List of works - Jelle J Goeman

A Cochran-Armitage-type and a score-free global test for multivariate ordinal data

scientific article

A Goodness-of-Fit Test for Multinomial Logistic Regression

scientific article published on 01 December 2006

A Kinome-Wide Small Interfering RNA Screen Identifies Proviral and Antiviral Host Factors in Severe Acute Respiratory Syndrome Coronavirus Replication, Including Double-Stranded RNA-Activated Protein Kinase and Early Secretory Pathway Proteins.

scientific article published on 3 June 2015

A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging

scientific article published on June 2013

A global test for groups of genes: testing association with a clinical outcome

scientific article published on January 2004

A global × global test for testing associations between two large sets of variables

scientific article

A microarray study on the effect of four hormone therapy regimens on gene transcription in whole blood from healthy postmenopausal women.

scientific article published on 2 January 2012

A multiple testing method for hypotheses structured in a directed acyclic graph

scientific article

A region-based multiple testing method for hypotheses ordered in space or time

scientific article published on February 2015

A test for comparing two groups of samples when analyzing multiple omics profiles

scientific article

An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs

scientific article published on 04 October 2014

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack

scientific article published on 9 February 2016

Analyzing gene expression data in terms of gene sets: methodological issues

scientific article

Assessing the translational landscape of myogenic differentiation by ribosome profiling.

scientific article

Autocorrelated logistic ridge regression for prediction based on proteomics spectra.

scientific article published on 21 February 2008

Common disease signatures from gene expression analysis in Huntington's disease human blood and brain

scientific article published on August 2016

Contribution to the discussion of "A critical evaluation of the current 'p-value controversy"'.

scientific article published on 25 April 2017

Correction: Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R.

scientific article published on 10 May 2012

Corrigendum: DNA methylation signatures link prenatal famine exposure to growth and metabolism

scientific article published on 7 July 2015

Cross-sectional serum metabolomic study of multiple forms of muscular dystrophy

scientific article published on 14 February 2018

DNA methylation signatures link prenatal famine exposure to growth and metabolism

scientific article

Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2.

scientific article published on 21 November 2017

Deep sequencing to reveal new variants in pooled DNA samples

scientific article published in December 2009

Dlx1 and Rgs5 in the ductus arteriosus: vessel-specific genes identified by transcriptional profiling of laser-capture microdissected endothelial and smooth muscle cells

scientific article published on 28 January 2014

Drug Survival Studies in Dermatology:Principles, Purposes, and Pitfalls

scientific article

Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae

scientific article published on 01 November 2020

Efficient approximate k-fold and leave-one-out cross-validation for ridge regression

scientific article published on 24 January 2013

Endogenous HLA class II epitopes that are immunogenic in vivo show distinct behavior toward HLA-DM and its natural inhibitor HLA-DO.

scientific article published on 13 August 2012

Enhancing scatterplots with smoothed densities.

scientific article published on 22 January 2004

Epigenomic Analysis of Sézary Syndrome Defines Patterns of Aberrant DNA Methylation and Identifies Diagnostic Markers

scientific article published on 22 April 2016

Fetal mesenchymal stromal cells differentiating towards chondrocytes acquire a gene expression profile resembling human growth plate cartilage

scientific article

Focused human gene expression profiling using dual-color reverse transcriptase multiplex ligation-dependent probe amplification

scientific article published on 24 April 2015

Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways

scientific article

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

scientific article published on 10 June 2008

Genes involved in the osteoarthritis process identified through genome wide expression analysis in articular cartilage; the RAAK study.

scientific article

Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes

scientific article (publication date: 15 September 2007)

Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing

scientific article

Hommel's procedure in linear time

scientific article published on 05 September 2018

Human leukocyte antigen-DO regulates surface presentation of human leukocyte antigen class II-restricted antigens on B cell malignancies

scientific article published on 14 February 2014

Human papillomavirus and post-transplant cutaneous squamous-cell carcinoma: a multicenter, prospective cohort study

scientific article published on 11 October 2017

Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood

scientific article

Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array

scientific article published on 06 August 2013

Identification of biomarkers for tuberculosis disease using a novel dual-color RT-MLPA assay.

scientific article

Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome

scientific article published in PLoS ONE

Inhibition of Gsk3β in cartilage induces osteoarthritic features through activation of the canonical Wnt signaling pathway.

