Publication overview

2-DE and MS analysis of key proteins in the adhesion of Lactobacillus plantarum, a first step toward early selection of probiotics based on bacterial biomarkers

Izquierdo, E.Horvatovich, P.Marchioni, E.oude-Werner, D.Sanz, Y.Ennahar, S.

Electrophoresis 2009, 30(6): 949

http://www.ncbi.nlm.nih.gov/pubmed/19309013

Large Scale Analysis of Small Repeats via Mining of the Human Genome

Van den Berg, I.Bosnacki, DraganHilbers, Peter A. J.

Database and Expert Systems Applications, DEXA, International Workshops, Linz, Austria, August 31-September 4, 2009, Proceedings 2009: 198

Mining Maximal Frequent Subgraphs in KEGG Reaction Networks

Ligtenberg, Willem P. A.Bosnacki, DraganHilbers, Peter A. J.

Database and Expert Systems Applications, DEXA, International Workshops, Linz, Austria, August 31-September 4, 2009, Proceedings 2009: 213

Identifying the Components

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

Data Mining and Knowledge Discovery 2009, 19(2): 176

Modeling and Identification of a Gene Regulatory Network Programming Erythropoiesis

de Vos, D. L.

CWI.Modelling, Analysis and Simulation [MAS 2009

http://www.narcis.info/publication/RecordID/oai:cwi.nl:14701

Defining gene and QTL networks

Jansen, R. C.Tesson, B. M.Fu, J.Yang, Y.McIntyre, L. M.

Curr.Opin.Plant Biol. 2009

http://www.ncbi.nlm.nih.gov/pubmed/19196544

Parametrization and penalties in spline models with an application to survival analysis

Costa, M.Shaw, J.

Computational Statistics & Data Analysis 2009, 53(3): 657

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

Approximating a similarity matrix by a latent class model: a reappraisal of additive fuzzy clustering

ter Braak, C. J.Kourmpetis, Y. A.Kiers, H. A.Bink, M. C.

Comp Stat and Data Analysis 2009

Influence of sample storage duration on serum protein profiles assessed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS)

Gast, Marie-Christine W.van Gils, Carla H.Wessels, Lodewijk F. A.Harris, NathanBonfre...

Clinical Chemistry and Laboratory Medicine: CCLM / FESCC 2009, 47(6): 694

http://www.ncbi.nlm.nih.gov/pubmed/19416081

Tumor-expressed B7-H1 and B7-DC in relation to PD-1+ T-cell infiltration and survival of patients with cervical carcinoma

Karim, RezaulJordanova, Ekaterina S.Piersma, Sytse J.Kenter, Gemma G.Chen, LiepingBoe...

Clinical Cancer Research: An Official Journal of the American Association for Cancer Research 2009, 15(20): 6341

http://www.ncbi.nlm.nih.gov/pubmed/19825956

Influence of sample storage duration on serum protein profiles assessed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS)

Gast, M. C.Van Gils, C. H.Wessels, L. F.Harris, N.Bonfrer, J. M.Rutgers, E. J.Schelle...

Clin.Chem.Lab Med. 2009, 47(6): 694

http://www.ncbi.nlm.nih.gov/pubmed/19416081

Gene expression profiling of the forming atrioventricular node using a novel tbx3-based node-specific transgenic reporter

Horsthuis, T.Buermans, H. P.Brons, J. F.Verkerk, A. O.Bakker, M. L.Wakker, V.Clout, D...

Circ.Res. 2009, 105(1): 61

http://www.ncbi.nlm.nih.gov/pubmed/19498200

Exploring the analysis of structured metabolomics data

Verouden, M. P. H.Westerhuis, J. A.van der Werf, M. J.Smilde, A. K.

Chemometrics and Intelligent Laboratory Systems 2009

http://www.sciencedirect.com/science/article/B6TFP-4WCTWJ8-1/2/f04b2e2...

Global analysis of multiple gas chromatography-mass spectrometry (GC/MS) data sets: a method for resolution of co-eluting components

van Stokkum, I. H. M.Mullen, K. M.Mihaleva, V. V.

Chemometrics and Intelligent Laboratory Systems 2009

http://dx.doi.org/10.1016/j.chemolab.2008.10.004

Phylogeny of the CDC25 homology domain reveals rapid differentiation of Ras pathways between early animals and fungi

van Dam, T. J.Rehmann, H.Bos, J. L.Snel, B.

Cell Signal. 2009

http://www.ncbi.nlm.nih.gov/pubmed/19567266

The alpha-kinase family: an exceptional branch on the protein kinase tree

Middelbeek, J.Clark, K.Venselaar, H.Huynen, M. A.van Leeuwen, F. N.

