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Publication overview

Proteomic profiling of plasma and serum in elderly patients with delirium

van Munster, Barbaravan Breemen, MarielleMoerland, PerrySpeijer, DaveDe Rooij, Sophia...

The Journal of neuropsychiatry and clinical neurosciences 2009, 21(3): 284

http://dx.doi.org/10.1176/appi.neuropsych.21.3.284

Multi-way analysis of lfux distributions across multiple conditions

Verouden, M. P. H.Notebaart, R. A.Westerhuis, J. A.van der Werf, M. J.Teusink, B.Smil...

Journal of Chemometrics 2009, 23: 7

Regression by L1 regularization of smart contrasts and sums (ROSCAS) beats PLS and elastic net in latent variable model

ter Braak, C. J. F.

Journal of Chemometrics 2009

Suppression of inflammatory signaling in monocytes from patients with coronary artery disease

Schirmer, S. H.Fledderus, J. O.van der Laan, A. M.van der Pouw-Kraan, T. C.Moerland, ...

J.Mol.Cell Cardiol. 2009, 46(2): 177

http://www.ncbi.nlm.nih.gov/pubmed/19059264

PDB_REDO: automated re-refinement of X-ray structure models in the PDB

Joosten, R. P.Salzemann, J.Bloch, V.Stockinger, H.Berglund, A. C.Blanchet, C.Bongcam-...

J.Appl.Cryst. 2009, 42: 376

Organ-specific attenuation of murine hepatitis virus strain A59 by replacement of catalytic residues in the putative viral cyclic phosphodiesterase ns2

Roth-Cross, J. K.Stokes, H.Chang, G.Chua, M. M.Thiel, V.Weiss, S. R.Gorbalenya, A. E....

J Virol. 2009, 83(8): 3743

http://www.ncbi.nlm.nih.gov/pubmed/19176619

Biochemical characterization of arterivirus nonstructural protein 11 reveals the nidovirus-wide conservation of a replicative endoribonuclease

Nedialkova, D. D.Ulferts, R.van den, Born E.Lauber, C.Gorbalenya, A. E.Ziebuhr, J.Sni...

J Virol. 2009, 83(11): 5671

http://www.ncbi.nlm.nih.gov/pubmed/19297500

The crystal structures of Chikungunya and Venezuelan equine encephalitis virus nsP3 macro domains define a conserved adenosine binding pocket

Malet, H.Coutard, B.Jamal, S.Dutartre, H.Papageorgiou, N.Neuvonen, M.Ahola, T.Forrest...

J Virol. 2009, 83(13): 6534

http://www.ncbi.nlm.nih.gov/pubmed/19386706

Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites

van Velzen, E. J.Westerhuis, J. A.van Duynhoven, J. P.van Dorsten, F. A.Grun, C. H.Ja...

J Proteome Res 2009, 8(7): 3317

http://www.ncbi.nlm.nih.gov/pubmed/19374449

Analyzing longitudinal microbial metabolomics data

Rubingh, C. M.Bijlsma, S.Jellema, R. H.Overkamp, K. M.van der Werf, M. J.Smilde, A. K...

J Proteome Res 2009, 8(9): 4319

http://www.ncbi.nlm.nih.gov/pubmed/19624157

The effect of preanalytical factors on stability of the proteome and selected metabolites in cerebrospinal fluid (CSF)

Rosenling, T.Slim, C. L.Christin, C.Coulier, L.Shi, S.Stoop, M. P.Bosman, J.Suits, F....

J Proteome Res 2009, 8(12): 5511

http://www.ncbi.nlm.nih.gov/pubmed/19845411

Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems

Vreede, J.Wolf, M. G.de Leeuw, S. W.Bolhuis, P. G.

J Phys.Chem.B 2009, 113(18): 6484

http://www.ncbi.nlm.nih.gov/pubmed/19358572

Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member

Narayanan, B.Niu, W.Joosten, H. J.Li, Z.Kuipers, R. K.Schaap, P. J.Dunaway-Mariano, D...

J Mol.Biol. 2009, 386(2): 486

http://www.ncbi.nlm.nih.gov/pubmed/19133276

Further clinical and molecular delineation of the 9q subtelomeric deletion syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype

Kleefstra, T.van Zelst-Stams, W. A.Nillesen, W. M.Cormier-Daire, V.Houge, G.Foulds, N...

J Med Genet 2009, 46(9): 598

http://www.ncbi.nlm.nih.gov/pubmed/19264732

Systems biology towards life in silico: mathematics of the control of living cells

Westerhoff, H. V.Kolodkin, A.Conradie, R.Wilkinson, S. J.Bruggeman, F. J.Krab, K.van ...

J Math.Biol. 2009, 58(1): 7

http://www.ncbi.nlm.nih.gov/pubmed/18278498

Improved cholesterol phenotype analysis by a model describing how lipoprotein lifecycle processes depend on particle size

van Schalkwijk, D. B.van Ommen, B.van Bochhove, K.Rensen, P. C. N.Havekes, L. M.van d...

