Research Topics
Species | Jelle J GoemanSummaryAffiliation: Leiden University Medical Center Country: The Netherlands Publications
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Detail Information
Publications
A global test for groups of genes: testing association with a clinical outcomeJelle J Goeman
Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
Bioinformatics 20:93-9. 2004..Groups of genes may be any size from a single gene to all genes on the chip (e.g. known pathways, specific areas of the genome or clusters from a cluster analysis)...- Testing association of a pathway with survival using gene expression dataJelle J Goeman
Department of Medical Statistics, Leiden University Medical Center, The Netherlands
Bioinformatics 21:1950-7. 2005..A recent surge of interest in survival as the primary clinical endpoint of microarray studies has called for an extension of the Global Test methodology to survival... 
Autocorrelated logistic ridge regression for prediction based on proteomics spectraJelle J Goeman
Leiden University Medical Center
Stat Appl Genet Mol Biol 7:Article10. 2008..The method is applied to the analysis of proteomics mass spectra...- L1 penalized estimation in the Cox proportional hazards modelJelle J Goeman
Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
Biom J 52:70-84. 2010..An R package, penalized, that implements the method, is available on CRAN... - Multiple testing on the directed acyclic graph of gene ontologyJelle J Goeman
Department of Medical Statistics, Postzone S5 P, P O Box 9600, 2300 RC Leiden, The Netherlands
Bioinformatics 24:537-44. 2008..Current methods for multiplicity adjustment do not make use of the graph structure of Gene Ontology (GO) when testing for association of expression profiles of GO terms with a response variable... - Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiorityJelle J Goeman
Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
Stat Med 29:2117-25. 2010..Relationships with confidence intervals are explored, and the effectiveness of the three-sided testing approach is demonstrated in a number of recent clinical trials... - Analyzing gene expression data in terms of gene sets: methodological issuesJelle J Goeman
Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
Bioinformatics 23:980-7. 2007..We also argue that methods that competitively test each gene set against the rest of the genes create an unnecessary rift between single gene testing and gene set testing... - A goodness-of-fit test for multinomial logistic regressionJelle J Goeman
Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
Biometrics 62:980-5. 2006.... - Enhancing scatterplots with smoothed densitiesPaul H C Eilers
Department of Medical Statistics, Leiden University Medical Centre, The Netherlands
Bioinformatics 20:623-8. 2004..Scatterplots of microarray data generally contain a very large number of dots, making it difficult to get a good impression of their distribution in dense areas... - Deep sequencing to reveal new variants in pooled DNA samplesAstrid A Out
Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Hum Mutat 30:1703-12. 2009..We describe custom bioinformatics and statistics to optimize detection of rare variants and to estimate required sequencing depth. Our results provide directions for designing high-throughput analyses of candidate genes... - Endogenous HLA class II epitopes that are immunogenic in vivo show distinct behavior toward HLA-DM and its natural inhibitor HLA-DOAnita N Kremer
Department of Hematology, Leiden University Medical Center, The Netherlands
Blood 120:3246-55. 2012..This opens perspectives to exploit selective processing capacities as a new approach for targeted immunotherapy... 
Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7RWillemijn M Passtoors
Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
PLoS ONE 7:e27759. 2012....- Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesisErik F Hensen
Department of Otolaryngology and Head and Neck Surgery, Leiden University Medical Center, The Netherlands
BMC Med Genomics 2:25. 2009.... - Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencingSusanne Osanto
Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
PLoS ONE 7:e38298. 2012..Individual differentially expressed miRNAs may potentially serve as diagnostic or prognostic markers or future therapeutic targets in ccRCC. The biological relevance of candidate novel miRNAs is unknown at present... - Poly(A) binding protein nuclear 1 levels affect alternative polyadenylationEleonora de Klerk
Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
Nucleic Acids Res 40:9089-101. 2012.... - Resolving confusion of tongues in statistics and machine learning: a primer for biologists and bioinformaticiansMaarten van Iterson
Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
Proteomics 12:543-9. 2012..We explain differences and similarities in common terminology used in various domains, such as precision, recall, sensitivity and true positive rate. This primer can serve as a guide to the terminology used in these fields... - Literature-aided interpretation of gene expression data with the weighted global testRob Jelier
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
Brief Bioinform 12:518-29. 2011..Literature mining tools are therefore powerful additions to the toolbox for the interpretation of high-throughput genomics data... - Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: a pathway-based analysisErik F Hensen
Department of Otolaryngology and Head and Neck Surgery, Leiden University, Medical Centre, Leiden, The Netherlands
BMC Cancer 8:168. 2008..Here, we present an independent gene expression validation study of metastasized versus non-metastasized HNSCC... - Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genesRiny Janssen
Laboratory for Toxicology, Pathology, and Genetics, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
J Infect Dis 196:826-34. 2007..Only a proportion of children infected with RSV require hospitalization. Because known risk factors for severe disease, such as premature birth, cannot fully explain differences in disease severity, genetic factors have been implicated...