, 2-12.
  • H.R.C. Dietrich, J. Knoll, L.R. van den Doel, G.W.K. van Dedem, P.A.S.  Daran-Lapujade, L.J. van Vliet, R. Moerman, J.T. Pronk, and I.T. Young, Nanoarrays: A Method for Performing Enzymatic Assays, Analytical Chemistry, vol. 76, no. 14, 2004, 15 July, 4112-4117.
  • B.J. Vermolen, Y. Garini, and I.T. Young, 3D Restoration with multiple images acquired by a modified conventional microscope, Microscopy Research and Technique, vol. 64, no. 2, 2004, 113-125.
  • B. Rieger, H.R.C. Dietrich, L.R. van den Doel, and L.J. van Vliet, Diffusion of microspheres in sealed and open microarrays, Microscopy Research and Technique, vol. 65, no. 3, 2004, 218-225.
  • B. Rieger, C. Molenaar, R.W. Dirks, and L.J. van Vliet, Alignment of the cell nucleus from labeled proteins only for 4D in vivo imaging, Microscopy Research and Technique, vol. 64, no. 2, 2004, 142-150.

Conference Proceedings:

  • Y. Garini, V.G. Kutchoukov, A. Bossche, P.F.A. Alkemade, M.W. Docter, P.W. Verbeek, L.J. van Vliet, and I.T. Young, Toward the development of a three-dimensional midfield microscope, in: Tuan Vo-Dinh, Z. Gryczynski, J.R. Lakowicz (eds.), Plasmonics in Biology and Medicine, Proc. BiOS 2004 (January 24-29, San Jose, CA), Proc. SPIE, vol. 5327, 2004, 115-122.
  • V.P. Iordanov, B.P. Iliev, J. Bastemeijer, A. Bossche, P.M. Sarro, I.T. Young, H.R.C. Dietrich, L.R. van den Doel, G.W.K. van Dedem, A.R. Kroon, and M.J. Vellekoop, Integrated sensors for nanoliter bioluminescence and fluorescence bio-chemical analysis, in: G.C.M. Meijer (eds.), The sense of contact VI (Proc. Sensor workshop for industry and science, Wageningen, March 23), 2004, 1-6.
  • V.P. Iordanov, B.P. Iliev, J. Bastemeijer, A. Bossche, P.M. Sarro, I.T. Young, G.W.K. van Dedem, and M.J. Vellekoop, Integrated nanoliter sensors reactor chamber for DNA multiplication - thermal characterization, in: G.C.M. Meijer (eds.), The sense of contact VI (Proc. Sensor workshop for industry and science, Wageningen, March 23), 2004, 1-6.
  • V.G. Kutchoukov, G.O.F. Parikesit, Y. Garini, J. Slabbekoorn, and L.K. Nanver, Fabrication of biochemical nanodevices with self aligned electrodes, Proceedings of APCOT MNT, 2004, April, p. accepted.
  • I.T. Young, Y. Garini, H.R.C. Dietrich, W. van Oel, and G. Liqui Lung, LEDs for fluorescence microscopy, in: J.-A. Conchello, C.J. Cogswell, T. Wilson (eds.), Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XI (Proc. Conf. San Jose, CA, USA, Jan.27-29), Proc. SPIE, vol. 5324, 2004, 208-215.
  • G.O.F. Parikesit, V.G. Kutchoukov, W. van Oel, G. Liqui Lung, A. Bossche, I.T. Young, and Y. Garini, Optical detection of single molecules in nanofluidic chips, in: E.A. Dobisz, L.A. Eldada (eds.), Nanoengineering: Fabrication, Properties, Optics, and Devices (Proc. SPIE Annual Meeting 2004: Nanotechnology and Organic Materials), Proc. SPIE, vol. 5515, 2004, Oct., 109-116.
  • B.P. Iliev, V.P. Iordanov, J. Bastemeijer, A. Bossche, P.M. Sarro, I.T. Young, G.W.K. van Dedem, and M.J. Vellekoop, Integrated nanoliter sensor reactor chamber for PCR analysis - from the idea to a complete system, in: G.C.M. Meijer (eds.), The sense of contact VI (Proc. Sensor workshop for industry and science, Wageningen, March 23), 2004, 1-6.

Publications 2005
Journals:

  • Sherif F. Louis, Bart J. Vermolen, Yuval Garini, Ian T. Young, Amanda Guffei, Zelda Lichtensztejn, Fabien Kuttler, Tony C. Y. Chuang, Sharareh Moshir, Virginie Mougey, Alice Y. C. Chuang, Paul Donald Kerr, Thierry Fest, Petra Boukamp, and Sabine Mai, c-Myc induces chromosomal rearrangements through telomere and chromosome remodeling in the interphase nucleus, PNAS, 102:27, p. 9613-9618 (2005)
  • Bart J. Vermolen, Y. Garini, S. Mai, V. Mougey, T. Fest, T. C.-Y. Chuang, A. Y.-C. Chuang, L. Wark, I. T. Young, Characterizing the three-dimensional organization of telomeres, Cytometry Part A, 67A, p. 144-150 (2005)
  • Y. Garini, B.J. Vermolen, and I.T. Young, From micro to nano: recent advances in high-resolution microscopy, Current Opinion in Biotechnology, vol. 16, no. 1, 2005, 3-12.
  • S. Mai and Y. Garini, Oncogenic Remodeling of the Three-Dimensional Organization of the Interphase Nucleus: c-Myc Induces Telomeric Aggregates Whose Formation Precedes Chromosomal Rearrangements, Cell Cycle, vol. 4, no. 10, 2005, 1327-1331.
  • L.R. van den Doel, P.T. Nagy, L.J. van Vliet, and G.P. Neitzel, Regularized phase-tracker with iso-phase scanning strategy for analysis of dynamic interferograms of nonwetting droplets under excitation, Applied Optics (Optical Society of America), vol. 44, no. 14, 2005, 2695-2704.
  • B. J. Vermolen, S. Mai, L. Wark, C. A. Fordyce, C. J. Miller, H. Berman, A. Y. C. Chuang, T. Tlsty, I. T. Young, and Y. Garini, "The effect of deconvolution algorithms on the automatic analysis of telomeres in three-dimensional imaging," Submitted (2005).
  • Conference Proceedings:
  • B. J. Vermolen, I. T. Young, A. Chuang, L. Wark, T. Chuang, S. Mai, and Y. Garini, "Three-dimensional analysis tool for segmenting and measuring the structure of telomeres in mammalian nuclei," SPIE Proceedings 5699, 111-120 (2005).
  • M. W. Docter, I. T. Young, V. G. Kutchoukov, A. Bossche, P. F. A. Alkemade, and Y. Garini, "A novel concept for a mid-field microscope," Proceedings of SPIE 5703, 118-126 (2005).
  • H. R. C. Dietrich, R. L. v. d. Doel, W. Hoyer, W. v. Oel, G. L. Lung, Y. Garini, T. Jovin, and I. T. Young, "Adaptation of Nanoarrays for the Study of -synuclein aggregation - preliminary results," Proceedings of SPIE 5699, 395-402 (2005).
  • H. R. C. Dietrich, I. T. Young, and Y. Garini, "Gold nanoparticles: A novel application of spectral imaging in proteomics - preliminary results," Proceedings of SPIE 5694, 82-89 (2005).

