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Publication overview

Reducibility of gene patterns in ciliates usingthe breakpoint graph

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

Theor.Comput.Sci. 2006

http://www.liacs.nl/~rbrijder/index.shtml#PUBLICATIONS

Time-dependent hierarchical regulation analysis: deciphering cellular adaptation

Bruggeman, F. J.de, Haan J.Hardin, H.Bouwman, J.Rossell, S.van, Eunen K.Bakker, B. M....

Syst.Biol.(Stevenage.) 2006, 153(5): 318

http://www.ncbi.nlm.nih.gov/pubmed/16986307

A molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein?

Pastore, C.Adinolfi, S.Huynen, M. A.Rybin, V.Martin, S.Mayer, M.Bukau, B.Pastore, A.

Structure 2006, 14(5): 857

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

GTP-Ras disrupts the intramolecular complex of C1 and RA domains of Nore1

Harjes, E.Harjes, S.Wohlgemuth, S.Muller, K. H.Krieger, E.Herrmann, C.Bayer, P.

Structure 2006, 14(5): 881

http://www.ncbi.nlm.nih.gov/pubmed/16698549

Augmented embedding of dissimilarity data into (pseudo-) Euclidean space

Harol, A.Pekalska, E. M.Verzakov, S.Duin, R. P. W.

Structural, syntactic and statistical pattern recognition 2006, 4109: 613

Structural inference of sensor-based measurements

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

Structural, syntactic and statistical pattern recognition 2006, 4109: 41

A Markov Chain Monte Carlo version of the genetic Agorithm Differential Evolution: easy Bayesian computing for real parameter spaces

ter Braak, C. J. F.

Statistics and Computing 2006(16): 239

Assessing genetic effects in survival data by correlating martingale residuals with an application to age at onset of Huntington disease

Wintrebert, C. M.Zwinderman, A. H.Maat-Kievit, A.Roos, R. A.van Houwelingen, H. C.

Stat Med 2006, 25(18): 3190

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

Approximate sample size calculations with microarray data: an illustration

Ferreira, J. A.Zwinderman, A.

Stat Appl Genet Mol Biol 2006, 5

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

Why don't you see what I mean? Prospects and limitations od current automatic sign recognition research

Ten Holt, G. A.Hendriks, P.Andringa, T. C.

Sign Language Studies 2006, 6: 416

Introducing a population into a steady community: the critical case, the center manifold and the direction of bifurcation

Boldin, B.

SIAM Journal on Applied Mathematics 2006: 1424

Item sets that compress

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

SIAM Conference on Data Mining 2006

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

Toward automatic reconstruction of a highly resolved tree of life

Ciccarelli, F. D.Doerks, T.Von Mering, C.Creevey, C. J.Snel, B.Bork, P.

Science 2006, 311(5765): 1283

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

Factor correction as a tool to eliminate between-session variation in replicate experiments: application to molecular biology and retrovirology

Ruijter, J. M.Thygesen, H. H.Schoneveld, O. J.Das, A. T.Berkhout, B.Lamers, W. H.

Retrovirology 2006, 3: 2

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

A comparison of gene interaction measures

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

RECOMB '06 2006

http://people.cs.uu.nl/dejong/publications/recomb06.pdf

Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra

van Breukelen, B.Barendregt, A.Heck, A. J.van den Heuvel, R. H.

Rapid Commun Mass Spectrom 2006, 20: 2490

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

Specific peptides identified by MALDI-TOF Mass Spectrometry in placental tissue from pregnancies complicated by early onset preclampsia attained by laser capture dissection

de Groot, C. J. M.Guzel, C.Steegers-Theunissen, R. P. M.De Maat, M.Dirkxs, P.Roes, E....

Proteomics Clin.Appl. 2006

Comparison of electrophysiological models for human ventricular cells and tissues

ten Tusscher, K. H.Bernus, O.Hren, R.Panfilov, A. V.

Prog.Biophys.Mol.Biol. 2006, 90(1): 326

http://www.ncbi.nlm.nih.gov/pubmed/16002127

System reduction of nonlinear positive systems by linearization and truncation positive systems

van Schuppen, J. H.Hardin, H.

Proceedings of the 2nd multidisciplinary symposium on positive systems: theory and applications 2006

http://homepages.cwi.nl/%7Eschuppen/papers/publications.htm

Observers for linear positive systems

van Schuppen, J. H.Hardin, H.

Proc.International Symposium MTNS 2006

http://homepages.cwi.nl/~schuppen/papers/publications.htm
http://homepages.cwi.nl/~schuppen/papers/publications.html#5

Controlling methicillin-resistant Staphylococcus aureus: quantifying the effects of interventions and rapid diagnostic testing

Bootsma, M. C.Diekmann, O.Bonten, M. J.

Proc Natl.Acad.Sci.U.S.A 2006, 103(14): 5620

http://www.ncbi.nlm.nih.gov/pubmed/16565219

Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA synthesis

Minskaia, E.Hertzig, T.Gorbalenya, A. E.Campanacci, V.Cambillau, C.Canard, B.Ziebuhr,...

Proc Natl Acad Sci U S A 2006, 103(13): 5108

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

Haplotype Block Structure is Conserved across Mammals

Guryev, V.Smits, B. M.van de Belt, J.Verheul, M.Hubner, N.Cuppen, E.

PLoS Genet 2006, 2(7)

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

Traditional biomolecular structure determination by NMR spectroscopy allows for major errors

Nabuurs, S. B.Spronk, C. A.Vuister, G. W.Vriend, G.

PLoS Comput Biol 2006, 2(2)

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens

de Ridder, J.Uren, A.Kool, J.Reinders, M.Wessels, L.

