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Publication overview

Protein complex prediction using an integrative bioinformatics approach

van Berlo, R. J.Wessels, L. F.de Ridder, D.Reinders, M. J.

J Bioinform Comput Biol 2007, 5(4): 839

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

Protein complex prediction using an integrative bioinformatics approach

Berlo, R. J. P. V.Wessels, L. F. A.Ridder, D. D. E.Reinders, M. J. T.

J Bioinform Comput Biol 2007, 5(4): 839

Benchmarking protein classification algorithms via supervised cross-validation

Kertesz-Farkas, A.Dhir, S.Sonego, P.Pacurar, M.Netoteia, S.Nijveen, H.Kuzniar, A.Leun...

J Biochem Biophys Methods 2007

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

ReConn: Explore Beyond the Edges of Pathways,

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

ISCB 2007

Virtual Reality in Aid of 3D Echocardiography

Koning, A. H. J.Bol Raap, G.van den Bosch, A. E.Meijboom, F. J.Bogers, A. J. J. C.van...

International Journal of Computer Assisted Radiology and Surgery 2007, 2(1): 123

Review of designing interactions

de Bruin, J. S.

Interactions 2007, 14(6): 60

Gene expression profiling to predict outcome after chemoradiation in head and neck cancer

Pramana, J.van den Brekel, M. W.van Velthuysen, M. L.Wessels, L. F.Nuyten, D. S.Hofla...

Int.J.Radiat.Oncol.Biol Phys. 2007, 69(5): 1544

http://www.ncbi.nlm.nih.gov/pubmed/17931799

Inferring the distribution of inter-reaction intervals for diffusion-limited reactions on lattices

Kaandorp, J. A.Rodriguez, J. V.

Int.J.Mod.Phys.C. 2007

P systems with single passenger carriers

Gao, Y.Hoogeboom, H. J.

Int J of foundations of computer science 2007

http://dx.doi.org/10.1142/S0129054107005273

The use of multiple hierarchically independant Gene Ontology terms in gene function prediction and genome annotation

Kourmpetis, Y. A. I.van der Burgt, A.Bink, M. C. A. M.ter Braak, C. J. F.van Ham, R. ...

In Silico Biology 2007

MOVE: a multi-level ontology-based visualization and exploration framework for genomic networks

Bosman, D. W.Blom, E. J.Ogao, P. J.Kuipers, O. P.Roerdink, J. B.

In Silico Biol 2007, 7(1): 35

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

All-inclusive proteomics mapping of yeast RNA polymerase II and III reveals several novel phosphorylation sites

Mohammed, S.Lorenzen, K.Kerkhoven, R.van Breukelen, B.Vannini, A.Cramer, P.Heck, A. J...

In Press 2007

Efficient multiclass ROC approximation by decomposition via confusion matrix perturbation analysis

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

IEEE Transactions on Pattern Analysis and Machine Intelligencearticle PR Marcel 2007

Multimedia search without visual analysis:The value of linguistic and contextual information

de Jong, F.Westerveld, T.de Vries, A.

IEEE transaction on circuits and systems for video technology 2007, 17(3): 365

Evaluating the design of biological cells using a computer workbench

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

IEEE computer society 2007

Preserving privacy through data generation

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

ICDM 2007 2007

Interacting with Visualizations

Fikkert, W.Bierz, T.D'Ambros, M.Jankun-Kelly, T. J.Kerren, A.

Human-Centered Visualization Environments 2007, 4417: 77

MPP1 links the Usher protein network and the Crumbs protein complex in the retina

Gosens, I.van, Wijk E.Kersten, F. F.Krieger, E.van der, Zwaag B.Marker, T.Letteboer, ...

Hum Mol Genet 2007, 16(16): 1993

http://www.ncbi.nlm.nih.gov/pubmed/17584769

Heterogeneity of gene expression profiles in head and neck cancer

Pramana, J.Pimentel, N.Hofland, I.Wessels, L. F.van Velthuysen, M. L.Atsma, D.Rasch, ...

Head Neck 2007, 29(12): 1083

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

Current Protein & Peptide Science

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

Guest Editor 2007, 8(2)

Integration of known transcription factor binding potential with gene expression clustering to advance from co-expression to co-regulation

Clements, M.van Someren, E. P.Knijnenburg, T. A.Reinders, M. J. T.

Genomics, Proteomics & Bioinformatics 2007, 5(2): 86

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions

van Noort, V.Snel, B.Huynen, M. A.

Genome Biol 2007, 8(9)

http://www.ncbi.nlm.nih.gov/pubmed/17880677

Global transcriptional responses of fission and budding yeast to changes in copper and iron levels: a comparative study

Rustici, G.van Bakel, H.Lackner, D. H.Holstege, F. C.Wijmenga, C.Bahler, J.Brazma, A.

Genome Biol 2007, 8(5)

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

Multivariate analysis of complex gene expression and clinical phenotypes with genetic marker data

Beyene, J.Tritchler, D.Bull, S. B.Cartier, K. C.Jonasdottir, G.Kraja, A. T.Li, N.Nock...

Genet.Epidemiol. 2007, 31

http://www.ncbi.nlm.nih.gov/pubmed/18046768

Interleukin 10: a new risk marker for the development of restenosis after percutaneous coronary intervention

Monraats, P. S.Kurreeman, F. A.Pons, D.Sewgobind, V. D.de Vries, F. R.Zwinderman, A. ...

Genes Immun. 2007, 8(1): 44

http://www.ncbi.nlm.nih.gov/pubmed/17122782

Expression analysis of the family of 14-3-3 proteins in zebrafish development

Besser, J.Bagowski, C. P.Salas-Vidal, E.van Hemert, M. J.Bussmann, J.Spaink, H. P.