Publications 2006
Journals:

  • Garini, Y., Confocal 3D DNA cytometry: Assessment of required coefficient of variation by computer simulation, Cellular oncology, vol. 28, no. 3, 2006, 121-122.
  • Y. Garini, I.T. Young, and G. McNamara, Spectral Imaging: Principles and Applications, Cytometry Part A, vol. 69A, no. 8, 2006, 735-747.
  • V. Raz, F. Carlotti, B.J. Vermolen, E. van der Poel, W.C.R. Sloos, S. Knaan-Shanzer, A.A.F. de Vries, R.C. Hoeben, I.T. Young, H.J. Tanke, Y. Garini, and R.W. Dirks, Changes in lamina structure are followed by spatial reorganization of heterochromatic regions in caspase-8-activated human mesenchymal stem cells, Journal of Cell Science, vol. 119, no. 20, 2006, 4247-4256.
  • S. Mai and Y. Garini, The significance of telomeric aggregates in the interphase nuclei of tumor cells, Journal of Cellular Biochemistry, vol. 97, no. 5, 2006, 904-915.
  • M.W. Docter, I.T. Young, O.M. Piciu, A. Bossche, P.F.A. Alkemade, P.M. van den Berg, and Y. Garini, Measuring the wavelength-dependent divergence of transmission through sub-wavelength hole-arrays by spectral imaging, Optics Express, vol. 14, no. 20, 2006, 9477-9482.
  • D.J. Arndt-Jovin, D.S. Lidke, K.A. Lidke, B. Rieger, and T.M. Jovin, Quantum dots shed light on processes in living cells, SPIE Newsroom, vol. DOI:10.1117/2.1200605.0228, 2006, 1-3.
  • A.Caporali, L. Wark, B.J. Vermolen, Y. Garini, and S. Mai, Telomeric aggregates and end-to-end chromosomal fusions require myc box II, Oncogene, vol. doi:10.1038, 2006, 1-9 (AOP).
  • I.T. Young, Y. Garini, B.J. Vermolen, G.F. Liqui Lung, G. Brouwer, S. Hendrichs, J. Spoelstra, E. Wilhelm, M. Zaal, and M. el Morabit, Absolute fluorescence calibration, European Journal of Medical Genetics, vol. 48, no. 4, 2005 (2006), 533-533.
  • Conference Proceedings:
  • M.W. Docter, I.T. Young, O. Piciu, A. Bossche, P.F.A. Alkemade, P.M. van den Berg, and Y. Garini, Measuring the near-field of extraordinary transmission through a periodic hole-array, in: D.L. Andrews, J.-M. Nunzi, A. Ostendorf (eds.), Nanophotonics, Proc. Photonics Europe 2006 (Strasbourg, France, Apr.3-7), Proc. SPIE, vol. 6195, 2006, 1L/1-8.
  • I.T. Young, Y. Garini, B. Vermolen, G. Liqui Lung, G. Brouwer, S. Hendrichs, M. el Morabit, J. Spoelstra, E. Wilhelm, and M. Zaal, Absolute Fluorescence Calibration - Invited Paper, in: D.L. Farkas, D.V. Nicolau, R.C. Leif (eds.), Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IV (Proc. Photonics West 2006: Biomedical Optics (BiOS), San Jose, CA, USA, Jan. 21-26), Proc. SPIE, vol. 6088, 2006, 0U/1-9.
  • H.R.C. Dietrich, I.T. Young, and Y. Garini, Advances in the Development of a Novel Method to be used in Proteomics using Gold Nanobeads, Proc. Photonics West 2006: Biomedical Optics (BiOS), San Jose, CA, USA, Jan. 21-26), Proc. SPIE, vol. 6092, 2006, 0C/1-8.

