Jelle J Goeman

Summary

Affiliation: Leiden University Medical Center
Country: The Netherlands

Publications

  1. ncbi A global test for groups of genes: testing association with a clinical outcome
    Jelle J Goeman
    Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
    Bioinformatics 20:93-9. 2004
  2. ncbi Testing association of a pathway with survival using gene expression data
    Jelle J Goeman
    Department of Medical Statistics, Leiden University Medical Center, The Netherlands
    Bioinformatics 21:1950-7. 2005
  3. doi Autocorrelated logistic ridge regression for prediction based on proteomics spectra
    Jelle J Goeman
    Leiden University Medical Center
    Stat Appl Genet Mol Biol 7:Article10. 2008
  4. pmc Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data
    Kristina M Hettne
    Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
    BMC Med Genomics 6:2. 2013
  5. doi Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority
    Jelle 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
  6. doi Multiple testing on the directed acyclic graph of gene ontology
    Jelle J Goeman
    Department of Medical Statistics, Postzone S5 P, P O Box 9600, 2300 RC Leiden, The Netherlands
    Bioinformatics 24:537-44. 2008
  7. ncbi Analyzing gene expression data in terms of gene sets: methodological issues
    Jelle J Goeman
    Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Bioinformatics 23:980-7. 2007
  8. ncbi A goodness-of-fit test for multinomial logistic regression
    Jelle J Goeman
    Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
    Biometrics 62:980-5. 2006
  9. doi L1 penalized estimation in the Cox proportional hazards model
    Jelle J Goeman
    Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Biom J 52:70-84. 2010
  10. pmc A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging
    Seyed Yahya Anvar
    Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    Aging (Albany NY) 5:412-26. 2013

Collaborators

Detail Information

Publications27

  1. ncbi A global test for groups of genes: testing association with a clinical outcome
    Jelle 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)...
  2. ncbi Testing association of a pathway with survival using gene expression data
    Jelle 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...
  3. doi Autocorrelated logistic ridge regression for prediction based on proteomics spectra
    Jelle 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...
  4. pmc Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data
    Kristina M Hettne
    Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
    BMC Med Genomics 6:2. 2013
    ....
  5. doi Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority
    Jelle 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...
  6. doi Multiple testing on the directed acyclic graph of gene ontology
    Jelle 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...
  7. ncbi Analyzing gene expression data in terms of gene sets: methodological issues
    Jelle J Goeman
    Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Bioinformatics 23:980-7. 2007
    ..This article aims to clarify the assumptions behind different approaches and to indicate a preferential methodology of gene set testing...
  8. ncbi A goodness-of-fit test for multinomial logistic regression
    Jelle J Goeman
    Department of Medical Statistics, Leiden University Medical Center, P O Box 9604, 2300 RC Leiden, The Netherlands
    Biometrics 62:980-5. 2006
    ....
  9. doi L1 penalized estimation in the Cox proportional hazards model
    Jelle 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...
  10. pmc A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging
    Seyed Yahya Anvar
    Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    Aging (Albany NY) 5:412-26. 2013
    ..We suggest that PABPN1 levels regulate muscle cell aging and OPMD represents an accelerated muscle aging disorder. ..
  11. ncbi Enhancing scatterplots with smoothed densities
    Paul 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...
  12. doi Deep sequencing to reveal new variants in pooled DNA samples
    Astrid 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...
  13. doi Endogenous HLA class II epitopes that are immunogenic in vivo show distinct behavior toward HLA-DM and its natural inhibitor HLA-DO
    Anita 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...
  14. pmc Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R
    Willemijn M Passtoors
    Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
    PLoS ONE 7:e27759. 2012
    ....
  15. pmc Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis
    Erik F Hensen
    Department of Otolaryngology and Head and Neck Surgery, Leiden University Medical Center, The Netherlands
    BMC Med Genomics 2:25. 2009
    ....
  16. doi Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging
    Erik B van den Akker
    Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands The Delft Bioinformatics Lab, Delft University of Technology, PO Box 5031, 2600 GA, Delft, The Netherlands
    Aging Cell 13:216-25. 2014
    ..The hereby-detected age-associated and consistently coexpressed PPI modules therefore may provide a molecular basis for future research into mechanisms underlying human aging...
  17. pmc Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer
    Sabrina A H M van den Tillaart
    Leiden University Medical Center, Department of Gynecology, Leiden, The Netherlands
    PLoS ONE 8:e67414. 2013
    ..The overall genetic changes and CNA on specific chromosome-arms differed between histological types. No relation was found with the clinical parameters that currently dictate treatment choice. ..
  18. doi Efficient approximate k-fold and leave-one-out cross-validation for ridge regression
    Rosa J Meijer
    Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Postzone S5 P, P O Box 9604, 2300 RC Leiden, The Netherlands
    Biom J 55:141-55. 2013
    ..In order to demonstrate the method's performance, it will be applied to several microarray data sets. An R package penalized, which implements the method, is available on CRAN...
  19. pmc Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing
    Susanne 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...
  20. pmc Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation
    Eleonora de Klerk
    Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
    Nucleic Acids Res 40:9089-101. 2012
    ....
  21. doi Resolving confusion of tongues in statistics and machine learning: a primer for biologists and bioinformaticians
    Maarten 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...
  22. doi Literature-aided interpretation of gene expression data with the weighted global test
    Rob 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...
  23. ncbi Multiple hypothesis testing in genomics
    Jelle J Goeman
    Biostatistics, Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
    Stat Med 33:1946-78. 2014
    ..In our discussion, we take into account the exploratory nature of genomics experiments, looking at selection of genes before or after testing, and at the role of validation experiments. Copyright © 2014 John Wiley & Sons, Ltd. ..
  24. ncbi Major aging-associated RNA expressions change at two distinct age-positions
    Marius Gheorghe
    Department of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
    BMC Genomics 15:132. 2014
    ..Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expression trends in cross-sectional datasets...
  25. pmc Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways
    Joris Deelen
    Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
    Age (Dordr) 35:235-49. 2013
    ..In conclusion, this study shows that genetic variation in genes involved in the IIS and TM pathways is associated with human longevity...
  26. pmc Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: a pathway-based analysis
    Erik 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...
  27. ncbi Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes
    Riny 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...