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Publication overview

Analysis of mass spectrometry data using sub-spectra

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

BMC Bioinformatics 2009, 10

http://www.ncbi.nlm.nih.gov/pubmed/19208154

Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering

Menolascina, F.Bellomo, D.Maiwald, T.Bevilacqua, V.Ciminelli, C.Paradiso, A.Tommasi, ...

BMC Bioinformatics 2009, 10: 1

http://www.biomedcentral.com/1471-2105/10/s12/s4

Integrated analysis of DNA copy number and gene expression microarray data using gene sets

Menezes, R. X.Boetzer, M.Sieswerda, M.van Ommen, G. J.Boer, J. M.

BMC Bioinformatics 2009, 10: 203

http://www.ncbi.nlm.nih.gov/pubmed/19563656

designGG: an R-package and web tool for the optimal design of genetical genomics experiments

Li, Y.Swertz, M. A.Vera, G.Fu, J.Breitling, R.Jansen, R. C.

BMC Bioinformatics 2009, 10: 188

http://www.ncbi.nlm.nih.gov/pubmed/19538731

A journey to Semantic Web query federation in the life sciences

Cheung, K. H.Frost, H. R.Marshall, M. S.Prud'hommeaux, E.Samwald, M.Zhao, J.Paschke, ...

BMC Bioinformatics 2009, 10

http://www.ncbi.nlm.nih.gov/pubmed/19796394

Oncogenomic analysis of mycosis fungoides reveals major differences with S,zary syndrome

van Doorn, R.van Kester, M. S.Dijkman, R.Vermeer, M. H.Mulder, A. A.Szuhai, K.Knijnen...

Blood 2009, 113(1): 127

http://www.ncbi.nlm.nih.gov/pubmed/18832135

Specific promoter methylation identifies different subgroups of MLL-rearranged infant acute lymphoblastic leukemia, influences clinical outcome, and provides therapeutic options

Stumpel, Dominique J. P. M.Schneider, Paulinevan Roon, Eddy H. J.Boer, Judith M.de Lo...

Blood 2009, 114(27): 5490

http://www.ncbi.nlm.nih.gov/pubmed/19855078

Tight control of MEK-ERK activation is essential in regulating proliferation, survival, and cytokine production of CD34+-derived neutrophil progenitors

Geest, Christian R.Buitenhuis, MirandaGroot Koerkamp, Marian J. A.Holstege, Frank C. ...

Blood 2009, 114(16): 3402

http://www.ncbi.nlm.nih.gov/pubmed/19667405

Nonparametric Testing for DNA Copy Number Induced Differential mRNA Gene Expression

van Wieringen, Wessel N.van de Wiel, Mark A.

Biometrics 2009, 65(1): 19

http://apps.isiknowledge.com/full_record.do?product=UA&search_mode=Gen...

Correlating multiple SNPs and multiple disease phenotypes: penalized non-linear canonical correlation analysis

Waaijenborg, S.Zwinderman, A. H.

Bioinformatics 2009, 25(21): 2764

http://www.ncbi.nlm.nih.gov/pubmed/19689958

Response to MeSH UP: effective MeSH text classification for improved document retrieval

Trieschnigg, D.Pezik, P.Lee, V.de, Jong F.Kraaij, W.Rebholz-Schuhmann, D.

Bioinformatics 2009

MeSH Up: effective MeSH text classification for improved document retrieval

Trieschnigg, D.Pezik, P.Lee, V.de, Jong F.Kraaij, W.Rebholz-Schuhmann, D.

Bioinformatics 2009, 25(11): 1412

http://www.ncbi.nlm.nih.gov/pubmed/19376821

Literature-based priors for gene regulatory networks

Steele, E.Tucker, A.t Hoen, P. A.Schuemie, M. J.

Bioinformatics 2009, 25(14): 1768

http://www.ncbi.nlm.nih.gov/pubmed/19389730

Matrix correlations for high-dimensional data: the modified RV-coefficient

Smilde, A. K.Kiers, H. A.Bijlsma, S.Rubingh, C. M.van Erk, M. J.

Bioinformatics 2009, 25(3): 401

http://www.ncbi.nlm.nih.gov/pubmed/19073588

Testing significance relative to a fold-change threshold is a TREAT

McCarthy, Davis J.Smyth, Gordon K.

