Judith M Boer

Summary

Affiliation: Erasmus MC
Country: The Netherlands

Publications

  1. pmc Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions
    Maarten van Iterson
    Center for Human and Clinical Genetics and Leiden University Medical Center, Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2300 ZC Leiden, The Netherlands, Netherlands Bioinformatics Centre, P O Box 9101, 6500 HB Nijmegen, The Netherlands, Department of Epidemiology and Biostatistics, VU University Medical Center, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands and Department of Pediatric Oncology, Erasmus Medical Center Sophia Children s Hospital, Dr Molewaterplein 60, 3015 GJ Rotterdam, The Netherlands
    Nucleic Acids Res 41:e146. 2013
  2. pmc BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
    Eddy H van Roon
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Clin Epigenetics 5:2. 2013
  3. pmc Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    Peter A C 't Hoen
    The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nucleic Acids Res 36:e141. 2008
  4. pmc Gene expression variation between mouse inbred strains
    Rolf Turk
    Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
    BMC Genomics 5:57. 2004
  5. doi request reprint General power and sample size calculations for high-dimensional genomic data
    Maarten van Iterson
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Stat Appl Genet Mol Biol 12:449-67. 2013
  6. pmc Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
    Eddy H J van Roon
    Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
    Eur J Hum Genet 19:307-12. 2011
  7. pmc Human papillomavirus (HPV) upregulates the cellular deubiquitinase UCHL1 to suppress the keratinocyte's innate immune response
    Rezaul Karim
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    PLoS Pathog 9:e1003384. 2013
  8. ncbi request reprint Generation and characterization of transgenic mice with the full-length human DMD gene
    Peter A C 't Hoen
    Center for Human and Clinical Genetics, Leiden University Medical Center, Postal Zone S4 P, PO Box 9600, 2300 RC Leiden, The Netherlands
    J Biol Chem 283:5899-907. 2008
  9. pmc Filtering, FDR and power
    Maarten van Iterson
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, 1007 MB, The Netherlands
    BMC Bioinformatics 11:450. 2010
  10. pmc Integrated analysis of DNA copy number and gene expression microarray data using gene sets
    Renee X Menezes
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    BMC Bioinformatics 10:203. 2009