scientific article published on 27 August 2011

Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2. ⬇️

scientific article

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

scientific article published on 28 May 2015

L1 penalized estimation in the Cox proportional hazards model

scientific article

Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine

scientific article published on 03 April 2019

Literature-aided interpretation of gene expression data with the weighted global test

scientific article

Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer

scientific article published on 09 July 2013

MAGE-A3 immunotherapeutic as adjuvant therapy for patients with resected, MAGE-A3-positive, stage III melanoma (DERMA): a double-blind, randomised, placebo-controlled, phase 3 trial

scientific article published on 13 June 2018

Major aging-associated RNA expressions change at two distinct age-positions.

scientific article

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging

scientific article

MicroRNA classifier and nomogram for metastasis prediction in colon cancer.

scientific article

Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls

scientific article published on 07 October 2015

Multiple testing on the directed acyclic graph of gene ontology.

scientific article published on 18 January 2008

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

scientific article

Plea for routinely presenting prediction intervals in meta-analysis

scientific article published on 12 July 2016

Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation

scientific article

Prenatal exposure to apoE deficiency and postnatal hypercholesterolemia are associated with altered cell-specific lysine methyltransferase and histone methylation patterns in the vasculature

scientific article

Promoter CpG island hypermethylation in dysplastic nevus and melanoma: CLDN11 as an epigenetic biomarker for malignancy

scientific article published on 7 July 2014

Quantitative comparison of different iron forms in the temporal cortex of Alzheimer patients and control subjects.

scientific article published on 2 May 2018

Resolving confusion of tongues in statistics and machine learning: a primer for biologists and bioinformaticians.

scientific article published on 23 January 2012

Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects

scientific article published on 25 May 2017

Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis

scientific article

Small studies are more heterogeneous than large ones: a meta-meta-analysis

scientific article published on 02 April 2015

Sotos syndrome is associated with deregulation of the MAPK/ERK-signaling pathway.

scientific article

Testing association of a pathway with survival using gene expression data

scientific article

Testing goodness of fit in regression: a general approach for specified alternatives

scientific article published on 25 July 2012

The footprint of genome architecture in the largest genome expansion in RNA viruses

scientific article

The inheritance procedure: multiple testing of tree-structured hypotheses

scientific article published on 21 January 2012

The transcriptional response to chronic stress and glucocorticoid receptor blockade in the hippocampal dentate gyrus

scientific article

Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority

scientific article published on 01 September 2010

Tracking the progression of the human inner cell mass during embryonic stem cell derivation

scientific article published on 26 February 2012

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model.

scientific article published on 22 June 2018

Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R

scientific article (publication date: 2012)

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing

scientific article published on 6 September 2017

Variability in the analysis of a single neuroimaging dataset by many teams

scientific article published on 20 May 2020

List of works by Jelle J Goeman

A Cochran-Armitage-type and a score-free global test for multivariate ordinal data

A Goodness-of-Fit Test for Multinomial Logistic Regression

A Kinome-Wide Small Interfering RNA Screen Identifies Proviral and Antiviral Host Factors in Severe Acute Respiratory Syndrome Coronavirus Replication, Including Double-Stranded RNA-Activated Protein Kinase and Early Secretory Pathway Proteins.

A decline in PABPN1 induces progressive muscle weakness in oculopharyngeal muscle dystrophy and in muscle aging

A global test for groups of genes: testing association with a clinical outcome

A global × global test for testing associations between two large sets of variables

A microarray study on the effect of four hormone therapy regimens on gene transcription in whole blood from healthy postmenopausal women.

A multiple testing method for hypotheses structured in a directed acyclic graph

A region-based multiple testing method for hypotheses ordered in space or time

A test for comparing two groups of samples when analyzing multiple omics profiles

An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack

Analyzing gene expression data in terms of gene sets: methodological issues

Assessing the translational landscape of myogenic differentiation by ribosome profiling.

Autocorrelated logistic ridge regression for prediction based on proteomics spectra.

Common disease signatures from gene expression analysis in Huntington's disease human blood and brain

Contribution to the discussion of "A critical evaluation of the current 'p-value controversy"'.

Correction: Transcriptional Profiling of Human Familial Longevity Indicates a Role for ASF1A and IL7R.

Corrigendum: DNA methylation signatures link prenatal famine exposure to growth and metabolism

Cross-sectional serum metabolomic study of multiple forms of muscular dystrophy

DNA methylation signatures link prenatal famine exposure to growth and metabolism

Deep characterization of a common D4Z4 variant identifies biallelic DUX4 expression as a modifier for disease penetrance in FSHD2.

