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Publication overview

Visualizing Genome Expression and Regulatory Network Dynamics in Genomic and Metabolic Context

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

Computer Graphics Forum 2008

Selection of components and degrees of smoothing via lasso in high dimensional nonparametric additive models

Zheng, S.

Computational Statistics & Data Analysis 2008, 53(1): 164

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

Simultaneous selection of variables and smoothing parameters in structured additive regression models

Belitz, C.Lang, S.

Computational Statistics & Data Analysis 2008, 53(1): 61

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

Penalized Spline Estimation for Varying-Coefficient Models

Lu, YiqiangZhang, RiquanZhu, Liping

Communications in Statistics - Theory and Methods 2008, 37(14): 2249

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

Formal models of appraisal: Theory, specification and computational model

Broekens, J.de Groot, D.Kosters, W.

Cognitive Systems Research 2008, 9: 173

Parallel assessment of the impact of different hormone replacement therapies on breast density by radiologist- and computer-based analyses of mammograms

Pettersen, P. C.Raundahl, J.Loog, M.Nielsen, M.Tanko, L. B.Christiansen, C.

Climacteric. 2008, 11(2): 135

http://www.ncbi.nlm.nih.gov/pubmed/18365856

Interferon-{beta} Signaling Is Enhanced in Patients With Insufficient Coronary Collateral Artery Development and Inhibits Arteriogenesis in Mice

Schirmer, Stephan H.Fledderus, Joost O.Bot, Pieter T. G.Moerland, Perry D.Hoefer, Imo...

Circulation research 2008

http://dx.doi.org/10.1161/CIRCRESAHA.108.171827

Web resources for the glycoscientist

Lutteke, T.

Chembiochem 2008, 9(13): 2155

http://www.ncbi.nlm.nih.gov/pubmed/18693281

miRNA's: small changes, widespread effects

Linsen, S. E. V.Tops, B. B. J.Cuppen, E.

Cell Research 2008

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

Uren, A. G.Kool, J.Matentzoglu, K.de, Ridder J.Mattison, J.van, Uitert M.Lagcher, W.S...

Cell 2008, 133(4): 727

http://www.ncbi.nlm.nih.gov/pubmed/18485879

Improved hydrogen bond potentials to assess in silico protein folding

Wolf, M. G.de Leeuw, S. W.Vreede, J. C.Bolhuis, P. G.

CBSB 2008

Cyclooxygenase-2 inhibition inhibits c-Met kinase activity and Wnt activity in colon cancer

Tuynman, J. B.Vermeulen, L.Boon, E. M.Kemper, K.Zwinderman, A. H.Peppelenbosch, M. P....

Cancer Res. 2008, 68(4): 1213

http://www.ncbi.nlm.nih.gov/pubmed/18281498

Classification of paediatric acute myeloid leukaemia utilizing gene expression profiling

Balgobind, B. V.Heuvel-Eibrink, M. M.Menezes, R. X.Reinhardt, D.Hollink, I. H. I. M.P...

British Journal of Haematology 2008, 141: 105

ISI:000255032500286

Solutions for data integration in functional genomics: a critical assessment and case study

Smedley, D.Swertz, M. A.Wolstencroft, K.Proctor, G.Zouberakis, M.Bard, J.Hancock, J. ...

Brief.Bioinform. 2008, 9(6): 532

http://www.ncbi.nlm.nih.gov/pubmed/19112082

The relative value of operon predictions

Brouwer, R. W. W.Kuipers, O. P.Hijum, S. A. F. T.

Brief Bioinform 2008(9): 367

A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer

Reyal, F.van Vliet, M. H.Armstrong, N. J.Horlings, H. M.de Visser, K. E.Kok, M.Tesche...

Breast Cancer Res. 2008, 10(6)

http://www.ncbi.nlm.nih.gov/pubmed/19014521

Visualizing Co-occurrence of Self-Optimizing Fragment Groups

de Graaf, E. H.Kosters, W. A.

BNAIC 2008 2008: 81

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

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

BMC.Syst.Biol. 2008, 2(1): 111

http://www.ncbi.nlm.nih.gov/pubmed/19108747

Can subtle changes in gene expression be consistently detected with different microarray platforms?