Bioinformatics 2009, 25(6): 765

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/6/765

Fewer permutations, more accurate P-values

Knijnenburg, Theo A.Wessels, Lodewyk F. A.Reinders, Marcel J. T.Shmulevich, Ilya

Bioinformatics 2009, 25(12)

http://dx.doi.org/10.1093/bioinformatics/btp211

Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly

Dutilh, B. E.Huynen, M. A.Strous, M.

Bioinformatics 2009

http://www.ncbi.nlm.nih.gov/pubmed/19542148

Metabolite and reaction inference based on enzyme specificities

de Groot, M. J.van Berlo, R. J.van Winden, W. A.Verheijen, P. J.Reinders, M. J.de, Ri...

Bioinformatics 2009

http://www.ncbi.nlm.nih.gov/pubmed/19696044

MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context

Brouwer, R. W.van Hijum, S. A.Kuipers, O. P.

Bioinformatics 2009, 25(1): 139

http://www.ncbi.nlm.nih.gov/pubmed/19008250

PanCGH: a genotype-calling algorithm for pangenome CGH data

Bayjanov, J. R.Wels, M.Starrenburg, M.van, Hylckama V.Siezen, R. J.Molenaar, D.

Bioinformatics 2009, 25(3): 309

http://www.ncbi.nlm.nih.gov/pubmed/19129208

Mitochondrial proteome evolution and genetic disease

Huynen, M. A.de, Hollander M.Szklarczyk, R.

Biochim.Biophys Acta 2009

http://www.ncbi.nlm.nih.gov/pubmed/19328849

DNA dependent recruitment of DDX17 and other interacting proteins by the human androgen receptor

Wong, H. Y.Demmers, J. A.Bezstarosti, K.Grootegoed, J. A.Brinkmann, A. O.

Biochim Biophys Acta 2009, 1794(2): 193

http://www.ncbi.nlm.nih.gov/pubmed/19059367

Identification of progressors in osteoarthritis by combining biochemical and MRI-based markers

Dam, E. B.Loog, M.Christiansen, C.Byrjalsen, I.Folkerson, J.Nielsen, M.Qazi, A. A.Pet...

Arthritis research & therapy 2009: 1

http://arthritis-research.com/content/pdf/ar2774.pdf

Introduction to Ontologies in Data Mining Applications Using Ontologies in Biomedicine

Gibson, A. P.Stevens, R.

Artech House 2009

Estimating penalized spline regressions: theory and application to economics

Greiner, Alfred

Applied Economics Letters 2009, 16(18): 1831

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

Understanding the alphaviruses: Recent research on important emerging pathogens and progress towards their control

Gould, E. A.Coutard, B.Malet, H.Morin, B.Jamal, S.Weaver, S.Gorbalenya, A.Moureau, G....

Antiviral Res. 2009

http://www.ncbi.nlm.nih.gov/pubmed/19616028

Characterizing the precision of mass-spectrometry-based metabolic profiling platforms

Smilde, A. K.van der Werf, M. J.Schaller, J. P.Kistemaker, C.

Analyst 2009, 134(11): 2281

http://www.ncbi.nlm.nih.gov/pubmed/19838416

Metabolomics data exploration guided by prior knowledge

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

Anal Chim Acta 2009, 651(2): 173

http://www.ncbi.nlm.nih.gov/pubmed/19782808

Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease

Saada, A.Vogel, R. O.Hoefs, S. J.van den Brand, M. A.Wessels, H. J.Willems, P. H.Vens...

Am.J Hum.Genet. 2009, 84(6): 718

http://www.ncbi.nlm.nih.gov/pubmed/19463981

The biological coherence of human phenome databases

Oti, M.Huynen, M. A.Brunner, H. G.

Am J Hum Genet 2009, 85(6): 801

http://www.ncbi.nlm.nih.gov/pubmed/20004759

De AIDA toolbox: Een gecombineerde aanpak voor het beheren van kennis

Marshall, M. S.Roos, M.Meij, E.Katrenko, S.van Hage, W. R.Adriaans, P. W.