Deep sequencing to reveal new variants in pooled DNA samples

Dlx1 and Rgs5 in the ductus arteriosus: vessel-specific genes identified by transcriptional profiling of laser-capture microdissected endothelial and smooth muscle cells

Drug Survival Studies in Dermatology:Principles, Purposes, and Pitfalls

Dynamics of the bacterial gut microbiota during controlled human infection with Necator americanus larvae

Efficient approximate k-fold and leave-one-out cross-validation for ridge regression

Endogenous HLA class II epitopes that are immunogenic in vivo show distinct behavior toward HLA-DM and its natural inhibitor HLA-DO.

Enhancing scatterplots with smoothed densities.

Epigenomic Analysis of Sézary Syndrome Defines Patterns of Aberrant DNA Methylation and Identifies Diagnostic Markers

Fetal mesenchymal stromal cells differentiating towards chondrocytes acquire a gene expression profile resembling human growth plate cartilage

Focused human gene expression profiling using dual-color reverse transcriptase multiplex ligation-dependent probe amplification

Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways

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

Genes involved in the osteoarthritis process identified through genome wide expression analysis in articular cartilage; the RAAK study.

Genetic susceptibility to respiratory syncytial virus bronchiolitis is predominantly associated with innate immune genes

Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing

Hommel's procedure in linear time

Human leukocyte antigen-DO regulates surface presentation of human leukocyte antigen class II-restricted antigens on B cell malignancies

Human papillomavirus and post-transplant cutaneous squamous-cell carcinoma: a multicenter, prospective cohort study

Huntington's disease biomarker progression profile identified by transcriptome sequencing in peripheral blood

Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array

Identification of biomarkers for tuberculosis disease using a novel dual-color RT-MLPA assay.

Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome

Inhibition of Gsk3β in cartilage induces osteoarthritic features through activation of the canonical Wnt signaling pathway.

Inter-individual differences in CpG methylation at D4Z4 correlate with clinical variability in FSHD1 and FSHD2. ⬇️

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

L1 penalized estimation in the Cox proportional hazards model

Large-scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine

Literature-aided interpretation of gene expression data with the weighted global test

Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer

MAGE-A3 immunotherapeutic as adjuvant therapy for patients with resected, MAGE-A3-positive, stage III melanoma (DERMA): a double-blind, randomised, placebo-controlled, phase 3 trial

Major aging-associated RNA expressions change at two distinct age-positions.

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging

MicroRNA classifier and nomogram for metastasis prediction in colon cancer.

Multiple Testing of Gene Sets from Gene Ontology: Possibilities and Pitfalls

Multiple testing on the directed acyclic graph of gene ontology.

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

Plea for routinely presenting prediction intervals in meta-analysis

Poly(A) binding protein nuclear 1 levels affect alternative polyadenylation

Prenatal exposure to apoE deficiency and postnatal hypercholesterolemia are associated with altered cell-specific lysine methyltransferase and histone methylation patterns in the vasculature

Promoter CpG island hypermethylation in dysplastic nevus and melanoma: CLDN11 as an epigenetic biomarker for malignancy

Quantitative comparison of different iron forms in the temporal cortex of Alzheimer patients and control subjects.

Resolving confusion of tongues in statistics and machine learning: a primer for biologists and bioinformaticians.

Robin Hood: A cost-efficient two-stage approach to large-scale simultaneous inference with non-homogeneous sparse effects

Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis

Small studies are more heterogeneous than large ones: a meta-meta-analysis

Sotos syndrome is associated with deregulation of the MAPK/ERK-signaling pathway.

Testing association of a pathway with survival using gene expression data

Testing goodness of fit in regression: a general approach for specified alternatives

The footprint of genome architecture in the largest genome expansion in RNA viruses

The inheritance procedure: multiple testing of tree-structured hypotheses

The transcriptional response to chronic stress and glucocorticoid receptor blockade in the hippocampal dentate gyrus

Three-sided hypothesis testing: simultaneous testing of superiority, equivalence and inferiority

Tracking the progression of the human inner cell mass during embryonic stem cell derivation

Transcriptional profiling and biomarker identification reveal tissue specific effects of expanded ataxin-3 in a spinocerebellar ataxia type 3 mouse model.

Transcriptional profiling of human familial longevity indicates a role for ASF1A and IL7R

Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing

Variability in the analysis of a single neuroimaging dataset by many teams