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Publication overview

Silicon cell models: Construction, analysis and reduction

Bruggeman, F. J.Hardin, H. M.van Schuppen, J. H.Westerhoff, H. V.Bertau, M.Mosekilde,...

 2008: 403

Models of natural computation: gene assembly and membrane system

Brijder, R.

 2008

Interactive Visualization of Gene Regulatory Networks with Associated Gene Expression Time Series Data

Westenberg, M. A.van Hijum, S. A. F. T.Lulko, A. T.Kuipers, O. P.Roerdink, J. B. T. M...

Visualization in Medicine and Life Sciences 2007

Large changes in regulome size herald the main prokaryotic lineages

Cordero, O. X.Hogeweg, P.

Trends Genet. 2007, 23(10): 488

http://www.ncbi.nlm.nih.gov/pubmed/17692992

An Integrative Kernel Method Dealing With Diverse Measurement Noise in Classification

Landgrebe, T. C. W.Duin, R. P. W.

Transactions of the South African Institute of Electrical Engineersarticle PR Marcel 2007

The influence of established genetic variation in the haemostatic system on clinical restenosis after percutaneous coronary interventions

Pons, D.Monraats, P. S.de Maat, M. P.Pires, N. M.Quax, P. H.van Vlijmen, B. J.Rosenda...

Thromb.Haemost. 2007, 98(6): 1323

http://www.ncbi.nlm.nih.gov/pubmed/18064331

Genetic variation in thrombin-activatable fibrinolysis inhibitor (TAFI) is associated with the risk of splanchnic vein thrombosis

de Bruijne, E. L.Murad, S. D.de Maat, M. P.Tanck, M. W.Haagsma, E. B.van, Hoek B.Rose...

Thromb.Haemost. 2007, 97(2): 181

http://www.ncbi.nlm.nih.gov/pubmed/17264944

Cycles and communicating classes in membrane systems and molecular dynamics

Rozenberg, G.Muskulus, M.Houweling, S.Besozzi, D.Pescini, D.Cazzaniga, P.Brijder, R.

Theor.Comput.Sci. 2007

http://dx.doi.org/10.1016/j.tcs.2006.11.027

Quorum sensing p systems

Krasnogor, N.Gheorghe, M.Bernardini, F.

Theor.Comput.Sci. 2007

http://dx.doi.org/10.1016/j.tcs.2006.10.012

Computing and the natural sciences at CiE 2005

Back, T.Lowe, B.

Theor.Comput.Sci. 2007, 371(1): 1

Cross Language Information Retrieval for Biomedical Literature

Schuemie, M.Trieschnigg, D.Kraaij, W.

The Sixteenth Text REtrieval Conference (TREC 2007) 2007

PDB improvement starts with data deposition

Joosten, R. P.Vriend, G.

Science 2007, 317(5835): 195

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

An ontology based approach for data integration; An application in Biomedical Research

Kashyap, V.Cheung, K. H.Doherty, D.Samwald, M.Marshall, M. S.Luciano, J.Stephens, S.H...

Real-world Applications of Semantic Web Technology and Ontologies 2007

The association between delirium and the apolipoprotein E ϵ4 allele in the elderly

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

Psychiatr Genet 2007, 17(5): 261

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

Assignment of protein function and discovery of novel nucleolar proteins based on automatic analysis of MEDLINE

Schuemie, M.Chichester, C.Lisacek, F.Coute, Y.Roes, P. J.Sanchez, J. C.Kors, J.Mons, ...

Proteomics 2007, 7(6): 921

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

Identification of leptomeningeal metastasis-related proteins in cerebrospinal fluid of patients with breast cancer by a combination of MALDI-TOF, MALDI-FTICR and nanoLC-FTICR MS

Rompp, A.Dekker, L.Taban, I.Jenster, G.Boogerd, W.Bonfrer, H.Spengler, B.Heeren, R.Sm...

