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Publication overview

Genomics and Evolution of Nidovirales

Gorbalenya, A. E.Perlman, S.Gallagher, T.Snijder, E.

The Nidoviruses 2008

A note on an extreme case of the generalized optimal discriminant transformation

Loog, M.Wu, X. J.Lu, J. P.Yang, J. Y.Wang, S. T.Kittler, J.

Neurocomputing 2008, 72: 664

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

Guelen, L.Pagie, L.Brasset, E.Meuleman, W.Faza, M. B.Talhout, W.Eussen, B. H.de, Klei...

Nature 2008, 453(7197): 948

http://www.ncbi.nlm.nih.gov/pubmed/18463634

SNP and haplotype mapping for genetic analysis in the rat

Saar, K.Beck, A.Bihoreau, M. T.Birney, E.Brocklebank, D.Chen, Y.Cuppen, E.Demonchy, S...

Nat.Genet 2008, 40(5): 560

http://www.ncbi.nlm.nih.gov/pubmed/18443594

Distribution and functional impact of DNA copy number variation in the rat

Guryev, V.Saar, K.Adamovic, T.Verheul, M.van Heesch, S. A.Cook, S.Pravenec, M.Aitman,...

Nat.Genet 2008, 40(5): 538

http://www.ncbi.nlm.nih.gov/pubmed/18443591

Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans

Ahmed, Z. M.Masmoudi, S.Kalay, E.Belyantseva, I. A.Mosrati, M. A.Collin, R. W.Riazudd...

Nat Genet 2008, 40(11): 1335

http://www.ncbi.nlm.nih.gov/pubmed/18953341

Selectivity in enrichment of PKA RI and RII isoforms and their interactors using modified cAMP affinity resins

Aye, T. T.Mohammed, S.Toorn, H. W.Veen, T. A.Heyden, M. A.Scholten, A.Heck, A. J.

Mol.Cell Proteomics. 2008

http://www.ncbi.nlm.nih.gov/pubmed/19119138

Signature genes as a phylogenomic tool

Dutilh, B. E.Snel, B.Ettema, T. J.Huynen, M. A.

Mol.Biol.Evol. 2008, 25(8): 1659

http://www.ncbi.nlm.nih.gov/pubmed/18492663

Evolution of closely linked gene pairs in vertebrate genomes

Franck, E.Hulsen, T.Huynen, M. A.de Jong, W. W.Lubsen, N. H.Madsen, O.

Mol.Biol Evol. 2008, 25(9): 1909

http://www.ncbi.nlm.nih.gov/pubmed/18566020

Functional role of arginine 375 in transmembrane helix 6 of multidrug resistance protein 4 (MRP4/ABCC4)

El-Sheikh, A. A.van den Heuvel, J. J.Krieger, E.Russel, F. G.Koenderink, J. B.

Mol Pharmacol. 2008, 74(4): 964

http://www.ncbi.nlm.nih.gov/pubmed/18612080

A novel multi-objective optimization scheme for grid resource allocation

Kuijl, A.Emmerich, M. T. M.Li, H.

MGC 2008

Multiple sequence alignment

Pirovano, W.Heringa, J.

Methods Mol.Biol. 2008, 452: 143

http://www.ncbi.nlm.nih.gov/pubmed/18566763

Genetic algorithm based two-mode clustering of metabolomics data

Hageman, J. A.van den Berg, R. A.Westerhuis, J. A.van der Werf, M. J.Smilde, A. K.

Metabolomics 2008(4): 141

Stabilization due to predator interference: comparison of different analysis approaches

van Voorn, G. A.Stiefs, D.Gross, T.Kooi, B. W.Feudel, U.Kooijman, S. A.

Math.Biosci.Eng 2008, 5(3): 567

http://www.ncbi.nlm.nih.gov/pubmed/18616359

Een computerprogramma voor het leren van actieve en passieve gebarenschat aan ernstig slechthorende en dove kinderen

Spaai, G.Fortgens, G.Elzenaar, M.Wenners, E.Lichtenauer, J. F.Hendriks, E.de Ridder, ...

Logopedie en Foniatrie 2008, 80(2): 42

A Reasoning Framework for Solving Nonograms

Batenburg, K. J.Kosters, W. A.

Lecture Notes in Computer Science 2008: 372

On optimizing dissimilarity-based classifier using multi-level fusion strategies

Kim, S. W.Duin, R. P.