Publications 2007
Journals

  • M.W. Docter, P.M. van den Berg, P.F.A. Alkemade, V.G. Kutchoukov, O.A. Piciu, A. Bossche, I.T. Young, Y. Garini, Structured illumination microscopy using extraordinary transmission through sub-wavelength hole-arrays, Journal of Nanophotonics, vol 1, 011665, 10 pages, 2007.
  • P.F.A. Alkemade, M.W. Docter, V.G. Kutchoukov, Uniform ion beam milling of a non-flat surface at off-normal incidence and four azimuths, Journal of Microscopy, Vol 225, March 2007, 229-235.
  • R. Sarkar, A. Guffei, B.J. Vermolen, Y. Garini, S. Mai, Alterations of centromere positions in nuclei of immortalized and malignant mouse lymphocytes, Cytometry, Volume 71A, Number 6, January 2007, 386-392.
  • A. Caporali, L. Wark, B.J. Vermolen, Y. Garini, S. Mai, Telomeric aggregates and end-to-end chromosomal fusions require myc box II, Oncogene, 26(10), 2007, 1398-1406.
  • V. Raz, B.J. Vermolen, I.T. Young, R.W. Dirks, Y. Garini, Sililar spatial reorganization of lamina, telomeres and centromeres in senescent and apoptotic human mesenchymal stem cells, Chromosome research, 15, 2007.
  • G. van Dalen, P. Nootenboom, L.J. van Vliet, L. Voortman, C. Esveld, 2007. 3D imaging, analysis and modelling of porous cereal products using X-ray microtomography. Image analysis and stereology, 26, 169-177.
  • G. van Dalen, P. Nootenboom, L.J. van Vliet, L. Voortman, E. Esvevld, 2007. 3D imaging and analysis of porous cenreal products using X-ray microtomography. In s.n. (Ed.), ICS XII - 2007  (pp. 1-8).
  • A.W.M. van Eekeren, K. Schutte, O.R. Oudegeest, L.J. van Vliet. Performance evaluation of super-resolution reconstruction methods on real-world data. Eurasip journal on applied signal processing, 2007(ID 43953).
  • F.G.A. Faas, L.J. van Vliet, 2007. A crossing detector based on the structure tensor. Lecture notes in computer science, 4678, 212-220.
  • F.G.A. Faas, L.J. van Vliet, 2007. Junction detection and multi-orientation analysis using streamlines. Lecture notes in computer science, 4673, 718-725.
  • C.L. Luengo Hendriks, G.M.P. van Kempen, L.J. van Vliet, 2007. Improving the accuracy of isotropic granulometries. Pattern recognition letters, 28(7), 865-872.
  • S.T. Nevo, M. van Stralen, A.M. Vossepoel, J.H.C. Reiber, N. de Jong, A.F.W. van der Steen, J.G. Bosch, 2007. Automated tracking of the mitral valve annulus motion in apical echocardiographic images using multidimensional dynamic programming. Ultrasound in medicine and biology, 33, 1389-1399.
  • B.J. Vermolen, Y. Garini, S. Mai, V. Mougey, T. Fest, T.C.Y. Chuang, A.Y.C. Chuang, L. Wark, I.T. Young, 2007. Characterizing the three-dimensional organization of telomeres. Cytometry part a, 71A(5), 345.
  • Y.S. Wu , L.J. van Vliet , H.W. Frijlink, K. van der Voort Maarschalk, 2007. Pore size distribution in tablets measured with a morphological sieve. International journal of pharmaceutics, 342, 176-183.
  • Conference proceedings
  • H.R.C. Dietrich, B.J. Vermolen, B. Rieger, I.T. Young, Y. Garini, Y, A New Optical Method for Characterizing Single Molecule, Proceedings SPIE, 6444E, 2007
  • G.O.F. Parikesit, Y. Garini, I.T. Young, A branched U-turn nanofluidic device for continuous sorting of macromolecules, 3rd International Symp. on Separation and Characterization of Natural and Synthetic Macromolecules, 2007, 86.
  • G.O.F. Parikesit, A.P. Markensteijn, J. Westerweel, I.T. Young, Y. Garini, Free Flow Dielectrophoresis - A numerical Study, Proceedings of uTAS (Miniaturized Systems for Chemistry and Life Sciences, 2007, 221-223.
  • S. Brinkers, H.R.C. Dietrich, B.Rieger, I. Ted Young, Detection of DNA hybridization events using the diffusion constant in TPM experiments, Focus on Microscopy, Valencia, Spain, April 10-13, 2007
  • H.R.C. Dietrich, F.G.M. Wiertz, B.J. Vermolen, B. Rieger, H.A. Heering, I.T. Young and Y. Garini, The Detection of DNA-protein interactions under near-native biological conditions,13th International Workshop on "Single Molecule Spectrocopy and Ultrasensitive Analysis in the Life Sciences", Berlin, Germany, September 19-21, 2007
  • H.R.C. Dietrich, F.G.M. Wiertz, B.J. Vermolen, B. Rieger, H.A. Heering, I.T. Young and Y. Garini, The Detection of DNA-protein interactions under near-native biological conditions,Annual Dutch Meeting on Molecular and Cellualar Biophysics, Veldhoven, The Netherlands, October 1-2, 2007
  • S. Brinkers, H.R.C. Dietrich, B. Rieger, I.T. Young, Lab-on-a-ship for radipidly determining gene experssion, Annual Dutch Meeting on Molecular and Cellualar Biophysics, Veldhoven, The Netherlands, October 1-2, 2007
  • M. Baiker, J. Milles, A.M. Vossepoel, I. Que, E. Kaijzel, C.W.G.M. Lowik, J.C. Reiber, J. Dijkstra & Lelieveldt, BPF (EWI Ch. Computer Graphics) (2007). Fully automated whole-body registration in mice using an articulated skeleton atlas. In s.n. (Ed.), Proc. 4th IEEE Int. Symposium on Biomedical Imaging: From Nano tot Macro (pp. 728-731).
  • M.W.A. Caan, K.A. Vermeer, L.J. van Vliet, C.A. Grimbergen, F.M. Vos, 2007. Pruning datasets in discriminant analysis: a DTI study to Schizophrenia. In s.n. (Ed.), ISBI 2007, Proceedings 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (pp. 1340-1344).
  • M.W.A. Caan, K.A. Vermeer, L.J. van Vliet, C.A. Grimbergen, F.M. Vos, 2007. Pruning datasets in discriminant analysis: a DTI study to Schizophrenia. In FW Jansen, GEO Pierre, CJ Veenman & JWJ Heijnsdijk (Eds.), ASCI 2007: Proc. 13th Ann. Conf. of the Advanced School for Computing and Imaging (pp. 298-303). Delft: ASCI.
  • M. van de Giessen, F.M. Vos, S.D. Strackee, M. Maas, C.A. Grimbergen, L.J. van Vliet, G.J. Streekstra, 2007. Constrained registration of multiple rigid objects in close proximity: application in the wrist joint. In s.n. (Ed.), ISBI 2007, Proc. 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (pp. 704-707). IEEE.
  • M. van de Giessen, F.M. Vos, S.D. Strackee, M. Maas, C.A. Grimbergen, L.J. van Vliet, G.J. Streekstra, 2007. Constrained registration of multiple rigid objects in close proximity: application in the wrist joint. In FW Jansen, GEO Pierre, CJ Veenman & JWJ Heijnsdijk (Eds.), ASCI 2007 - Proc. 13th Ann. Conf. of the Advanced School for Computing and Imaging (pp. 252-256). Delft: ASCI.
  • O.M. Piciu, M.C. van der Krogt, F. Tatar, P.M. Sarro, A. Bossche, M.W. Docter, Y. Garini, I.T. Young, 2007. Nano-hole Arrays in Thin Au/Pd Film on Glass, for High Speed Molecular Analysis. In s.n. (Ed.), Proceedings of 5th IEEE Conference on Sensors (pp. 608-611). New York: IEEE.
  • O.M. Piciu, M.C. van der Krogt, M.W. Docter, Y. Garini, I.T. Young, P.M. Sarro, A. Bossche, 2007. Sub-wavelength apertures in Au/Pd film for fluorescence measurements. In s.n. (Ed.), Sub-wavelength apertures in Au/Pd film for fluorescence measurements Proceedings of Sense of contact 9 (pp. 1-4). Zeist, The Netherlands: sense of contact.
  • Rivera Rabelo, S.M. Luthi, L.J. van Vliet, 2007. Parameterization of meander-belt systems in high-resolution three-dimensional seismic data using the GeoTime cube and modern analogues. In RJ Davies, HW Posamentier, LJ Wood & JA Cartwright (Eds.), Seismic Geomorphology: Applications to Hydrpcarbon Exploration and production (pp. 121-137). London, UK: Geological Society London.
  • Tetyukhina, L.J. van Vliet, S.M. Luthi, C.P.A. Wapenaar, 2007. High-resolution clinoform characterization by 2-D model-driven seismic Bayesian inversion. In s.n. (Ed.), Proceedings SEG International Exposition and 77th Annual Meeting (pp. 1855-1859). Tulsa, OK, USA: SEG.
  • I.W.O. Serlie, F.M. Vos, R. Truyen, F.H. Post, L.J. van Vliet, 2007. Classifying CT Imaga Data Into Material Fractions by a scale and Rotation Invariant Edge Model. Ieee transactions on image processing, 16(12), 2891-2904.
  • K.A. Vermeer, N.J. Reus, F.M. Vos, H.G. Lemiil, A.M. Vossepoel, 2007. Spilt bundle detection in polarimetric images of the human retinal nerve fiber layer. Methods of information in medicine, 46(4), 425-431.
  • F.M. Vos, M.W.A. Caan, K.A. Vermeer, C.B.L.M. Majoie, G.J. den Heeten, L.J. van Vliet, 2007. Linear and kernel Fisher discriminant analysis for studying diffusion tensor images in Schizophrenia. In s.n. (Ed.), ISBI 2007, Proc. 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (pp. 764-767).