Cell Mol Life Sci 2009, 67(6): 875

http://www.ncbi.nlm.nih.gov/pubmed/20012461

Cyttron: A Virtualized Microscope supporting image integration and knowledge discovery

Kallergi, A.Bei, Y.Kok, P.Dijkstra, J.Abrahams, J. P.Verbeeek, F. J.

Cell Death and Disease Series 2009

Functional organization of the S. cerevisiae phosphorylation network

Fiedler, DorotheaBraberg, HannesMehta, MonikaChechik, GalCagney, GerardMukherjee, Par...

Cell 2009, 136(5): 952

http://www.ncbi.nlm.nih.gov/pubmed/19269370

Automated left ventricular delineation in X-ray angiograms: A validation study

Oost, E.Oemrawsingh, P.Reiber, J. H.Lelieveldt, B. P. F.

Catheterization and cardiovascular interventions 2009, 73(2): 231

http://www3.interscience.wiley.com/cgi-bin/fulltext/119877461/PDFSTART

eQTL Analysis in Mice and Rats in Methods in Molecular Biology

Tesson, B.Jansen, R. C.

Cardiovascular Genomics 2009

http://www.ncbi.nlm.nih.gov/pubmed/19763934

Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models

Jonker, M. J.Bruning, O.van, Iterson M.Schaap, M. M.van der Hoeven, T. V.Vrieling, H....

Carcinogenesis 2009

http://www.ncbi.nlm.nih.gov/pubmed/19696161

Life Sciences on the semantic web: the nerocommons and beyond

Ruttenberg, A.Rees, J.Samwald, M.Marshall, M. S.

Brief Bioinform 2009

Clinical proteomics in breast cancer: a review

Gast, Marie-Christine W.Schellens, Jan H. M.Beijnen, Jos H.

Breast Cancer Research and Treatment 2009, 116(1): 17

http://www.ncbi.nlm.nih.gov/pubmed/19082706

Concordance of clinical and molecular breast cancer subtyping in the context properative of chemotherapy response

de Ronde, J. J.Hannemann, J.Halfwerk, H.Mulder, L.Straver, M. E.Vrancken Peeters, Mjt...

Breast cancer research (online) 2009, 119(1): 119

http://www.springerlink.com/content/u45236132806k301/fulltext.pdf

Clinical proteomics in breast cancer: a review

Gast, M. C.Schellens, J. H.Beijnen, J. H.

Breast Cancer Res.Treat. 2009, 116(1): 17

http://www.ncbi.nlm.nih.gov/pubmed/19082706

Bootstrap confidence intervals in multi-level simultaneous component analysis

Timmerman, M. E.Kiers, H. A.Smilde, A. K.Ceulemans, E.Stouten, J.

Br J Math.Stat Psychol. 2009, 62: 299

http://www.ncbi.nlm.nih.gov/pubmed/18086338

Using R in Taverna: RShell v1.2

Wassink, I.Rauwerda, H.Neerincx, P. B.Vet, P. E.Breit, T. M.Leunissen, J. A.Nijholt, ...

BMC Res.Notes 2009, 2: 138

http://www.ncbi.nlm.nih.gov/pubmed/19607662

SigWinR; the SigWin-detector updated and ported to R

de Leeuw, W. C.Rauwerda, H.Inda, M.Bruning, O.Breit, T.

BMC Res.Notes 2009

OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

Neerincx, P. B.Rauwerda, H.Nie, H.Groenen, M. A.Breit, T.Leunissen, J. A.

BMC Proceedings 2009, 16(3)

Associating multiple longitudinal traits with high-dimensional single-nucleotide polymorphism data: application to the Framingham Heart Study

Waaijenborg, S.Zwinderman, A. H.

BMC Proc 2009, 3

http://www.ncbi.nlm.nih.gov/pubmed/20018039

Microarray data mining using Bioconductor packages

Nie, H.Neerincx, P. B.van der, Poel J.Ferrari, F.Bicciato, S.Leunissen, J. A.Groenen,...

BMC Proc 2009, 3

http://www.ncbi.nlm.nih.gov/pubmed/19615122

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis

Neerincx, P. B.Casel, P.Prickett, D.Nie, H.Watson, M.Leunissen, J. A.Groenen, M. A.Kl...

BMC Proc 2009, 3

http://www.ncbi.nlm.nih.gov/pubmed/19615109

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Hedegaard, J.Arce, C.Bicciato, S.Bonnet, A.Buitenhuis, B.Collado-Romero, M.Conley, L....