Journal of the Institute of Electronics Engineers of Korea, CI 2008, 5(3): 410

Second order structure of scale-space measurements

Markussen, B.Steenstrup Pedersen, K.Loog, M.

Journal of mathematical imaging and vision 2008, 31(2): 207

On the equivalence of linear dimensionality-reducing transformations

Loog, M.

Journal of Machine Learning research 2008, 9: 2489

Genomic studies in ageing research: the need to integrate genetic and gene expression approaches

Passtoors, W. M.Beekman, M.Gunn, D.Boer, J. M.Heijmans, B. T.Westendorp, R. G. J.Zwaa...

Journal of Internal Medicine 2008, 263(2): 153

ISI:000252557900005

Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

Belmamoune, M.verbeek, F. J.

Journal of Integrative Bioinformatics 2008, 5(2)

Towards Design Space Exploration for Biological Systems

Polstra, S.Pronk, T. E.Pimentel, A. D.Breit, T.

Journal of Computers 2008

Development of differential plasma cholesterol diagnosis using a computational model

van Schalkwijk, D. B.van Bochove, C.Havekes, L. M.van Ommen, B.Freidig, A. P.

Journal of Clinical Lipidology 2008, 5: 67

The geometry of ASCA

Smilde, A. K.Hoefsloot, H. C.Westerhuis, J. A.

Journal of Chemometrics 2008(22): 464

Validation of a simple method for measuring cranial deformities (plagiocephalometry)

van Adrichem, L. N.van Vlimmeren, L. A.Cadanova, D.Helders, P. J.Engelbert, R. H.van ...

J.Craniofac.Surg. 2008, 19(1): 15

http://www.ncbi.nlm.nih.gov/pubmed/18216659

Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts

Marques, I. J.Leito, J. T.Spaink, H. P.Testerink, J.Jaspers, R. T.Witte, F.van den, B...

J.Comp Physiol [B] 2008, 178(1): 77

http://www.ncbi.nlm.nih.gov/pubmed/17828398

Functional characterization of the cleavage specificity of the sapovirus chymotrypsin-like protease

Robel, I.Gebhardt, J.Mesters, J. R.Gorbalenya, A.Coutard, B.Canard, B.Hilgenfeld, R.R...

J Virol. 2008, 82(16): 8085

http://www.ncbi.nlm.nih.gov/pubmed/18550673

Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity

Decroly, E.Imbert, I.Coutard, B.Bouvet, M.Selisko, B.Alvarez, K.Gorbalenya, A. E.Snij...

J Virol. 2008, 82(16): 8071

http://www.ncbi.nlm.nih.gov/pubmed/18417574

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution

Kensche, P. R.van Noort, V.Dutilh, B. E.Huynen, M. A.

J R Soc Interface 2008

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

Highly robust, automated, and sensitive online TiO2-based phosphoproteomics applied to study endogenous phosphorylation in Drosophila melanogaster

Pinkse, M. W.Mohammed, S.Gouw, J. W.van, Breukelen B.Vos, H. R.Heck, A. J.

J Proteome.Res. 2008, 7(2): 687

http://www.ncbi.nlm.nih.gov/pubmed/18034456

Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo

Lemeer, S.Pinkse, M. W.Mohammed, S.van, Breukelen B.den, Hertog J.Slijper, M.Heck, A....

J Proteome.Res. 2008, 7(4): 1555

http://www.ncbi.nlm.nih.gov/pubmed/18307296

Rapid free energy calculation of peptide self-assembly by REMD umbrella sampling

Wolf, M. G.Jongejan, J. A.Laman, J. D.de Leeuw, S. W.

J Phys.Chem.B 2008, 112(43): 13493

http://www.ncbi.nlm.nih.gov/pubmed/18841883

Targeted SCX Based Peptide Fractionation for Optimal Sequencing by Collision Induced, and Electron Transfer Dissociation

van der Toorn, H. W. P.Mohammed, S.Gouw, J. W.van Breukelen, B.Heck, A. J.

J Pharm Biomed Anal 2008, 1(8): 379

Biclustering Sparse Binary Genomic Data

Van Uitert, M.Meuleman, W.Wessels, L.

J Comput Biol 2008

Insertional mutagenesis combined with acquired somatic mutations causes leukemogenesis following gene therapy of SCID-X1 patients

Howe, S. J.Mansour, M. R.Schwarzwaelder, K.Bartholomae, C.Hubank, M.Kempski, H.Brugma...