Publications 2008
Journals

  • M.W.A. Caan, L.J. van Vliet, C.B.L.M. Majoie, E.M. Aukemea, C.A. Grimbergen, F.M. Vos. Spatial consistency in 3D tract-based clustering statistics. Lecture notes in computer science, 5241(2008), 535-542.
  • K.R. Castleman, I.T. Young, 2008. Fundamentals of Microscopy. In Q. Wu, F.A. Merchant & K.R. Castleman (Eds.), Microscope Image Processing (pp. 11-25). Elsevier.
  • K.R. Castleman, I.T. Young, 2008. Introduction. In Q. Wu, F.A. Merchant & K.R. Castleman (Eds.), Microscope Image Processing (pp. 1-9). Elsevier.
  • J. Dijk, A.W.M. van Eekeren, K. Schutte, D.J. de Lange, L.J. van Vliet, 2008. Super-resolution reconstruction for maving point target detection. Optical engineering, 47 (09)(096401), 096401-1-096401-12.
  • R.J. van Heekeren, F.G.A. Faas, L.J. van Vliet, 2007. Finding the minimum-cost path without cutting corners. Lecture notes in computer science, 4522, 263-272.
  • G.O.F. Parikesit, A.P. Markesteijn, O.M. Piciu, A. Bossche, J. Westerweel, I.T. Young, Y. Garini,  2008. Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels. Biomicrofluidics, 2(024103), 1-14.
  • Q.T. Pham, L.J. van Vliet & K. Schutte. Robust super-resolution by minimizing a gaussian-weighted L2 error norm. In nn (Ed.), Journal of Physics: Conference Series 124, 2008, 012037 (pp. 1-20). IOP Publishing Ltd..
  • Q.T. Pham, L.J. van Vliet & K. Schutte. Robust super-resolution without regularization. In nn (Ed.), Journal of Physics: Conference Series 124, 2008, 012036 (pp. 1-20). IOP Publishing Ltd.
  • V.F. van Ravesteijn, F.M. Vos, I.W.O. Serlie, R. Truyen, L.J. van Vliet, 2008. Thin layer tissue classification for electronic cleansing of CT colonography data. Lecture notes in computer science, 190(5), 78-84.
  • I.W.O. Serlie, A.H. de Vries, L.J. van Vliet, C.Y. Nio, R. Truyen, F.M. Vos, 2008. Lesion conspicuity and efficiency of CT colonography with electronic cleansing based on a three-material transition model. American journal of roentgenology, 191(11), 1493-1502.
  • B.J. Vermolen, Y. Garini, I.T. Young, R.W. Dirks, V. Raz, 2008. Segmentation and analysis of the three-dimensional redistribution of nuclear components in human mesenchymal stem cells. Cytometry part a, 816-824.
  • B.J. Vermolen, I.T. Young, Y. Garini , 2008. 3D-sky: decreasing the acquisition time in fourier spectroscopy using one-sided interferograms, a simulation. In 3D-sky: decreasing the acquisition time in fourier spectroscopy using one-sided interferograms, a simulation (pp. 127-127).
  • B.J. Vermolen, I.T. Young, V. Raz, Y. Garini, 2008. Teloview: dot-like segmentation using a gaussian scale space approach and applications. In Teloview: dot-likw segmentation using a gaussian scale space approach and applications (pp. 219-219).
  • F.M. Vos, C. van Wijk, V.F. van Ravesteijn, I.W.O. Serlie, S.E. Grigorescu, F.H. Post, R. Truyen, J. Stoker, L.J. van Vliet, 2008. Recent advances in techniques for CT colonography: electronic cleansing and CAD. International journal of computer assisted radiology and surgery, 3 (Suppl 1), S188-S198.
  • J. Vermeulen, S. Kalitzin, J. Parra, E. Dekker, A.M. Vossepoel F. Lopes da Silva, 2008. Non-provocative diagnostics of photosensitivity using visually evoked potentials. Clinical neurophysiology, 119(4), 842-852.
  • van Wijk, J. Florie, C.Y. Nio, E. Dekker, A.H. de Vries, H.W. Venema, L.J. van Vliet, J. Stoker, F.M. Vos, 2008. Protrusion method for automated estimation of polyp size on CT colonography. American journal of roentgenology, 190(5), 1279-1285.
  • Y.S. Wu, L.J. van Vliet, H.W. Frijlink, I. Stokroos, K.V. Maarschalk, 2008. Pore direction in relation to anisotropy of mechanical strength in a cubic starch compact. Aaps pharmscitech, 9(2), 528-535.
  • Y.S. Wu , H.W. Frijlink, L.J. van Vliet, K. van der Voort Maarschalk, 2008. Pore shape in de sodium chloride matrix of tablets after the addition of starch as a second component. European journal of pharmaceutics and biopharmaceutics, 70 (2), 539-543.
  • M.W.A. Caan, L.J. van Vliet, A.W. de Vries, C.A. Grimbergen, H.G. Khedoe, F.M. Vos, E.M. Akkerman, 2008. Generating fiber crossing phantoms out of experimental dwis. In Generating fiber crossing phantoms out of experimental dwis (pp. 110-115). Delft: Advanced School for Computing and Imaging (ASCI).
  • S. Brinkers, H.R.C. Dietrich, B. Rieger, I.T. Young, 2008. Single molecule RNA detection: fast and sensitive gene profiling. (pp. 108-108).
  • S. Brinkers, H.R.C. Dietrich, B. Rieger, Y. Garini, I.T. Young, 2008. Fast, sensitive determination of gene expression. In Fast, sensitive determination of gene expression (pp. 228-228)
  • Conference proceedings
  • A.W.M. van Eekeren, K. Schutte, L.J. van Vliet, 2008. Super-resolution on small moving objects. In nn (Ed.), Proceedings 15th International Conference on Image Processing, San Diego, California (pp. 1248-1251). Los Alamitos: IEEE Signal Processing Society Press.
  • A.W.M. van Eekeren, K. Schutte, O.R. Oudegeest, L.J. van Vliet, 2007. Super-resolution on moving objects using a polygon-based object description. In F.W. Jansen, G.E.O. Pierre, C.J. Veenman, J.W.J. Heijnsdijk (Eds.), Proc. 13th Annual Conference of the Advanced School for Computing and Imaging (pp. 317-321). Delft: ASCI.
  • P.H. Kitslaar, H.A. Marquering, G. Koning, A.M. Vossepoel, W.J. Jukema, J.J. Bax, M. Nieber,  J.H.C. Reiber, 2008. Automated determination of optimal angiographic viewing angles for coronary artery bifurcations from CTA data. Proceedings SPIE, 6918, 1-10.
  • O.M. Piciu, M.W. Docter, M.C. van der Krogt,, Y. Garini, I.T. Young, P.M. Sarro, A. Bossche, 2008. Fabrication and optical characterization of nano-hole arrays in gold and gold/palladium films on glass. Institution of mechanical engineers. Proceedings. part N: Journal of nanoengineering and nanosystems, 221(3), 107-114.
  • V.F. van Ravesteijn, L.J. van Vliet, F.M. Vos, 2008. Thin Layer Tissue Classification for Electronic Cleansing of CT Colonography Data. In H Yoshida (Ed.), Proceedings of the MICCAI 2008 Workshop on Computational and Visualization Challenges in the New Era of Virtual Colonoscopy  (pp. 78-84).
  • V.F. van Ravesteijn, F.M. Vos, I.W.O. Serlie, L.J. van Vliet, 2008. Thin layer tissue classification for electronic cleansing of CT colonography data. In Proc. 14th Annual Conference of the Advanced School for Computing and Imaging (pp. 355-361). Delft: ASCI.
  • Tetyukhina, S.M. Luthi, L.J. van Vliet, C.P.A. Wapenaar, 2008. High-resolution reservoir characterization by 2-D model-driven seismic Bayesian inversion: an example from a Tertiary deltaic clinoform, system in the North Sea. In s.n. (Ed.), SEG International Exposition and 78th Annual Meeting (pp. 1880-1884). Tulsa, OK, USA: SEG.
  • Tetyukhina, S.M. Luthi, L.J. van Vliet, C.P.A. Wapenaar, 2008. High-resolution characterization of the North Sea fluvio-deltaic system by seismic Bayesian inversion. In s.n. (Ed.), 9th Nederlands Aardwetenschappelijk Congress (pp. 254). The Netherlands: NAC.
  • I.T. Young, M. el Morabit, G.F. Liqui Lung, B.J. Vermolen, 2008. Photonic Calibration for Fluorescence Microscopy. Proceedings SPIE, 6859(685915).

