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Publication overview

Creatine kinase in energy metabolic signaling in muscle

Kongas, O.van Beek, J. H. G. M.

Nature Proceedings 2007

http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=BIO...

Beyond standardization: dynamic software infrastructures for systems biology

Swertz, M. A.Jansen, R. C.

Nat Rev Genet 2007, 8(3): 235

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

MetaNetwork: a computational protocol for the genetic study of metabolic networks

Fu, J.Swertz, M. A.Keurentjes, J. J.Jansen, R. C.

Nat Protoc 2007, 2(3): 685

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

MMTV insertional mutagenesis identifies genes, gene families and pathways involved in mammary cancer

Theodorou, V.Kimm, M. A.Boer, M.Wessels, L.Theelen, W.Jonkers, J.Hilkens, J.

Nat Genet 2007, 39(6): 759

http://dx.doi.org/10.1038/ng2034

Dichotomy in post-genomic microbiology

Felis, G. E.Molenaar, D.Dellaglio, F.Hylckama Vlieg, J. E.

Nat Biotechnol 2007, 25(8): 848

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

Personalization on a peer-to-peer television system

Wang, J.Pouwelse, J.Fokker, J.de Vries, A. P.Reinders, M. J. T.

Multimedia Tools and Applications 2007

Chromosome rearrangements and the evolution of genome structuring and adaptability

Crombach, A.Hogeweg, P.

Mol.Biol.Evol. 2007, 24(5): 1130

http://www.ncbi.nlm.nih.gov/pubmed/17322554

The use of in vitro peptide binding profiles and in silico ligand-receptor interaction profiles to describe ligand-induced conformations of the retinoid X receptor alpha ligand-binding domain

Folkertsma, S.van Noort, P. I.de Heer, A.Carati, P.Brandt, R.Visser, A.Vriend, G.de V...

Mol Endocrinol 2007, 21(1): 30

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

A tutorial for DNA microarray expression-profiling

van Bakel, H.Holstege, F. C. P.

Mol Cell Tutorial 2007

Identification of glioma neovascularization-related proteins by using MALDI-FTMS and nano-LC fractionation to microdissected tumor vessels

Mustafa, D. A.Burgers, P. C.Dekker, L. J.Charif, H.Titulaer, M. K.Smitt, P. A.Luider,...

Mol Cell Proteomics 2007, 6(7): 1147

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

Towards a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae

Collins, S. R.Kemmeren, P.Zhao, X. C.Greenblatt, J. F.Spencer, F.Holstege, F. C.Weiss...

Mol Cell Proteomics 2007

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

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes

de Groot, M. J.ran-Lapujade, P.van Breukelen, B.Knijnenburg, T. A.de Hulster, E. A.Re...

Microbiology 2007, 153: 3864

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

Heteroclinic orbits indicate overexploitation in predator-prey systems with a strong Allee effect

van Voorn, G. A.Hemerik, L.Boer, M. P.Kooi, B. W.

Math.Biosci. 2007, 209(2): 451

http://www.ncbi.nlm.nih.gov/pubmed/17521681

A new class of non-linear stochastic population models with mass conservation

Kooijman, S. A.Grasman, J.Kooi, B. W.

Math.Biosci. 2007, 210(2): 378

http://www.ncbi.nlm.nih.gov/pubmed/17659307

A biodiversity-inspired approach to aquatic ecosystem modelling

Bruggeman, J.Kooijman, S. A. L. M.

Limnol Oceanogr 2007

Ectopic retroviral expression of LMO2, but not IL2Rgamma, blocks human T-cell development from CD34+ cells: implications for leukemogenesis in gene therapy

Pike-Overzet, K.de Ridder, D.Weerkamp, F.Baert, M. R. M.Verstegen, M. M. A.Brugman, M...

Leukemia 2007, 21(4): 754

http://dx.doi.org/10.1038/sj.leu.2404563

From micro to macro: how the overlap graph determines the reduction graph in ciliates

Rozenberg, G.Brijder, R.Hoogeboom, H. J.

Lecture Notes in Computer Science 2007

http://dx.doi.org/10.1007/978-3-540-74240-1_14

Kernel Combination Versus Classifier Combination

Lee, S. W.Verzakov, S.Duin, R. P. W.