Collaborators

Detail Information

Publications20

  1. pmc Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions
    Maarten van Iterson
    Center for Human and Clinical Genetics and Leiden University Medical Center, Leiden Genome Technology Center, Leiden University Medical Center, Einthovenweg 20, 2300 ZC Leiden, The Netherlands, Netherlands Bioinformatics Centre, P O Box 9101, 6500 HB Nijmegen, The Netherlands, Department of Epidemiology and Biostatistics, VU University Medical Center, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands and Department of Pediatric Oncology, Erasmus Medical Center Sophia Children s Hospital, Dr Molewaterplein 60, 3015 GJ Rotterdam, The Netherlands
    Nucleic Acids Res 41:e146. 2013
    ..Using the same study, we showed the advantages of the global test over Pearson correlation and lasso. We conclude that our integrated approach successfully identifies regulated microRNAs and their targets. ..
  2. pmc BRAF mutation-specific promoter methylation of FOX genes in colorectal cancer
    Eddy H van Roon
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Clin Epigenetics 5:2. 2013
    ..We studied genome-wide DNA methylation differences between colorectal tumors carrying a BRAF mutation and BRAF wildtype tumors...
  3. pmc Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms
    Peter A C 't Hoen
    The Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Nucleic Acids Res 36:e141. 2008
    ..We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies...
  4. pmc Gene expression variation between mouse inbred strains
    Rolf Turk
    Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, Nederland
    BMC Genomics 5:57. 2004
    ..In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred strains using spotted oligonucleotide microarrays...
  5. doi request reprint General power and sample size calculations for high-dimensional genomic data
    Maarten van Iterson
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    Stat Appl Genet Mol Biol 12:449-67. 2013
    ..Furthermore, we compare our proposed method for estimation of the density of effect sizes from pilot data with a recent proposed method specific for two group comparisons...
  6. pmc Tumour-specific methylation of PTPRG intron 1 locus in sporadic and Lynch syndrome colorectal cancer
    Eddy H J van Roon
    Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
    Eur J Hum Genet 19:307-12. 2011
    ..The high sensitivity and specificity for the PTPRG intron 1 methylation in both sporadic and hereditary colon cancers support biomarker potential for early detection of colon cancer...
  7. pmc Human papillomavirus (HPV) upregulates the cellular deubiquitinase UCHL1 to suppress the keratinocyte's innate immune response
    Rezaul Karim
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    PLoS Pathog 9:e1003384. 2013
    ..This identifies UCHL1 as a negative regulator of PRR-induced immune responses and consequently its virus-increased expression as a strategy for hrHPV to persist...
  8. ncbi request reprint Generation and characterization of transgenic mice with the full-length human DMD gene
    Peter A C 't Hoen
    Center for Human and Clinical Genetics, Leiden University Medical Center, Postal Zone S4 P, PO Box 9600, 2300 RC Leiden, The Netherlands
    J Biol Chem 283:5899-907. 2008
    ..In addition, the hDMD mouse can be used to study the influence of the genomic context on deletion and recombination frequencies, genome stability, and gene expression regulation...
  9. pmc Filtering, FDR and power
    Maarten van Iterson
    Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, 1007 MB, The Netherlands
    BMC Bioinformatics 11:450. 2010
    ..However, filtering may introduce a bias on the multiple testing correction. The precise amount of bias depends on many quantities, such as fraction of probes filtered out, filter statistic and test statistic used...
  10. pmc Integrated analysis of DNA copy number and gene expression microarray data using gene sets
    Renee X Menezes
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    BMC Bioinformatics 10:203. 2009
    ..Furthermore, some copy number changes extend over larger chromosomal regions affecting the expression levels of multiple resident genes...
  11. 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
    ....
  12. pmc Human papillomavirus deregulates the response of a cellular network comprising of chemotactic and proinflammatory genes
    Rezaul Karim
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    PLoS ONE 6:e17848. 2011
    ..In summary, our comprehensive expression profiling approach revealed that HPV16 and 18 coordinate a broad deregulation of the keratinocyte's inflammatory response, and contributes to the understanding of virus persistence...
  13. pmc Early onset MSI-H colon cancer with MLH1 promoter methylation, is there a genetic predisposition?
    Eddy H J van Roon
    Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
    BMC Cancer 10:180. 2010
    ..As this type of colon cancer is associated with high ages, young patients bearing this type of malignancy are rare and could provide additional insight into the etiology of sporadic MSI-H colon cancer...
  14. pmc The homeobox gene MEIS1 is methylated in BRAF (p.V600E) mutated colon tumors
    Ashwin A Dihal
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    PLoS ONE 8:e79898. 2013
    ..In conclusion, BRAF (p.V600E) colon tumors showed significant MEIS1 promoter methylation, which was associated with decreased MEIS1 gene expression. ..
  15. doi request reprint Specific promoter methylation identifies different subgroups of MLL-rearranged infant acute lymphoblastic leukemia, influences clinical outcome, and provides therapeutic options
    Dominique J P M Stumpel
    Department of Pediatric Oncology Hematology, Erasmus Medical Center Sophia Children s Hospital, Rotterdam, The Netherlands
    Blood 114:5490-8. 2009
    ..Therefore, inhibition of aberrant DNA methylation may be an important novel therapeutic strategy for MLL-rearranged ALL in infants...
  16. doi request reprint Oncogenomic analysis of mycosis fungoides reveals major differences with Sezary syndrome
    Remco van Doorn
    Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
    Blood 113:127-36. 2009
    ..Furthermore, our analysis uncovered genomic differences between MF and Sz, which suggest that the molecular pathogenesis and therefore therapeutic requirements of these cutaneous T-cell lymphomas may be distinct...
  17. pmc Can subtle changes in gene expression be consistently detected with different microarray platforms?
    Paola Pedotti
    Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
    BMC Genomics 9:124. 2008
    ..Here we address the performance and the overlap in the detection of differentially expressed genes for five different microarray platforms in a challenging biological context where differences in gene expression are few and subtle...
  18. ncbi request reprint Microarray data analysis: a hierarchical T-test to handle heteroscedasticity
    Renee X de Menezes
    Department of Medical Statistics, Leiden University Medical Center, PO Box 9604, 2300 RC Leiden, The Netherlands
    Appl Bioinformatics 3:229-35. 2004
    ..This approach can be extended to cases where there are more than two groups...
  19. doi request reprint Tumor-expressed B7-H1 and B7-DC in relation to PD-1+ T-cell infiltration and survival of patients with cervical carcinoma
    Rezaul Karim
    Departments of Center for Human and Clinical Genetics, Immunohematology and Blood Transfusion, Clinical Oncology, Pathology, and Gynecology, Leiden University Medical Center, Leiden, The Netherlands
    Clin Cancer Res 15:6341-7. 2009
    ..The aim of this study was to determine B7-H1, B7-DC, and PD-1 expression in cervical carcinoma...
  20. ncbi request reprint Large-scale gene expression analysis of human skeletal myoblast differentiation
    Ellen Sterrenburg
    Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333 AL Leiden, The Netherlands
    Neuromuscul Disord 14:507-18. 2004
    ..Further study of these genes can bring new insights into the process of muscle differentiation, and they are candidate genes for neuromuscular disorders with an as yet unidentified cause...