Thesis 2008

  • M.W. Docter (13 oktober 2008). Midfield microscope: exploring the extraordinary. TUD Technische Universiteit Delft (108 pag.) (Enschede: PrintPartners Ipskamp). Prom./coprom.: Prof.dr. I.T. Young, dr. Y. Garini.

 

Imaging cells inside organisms
  • Braakman N, Matysik J, van Duinen SG, Verbeek F, Schliebs R,.de Groot HJM, Alia A (2006). Longitudinal assessment of Alzheimer’s β-Amyloid plaque development in transgenic mice monitored by in vivo magnetic resonance microimaging, J. of Magn. Res. Imaging, 24, 530-536
  • Kabli S, Alia, Spaink HP, Verbeek FJ, de Groot HJM (2006). Magnetic Resonance Microscopy of the Adult Zebrafish, Zebrafish, 3, 4, 431-439
  • Kabli, S., Spaink, H.P., Groot, H.J.M.d., Alia, A. , In Vivo high resolution magnetic resonance spectroscopy of the adult Zebrafish brain at 9.4T, Proc. Intl. Mag. Reson. Med., vol. 16, pp. 113. 2008
  • Kabli, S., Spaink, H.P., De Groot, H.J.M., Alia, A. , In Vivo Metabolite Profile of Adult Zebrafish Brain Obtained by High-Resolution Localized Magnetic Resonance Spectroscopy, Journal of Magnetic Resonance Imaging, vol. 29, no. 2, pp. 275-281. 2009
  • Thesis S. Kabli Oct. 2009

 