J Lipid Research 2009

Influence of clotting time on the protein composition of serum samples based on LC-MS data

Govorukhina, N. I.de, Vries M.Reijmers, T. H.Horvatovich, P.van der Zee, A. G.Bischof...

J Chromatogr.B Analyt.Technol.Biomed Life Sci. 2009, 877(13): 1281

http://www.ncbi.nlm.nih.gov/pubmed/18996063

QSAR models for predicting the similarity in binding profiles for pairs of protein kinases and the variation of models between experimental data sets

Sheridan, R. P.Nam, K.Maiorov, V. N.McMasters, D. R.Cornell, W. D.

J Chem Inf Model 2009, 49(8): 1974

http://www.ncbi.nlm.nih.gov/pubmed/19639957

Exportin 4 mediates a novel nuclear import pathway for Sox family transcription factors

Gontan, C.Guttler, T.Engelen, E.Demmers, J.Fornerod, M.Grosveld, F. G.Tibboel, D.Gorl...

J Cell Biol 2009, 185(1): 27

http://www.ncbi.nlm.nih.gov/pubmed/19349578

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

Doreleijers, J. F.Vranken, W. F.Schulte, C.Lin, J.Wedell, J. R.Penkett, C. J.Vuister,...

J Biomol NMR 2009, 45(4): 389

http://www.ncbi.nlm.nih.gov/pubmed/19809795

How to do recombination in evolution strategies: An empirical study

Chen, J.Emmerich, M. T. M.Li, R.Kok, J.Back, T.

IWINAC 2009

A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder

Littink, K. W.van Genderen, M. M.Collin, R. W.Roosing, S.de Brouwer, A. P.Riemslag, F...

Invest Ophthalmol.Vis Sci 2009, 50(5): 2344

http://www.ncbi.nlm.nih.gov/pubmed/19074807

Correlating MALDI and SIMS imaging mass spectrometric datasets of biological tissue surfaces

Eijkel, G. B.Kukrer Kaleta, B.van der Wiel, I. M.Kros, J. M.Luider, T. M.Heeren, R. M...

Interface Anal. 2009, 41(8): 675

http://www3.interscience.wiley.com/cgi-bin/fulltext/122512410/PDFSTART

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

Roel, G.Gent, Y.Peterson-Maduro, J.Verbeek, F.Destree, O.

Int.Journal of Developmental Biology 2009

http://www.ncbi.nlm.nih.gov/pubmed/19123129

Zebrafish development and regeneration: new tools for biomedical research

Brittijn, S. A.Duivesteijn, S. J.Belmamoune, M.Bertens, L. F.Bitter, W.de Bruijn, J. ...

Int J Dev.Biol. 2009, 53(5): 835

http://www.ncbi.nlm.nih.gov/pubmed/19557689

Personalization of tagging systems

Wang, J.Clements, M.Yang, J.de Vries, A. P.Reinders, M. J. T.

Information processing & management 2009, 46: 58

http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VC8-4WWFN9R-...

The influence of personalization on tag query length in social media search

Clements, M.de Vries, A. P.Reinders, M. J. T.

Information processing & management 2009: 1

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VC8-4WCT02F...

Predicting metabolic fluxes using gene expression differences as constrains

van Berlo, R. J. P.de Ridder, D.Daran, J. M.Daran-Lapujade, P. A. S.Teusink, B.Reinde...

Ieee-acm transactions on computational biology and bioinformatics 2009: 1

http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=05066963

Evolutionary optimization of kernel weights improves protein complex comembership prediction

Hulsman, MarcReinders, Marcel J. T.de Ridder, Dick

IEEE/ACM Trans Comput Biol Bioinform 2009, 6(3): 427

http://dx.doi.org/10.1109/TCBB.2008.137

Automated detection of regional wall motion abnormalities based on a statistical model applied to multiscale short-axis cardiac MR images

Suinesiaputra, A.Frangi, A. F.Kaandorp, T. A. M.Lamb, H. J.Bax, J. J.Reiber, J. H. C....

Ieee transactions on medical imaging 2009, 28(4): 595

http://ieeexplore.ieee.org/search/wrapper.jsp?arnumber=4781566

Dimensionality reduction of hyperspectral data via spectral feautre extraction

Mojaradi, B.brishami-Moghaddam, H.Zoej, M. J. V.Duin, R. P. W.

Ieee transactions on geoscience and remote sensing 2009, 47(7): 2091

Sign language perception research for improving automatic sign language recognition

Ten Holt, G. A.Arendsen, J.de Ridder, H.van Doorn, A. J.Reinders, M. J. T.Hendriks, E...

Human Vision and Electronic Imaging XIV, Proceedings of SPIE IS&T Electronic Imaging 2009, 7240

A critical view of metabolic network adaptations

Papp, B.Teusink, B.Notebaart, R. A.