J Clin.Invest 2008, 118(9): 3143

http://www.ncbi.nlm.nih.gov/pubmed/18688286

Statistical data processing in clinical proteomics

Smit, S.Hoefsloot, H. C.Smilde, A. K.

J Chromatogr.B Analyt.Technol.Biomed Life Sci. 2008, 866(1): 77

http://www.ncbi.nlm.nih.gov/pubmed/18033744

Identification by a differential proteomic approach of the induced stress and redox proteins by resveratrol in the normal and diabetic rat heart

Dekkers, D. H.Bezstarosti, K.Gurusamy, N.Luijk, K.Verhoeven, A. J.Rijkers, E. J.Demme...

J Cell Mol Med 2008, 12(5): 1677

http://www.ncbi.nlm.nih.gov/pubmed/18194459

The in vitro RNA synthesizing activity of the isolated arterivirus replication/transcription complex is dependent on a host factor

van Hemert, M. J.de Wilde, A. H.Gorbalenya, A. E.Snijder, E. J.

J Biol Chem. 2008, 283(24): 16525

http://www.ncbi.nlm.nih.gov/pubmed/18411274

Role of the alpha-kinase domain in transient receptor potential melastatin 6 channel and regulation by intracellular ATP

Thebault, S.Cao, G.Venselaar, H.Xi, Q.Bindels, R. J.Hoenderop, J. G.

J Biol Chem 2008, 283(29): 19999

http://www.ncbi.nlm.nih.gov/pubmed/18490453

Automated, feature-based image alignment for high-resolution imaging mass spectrometry of large biological samples

Broersen, A.van, Liere R.Altelaar, A. F.Heeren, R. M.McDonnell, L. A.

J Am.Soc.Mass Spectrom. 2008, 19(6): 823

http://www.ncbi.nlm.nih.gov/pubmed/18403214

Quantitative prediction of amyloid fibril growth of short peptides from simulations: calculating association constants to dissect side chain importance

Wolf, M. G.Jongejan, J. A.Laman, J. D.de Leeuw, S. W.

J Am.Chem.Soc. 2008, 130(47): 15772

http://www.ncbi.nlm.nih.gov/pubmed/18983145

Time-Course of Cytokines During Delirium in Elderly Patients with Hip Fractures

van Munster, B. C.Korevaar, J. C.Zwinderman, A. H.Levi, M.Wiersinga, W. J.de Rooij, S...

J Am Geriatr.Soc. 2008

http://www.ncbi.nlm.nih.gov/pubmed/18691278

Creating gene set activity profiles with time-series expression data

Knijnenburg, T. A.Wessels, L. F. A.Reinders, M. J. T.

International Journal of Bioinformatics Research and ApplicationsKnijnenburg2007a 2008

Zebrafish Developmental Patterning: New Tools for Medical Research

Richardson, M. K.Bertens, L. F. M.Belmamoune, M.verbeek, F. J.

Int.Journal of Developmental Biology 2008

Screen of MicroRNA targets in zebrafish using heterogeneous data sources; a case study for dre-miR-10 and dre-miR-196

Zhang, F.Yanju,Woltering, J. M.Verbeek, F.

Int.J.of Mathematical, Physical and Engineering Sciences 2008

Continuation of connecting orbits in 3d-ODEs (I) point-to-cycle connections

Kooi, B. W.van Voorn, G. A.Doedel, E. J.Kuznetzov, Y. A.

Int.J.of Bifurcation and Chaos 2008

https://www.researchgate.net/publication/1894054_Continuation_of_conne...

Literature-based concept profiles for gene annotation: the issue of weighting

Jelier, R.Schuemie, M. J.Roes, P. J.van Mulligen, E. M.Kors, J. A.

Int.J Med.Inform. 2008, 77(5): 354

http://www.ncbi.nlm.nih.gov/pubmed/17827057

On the measurement of genetic interactions

Franke, L.de Jong, E. D.Siebes, A.

Int. Symposium of CLS 2008

http://www.cs.uu.nl/groups/ADA/people/siebes/

Probabilistic relevance ranking for collaborative filtering

Wang, J.Robertson, S.de Vries, A. P.Reinders, M. J. T.

Information Retrieval 2008: 477

Structuring mined knowledge for the support of hypothesis generation in molecular biology

Roos, M.Marshall, M. S.Gibson, A. P.Adriaans, P. W.

In Proceedings First International Workshop on Semantic Web Applications and Tools for Life Science 2008