Databases, modeling and visualization
  • 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.
  • L. De Raedt, T. Washio, and J.N. Kok, editors. Advances in Mining Graphs, Trees and Sequences, volume 124 of Frontiers in Artificial Intelligence and Applications. June 2005.
  • Yun Chi, Siegfried Nijssen, R. R. Muntz, and Joost N. Kok. Frequent subtree mining-an overview. In Fundamenta Informaticae, volume 66, pages 161-198. IOS Press, 2005.
  • Christiaan Henkel and Joost N. Kok. Towards evolutionary DNA computing. In Lecture Notes in Computer Science, volume 3661, pages 244-259, 2005.
  • P. O'Neill, K. Fraser, Z. Wang, P. Kellam, J. N. Kok, and X. Liu. Pyramidic clustering of large scale microarray images. In The Computer Journal. Oxford University Press, 2005.
  • Elena V. Samsonova, Thomas Bäck, Joost N. Kok, and Adriaan P. IJzerman. Reliable hierarchical clustering with the self-organizing map. In IDA 2005, pages 385-396. 2005.
  • A. Fazel Famili, Joost N. Kok, José Manuel Pe na, Arno Siebes, and A. J. Feelders. Advances in Intelligent Data Analysis VI, 6th International Symposium on Intelligent Data Analysis, IDA 2005, Madrid, Spain, September 8-10, 2005, Proceedings. Springer, 2005.
  • Eric-Wubbo Lameijer, Adriaan P. IJzerman, and Joost N. Kok. The molecule evoluator: an interactive evolutionary algorithm for designing drug molecules. In Hans-Georg Beyer and Una-May O'Reilly, editors, Genetic and Evolutionary Computation Conference, GECCO 2005, Proceedings, Washington DC, USA,, pages 1969-1976. ACM, 2005.
  • Takashi Washio, Luc De Raedt, and Joost N. Kok. Advances in mining graphs, trees and sequences. Fundamenta Informaticae, 66, 2005.
  • E.V. Samsonova, J.N. Kok, and A.P. IJzerman. Treesom: Cluster analysis in the self-organizing map. In 5th Workshop on Self-Organizing Maps (WSOM), pages 429-438, 2005.
  • Eric-Wubbo Lameijer, Ad IJzerman, and Joost Kok. Using data mining to improve mutation in a tool for molecular evolution. In 2005 IEEE Congress on Evolutionary Computation. 2005.
  • Eric-Wubbo Lameijer, Thomas Bäck, Joost N. Kok, and Ad P. Ijzerman. Evolutionary algorithms in drug design. Natural Computing, 4:177-243, 2005.
  • Sander M. Bohte and Joost N. Kok. Applications of spiking neural networks, Information Processing Letters, 95:519-520, 2005.
  • 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.
  • 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 (2006).
  • 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
  • Ofer M. Shir, Joost N. Kok, Thomas Bäck, Marc J. J. Vrakking: Learning the Complete-Basis-Functions Parameterization for the Optimization of Dynamic Molecular Alignment by ES. IDEAL 2006, Lecture Notes in Computer Science 4224: 410-418
  • Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman: The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules. Journal of Chemical Information and Modeling 46(2): 545-552 (2006)
  • Eric-Wubbo Lameijer, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman: Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés". Journal of Chemical Information and Modeling 46(2): 553-562 (2006)
  • Jeroen Kazius, Siegfried Nijssen, Joost N. Kok, Thomas Bäck, Adriaan P. IJzerman: Substructure Mining Using Elaborate Chemical Representation. Journal of Chemical Information and Modeling 46(2): 597-605 (2006)
  • Christiaan V. Henkel, Thomas Bäck, Joost N. Kok, Grzegorz Rozenberg and Herman P. Spaink, DNA computing of solutions to knapsack problems, Biosystems, doi:10.1016/j.biosystems.2006.06.001.
  • Elena V. Samsonova, Joost N. Kok and Ad P. IJzerman, TreeSOM: Cluster analysis in the self- organizing map, Neural Networks Pages: 935 – 949, Volume 19, Issue 6, (July 2006)
  • Siegfried Nijssen, Joost N. Kok, Multi-class Correlated Pattern Mining, Knowledge Discovery in Inductive Databases, 4th International Workshop, KDID 2005, Porto, Portugal, October 3, 2005, Revised Selected and Invited Papers. Lecture Notes in Computer Science 3933, Springer 2006, pages 165-187, 2006.
  • Farhad Arbab, Joost N. Kok, Interaction and Coordination of Tools for Structured Data, Proceedings ISoLA, Lecture Notes in Computer Science Volume 4313, 2006, pages 1-8.
  • C. Soares, E.H. de Graaf, J.N. Kok and W.A. Kosters, Sequence Mining on Web Access Logs:  A Case Study, BNAIC 2006, Namur, Belgium, 5-6 October 2006; Proceedings pp. 291-298 (P.-Y. Schobbens, W. Vanhoof and G. Schwanen, editors).
  • Siegfried Nijssen, Joost N. Kok, Multi-class Correlated Pattern Mining, BNAIC 2006, Namur, Belgium, 5-6 October 2006; Proceedings pp. 411-412 (P.-Y. Schobbens, W. Vanhoof and G. Schwanen, editors).
  • Siegfried Nijssen, Joost N. Kok, Frequent Subgraph Miners: Runtimes
  • Don't Say Everything, Mining and Learning with Graphs (MLG 2006), Workshop held with ECML/PKDD 2006 in Berlin.
  • Ofer M. Shir, Christian Siedschlag, Thomas Bäck, and Marc J.J. Vrakking. Niching in evolution strategies and its application to laser pulse shaping. In Artificial Evolution, 7th International Conference, Evolution Artificielle, EA 2005, volume 3871 of Lecture Notes in Computer Science. Springer Verlag (2006).
  • Michael T. M. Emmerich, Jochen Hundemer, Mihai-Christian Varcol, Boris Naujoks, and Moustafa Abdel-Maksoud. Design optimization of ship propellers by means of advanced metamodel-assisted evolution strategies. In Proceedings ERCOFTAC 2006 Int'l Conference on Design Optimization, Las Palmas, Gran Canaria, 2006.
  • Michael T.M. Emmerich, Maren Urselmann, Jochen Till, Guido Sand, and Sebastian Engell. Hybrid ea/mip method for solving two-stage stochastic programming problems in chemical batch scheduling. In 7th International Conference on Adaptive Computing in Design and Manufacture (ACDM 2006), LNCS 3907, Bristol, U.K, 2006. IP-CC Press.
  • Michael Emmerich. Sms-emoa: Multiobjective selection based on dominated hypervolume. European Journal of Operational Research, 2006.
  • Ernst G.P. Bovenkamp, Jeroen Eggermont, Rui Li, Michael T.M. Emmerich, Thomas Bäck, J. Dijkstra, and J.H.C. Reiber. Optimizing IVUS Lumen Segmentations using Evolutionary Algorithms. In Medical Image Computing and Computer-Assisted Intervention, Kopenhagen, Denmark, 2006.
  • Jeroen Eggermont, Ernst G.P. Bovenkamp, Rui Li, Michael T.M. Emmerich, Thomas Bäck, J. Dijkstra, and J.H.C. Reiber. Extending nk landscapes to the mixed-integer domain. In 18th Belgium-Netherlands Conference on Artificial Intelligence, Namen, Belgium, october 5-6 2006.