HFSP J 2009, 3(1): 24

http://www.ncbi.nlm.nih.gov/pubmed/19492021

Folding defects in P-type ATP 8B1 associated with hereditary cholestasis are ameliorated by 4-phenylbutyrate

van der Velden, L. M.Stapelbroek, J. M.Krieger, E.van den Berghe, P. V.Berger, R.Verh...

Hepatology 2009, 51(1): 286

http://www.ncbi.nlm.nih.gov/pubmed/19918981

Reduced expression of ATP7B affected by Wilson disease-causing mutations is rescued by pharmacological folding chaperones 4-phenylbutyrate and curcumin

van den Berghe, P. V.Stapelbroek, J. M.Krieger, E.de, Bie P.van de Graaf, S. F.de Gro...

Hepatology 2009, 50(6): 1783

http://www.ncbi.nlm.nih.gov/pubmed/19937698

Modulation of glycosphingolipid metabolism significantly improves hepatic insulin sensitivity and reverses hepatic steatosis in mice

Bijl, NoraSokolovic,MilkaVrins, CarlosLangeveld, MirjamMoerland, PerryOttenhoff, Roel...

Hepatology 2009, 9999(999)

http://dx.doi.org/10.1002/hep.23175

Situational awareness support to enhance teamwork in collaborative working environments

Kulyk, O.van Dijk, E. M. A. G.van der Vet, P. E.Nijholt, A.Whitworth, B.de Moor, A.

Handbook on Socio-Technical Design and Social Networking Systems 2009: 635

Role of the C-terminal linear region of EGF-like growth factors in ErbB specificity

van der Woning, S. P.Venselaar, H.van, Rotterdam W.Jacobs-Oomen, S.van Leeuwen, J. E....

Growth Factors 2009, 27(3): 163

http://www.ncbi.nlm.nih.gov/pubmed/19384683

Repertoire and evolution of miRNA genes in four divergent nematode species

de Wit, ElzoLinsen, Sam E. V.Cuppen, EdwinBerezikov, Eugene

Genome Research 2009, 19(11): 2064

http://www.ncbi.nlm.nih.gov/pubmed/19755563

Asymmetric relationships between proteins shape genome evolution

Notebaart, R. A.Kensche, P. R.Huynen, M. A.Dutilh, B. E.

Genome Biol. 2009, 10(2)

http://www.ncbi.nlm.nih.gov/pubmed/19216750

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication

Szklarczyk, R.Huynen, M. A.

Genome Biol 2009, 10(11)

http://www.ncbi.nlm.nih.gov/pubmed/19930686

High-resolution genetic mapping of mammalian motor activity levels in mice

Kas, M. J. H.de Mooij-van Malsen, J. G.de Krom, M.van Gassen, K. L. I.van Lith, H. A....

Genes, Brain, and Behavior 2009, 8(1): 13

http://www.ncbi.nlm.nih.gov/pubmed/18721260

The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation

Soler, E.ndrieu-Soler, C.de, Boer E.Bryne, J. C.Thongjuea, S.Stadhouders, R.Palstra, ...

Genes Dev 2009, 24(3): 277

http://www.ncbi.nlm.nih.gov/pubmed/20123907

Enhancing search space diversity in multi-objective evloutionary drug molecule desing using niching

Kruisselbrink, J. W.Aleman, A.Emmerich, M. T. M.Ijzerman, A. P.Bender, A.Back, T.van ...

GECCO 2009

Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation

Guryev, VictorCuppen, Edwin

FEBS Letters 2009, 583(11): 1668

http://www.ncbi.nlm.nih.gov/pubmed/19379744

Gaucher disease: a model disorder for biomarker discovery

Boot, R. G.van Breemen, M. J.Wegdam, W.Sprenger, R. R.de, Jong S.Speijer, D.Hollak, C...

Expert Rev Proteomics 2009, 6(4): 411

http://www.ncbi.nlm.nih.gov/pubmed/19681676

Stability from structure: metabolic networks are unlike other biological networks

van Nes, P.Bellomo, D.Reinders, M. J. T.de Ridder, D.

EURASIP J Bioinform Syst Biol 2009

http://dx.doi.org/10.1155/2009/630695

Video enhancement and restoration

Lagendijk, R. L.Biemond, J.Rares, A.Reinders, M. J. T.

The essential guide to video processing -second edition 2009: 69

http://www.amazon.com/Essential-Guide-Video-Processing/dp/0123744563/r...

Talking to chromatin: post-translational modulation of polycomb group function

Niessen, H. E.Demmers, J. A.Voncken, J. W.

Epigenetics.Chromatin. 2009, 2(1): 10

http://www.ncbi.nlm.nih.gov/pubmed/19723311

Cotranslational assembly of the yeast SET1C histone methyltransferase complex

Halbach, Andr ªZhang, HaidiWengi, AgnieszkaJablonska, ZofiaGruber, Isabel M. L.Halbei...

The EMBO Journal 2009, 28(19): 2959

http://www.ncbi.nlm.nih.gov/pubmed/19713935