PLoS Comput Biol 2006, 2(12)

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

The Complementary Extractable and Ester-Bound Lipids in a Soil Profile Under Pine

Nierop, K. G. J.Jansen, B.Hageman, J. A.Verstraten, J. M.

Plant Soil 2006: 1

CDNA array analysis of stress-induced gene expression in barley androgenesis

Maraschin, S. D. F.Caspers, M.Potokina, E.Wulfert, F.Graner, A.Spaink, H. P.Wang, M.

Physiologia Plantarum 2006(127): 535

Comment on "Linking population-level models with growing networks: a class of epidemic models"

Bootsma, M. C.Diekmann, O.

Phys.Rev.E.Stat.Nonlin.Soft.Matter Phys. 2006, 74(1): 18101

http://www.ncbi.nlm.nih.gov/pubmed/16907218

Cell model for efficient simulation of wave propagation in human ventricular tissue under normal and pathological conditions

ten Tusscher, K. H.Panfilov, A. V.

Phys.Med.Biol. 2006, 51(23): 6141

http://www.ncbi.nlm.nih.gov/pubmed/17110776

Gene expression profiling to monitor therapeutic and adverse effects of antisense therapies for Duchenne Muscular Dystrophy

t Hoen, P. A. C.Van der Wees, C. S. C.Turk, R.Goyenvalle, A.Danos, O.Garcia, L.van Om...

Pharmacogenomics 2006, 7: 281

The interaction between classification and rejection performance for distance-based reject-option classifiers

Landgrebe, T. C. W.Tax, D. M. J.Paclik, P.Duin, R. P.

Pattern Recognition Letters 2006, 27: 908

Random subspace method for multivariate feature selection

Lai, C.Reinders, M.Wessels, L.

Pattern Recognition Letters 2006, 27: 1067

Artifacts of Markov blanket filtering based on discretized features in small sample size applications

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

Pattern Recognition Letters 2006, 27: 709

Experimental study on prototype optimisation algorithms for prototype-based classification in vector spaces

Lozano, M.Sotoca, J. M.Sanchez, J. S.Pla, F.Pekalska, E. M.Duin, R. P.

Pattern Recognition 2006, 39: 1827

The straight-chain lipid biomarker composition of dominant biomarss formers along two altitudinal transects in the Ecuadorian Andes

Jansen, B.Nierop, K. G. J.Hageman, J. A.Cleef, A. M.Verstraten, J. M.

Organic Geochemistry Org.Geochem. 2006, 37: 1514

Evolutionary algorithms in the optimization of dynamic molecular alignment

Siedschlag, C.Shir, O. M.Back, T.Vrakking, M. J. J.

Optics Communications 2006, 264: 511

Cross-Platform Array Comparative Genomic Hybridization (array CGH) Meta-Analysis Separates Hematopoietic and Mesenchymal from Epithelial Tumors

Jong, K.Marchiori, E.van der Vaart, A.Chin, S. F.Carvalho, B.Tijssen, M.Eijk, P. P.va...

Oncogene, advanced online publication 2006(10)

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

Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes

Tiffin, N.Adie, E.Turner, F.Brunner, H. G.van Driel, M. A.Oti, M.Lopez-Bigas, N.Ouzou...

Nucleic Acids Res 2006, 34(10): 3067

Sequence comparison by sequence harmony identifies subtype-specific functional sites

Pirovano, W.Feenstra, K. A.Heringa, J.

Nucleic Acids Res 2006, 34(22): 6540

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

Cloning and expression of new microRNAs from zebrafish

Kloosterman, W. P.Steiner, F. A.Berezikov, E.de Bruijn, E.van de Belt, J.Verheul, M.C...

Nucleic Acids Res 2006, 34(9): 2558

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

BAGEL: a web-based bacteriocin genome mining tool

de Jong, A.van Hijum, S. A.Bijlsma, J. J.Kuipers, O. P.

Nucleic Acids Res 2006, 34

Mouse microRNA profilies determined with a new and sensitive cloning method

Takada, S.Berezikov, E.Yamashita, Y.Lagos-Quitana, M.Kloosterman, W.Enomoto, M.Hatana...

Nucl.Acids Res. 2006, 34

From outliers to prototypes: Ordering data

Harmeling, S.Dornhege, G.Tax, D. M. J.Meinecke, F.Muller, K.

Neurocomputing 2006, 69: 1608

Gene expression profiling highlights defective myogenesis in DMD patients and a possible role for bone morphogenetic protein 4

Sterrenburg, E.van der Wees, C. G.White, S. J.Turk, R.de Menezes, R. X.van Ommen, G. ...

Neurobiol Dis 2006, 23(1): 228

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

TreeSOM: Cluster analysis in the self-organizing map

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

Neural Networks 2006, 19(6): 935

Reconn, a new tool for pathway visualization and generation

Ligtenberg, W.P.A.Hilbers, P.A.J.

Netherlands Bioinformatics Conference 2006

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Strous, M.Pelletier, E.Mangenot, S.Rattei, T.Lehner, A.Taylor, M. W.Horn, M.Daims, H....

Nature 2006, 440(7085): 790

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

Gene therapy: is IL2RG oncogenic in T-cell development?

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

Nature 2006, 443(7109)

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

Modelling strategies for the industrial exploitation of lactic acid bacteria

Teusink, B.Smid, E. J.

Nat Rev Microbiol 2006, 4(1): 46

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

Diversity of microRNAs in human and chimpanzee brain

Berezikov, E.Thuemmler, F.van Laake, L. W.Kondova, I.Bontrop, R.Cuppen, E.Plasterk, R...

Nat Genet 2006, 38(12): 1375

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