  • Michael T.M. Emmerich, Rui Li, Jeroen Eggermont, Ernst G.P. Bovenkamp, Th. Bäck, J. Dijkstra, and J.H.C. Reiber. Optimizing Parameters of Coronary Vessel Image Analysis using Evolution Strategies. In 18th Belgium-Netherlands Conference on Artificial Intelligence, Namen, Belgium, october 5-6 2006.
  • Rui Li, Michael T.M. Emmerich, Jeroen Eggermont, Ernst G.P. Bovenkamp, Thomas Bäck, J. Dijkstra, and J.H.C. Reiber. Mixed-integer nk landscapes. Parallel Problem Solving from Nature (PPSN), 2006.
  • Rui Li, Michael T.M. Emmerich, Jeroen Eggermont, Ernst G.P. Bovenkamp, Thomas Bäck, J. Dijkstra, and J.H.C. Reiber. Mixed-Integer Optimization of Coronary Vessel Image Analysis using Evolution Strategies. In M. Keijzer et al, editor, GECCO '06: Proceedings of the 8th annual conference on Genetic and evolutionary computation, pages 1645-1652, Seattle, WA, USA, 2006.
  • Rui Li, Michael T.M. Emmerich, Ernst G.P. Bovenkamp, Jeroen Eggermont, Thomas Bäck, J. Dijkstra, and J.H.C. Reiber. Mixed-Integer Evolution Strategies and Their Application to Intravascular Ultrasound Image Analysis. In F. Rothlauf et al, editor, Proceedings of the 8th European Workshop on Evolutionary Computation in Image Analysis and Signal Processing (EvoIASP), volume 3907 of LNCS, pages 415-426, Budapest, Hungary, 10-12 April 2006. Springer Verlag.
  • Rui Li, Michael T.M. Emmerich, Thomas Bäck, Ernst G.P. Bovenkamp, J. Eggermont, J. Dijkstra, and J.H.C. Reiber. Optimizing Parameters of Intravascular Ultrasound Image Analysis Systems using Mixed-Integer Evolution Strategies. LNCS 3907, pages 283-284, Bristol, UK, 2006. Adaptive Computing in Design and Manufacture (ACDM), IP-CC Press.
  • Ron Breukelaer, Michael Emmerich, and Thomas Bäck. On interactive evolution strategies. In Applications of Evolutionary Computing EvoWorkshops 2006: EvoINTERACTION, volume 3907 of Lecture Notes in Computer Science, pages 530-541, Budapest, Hungary, April 2006. Springer Berlin / Heidelberg.
  • J. Jakumeit, M. Emmerich, and F. Hediger. Inverse modeling and numerical optimization of heater temperatures in a bridgman process. In Modelling of Casting, Welding and Advanced Solidification Processes XI (MCWASP Conference), Opio, France, May 28 - June 2 2006.
  • Michael T.M. Emmerich, Ofer Shir, and Thomas Bäck. Multi-criteria optimization in laser pulse shaping using evolutionary algorithms and kriging metamodels. In MCDM2006, Chania, Greece, June 19-23 2006.
  • M. Emmerich and A. Deutz. A family of test problems with pareto-fronts of variable curvature based on super-spheres. In MCDM 2006, Chania, Greece, June 19-23 2006.
  • Ofer M. Shir, Christian Siedschlag, Thomas Bäck, and Marc J.J. Vrakking. Evolutionary algorithms in the optimization of dynamic molecular alignment. In IEEE WCCI, Vancouver, BC, Canada, July 2006. IEEE.
  • Ofer M. Shir, Christian Siedschlag, Thomas Bäck, and Marc J.J. Vrakking. The complete-basis-functions parameterization in es and its application to laser pulse shaping. In GECCO '06: Proceedings of the 8th annual conference on Genetic and evolutionary computation, pages 1769-1776, New York, NY, USA, July 2006. ACM Press.
  • Christian Siedschlag, Ofer M. Shir, Thomas Bäck, and Marc J.J. Vrakking. Evolutionary algorithms in the optimization of dynamic molecular alignment. Optics Communications, 264(2):511-518, August 2006.
  • Ofer M. Shir and Thomas Bäck. Niche radius adaptation in the cma-es niching algorithm. In 9th International Conference on Parallel Problem Solving from Nature (PPSN IX), volume 4193 of Lecture Notes in Computer Science, pages 142-151, Reykjavik, Iceland, October 2006. Springer Berlin / Heidelberg.
  • E.H. de Graaf and W.A. Kosters, Mining for Stable Patterns: Regular Intervals between Occurrences,
  • 18th Belgium-Netherlands Conference on Artificial Intelligence (BNAIC 2006), Namur, Belgium, 5-6 October 2006; Proceedings pp. 149-155 (P.-Y. Schobbens, W. Vanhoof and G. Schwanen, editors).
  • J. Broekens, T. Cocx and W.A. Kosters, Object-Centered Interactive Multi-Dimensional Scaling: Ask the Expert, 18th Belgium-Netherlands Conference on Artificial Intelligence (BNAIC 2006),
  • Namur, Belgium, 5-6 October 2006; Proceedings pp. 59-66 (P.-Y. Schobbens, W. Vanhoof and G. Schwanen, editors).
  • E.H. de Graaf, J.M. de Graaf and W.A. Kosters, Using Consecutive Support for Genomic Profiling,
  • ECML/PKDD-2006 Workshop on Data and Text Mining for Integrative Biology, Proceedings pp. 16-27 (M. Hilarion and C. Nédellec, editors), Berlin, Germany, 18 September 2006.
  • K.J. Batenburg and W.A. Kosters, A Neural Network Approach to Real-time Discrete Tomography, International Workshop on Combinatorial Image Analysis (IWCIA) 2006, Berlin, Germany, 19-21 June, Lecture Notes in Computer Science 4040, (Ralf Reulke, Ulrich Eckardt, Boris Flach, Uwe Knauer, Konrad Polthier (editors)), pp. 389-403, 2006.
  • Joost N. Kok, Jacek Koronacki, Ramon López de Mántaras, Stan Matwin, Dunja Mladenic, Andrzej Skowron: Machine Learning: ECML 2007, 18th European Conference on Machine Learning, Warsaw, Poland, September 17-21, 2007, Proceedings Springer 2007 125
  • Joost N. Kok, Jacek Koronacki, Ramon López de Mántaras, Stan Matwin, Dunja Mladenic, Andrzej Skowron: Knowledge Discovery in Databases: PKDD 2007, 11th European Conference on Principles and Practice of Knowledge Discovery in Databases, Warsaw, Poland, September 17-21, 2007, Proceedings Springer 2007 124
  • Edgar H. de Graaf, Joost N. Kok, Walter A. Kosters: Clustering Improves the Exploration of Graph Mining Results. AIAI 2007: 13-20 123 
  • Fabrice Colas, Pavel Paclík, Joost N. Kok, Pavel Brazdil: Does SVM Really Scale Up to Large Bag of Words Feature Spaces? IDA 2007: 296-307 122
  • Ofer M. Shir, Joost N. Kok, Thomas Bäck, Marc J. J. Vrakking: Gaining Insights into Laser Pulse Shaping by Evolution Strategies. IWINAC (1) 2007: 467-477 121
  • Hendrik Blockeel, Tijn Witsenburg, Joost N. Kok: Graphs, Hypergraphs, and Inductive Logic Programming. MLG 2007 120
  • Edgar H. de Graaf, Joost N. Kok, Walter A. Kosters: Clustering Co-occurrence of Maximal Frequent Patterns in Streams CoRR abs/0705.0588: (2007) 119
  • Edgar H. de Graaf, Joost N. Kok, Walter A. Kosters: Clustering with Lattices in the Analysis of Graph Patterns CoRR abs/0705.0593: (2007) 118