Pedotti, P.t Hoen, P. A.Vreugdenhil, E.Schenk, G. J.Vossen, R. H.Ariyurek, Y.de, Holl...

BMC.Genomics 2008, 9(1): 124

http://www.ncbi.nlm.nih.gov/pubmed/18331641

Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: a pathway-based analysis

Hensen, E. F.De Herdt, M. J.Goeman, J. J.Oosting, J.Smit, V. T.Cornelisse, C. J.Baate...

BMC.Cancer 2008, 8: 168

http://www.ncbi.nlm.nih.gov/pubmed/18544165

Haptoglobin phenotype is not a predictor of recurrence free survival in high-risk primary breast cancer patients

Gast, M. C.van, Tinteren H.Bontenbal, M.van Hoesel, R. Q.Nooij, M. A.Rodenhuis, S.Spa...

BMC.Cancer 2008, 8: 389

http://www.ncbi.nlm.nih.gov/pubmed/19108738

Presenting and exploring biological pathways with PathVisio

van Iersel, M. P.Kelder, T.Pico, A. R.Hanspers, K.Coort, S.Conklin, B. R.Evelo, C.

BMC.Bioinformatics. 2008, 9: 399

http://www.ncbi.nlm.nih.gov/pubmed/18817533

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

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

BMC.Bioinformatics. 2008, 9: 88

http://www.ncbi.nlm.nih.gov/pubmed/18257918

R/parallel--speeding up bioinformatics analysis with R

Vera, G.Jansen, R. C.Suppi, R. L.

BMC.Bioinformatics 2008, 9: 390

http://www.ncbi.nlm.nih.gov/pubmed/18808714

SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences

Inda, M. A.Van Batenburg, M. F.Roos, M.Belloum, A. S.Vasunin, D.Wibisono, A.van Kampe...

BMC Res.Notes 2008, 1: 63

http://www.ncbi.nlm.nih.gov/pubmed/18710516

Salvaging Affymetrix probes after probe-level re-annotation

de Leeuw, W. C.Rauwerda, H.Jonker, M. J.Breit, T. M.

BMC Res.Notes 2008, 1: 66

http://www.ncbi.nlm.nih.gov/pubmed/18710586

In Silico Identification of T-boxes: to Study Their Propagation and to Improve the Functional Annotation of Transport Systems

Wels, M.Groot Kormelink, T.Kleerebezem, M.Siezen, R. J.Francke, C.

BMC Genomics 2008

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

van Vliet, M. H.Reyal, F.Horlings, H. M.van, de V.Reinders, M. J.Wessels, L. F.

BMC Genomics 2008, 9: 375

http://www.ncbi.nlm.nih.gov/pubmed/18684329

Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo

Troost, F. J.van, Baarlen P.Lindsey, P.Kodde, A.de Vos, W. M.Kleerebezem, M.Brummer, ...

BMC Genomics 2008, 9: 374

http://www.ncbi.nlm.nih.gov/pubmed/18681965

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns

Ricard, G.de Graaf, R. M.Dutilh, B. E.Duarte, I.van Alen, T. A.van Hoek, A. H.Boxma, ...

BMC Genomics 2008, 9: 587

http://www.ncbi.nlm.nih.gov/pubmed/19061489

A genome-wide SNP panel for mapping and association studies in the rat

Nijman, I. J.Kuipers, S.Verheul, M.Guryev, V.Cuppen, E.

BMC Genomics 2008, 9: 95

http://www.ncbi.nlm.nih.gov/pubmed/18298839

BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

Hulsen, T.de, Vlieg J.Alkema, W.

BMC Genomics 2008, 9(1): 488

http://www.ncbi.nlm.nih.gov/pubmed/18925949

Comparing the old and new generation SELDI-TOF MS:implications for serum protein profiling

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

BMC Genomics 2008

http://dx.doi.org/10.1186/1755-8794-1-4

HaploSNPer: a web-based allele and SNP detection tool

Tang, J.Leunissen, J. A.Voorrips, R. E.van der Linden, G. C.Vosman, B.

BMC Genet 2008, 9(1): 23

http://www.ncbi.nlm.nih.gov/pubmed/18307806

Estimating effects of rare haplotypes on failure time using a penalized Cox proportional hazards regression model

Souverein, O. W.Zwinderman, A. H.Jukema, J. W.Tanck, M. W.