Lecture Notes in Computer Science 2007(4472): 22

On Combining Dissimilarity-Based Classifiers to Solve the Small Sample Size Problem for Appearance-Based Face Recognition

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

Lecture Notes in Computer Science 2007(4509): 110

A string-baed model for simple gene assembly

Brijder, R.Petre, I.Langille, M.

Lecture Notes in Computer Science 2007

http://dx.doi.org/10.1007/978-3-540-74240-1_15

Characterizing reduction graphs for gene assembly in ciliates

Brijder, R.Hoogeboom, H. J.

Lecture Notes in Computer Science 2007

http://dx.doi.org/10.1007/978-3-540-73208-2_14

Group-induced vector spaces

Bicego, M.Pekalska, E.Duin, R. P. W.

Lecture Notes in Computer Science 2007(4472): 190

Producer/Consumer in membrane systems and petri nets

Bernardini, F.Gheorghe, M.

Lecture Notes in Computer Science 2007

http://dx.doi.org/10.1007/978-3-540-73001-9_5

Validation of SELDI TOF MS serum protein profiles for renal cell carcinoma in new populations

Engwegen, J. Y.Mehra, N.Haanen, J. B.Bonfrer, J. M.Schellens, J. H.Voest, E. E.Beijne...

Lab Invest 2007

On the generality of crowding: Visual crowding in size, saturation, and hue compared to orientation

van den Berg, R.Roerdink, J. B.Cornelissen, F. W.

Journal of Vision 2007, 7(2): 1

TIMP: an R package for modeling multi-way spectroscopic measures

Mullen, K. M.van Stokkum, I. H. M.

Journal of Statistical Software 2007, 18

http://www.jstatsoft.org/v18/i03/

An introduction to the special volume "Spectroscopy and Chemometrics in R"

Mullen, K. M.van Stokkum, I. H. M.

Journal of Statistical Software 2007, 18

http://www.jstatsoft.org/v18/i01/

FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks

Binsl, T. W.Mullen, K. M.van Stokkum, I. H. M.Heringa, J.van Beek, J. H. G. M.

Journal of Statistical Software 2007, 18(7): 1

VLAM-G: Interactive Data Driven Workflow Engine for Grid-enabled Resources

Korkhov, V.Vasyunin, A.Wibisono, A.Belloum, A.Inda, M.Roos, M.Breit, T.de Laat, C.Her...

Journal of Scientific Programming 2007

Developmental Anatomy Ontology of Zebrafish: an Integrative semantic framework

Belmamoune, M.verbeek, F. J.

Journal of Integrative Bioinformatics 2007

Algorithms for separable nonlinear least squares with application to modelling time-resolved spectra

Mullen, K. M.Vengris, M.van Stokkum, I. H. M.

Journal of Global Optimization 2007, 38: 201

Grey Component Analysis

Westerhuis, J. A.Derks, E. P. P. A.Hoefsloot, H. C. J.Smilde, A. K.

Journal of Chemometrics 2007

Comparative Urine Analysis by Liquid Chromatography-Mass Spectrometry and Multivariate Statistics: Method Development, Evaluation, and Application to Proteinuria

Kemperman, R. F.Horvatovich, P. L.Hoekman, B.Reijmers, T. H.Muskiet, F. A.Bischoff, R...

J.Proteome Res. 2007, 6(1): 194

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

A flexible approach to induced fit docking

Nabuurs, S. B.Wagener, M.de, Vlieg J.

J.Med.Chem. 2007, 50(26): 6507

http://www.ncbi.nlm.nih.gov/pubmed/18031000

The M235T polymorphism in the angiotensinogen gene is associated with the risk of malignant hypertension in white patients

van den Born, B. J.van Montfrans, G. A.Uitterlinden, A. G.Zwinderman, A. H.Koopmans, ...

J.Hypertens. 2007, 25(11): 2227

http://www.ncbi.nlm.nih.gov/pubmed/17921816

Influence of (sub)mesoscale eddies on the soft-tissue carbon pump

Dijkstra, H. A.Omta, A. W.Kooijman, S. A. L. M.