Proteomics 2007, 7(3): 474

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

How to distinguish healthy from diseased? Classification strategy for mass spectrometry-based clinical proteomics

Hendriks, M. M. W. B.Smit, S.Akkermans, W. L. M. W.Reijmers, T. H.Eilers, P. H.Hoefsl...

Proteomics 2007, 7(20): 3672

Evolution of prokaryotic subtilases: Genome-wide analysis reveals novel subfamilies with different catalytic residues

Siezen, R. J.Renckens, B.Boekhorst, J.

Proteins 2007

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

Combining substrate dynamics, binding statistics, and energy barriers to rationalize regioselective hydroxylation of octane and lauric acid by CYP102A1 and mutants

Feenstra, K. A.Starikov, E. B.Urlacher, V. B.Commandeur, J. N.Vermeulen, N. P.

Protein Sci 2007, 16(3): 420

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

Lightweight gene name normalization by dictionary lookup

Schuemie, M.Jelier, R.Kors, J. A.Peregrine,

Proceedings of the Biocreative 2 2007

Analysis of Mass Spectrometry data using Wavelets and Sub-spectra

Meuleman, W.Engwegen, J. Y.Gast, M. C.Reinders, M. J. T.Wessels, L. F. A.

Proceedings of the 13th Annual conference of the Advanced school for computing and imaging 2007

An integrative kernel method dealing with diverse measurement noise in classification

Li, Y.de Ridder, D.Duin, R. P. W.Reinders, M. J. T.

Proceedings of the 13th Annual conference of the Advanced school for computing and imaging 2007: 127

Discovering cooperating oncogenes by statistical co-occurence analysis

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

Proceedings of the 13th Annual conference of the Advanced school for computing and imaging 2007: 166

Thesaurus-based feedback to support mixed search and browsing environments

Meij, E.de Rijke, M.

Proceedings of the 11th European Conference on Digital Libraries (ECDL 2007) 2007

A hybrid approach to modelling biological systems

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

Proceedings 8th workshop on membrane computing 2007

http://www.liacs.nl/CS/TCS/search.cgi?name=Romero-Campero&title=Romero...

The effect of public health measures on the 1918 influenza pandemic in U.S. cities

Bootsma, M. C.Ferguson, N. M.

Proc Natl.Acad.Sci.U.S.A 2007, 104(18): 7588

http://www.ncbi.nlm.nih.gov/pubmed/17416677

Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function

Szklarczyk, R.Heringa, J.Pond, S. K.Nekrutenko, A.

Proc Natl Acad Sci U S A 2007, 104(31): 12807

http://www.ncbi.nlm.nih.gov/pubmed/17652172

The fluxes through glycolytic in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels

ran-Lapujade, J. M. D. P.Rossell, S.van Gulik, W. M.Luttik, M. A. H.de Groot, M. J. L...

Proc Natl Acad Sci U S A 2007, 104(40): 15753

Structural diversity in twin-arginine signal peptide-binding proteins

Maillard, J.Spronk, C. A.Buchanan, G.Lyall, V.Richardson, D. J.Palmer, T.Vuister, G. ...

Proc Natl Acad Sci U S A 2007, 104(40): 15641

http://www.ncbi.nlm.nih.gov/pubmed/17901208

Somatic loss of BRCA1 and p53 in mice induces mammary tumors with features of human BRCA1-mutated basal-like breast cancer

Liu, X.Holstege, H.van der Gulden, H.Treur-Mulder, M.Zevenhoven, J.Velds, A.Kerkhoven...

Proc Natl Acad Sci U S A 2007, 104(29): 12111

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

CCR4/NOT complex associates with the proteasome and regulates histone methylation

Laribee, R. N.Shibata, Y.Mersman, D. P.Collins, S. R.Kemmeren, P.Roguev, A.Weissman, ...

Proc Natl Acad Sci U S A 2007, 104(14): 5836

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

Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication

Jiang, P.Faase, J. A.Toyoda, H.Paul, A.Wimmer, E.Gorbalenya, A. E.

