Publication overview

Solution structure of the second PDZ domain of the neuronal adaptor X11alpha and its interaction with the C-terminal peptide of the human copper chaperone for superoxide dismutase

Duquesne, A. E.Ruijter, M.Brouwer, J.Drijfhout, J. W.Nabuurs, S. B.Spronk, C. A.Vuist...

J Biomol NMR 2005, 32(3): 209

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Reconstruction of the complete ouabain-binding pocket of Na,K-ATPase in gastric H,K-ATPase by substitution of only seven amino acids

Qiu, L. Y.Krieger, E.Schaftenaar, G.Swarts, H. G.Willems, P. H.De Pont, J. J.Koenderi...

J Biol Chem 2005, 280(37): 32349

Erythrocyte antioxidant defense response against cigarette smoking in humans--the glutathione S-transferase vulnerability

Orhan, H.Evelo, C. T.Sahin, G.

J Biochem Mol Toxicol 2005, 19(4): 226

Exploring Lactobacillus plantarum genome diversity by using microarrays

Molenaar, D.Bringel, F.Schuren, F. H.de Vos, W. M.Siezen, R. J.Kleerebezem, M.

J Bacteriol 2005, 187(17): 6119

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Metabolic models for rational improvement of lactic acid bacteria as cell factories

Smid, E. J.van Enckevort, F. J.Wegkamp, A.Boekhorst, J.Molenaar, D.Hugenholtz, J.Siez...

J Appl Microbiol 2005, 98(6): 1326

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

MPP5 recruits MPP4 to the CRB1 complex in photoreceptors

Kantardzhieva, A.Gosens, I.Alexeeva, S.Punte, I. M.Versteeg, I.Krieger, E.Neefjes-Mol...

Invest Ophthalmol.Vis Sci 2005, 46(6): 2192

http://www.ncbi.nlm.nih.gov/pubmed/15914641

Applications of spiking neural networks

Bohte, S. M.Kok, J. N.

Information Processing Letters 2005, 95(6): 519

Frequent subtree mining-an overview

Yun, ChiNijssen, S.Muntz, R. R.Kok, J. N.

In Fundamenta informaticae 2005, 66: 161

The nearest subclass classifier: a compromise between the nearest mean and nearest neighbor classifier

Veenman, C. J.Reinders, M. J.

IEEE Trans Pattern Anal Mach Intell 2005, 27(9): 1417

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Reliable Hierarchical Clustering with the Self-organizing Map

Samsonova, E. V.Baeck, T.Kok, J. N.Ijzerman, A. P.

IDA 2005: 385

Dynamics of reentrant arrhythmias in the human ventricles

Ten Tusscher, K. H. W. J.Panfilov, A. V.Hren, R.

Heart Rhythm 2005: 260

A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays

Alberts, R.Terpstra, P.Bystrykh, L. V.de Haan, G.Jansen, R. C.

Genetics 2005, 171(3): 1437

Niching in evolution strategies

Shir, O. M.Back, T.

GECCO 2005: 915

Advancing in Mining GRaphs, Trees and Sequences

Washio, T.Raedt, L.Kok, J. N.

Fundamental Information 2005, 66: 1

Comparative and functional genomics of lactococci

Kok, J.Buist, G.Zomer, A. L.van Hijum, S. A.Kuipers, O. P.

FEMS Microbiol Rev 2005, 29(3): 411

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Variation and evolution of biomolecular systems: searching for functional relevance

Huynen, M. A.Gabaldon, T.Snel, B.

FEBS Lett 2005, 579(8): 1839

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Gene expression and digit homology in the chicken embryo wing

Welten, M. C.verbeek, F. J.Meijer, A. H.Richardson, M. K.

Evol Dev 2005, 7(1): 18

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

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

Corredor-Adamez, M.Welten, M. C.Spaink, H. P.Jeffery, J. E.Schoon, R. T.de Bakker, M....

Evol Dev 2005, 7(5): 362

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Presentation of the tool ReConn

Ligtenberg, W.P.A.

Cytoscape developers meeting 2005

Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family

Cases, M.Garcia-Serna, R.Hettne, K.Weeber, M.van der Lei, J.Boyer, S.Mestres, J.

Curr Top Med Chem 2005, 5(8): 763

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

The nuclear receptor ligand-binding domain: a family-based structure analysis

Folkertsma, S.van Noort, P. I.Brandt, R. F.Bettler, E.Vriend, G.de Vlieg, J.

Curr Med Chem 2005, 12(9): 1001

Confidence intervals for prohabilistic network classifiers

Egmont-Petersen, M.Feelders, A.Baesens, B.

Computational Statistics and Data Analysis 2005, 49(4): 998

Local structure prediction of proteins

Simossis, V. A.Heringa, J.

Computational Methods for Protein Structure Prediction and Modeling 2005: 207

Local structure prediction of proteins

George, R. A.Simossis, V. A.Heringa, J.

Computational Methods for Protein Structure Prediction and Modeling 2005

Pyramidic Clustering of Large-Scale Microarray Images

O'Neill, P.Fraser, K.Zidong, W.Kellam, P.Kok, J. N.Liu, X.

Comput.J 2005, 48(4): 466

Tumor profiling turmoil

Roepman, P.Holstege, F. C.