J.Geophys.Res. 2007

http://www.phys.uu.nl/%7Edijkstra/pubs2006.html

FOXO3a induces differentiation of Bcr-Abl-transformed cells through transcriptional down-regulation of Id1

Birkenkamp, K. U.Essafi, A.van, der V.da, Costa M.Hui, R. C.Holstege, F.Koenderman, L...

J.Biol.Chem. 2007, 282(4): 2211

http://www.ncbi.nlm.nih.gov/pubmed/17132628

Likelihood of crystallization: experimental and computational approaches

Carugo, O.jnovic-Carugo, K.Gorbalenya, A. E.Tucker, P.

J.Appl.Cryst. 2007, 40: 392

Human coronavirus 229E papain-like proteases have overlapping specificities but distinct functions in viral replication

Ziebuhr, J.Schelle, B.Karl, N.Minskaia, E.Bayer, S.Siddell, S. G.Gorbalenya, A. E.Thi...

J Virol 2007

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

Arterivirus Subgenomic mRNA Synthesis and Virion Biogenesis Depend on the Multifunctional nsp1 Autoprotease

Tijms, M. A.Nedialkova, D. D.Zevenhoven-Dobbe, J. C.Gorbalenya, A. E.Snijder, E. J.

J Virol 2007, 81(19): 10496

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

Structural and functional characterization of sapovirus RNA-dependent RNA polymerase

Fullerton, S. W.Blaschke, M.Coutard, B.Gebhardt, J.Gorbalenya, A.Canard, B.Tucker, P....

J Virol 2007, 81(4): 1858

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

Examples of NIR based real time release in tablet manufacturing

Skibsted, E. T.Westerhuis, J. A.Smilde, A. K.Witte, D. T.

J Pharm Biomed Anal 2007, 43(4): 1297

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

Identification of novel biomarkers in pediatric primitive neuroectodermal tumors and ependymomas by proteome-wide analysis

de Bont, J. M.den Boer, M. L.Kros, J. M.Passier, M. M.Reddingius, R. E.Smitt, P. A.Lu...

J Neuropathol Exp Neurol 2007, 66(6): 505

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

Evidence for functional significance of the permuted C motif in Co2+-stimulated RNA-dependent RNA polymerase of infectious bursal disease virus

Letzel, T.Mundt, E.Gorbalenya, A. E.

J Gen Virol 2007, 88: 2824

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

Gene-expression and immunohistochemical study of specific T-cell subsets and accessory cell types in the transformation and prognosis of follicular lymphoma

Glas, A. M.Knoops, L.Delahaye, L.Kersten, M. J.Kibbelaar, R. E.Wessels, L. A.van Laar...

J Clin Oncol 2007, 25(4): 390

http://dx.doi.org/10.1200/JCO.2006.06.1648

Gammaretrovirus-mediated correction of SCID-X1 is associated with skewed vector integration site distribution in vivo

Schwarzwaelder, K.Howe, S. J.Schmidt, M.Brugman, M. H.Deichmann, A.Glimm, H.Schmidt, ...

J Clin Invest 2007, 117(8): 2241

http://dx.doi.org/10.1172/JCI31661

Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy

Deichmann, A.Hacein-Bey-Abina, S.Schmidt, M.Garrigue, A.Brugman, M. H.Hu, J.Glimm, H....

J Clin Invest 2007, 117(8): 2225

http://dx.doi.org/10.1172/JCI31659

Evaluation of techniques for increasing recall in a dictionary approach to gene and protein name identification

Schuemie, M. J.Mons, B.Weeber, M.Kors, J. A.

J Biomed Inform 2007, 40(3): 316

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

Gene expression profiling of liver cells after copper overload in vivo and in vitro reveals new copper-regulated genes

Muller, P.van Bakel, H.van de Sluis, B.Holstege, F.Wijmenga, C.Klomp, L. W.

J Biol Inorg Chem 2007, 12(4): 495

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

Role of the synthase domain of Ags1p in cell wall alpha-glucan biosynthesis in fission yeast

Vos, A.Dekker, N.Distel, B.Leunissen, J. A.Hochstenbach, F.

J Biol Chem 2007, 282(26): 18969

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