Agro Informatica 2009, 21(4): 5

Gestures to Intuitively Control Large Displays

Fikkert, W.van der Vet, P. E.Rauwerda, H.Breit, T.Nijholt, A.Sales Dias, M.Gibet, S.W...

Advances in Gesture-Based Human-Computer Interaction and Simulation 2009: 199

Navigation 3D sans Reconstruction Explicite

Peyras, J.Bartoli, A.Georgel, P.Loog, M.

Actes des Orasis09 2009: 1

http://orasis09.irisa.fr/articles/35.pdf

Structure of the C-terminal domain of nsp4 from feline coronavirus

Manolaridis, I.Wojdyla, J. A.Panjikar, S.Snijder, E. J.Gorbalenya, A. E.Berglind, H.N...

Acta Crystallogr.D.Biol.Crystallogr. 2009, 65: 839

http://www.ncbi.nlm.nih.gov/pubmed/19622868

Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

Joosten, R. P.Womack, T.Vriend, G.Bricogne, G.

Acta Crystallogr.D.Biol.Crystallogr. 2009, 65: 176

http://www.ncbi.nlm.nih.gov/pubmed/19171973

Structure of the X (ADRP) domain of nsp3 from feline coronavirus

Wojdyla, J. A.Manolaridis, I.Snijder, E. J.Gorbalenya, A. E.Coutard, B.Piotrowski, Y....

Acta Crystallogr D Biol Crystallogr 2009, 65: 1292

http://www.ncbi.nlm.nih.gov/pubmed/19966415

Realization theory for rational systems: Minimal reational realizations

Nemcova, J.van Schuppen, J. H.

Acta Applicandae Mathematicae 2009

2D/3D registration of micro-ct data to multi-view photographs based on a 3D distance map

Wildeman, M. H.Baiker, M.Reiber, J. H. C.Lowik, C. W. G. M.Reinders, M. J. T.Lelievel...

2009 6th IEEE International Symposium on Biomedical Imaging: From Nano to Macro proceedings 2009: 987

http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=5192959&isYear=2...

Identification of cellular dynamic patterns resulting from repetitive photobleaching using independent component analysis

van Gemert, A. M. C.Jost, C. R.van der Laan, A. M. A.Dirks, R. W.Reiber, J. H. C.Tank...

2009 6th IEEE International Symposium on Biomedical Imaging: From Nano to Macro proceedings 2009: 1382

http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=5192959&isYear=2...

Quantative comparison of spot detection methods in live-cell fluoresence microscopy imaging

Smal, I.Loog, M.Niessen, W.Meijering, E.

2009 6th IEEE International Symposium on Biomedical Imaging: From Nano to Macro proceedings 2009: 1178

http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=5192959&isYear=2...

Markerless human motion and pose recognition

Huo, F.Hendriks, E. A.Paclik, P.Oomes, A. H. J.

10th Workshop on Image Analysis for Multimedia Interactive Services, 2009 2009: 13

http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=5031414&isYear=2...

A pathway approach to align regulatory-metabolic networks

Li, Y.Bot, J.Reinders, M.de Ridder, D.

8th CSB2009 2009

http://ict.ewi.tudelft.nl/pub/yunlei/055Li.pdf

Specificity enhancement in microRNA target prediction through knowledge discovery

Zhang, Y.de Bruin, J.Verbeek, F.

 2009

Towards quantitative spatio-temporal gene expression measurements in mice

Wildeman, M.

 2009

Feasibility Analysis for Hardware Acceleration of Pattern Recognition Algorithms

van Wijnen, P.

 2009

Compressing Tags to Find Interesting Media Groups

van Leeuwen, M.Bonchi, F.Sigurbjörnsson, B.Siebes, A.

 2009, 18: 1147

Ibidas: to serve and to protect

van Kouteren, P.

 2009

FPGA Hardware acceleration of co-occurring aberrations in aCHG data

van der Leije, M.

 2009

Logic gene network design: a CAD tool based on modularity and standardization

van den Berg, B. A.

 2009

Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels

van Berlo, R. J. P.de Groot, M. J. L.Reinders, M. J. T.de Ridder, D.

 2009: 1

http://ict.ewi.tudelft.nl/pub/dick/ict200901.pdf