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, IlyaBioinformatics 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, AlfredApplied 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