Proc Natl Acad Sci U S A 2007, 104(22): 9457

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

The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms

Ingham, C. J.Sprenkels, A.Bomer, J.Molenaar, D.van den, Berg A.van, Hylckama V.de Vos...

Proc Natl Acad Sci U S A 2007, 104(46): 18217

http://www.ncbi.nlm.nih.gov/pubmed/17989237

From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism

Gabaldon, T.Huynen, M. A.

PLoS.Comput.Biol. 2007, 3(11)

http://www.ncbi.nlm.nih.gov/pubmed/17983265

Module-based outcome prediction using breast cancer compendia

van Vliet, M.Klijn, C. N.Wessels, L. F. A.Reinders, M. J. T.

PloS ONE 2007

A first look at ARFome: Dual-coding genes in mamalian genomes

Chung, W.Wadhawan, S.Szklarczyk, R.Pond, S. K.Nekrutenko, A.

PLoS Comput Biol 2007

Dual-coding eukaryotic genes defy statistical odds

Chung, W.Wadhawan, S.Szklarczyk, R.Nekrutenko, A.

PLoS Comput Biol 2007

Transcriptome-based identification of pro- and antioxidative gene expression in kidney cortex of nitric oxide-depleted rats

Wesseling, S.Joles, J. A.van Goor, H.Bluyssen, H. A.Kemmeren, P.Holstege, F. C.Kooman...

Physiol Genomics 2007, 28(2): 158

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

Estimating grassland biomass using SVM band shaving of hyperspectral data

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

Photogrammetric engineering and remote sensing 2007, 73(10): 1141

Literature-based compound profiling: application to toxicogenomics

Frijters, R.Verhoeven, S.Alkema, W.van, Schaik R.Polman, J.

Pharmacogenomics. 2007, 8(11): 1521

http://www.ncbi.nlm.nih.gov/pubmed/18034617

Classification in the presence of class noise using a probabilistic kernel fisher method

Li, Y.Wessels, L. F. A.de Ridder, D.Reinders, M. J. T.

Pattern Recognition 2007, 40: 3349

Approximating the multiclass ROC by pairwise analysis

Landgrebe, T. C. W.Duin, R. P. W.

Pattern Recogn.Lett. 2007, 28(131279176): 1747

Pairwise feature evaluation for constructing reduced representations

Harol, A.Lai, C.kalska, E.x017c,bieta,Duin, R. P. W.

Pattern Anal.Appl. 2007, 10(11229120): 55

Oncogenic pathways impinging on the G(2)-restriction point

Foijer, F.Simonis, M.van Vliet, M.Wessels, L.Kerkhoven, R.Sorger, P. K.Te Riele, H.

Oncogene 2007

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

STRING 7--recent developments in the integration and prediction of protein interactions

Von Mering, C.Jensen, L. J.Kuhn, M.Chaffron, S.Doerks, T.Kruger, B.Snel, B.Bork, P.

Nucleic Acids Res. 2007, 35

http://www.ncbi.nlm.nih.gov/pubmed/17098935

Primer3Plus, an enhanced web interface to Primer3

Untergasser, A.Nijveen, H.Rao, X.Bisseling, T.Geurts, R.Leunissen, J. A.

Nucleic Acids Res 2007, 35

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

A Protein Classification Benchmark collection for machine learning

Sonego, P.Pacurar, M.Dhir, S.Kertesz-Farkas, A.Kocsor, A.Gaspari, Z.Leunissen, J. A.P...

Nucleic Acids Res 2007, 35

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

Reconstructing the evolution of the mitochondrial ribosomal proteome

Smits, P.Smeitink, J. A.van den Heuvel, L. P.Huynen, M. A.Ettema, T. J.

Nucleic Acids Res 2007, 35(14): 4686

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

Sequence harmony: detecting functional specificity from alignments

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

Nucleic Acids Res 2007, 35

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

Identifying foldable regions in protein sequence from the hydrophobic signal

Pang, C. N. I.Lin, K.Wouters, M. A.Heringa, J.George, R. A.

Nucl.Acids Res. 2007