  • Edgar H. de Graaf, Joost N. Kok, Walter A. Kosters: Mining Patterns with a Balanced Interval CoRR abs/0705.1110: (2007)
  • Peter kok, Boudewijn lelieveldt, Charl Botha, Frist Post, Eric kaijzel, Ivo Que, Clemens Lowik, Johan Reiber, Jouke Dijkstra. INTEGRIM: An image fusion tool for visualization and interpretation of micro-CT and multi-view BLI imaging. Proc. fifth annual meeting of the society for molecular imaging, Hawai 2006, pp296-297.
  • P. Kok, J. Dijkstra, C. P. Botha, F. H. Post, E. Kaijzel, I. Que, C.W.G.M. Lowik, J.H.C. Reiber, B. P. F. Lelieveldt. Integrated visualization of multi-angle bioluminescence imaging and micro CT. Proc. SPIE Medical Imaging 2007, paper nr 6509 65.
  • M. Baiker, J. Milles, A. M. Vossepoel, I. Que, E. L. Kaijzel, C. W. G. M. Löwik, J. H. C. Reiber, J. Dijkstra, B. P. F. Lelieveldt. Fully automated whole-body registration in Mice using an articulated skeleton atlas. Proc. ISBI 2007. (in press)
  • A.E.H. Scheenstra, J. Dijkstra, R.C.G. van de Ven, L. van der Weerd, J.H. C. Reiber. Semi-automated registration of single histology sections with ex vivo MRM volumes. Proc. ASCI Conference 2006. pp 400-405.
  • A.E.H. Scheenstra, J. Dijkstra, R.C.G. van de Ven, L. van der Weerd, J.H. C. Reiber. Automated Registration of Histology sections with ex-vivo MRM volumes. Proc. ISMRM 2006 pp 2012.
  • Y.Z. Wadghiri, M. Douadi, A. Boutajangout, A.A. Asuni, A. Scheenstra, F. Behloul-Admiraal and E.M. Sigurdsson. In Vivo μMEMRI Reveals Age-Dependent Hippocampal Dysfunction in a Tangle Mouse Model of Dementia. ISMRM 2007. (in press)   
  • A.E.H. Scheenstra, J. Dijkstra, R.C.G. van de Ven, L. van der Weerd, J.H.C. Reiber. Automated segmentation of the ex vivo mouse brain. Proc. SPIE Medical Imaging 2007. (in press)
  • A.E.H. Scheenstra, J. Dijkstra, R.C.G. van de Ven, L. van der Weerd, J.H. C. Reiber. Automated edge-driven markov random filed segmentation of ex vivo mouse brain MRM images. Proceedings 2007 IEEE International Symposium on Biomedical Imaging (ISBI 2007): from nano to macro. IEEE, ISBI 2007: 1292-5.
  • Li R, Eggermont J, Emmerich MTM, Bovenkamp EGP, Bäck Th, Dijkstra J, Reiber JHC. Towards dynamic fitness based partitioning for intravasculair ultrasound image analysis. In: Applications of Evolutionary Computing. M. Giacobini et al (Eds.). Evo Workshops 2007, LNCS 4448, Springer-Verlag Berlin Heidelberg 2007: 391-8.
  • Eggermont J, Li R, Bovenkamp EGP, Marquering H, Emmerich MTM, Lugt A van der, Bäck Th, Dijkstra J, Reiber JHC. Optimizing computed tomographic angiography image segmentation using fitness based partitioning. In: Applications of Evolutionary Computing. M. Giacobini et al (Eds). LNCS series 4974. Springer-Verlag Berlin Heidelberg 2008: 275-84.
  • Bovenkamp EGP, Dijkstra J, Bosch JG, Reiber JHC. User-agent cooperation in multiagent IVUS image segmentation. IEEE Transactions on Medical Imaging 2009: 28 (1): 94-105
  • Jeroen S. de Bruin, Joost N. Kok, Nada Lavrac, Igor Trajkovski: On the Design of Knowledge Discovery Services Design Patterns and Their Application in a Use Case Implementation. ISoLA 2008: 649-662
  • Fabrice Colas, Ingrid Meulenbelt, Jeanine J. Houwing-Duistermaat, Margreet Kloppenburg, Iain Watt, Stephanie M. van Rooden, Martine Visser, Johan Marinus, Edward O. Cannon, Andreas Bender, Jacobus J. van Hilten, P. Eline Slagboom, Joost N. Kok: A Scenario Implementation in Rfor Subtype Discovery Examplified on Chemoinformatics Data. ISoLA 2008: 669-683 2007 126
  • Juan Chen, Michael T. M. Emmerich, Rui Li, Joost N. Kok, Thomas Bäck: How to Do Recombination in Evolution Strategies: An Empirical Study. IWINAC (1) 2009: 223-232
  • 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
  • Lenneke W.A van Hooijdonk, Muhammad Ichwan, Thomas F. Dijkmans, Theo G. Schouten, Fons J. Verbeek, Erno Vreugdenhil, Carlos P. Fitzsimons (2008) Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression. BMC Neuroscience 10:2
  • Dmitrieva, J., Verbeek F.J. (2008) Information Visualization from Ontology Proc.  Proceedings 5th international conference on formal ontology in information systems.
  • 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
  • Belmamoune M. and Fons J. 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
  • 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
  • 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
  • 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
  • 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
  • Dmitrieva, J., Verbeek, F.J. (2009) Multi-view Ontology Visualization. Proceedings 11th International Protege Conference  (http://protege.stanford.edu/conference/2009/abstracts/S9P3Dmitrieva.pdf)
  • 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.
  • Papakonstantinou, C., Ioannis Panagiotou, I., Verbeek, F.J. (2009) Tag Based Meta-Search for Browsing the Web: The TicTag Application. Proceedings HCI 2009, Cambridge, United Kingdom (In Press).
  • 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)
  • Papakonstantinou, C., Ioannis Panagiotou, I., Verbeek, F.J. (2009) Tag Based Meta-Search for Browsing the Web: The TicTag Application. Proceedings CHI-NL, Leiden, The Netherlands
  • 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. Proceedings Workshop Emotion and Computing, Paderborn, Germany (In Press)INCF TaskForce Atlassing  (2009) The INCF Digital Atlassing Program – Report in Digital Atlassing Standards in the Rodent Mouse Brain. INCF, -Karolinska Institutet, Stockholm, Sweden.
  • Liefaard LC, Ploeger BA, Molthoff CF, de Jong HW, Dijkstra J, van der Weerd L, Lammertsma AA, Danhof M, Voskuyl RA. Changes in GABAA receptor properties in amygdala kindled animals: in vivo studies using [11C] flumazenil and positron emission tomography. Epilepsia. 2009 Jan;50(1):88-98. Epub 2008 Aug 25. 4:
  • Scheenstra AE, van de Ven RC, van der Weerd L, van den Maagdenberg AM, Dijkstra J, Reiber JH. Automated segmentation of in vivo and ex vivo mouse brain  magnetic resonance images. Mol Imaging. 2009 Jan-Feb;8(1):35-44.
  • Lowik CW, Kaijzel EL, Que I, Van der Pluijm G, Kok P, Lelieveldt BP, Dijkstra J. Non-invasive 3D multi-modality imaging of tumor progression and osteolytic bone metastases in mouse models of cancer BONE, 8756-3282, JUN 2007 (40) 6 Suppl. 2 S230
  • Thesis Alize Scheenstra (defense beginning 2010)

 

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