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Publication overview

Approaches to microRNA discovery

Berezikov, E.Cuppen, E.Plasterk, R. H.

Nat Genet 2006, 38

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

Analogie based video editing

Yan, W. Q.Wang, J.Kankanhalli, M. S.

Multimedia systems 2006, 11: 3

Nuclear pore components are involved in the transcriptional regulation of dosage compensation i Drosophila

Mendjan, S.Taipale, M.Kind, J.Gebhardt, P.Scheider, M.Vermeulen, M.Buscaino, A.Duncan...

Mol.Cell. 2006, 21: 811

Feed-forward loop circuits as a side effect of genome evolution

Cordero, O. X.Hogeweg, P.

Mol.Biol.Evol. 2006, 23(10): 1931

http://www.ncbi.nlm.nih.gov/pubmed/16840361

When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

Kresnowati, M. T.van Winden, W. A.Almering, M. J.ten Pierick, A.Ras, C.Knijnenburg, T...

Mol Syst Biol 2006, 2: 49

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

GRIS: Glycoprotein-hormone receptor information system

Van Durme, J.Horn, F.Costagliola, S.Vriend, G.Vassart, G.

Mol Endocrinol 2006, 20(9): 2247

A Quest for Human and Mouse Embryonic Stem Cell-specific Proteins

van Hoof, D.Passier, R.Ward-Van Oostwaard, D.Pinkse, M. W.Heck, A. J.Mummery, C. L.Kr...

Mol Cell Proteomics 2006, 5(7): 1261

Mass spectrometric identification of human prostate cancer-derived proteins in serum of xenograft-bearing mice

van den Bemd, G. J.Krijgsveld, J.Luider, T. M.van Rijswijk, A. L.Demmers, J. A.Jenste...

Mol Cell Proteomics 2006

Uncleaved TFILA is a substrate for Taspase 1 and active in transcription

Zhou, H.Spicuglia, S.Hsieh, J. J.Mitsiou, D. J.Hoiby, T.Veenstra, G. J.Korsmeyer, S. ...

Mol Cell Biol 2006, 26(7): 2728

A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin

Vermeulen, M.Walter, W.Le Guezennec, X.Kim, J.Edayathumangalam, R. S.Lasonder, E.Luge...

Mol Cell Biol 2006, 26(14): 5226

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

Peroxisome proliferator-activated receptor subtype- and cell-type-specific activation of genomic target genes upon adenoviral transgene delivery

Nielsen, R.Grontved, L.Stunnenberg, H. G.Mandrup, S.

Mol Cell Biol 2006, 26(15): 5698

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

Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA

Andrau, J. C.van de Pasch, L.Lijnzaad, P.Bijma, T.Koerkamp, M. G.van de Peppel, J.Wer...

Mol Cell 2006, 22(2): 179

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

Dont' Say Everything, Mining and Learning with Graphs

Nijssen, S.Kok, J. N. Series, Editor

MLG 2006 with ECML/PKDD 2006 2006

The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment

Boekhorst, J.Wels, M.Kleerebezem, M.Siezen, R. J.

Microbiology 2006, 152: 3175

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

Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria

Boekhorst, J.Helmer, Q.Kleerebezem, M.Siezen, R. J.

Microbiology 2006, 152: 273

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

How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria

Deutscher, J.Francke, C.Postma, P. W.

Microbiol Mol Biol Rev 2006, 70(4): 939

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

Membrane systems with external control

Rozenberg, G.Cavaliere, M.Brijder, R.

Lecture Notes in Computer Science 2006

A modeling approach based on p systems with bounded parallelism

Romero-Campero, F. J.Bernardini, F.

Lecture Notes in Computer Science 2006

Computational comleteness of tissue p systems with conditional uniport

Bernardini, F.Verlan, S.Margensten, M.Gheorghe, M.

Lecture Notes in Computer Science 2006

Tissue p systems with communication modes

Bernardini, F.Freund, R. W.

Lecture Notes in Computer Science 2006

Applicability of loop recombination in ciliates using the breakpoint graph

Brijder, R.Muskulus, M.Hoogeboom, H. J.

Lecture Notes in Bioinformatics 2006

Compression Picks Item Sets That Matter

van Leeuwen, M.Vreeken, J.Siebes, A.

Knowledge Discovery in Databases: PKDD 2006: 585

http://www.springerlink.com/content/2513p1jq6p22527t/

Model selection and estimation in regression with grouped variables

Yuan, MingLin, Yi

Journal of the Royal Statistical Society Series B 2006, 68(1): 49

http://dx.doi.org/10.1111/j.1467-9868.2005.00532.x

Testing against a high-dimensional alternative

Goeman, J. J.Geer, S. A.Houwelingen, H. C.

Journal of the Royal Statistical Society 2006: 477

Accretive serial modular growth of the demosponge: ultrastructural and magnetic resonance imaging of the silicious skeleton

Manz, B.Belikov, S. I.Mietchen, D.Rotenberg, M.Kaluzhnaya, O. V.Kaandorp, J. A.Reiber...

Journal of Structural Biology 2006

Proteolytic processing of the Equine arteritis virus replicase polyprotein pp1a: importance of the major and minor processingpathways and internal cleavage of non-structural protein 7

van Aken, D.Zevenhoven-Dobbe, J. C.Gorbalenya, A. E.Snijder, E. J.

J.Gen.Virol. 2006, 87: 3473

Maximum likelihood Scaling (MALS)

Hoefsloot, H. C. J.Verouden, M. P. H.Westerhuis, J. A.Smilde, A. K.