Gene Expr.Patterns. 2007, 7(4): 511

http://www.ncbi.nlm.nih.gov/pubmed/17127101

The second harmonic generation case-study as a gateway for es to quantum control problems

Shir, O. M.Back, T.

GECCO 2007: 713

Multiset-based self-assembly of graphs

Bernardini, F.Zandron, C.Rozenberg, G.Brijder, R.

Fundamenta Informaticae 2007

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

Regulation of pentose catabolic pathway genes of aspergillus niger

de Groot, M.van den Dool, C.Wosten, H.Levisson, M.van Kuyk, P.Ruijter, G.de Vries, R.

Food Technology and Biotechnology 2007, 45(2): 134

Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae

Abbott, D. A.Knijnenburg, T. A.de Poorter, L. M. I.Reinders, M. J. T.Pronk, J. T.van ...

FEMS Yeast Res 2007, 7(6): 819

http://dx.doi.org/10.1111/j.1567-1364.2007.00242.x

ReConn: Connecting Cytoscape to the Reactome database

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

FEBS SysBio 2007

Effect of regional sympathetic denervation affects the relation between canine local myocardial blood flow and oxygen consumption

Alders, D. J.Cornelussen, R. N.Prinzen, F. W.Specht, P. A.Noble, M. I.Drake-Holland, ...

Exp Physiol 2007, 92(3): 541

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

Classification of cell fates with support vector machine learning

Shir, O. M.Raz, V.Dirks, R. W.Back, T.

EvoBio 2007: 258

Influence of diffuse fibrosis on wave propagation in human ventricular tissue

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

Europace. 2007, 9

http://www.ncbi.nlm.nih.gov/pubmed/17959692

Identification of candidate transcriptional modulators involved in successful regeneration after nerve injury

Stam, F. J.MacGillavry, H. D.Armstrong, N. J.de Gunst, M. C.Zhang, Y.van Kesteren, R....

Eur.J Neurosci. 2007, 25(12): 3629

http://www.ncbi.nlm.nih.gov/pubmed/17610582

Diagnostic criteria for congenital long QT syndrome in the era of molecular genetics: do we need a scoring system?

Hofman, N.Wilde, A. A.Kaab, S.van, Langen I.Tanck, M. W.Mannens, M. M.Hinterseer, M.B...

Eur.Heart J 2007, 28(5): 575

http://www.ncbi.nlm.nih.gov/pubmed/17090615

Influence of LDL-receptor mutation type on age at first cardiovascular event in patients with familial hypercholesterolaemia

Souverein, O. W.Defesche, J. C.Zwinderman, A. H.Kastelein, J. J.Tanck, M.

Epub 2007

Possible role of the innate immunity in temporal lobe epilepsy

van Gassen, K. L.de, Wit M.Groot Koerkamp, M. J.Rensen, M. G.van Rijen, P. C.Holstege...

Epilepsia 2007

http://www.ncbi.nlm.nih.gov/pubmed/18076643

Critical roles for a genetic code alteration in the evolution of the genus Candida

Silva, R. M.Paredes, J. A.Moura, G. R.Manadas, B.Lima-Costa, T.Rocha, R.Miranda, I.Go...

EMBO J. 2007, 26(21): 4555

http://www.ncbi.nlm.nih.gov/pubmed/17932489

Machine Learning

Kok, J.Koronacki, J.Lopez de Mantaras, R.Matwin, S.Mladenic, D.Skowron, A.

ECML, 18th European Conference on Machine Learning 2007

Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects

van Baarlen, P.van, Belkum A.Thomma, B. P.

Drug Discov.Today 2007, 12(3): 167

http://www.ncbi.nlm.nih.gov/pubmed/17275738

ReConn (demo)

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

Cytoscape Retreat Biology 2007

Variation of CNV distribution in five different ethnic populations

White, S. J.Vissers, L. E.Geurts van, Kessel A.de Menezes, R. X.Kalay, E.Lehesjoki, A...

Cytogenet.Genome Res. 2007, 118(1): 19

http://www.ncbi.nlm.nih.gov/pubmed/17901696

Tribler: A social-based peer-to-peer system

Pouwelse, J.Garbacki, P.Wang, J.Bakker, A.Yang, J.Iosup, A.Epema, D.Reinders, M.van S...

Concurrency and computation: practice and experiencePouwelse2007 2007

Computational techniques for spatial logistic regression with large data sets

Paciorek, Christopher J.

Computational Statistics & Data Analysis 2007, 51(8): 3631

http://apps.isiknowledge.com//InboundService.do?SID=W1hgMN9FP@9AppAFiO...

Parsimonious additive models

Avalos, MartaGrandvalet, YvesAmbroise, Christophe

Computational Statistics & Data Analysis 2007, 51(6): 2851

http://apps.isiknowledge.com//InboundService.do?SID=W1hgMN9FP@9AppAFiO...

Tools for computational processing of LC-MS datasets: a user's perspective

Codrea, M. C.Jimenez, C. R.Heringa, J.Marchiori, E.

Comput Methods Programs Biomed. 2007, 86(3): 281

http://www.ncbi.nlm.nih.gov/pubmed/17459516

Validation of protein structure models

Joosten, R. P.Chinea, G.Kleywegt, G. J.Vriend, G.

Comprehensive Medical Chemistry II 2007, 3: 507

A multivariate version of the Benjamini-Hochberg method

Ferreira, J. A.Nyangoma, S. O.

COBRA Preprint Series 2007

http://biostats.bepress.com/cobra/ps/art24

The modular nature of genetic diseases

Oti, M.Brunner, H. G.

Clin Genet 2007, 71(1): 1

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