Cell Cycle 2005, 4(5): 659

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Substantial changes in gene expression of Wnt, MAPK and TNFalpha pathways induced by TGF-beta1 in cervical cancer cell lines

Kloth, J. N.Fleuren, G. J.Oosting, J.de Menezes, R. X.Eilers, P. H.Kenter, G. G.Gorte...

Carcinogenesis 2005, 26(9): 1493

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Inhibition of a new differentiation pathway in neuroblastoma by copy number defects of N-myc, Cdc42, and nm23 genes

Valentijn, L. J.Koppen, A.van Asperen, R.Root, H. A.Haneveld, F.Versteeg, R.

Cancer Res 2005, 65(8): 3136

Phox2B mutations and the Delta-Notch pathway in neuroblastoma

van Limpt, V.Chan, A.Schramm, A.Eggert, A.Versteeg, R.

Cancer Lett 2005, 228(1): 59

Biological effects of TrkA and TrkB receptor signaling in neuroblastoma

Schramm, A.Schulte, J. H.Astrahantseff, K.Apostolov, O.Limpt, V.Sieverts, H.Kuhfittig...

Cancer Lett 2005, 228(1): 143

Online text mining tools to support discovery in the life sciences

Weeber, M.Kors, J. A.Mons, B. Series, Editor

Briefings in Bioinformatics 2005

Combining microarrays and genetic analysis

Alberts, R.Fu, J.Swertz, M. A.Lubbers, L. A.Albers, C. J.Jansen, R. C.

Brief Bioinform 2005, 6(2): 135

No common denominator for breast cancer lymph node metastasis

Weigelt, B.Wessels, L. F.Bosma, A. J.Glas, A. M.Nuyten, D. S.He, Y. D.Dai, H.Peterse,...

Br J Cancer 2005, 93(8): 924

A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data

van Hijum, S. A.de Jong, A.Baerends, R. J.Karsens, H. A.Kramer, N. E.Larsen, R.den He...

BMC Genomics 2005, 6(1): 77

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Muscle regeneration in dystrophin-deficient mdx mice studied by gene expression profiling

Turk, R.Sterrenburg, E.de Meijer, E. J.van Ommen, G. J.den Dunnen, J. T.Hoen, P. A.

BMC Genomics 2005, 6: 98

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences

Guryev, V.Berezikov, E.Cuppen, E.

BMC Genomics 2005, 6(1): 10

Dissecting systems-wide data using mixture models: application to identify affected cellular processes

Svensson, J. P.de Menezes, R. X.Turesson, I.Giphart-Gassler, M.Vrieling, H.

BMC Bioinformatics 2005, 6: 177

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Thesaurus-based disambiguation of gene symbols

Schijvenaars, B. J.Mons, B.Weeber, M.Schuemie, M. J.van Mulligen, E. M.Wain, H. M.Kor...

BMC Bioinformatics 2005, 6: 149

Which gene did you mean?

Mons, B.

BMC Bioinformatics 2005, 6: 142

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data

Jain, NitinCho, HyungJunO'Connell, MichaelLee, Jae

BMC Bioinformatics 2005, 6(1): 187

http://www.biomedcentral.com/1471-2105/6/187

Targeted discovery tools: proteomics and chromatin immunoprecipitation-on-chip

Le Guezennec, X.Brinkman, A. B.Vermeulen, M.Denissov, S. G.Gazziola, C.Lohrum, M. E.S...

BJU Int 2005, 96: 16

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Locally Adaptive Function Estimation for Binary Regression Models

Jerak, AlexanderLang, Stefan

Biometrical Journal 2005, 47(2): 151

http://apps.isiknowledge.com//InboundService.do?SID=W1hgMN9FP@9AppAFiO...

A protocol for building and evaluating predictors of disease state based on microarray data

Wessels, L. F.Reinders, M. J.Hart, A. A.Veenman, C. J.Dai, H.He, Y. D.van't Veer, L. ...

Bioinformatics 2005, 21(19): 3755

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

A simple and fast secondary structure prediction method using hidden neural networks

Lin, K.Simossis, V. A.Taylor, W. R.Heringa, J.

Bioinformatics 2005, 21(2): 152

The properties of protein family space depend on experimental design

Kunin, V.Teichmann, S. A.Huynen, M. A.Ouzounis, C. A.

Bioinformatics 2005, 21(11): 2618

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Predicting gene function through systematic analysis and quality assessment of high-throughput data

Kemmeren, P.Kockelkorn, T. T.Bijma, T.Donders, R.Holstege, F. C.

Bioinformatics 2005, 21(8): 1644

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes

Jelier, R.Jenster, G.Dorssers, L. C.van der Eijk, C. C.van Mulligen, E. M.Mons, B.Kor...

Bioinformatics 2005, 21(9): 2049

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Testing association of a pathway with survival using gene expression data

Goeman, J. J.Oosting, J.Cleton-Jansen, A. M.Anninga, J. K.van Houwelingen, H. C.

Bioinformatics 2005, 21(9): 1950

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes

Gabaldon, T.Huynen, M. A.

Bioinformatics 2005, 21

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...

Quantile smoothing of array CGH data

Eilers, P. H.de Menezes, R. X.

Bioinformatics 2005, 21(7): 1146

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&d...