J.Chemometrics 2006

Visual search near threshold: Some features are more equal than others

Hannus, A.van den Berg, R.Bekkering, H.Roerdink, J. B.Cornelissen, F. W.

J Vis 2006, 6(4): 523

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

Mutagenesis analysis of the nsp4 main proteinase reveals determinants of arterivirus replicase polyprotein autoprocessing

van Aken, D.Snijder, E. J.Gorbalenya, A. E.

J Virol 2006, 80(7): 3428

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

Evidence for functional protein interactions required for poliovirus RNA replication

Teterina, N. L.Levenson, E.Rinaudo, M. S.Egger, D.Bienz, K.Gorbalenya, A. E.Ehrenfeld...

J Virol 2006, 80(11): 5327

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

Site-directed mutagenesis of the Nidovirus replicative endoribonuclease NendoU exerts pleiotropic effects on the arterivirus life cycle

Posthuma, C. C.Nedialkova, D. D.Zevenhoven-Dobbe, J. C.Blokhuis, J. H.Gorbalenya, A. ...

J Virol 2006, 80(4): 1653

Discussion of 'Bayesian palaeoclimate reconstruction' by J. Haslett et al

ter Braak, C. J. F.

J Roy Stat 2006(169): 431

Analysis of the cGMP/cAMP interactome using a chemical proteomics approach in mammalian heart tissue validates sphingosine kinase type 1-interacting protein as a genuine and highly abundant AKAP

Scholten, A.Poh, M. K.van Veen, T. A.van Breukelen, B.Vos, M. A.Heck, A. J.

J Proteome Res 2006, 5(6): 1435

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

In-gel isoelectric focusing of peptides as a tool for improved protein identification

Krijgsveld, J.Gauci, S.Dormeyer, W.Heck, A. J.

J Proteome Res 2006, 5(7): 1721

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

Fast empirical pKa prediction by Ewald summation

Krieger, E.Nielsen, J. E.Spronk, C. A.Vriend, G.

J Mol Graph Model 2006, 25(4): 481

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

QCRNA 1.0: A database of quantum calculations for RNA catalysis

Giese, T. J.Gregersen, B. A.Liu, Y.Nam, K.Mayaan, E.Moser, A.Range, K.Faza, O. N.Lope...

J Mol Graph Model 2006, 25(4): 423

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

Predicting disease genes using protein-protein interactions

Oti, M.Snel, B.Huynen, M. A.Brunner, H. G.

J Med Genet 2006, 43: 691

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

Longitudinal Assessment of Alzheimer's Beta-Amyloid Plaque Development in Transgenic Mice Monitored by in Vivo Magnetic Resonance Microimaging

Braakman, N.Matysik, J.van Duinen, S. G.Verbeek, F.Schliebs, R.de Groot, H. J.Alia, A...

J Magn Reson Imaging 2006, 24(3): 530

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

Identification of protease and ADP-ribose 1''-monophosphatase activities associated with transmissible gastroenteritis virus non-structural protein 3

Putics, A.Gorbalenya, A. E.Ziebuhr, J.

J Gen Virol 2006, 87: 651

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

Analysis of human serum by liquid chromatography-mass spectrometry: improved sample preparation and data analysis

Govorukhina, N. I.Reijmers, T. H.Nyangoma, S. O.van der Zee, A. G.Jansen, R. C.Bischo...

J Chromatogr A. 2006, 1120: 142

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

Substructure Mining Using Elaborate Chemical Representation

Nijssen, S.Kok, J.Back, T.Ijzerman, A. P.

J Chem Inf Model 2006, 46(2): 597

Mining a chemical database for fragment co-occurrence: discovery of "chemical cliches"

Lameijer, E. W.Kok, J. N.Back, T.Ijzerman, A. P.

J Chem Inf Model 2006, 46(2): 553

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

Substructures mining using elaborate chemical representation

Kazius, J.Nijssen, S.Kok, J.Back, T.Ijzerman, A. P.

J Chem Inf Model 2006, 46(2): 597

The molecule evoluator. An interactive evolutionary algorithm for the design of drug-like molecules

Lameijer, E. W.Kok, J. N.Back, T.Ijzerman, A. P.

J Chem Inf and Mod 2006, 46: 545

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

Diks, S. H.Bink, R. J.van de Water, S.Joore, J.van Rooijen, C.verbeek, F. J.den Herto...

J Cell Biol 2006, 174(4): 581

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

Negative constraints underlie the ErbB specificity of epidermal growth factor-like ligands

van der Woning, S. P.van, Rotterdam W.Nabuurs, S. B.Venselaar, H.Jacobs-Oomen, S.Wing...

J Biol Chem 2006, 281(52): 40033

http://www.ncbi.nlm.nih.gov/pubmed/17032651

A genome-scale model of Lactobacillus plantarum: an essential tool for integration of functional genomics data and for exploring metabolic capacities

Teusink, B.Wiersma, A.Francke, C.Molenaar, D.Siezen, R. J.Smid, E. J.

J Biol Chem 2006, 281: 40041

Evaluation of a gene network extraction method on synthetic data

de Jong, E. D.Siebes, A.

ISNB '06 2006

http://people.cs.uu.nl/dejong/publications/isnb.pdf

Estimating spatial patterns of biomass and nitrogen status grasslands through imaging spectrometry

Clevers, J. G. P. W.Van der Heijden, G. W. A. M.Verzakov, S.Schaepman, M.

International archives of photogrammetry, remote sensing and spatial information sciences, ISPRS WG VII/1 2006: 56

Mixtures of Monotone Networks for Prediction

Velikova, M.Daniels, H.Feelders, A.

Intern J of Computational Intelligence 2006, 3(3): 204