BMC Genet 2008, 9: 9

http://www.ncbi.nlm.nih.gov/pubmed/18221501

Complex fate of paralogs

Szklarczyk, R.Huynen, M. A.Snel, B.

BMC Evol.Biol. 2008, 8: 337

http://www.ncbi.nlm.nih.gov/pubmed/19094234

LocateP: Genome-scale subcellular-location predictor for bacterial proteins

Zhou, M.Boekhorst, J.Francke, C.Siezen, R. J.

BMC Bioinformatics 2008, 9(1): 173

http://www.ncbi.nlm.nih.gov/pubmed/18371216

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation

Titulaer, M. K.Mustafa, D. A.Siccama, I.Konijnenburg, M.Burgers, P. C.Andeweg, A. C.S...

BMC Bioinformatics 2008, 9: 133

http://www.ncbi.nlm.nih.gov/pubmed/18312684

The meaning of alignment: lessons from structural diversity

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

BMC Bioinformatics 2008, 9: 556

http://www.ncbi.nlm.nih.gov/pubmed/19105835

Conserved co-expression for candidate disease gene prioritization

Oti, M.van, Reeuwijk J.Huynen, M. A.Brunner, H. G.

BMC Bioinformatics 2008, 9: 208

http://www.ncbi.nlm.nih.gov/pubmed/18433471

Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data

Li, P.Castrillo, J. I.Velarde, G.Wassink, I.Soiland-Reyes, S.Owen, S.Withers, D.Oinn,...

BMC Bioinformatics 2008, 9: 334

http://www.biomedcentral.com/1471-2105/9/334

Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease

Jelier, R.t Hoen, P. A.Sterrenburg, E.den Dunnen, J. T.van Ommen, G. J.Kors, J. A.Mon...

BMC Bioinformatics 2008, 9: 291

http://www.ncbi.nlm.nih.gov/pubmed/18577208

High-throughput bioinformatics with the Cyrille2 pipeline system

Fiers, M. W.van der, Burgt A.Datema, E.de Groot, J. C.van Ham, R. C.

BMC Bioinformatics 2008, 9: 96

http://www.ncbi.nlm.nih.gov/pubmed/18269742

A novel (Leu183Pro-)mutation in the HFE-gene co-inherited with the Cys282Tyr mutation in two unrelated Dutch hemochromatosis patients

Swinkels, D. W.Venselaar, H.Wiegerinck, E. T.Bakker, E.Joosten, I.Jaspers, C. A.Vasme...

Blood Cells Mol Dis 2008, 40(3): 334

http://www.ncbi.nlm.nih.gov/pubmed/18042412

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

Robinson, M. D.Smyth, G. K.

BIOSTATISTICS 2008, 9(2): 321

http://apps.isiknowledge.com/full_record.do?product=WOS&search_mode=Ge...

Fast in silico protein folding by introduction of alternating hydrogen bond potentials

Wolf, M. G.de Leeuw, S. W.

Biophys.J 2008, 94(10): 3742

http://www.ncbi.nlm.nih.gov/pubmed/18434590

Concentration dependence of alpha-synuclein fibril length assessed by quantitative atomic force microscopy and statistical-mechanical theory

van Raaij, M. E.van, Gestel J.Segers-Nolten, I. M.de Leeuw, S. W.Subramaniam, V.

Biophys.J 2008, 95(10): 4871

http://www.ncbi.nlm.nih.gov/pubmed/18676659

Quantitative atomic force microscopy establishes free energy parameters of amyloid fibril formation

Segers-Nolten, I. M.Subramaniam, V.de Leeuw, S. W.van Raaij, M. E.van Gestel, J. A. M...

Biophys J 2008

Detection of colorectal cancer by serum and tussue protein profiling: a prospective study in a population at risk

Engwegen, J. Y.Depla, A. C. T. M.Smits, M. E.Cats, A.Tuynman, H.Heukelem, H. A.Snel, ...

Biomarker Insights 2008: 375

E-BioFlow: different perspectives on scientific workflows

Wassink, I.Rauwerda, H.van der Vet, P. E.Breit, T.Nijholt, A.

Bioinformatics. 2008