BMC Proc 2009, 3

http://www.ncbi.nlm.nih.gov/pubmed/19615118

Lentivirus-mediated transgene delivery to the hippocampus reveals sub-field specific differences in expression

van Hooijdonk, L. W. A.Ichwan, M.Dijkmans, T. F.Schouten, T. G.verbeek, F. J.Vreugden...

BMC Neuroscience 2009

Validation of previously identified serum biomarkers for breast cancer with SELDI-TOF MS: a case control study

van Winden, Annemieke WjGast, Marie-Christine W.Beijnen, Jos H.Rutgers, Emiel JthGrob...

BMC Medical Genomics 2009, 2: 4

http://www.ncbi.nlm.nih.gov/pubmed/19152674

Relative power and sample size analysis on gene expression profiling data

van Iterson, M.t Hoen, P. A. C.Pedotti, P.Hooiveld, Gjejden Dunnen, J. T.van Ommen, G...

BMC Genomics 2009, 10(1): 439

http://www.biomedcentral.com/1471-2164/10/439

Relative power and sample size analysis on gene expression profiling data

van, Iterson M.t Hoen, P. A.Pedotti, P.Hooiveld, G. J.den Dunnen, J. T.van Ommen, G. ...

BMC Genomics 2009, 10: 439

http://www.ncbi.nlm.nih.gov/pubmed/19758461

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome

Severing, E. I.van Dijk, A. D.Stiekema, W. J.van Ham, R. C.

BMC Genomics 2009, 10: 154

http://www.ncbi.nlm.nih.gov/pubmed/19358722

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data

Knijnenburg, Theo A.Daran, Jean Marcvan den Broek, Marcel A.ran-Lapujade, Pascale Asd...

BMC Genomics 2009, 10

http://dx.doi.org/10.1186/1471-2164-10-53

The hydrogenosomes of Psalteriomonas lanterna

de Graaf, R. M.Duarte, I.van Alen, T. A.Kuiper, J. W.Schotanus, K.Rosenberg, J.Huynen...

BMC Evol Biol 2009, 9: 287

http://www.ncbi.nlm.nih.gov/pubmed/20003182

A close examination of double filtering with fold change and t test in microarray analysis

Zhang, SongCao, Jing

BMC Bioinformatics 2009, 10(1): 402

http://www.biomedcentral.com/1471-2105/10/402

Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks

Waaijenborg, S.Zwinderman, A. H.

BMC Bioinformatics 2009, 10: 315

http://www.ncbi.nlm.nih.gov/pubmed/19785734

Knowledge driven decomposition of tumor expression profiles

van Vliet, M. H.Wessels, L. F.Reinders, M. J.

BMC Bioinformatics 2009, 10

http://www.ncbi.nlm.nih.gov/pubmed/19208120

A structured overview of simultaneous component based data integration

Van Deun, K.Smilde, A. K.van der Werf, M. J.Kiers, H. A.Van, Mechelen I.

BMC Bioinformatics 2009, 10: 246

http://www.ncbi.nlm.nih.gov/pubmed/19671149

Integrating functional genomics data using maximum likelihood based simultaneous component analysis

van den Berg, R. A.Van, Mechelen I.Wilderjans, T. F.Van, Deun K.Kiers, H. A.Smilde, A...

BMC Bioinformatics 2009, 10: 340

http://www.ncbi.nlm.nih.gov/pubmed/19835617

Improving the analysis of designed studies by combining statistical modelling with study design information

Thissen, U.Wopereis, S.van den Berg, S. A.Bobeldijk, I.Kleemann, R.Kooistra, T.van Di...

BMC Bioinformatics 2009, 10: 52

http://www.ncbi.nlm.nih.gov/pubmed/19200393

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Sontrop, HermanMoerland, Perryvan den Ham, Ren ªReinders, MarcelVerhaegh, Wim

BMC Bioinformatics 2009, 10: 389

http://dx.doi.org/10.1186/1471-2105-10-389

SNAD: sequence name annotation-based designer

Sidorov, I. V.Reshetov, D.Gorbalenya, A.

BMC Bioinformatics 2009

http://www.biomedcentral.com/1471-2105/10/251

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

Roos, M.Marshall, M. S.Gibson, A. P.Schuemie, M.Meij, E.Katrenko, S.van Hage, W. R.Kr...

BMC Bioinformatics 2009, 10

http://www.ncbi.nlm.nih.gov/pubmed/19796406

Structure and Function Analysis of Flexible Alignment Regions in Proteins

Pirovano, W.van der Reijden, A.Feenstra, K. A.Heringa, J.

BMC Bioinformatics 2009

http://www.biomedcentral.com/1471-2105/10/S13/P6