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Author Details

Patrick Kemmeren
Princess Maxima Center for Pediatric Oncology
2002
55
29
Nevan J Krogan (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37400763Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS.BMC Cancer2023
37060567Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia.Cell Rep2023
35085008Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing.JCO Precis Oncol2022
36182817Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program 'iTHER'.Eur J Cancer2022
36230794Molecular Characterization Reveals Subclasses of 1q Gain in Intermediate Risk Wilms Tumors.Cancers (Basel)2022
35916583Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes.EMBO Mol Med2022
33306797Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations.Mol Biol Evol2021
33654267Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology.NPJ Precis Oncol2021
34615983A systematic analysis of genetic interactions and their underlying biology in childhood cancer.Commun Biol2021
31562204DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas.Clin Cancer Res2020
31887709Kaposiform hemangioendothelioma and tufted angioma - (epi)genetic analysis including genome-wide methylation profiling.Ann Diagn Pathol2020
33280256Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.Mol Syst Biol2020
32685929An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions.STAR Protoc2020
32161258An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity.Nat Commun2020
30568311Next-generation phenotyping using computer vision algorithms in rare genomic neurodevelopmental disorders.Genet Med2019
31083661The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interaction pattern.PLoS Comput Biol2019
30221560The clinical implementation of copy number detection in the age of next-generation sequencing.Expert Rev Mol Diagn2018
27979920Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters.EMBO J2017
28257504Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation.PLoS One2017
26939894An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation.Sci Rep2016
27626671Proteome-wide Changes in Protein Turnover Rates in C. elegans Models of Longevity and Age-Related Disease.Cell Rep2016
26700642A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.BMC Biol2015
24952590Cell cycle population effects in perturbation studies.Mol Syst Biol2014
25215507De-novo learning of genome-scale regulatory networks in S. cerevisiae.PLoS One2014
25157590The genomic landscape of compensatory evolution.PLoS Biol2014
24766815Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.Cell2014
24324601The role of Ctk1 kinase in termination of small non-coding RNAs.PLoS One2013
22697265Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.BMC Genomics2012
21596317The specificity and topology of chromatin interaction pathways in yeast.Mol Cell2011
20620961A consensus of core protein complex compositions for Saccharomyces cerevisiae.Mol Cell2010
21145464Functional overlap and regulatory links shape genetic interactions between signaling pathways.Cell2010
20959818Epistatic relationships reveal the functional organization of yeast transcription factors.Mol Syst Biol2010
19269370Functional organization of the S. cerevisiae phosphorylation network.Cell2009
19690564A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system.Mol Syst Biol2009
19713935Cotranslational assembly of the yeast SET1C histone methyltransferase complex.EMBO J2009
19401678Adaptable gene-specific dye bias correction for two-channel DNA microarrays.Mol Syst Biol2009
17200106Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.Mol Cell Proteomics2007
17389396CCR4/NOT complex associates with the proteasome and regulates histone methylation.Proc Natl Acad Sci U S A2007
17047089Transcriptome-based identification of pro- and antioxidative gene expression in kidney cortex of nitric oxide-depleted rats.Physiol Genomics2007
16489042Multiple robust signatures for detecting lymph node metastasis in head and neck cancer.Cancer Res2006
15699468Nitric oxide-dependent and nitric oxide-independent transcriptional responses to high shear stress in endothelial cells.Hypertension2005
15837421Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.Mol Cell2005
15980578GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.Nucleic Acids Res2005
15640797An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas.Nat Genet2005
15531615Predicting gene function through systematic analysis and quality assessment of high-throughput data.Bioinformatics2005
15105828From microarray data to results. Workshop on genomic approaches to microarray data analysis.EMBO Rep2004
15215431Expression Profiler: next generation--an online platform for analysis of microarray data.Nucleic Acids Res2004
15242832Nitric oxide donor induces temporal and dose-dependent reduction of gene expression in human endothelial cells.Am J Physiol Heart Circ Physiol2004
12519949ArrayExpress--a public repository for microarray gene expression data at the EBI.Nucleic Acids Res2003
14744115ArrayExpress: a public database of gene expression data at EBI.C R Biol2003
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Collaborators

Frank C P Holstege
Princess Maxima Center for Pediatric Oncology
Co-authored papers 37
Philip Lijnzaad
Princess Maxima Center for Pediatric Oncology
Co-authored papers 14
Dik van Leenen
Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University
Co-authored papers 12
Mariel O Brok
Princess Maxima Center for Pediatric Oncology
Co-authored papers 8
Jayne Y Hehir-Kwa
Princess Maxima Center for Pediatric Oncology
Co-authored papers 8
Marian J A Groot Koerkamp
Princess Maxima Center for Pediatric Oncology Research
Co-authored papers 8
Thanasis Margaritis
Princess Maxima Center for Pediatric Oncology
Co-authored papers 7
Joris J Benschop
Center for Molecular Medicine, University Medical Center Utrecht
Co-authored papers 7
Nathalie Brabers
University Medical Centre Utrecht, Universiteitsweg
Co-authored papers 6
Tineke L Lenstra
the Netherlands Cancer Institute, Oncode Institute
Co-authored papers 6
Sander R van Hooff
Princess Maxima Center for Pediatric Oncology
Co-authored papers 6
Nevan J Krogan (CM4AI)
University of California San Francisco
Co-authored papers 5
Katrin Sameith
Center for Molecular and Cellular Bioengineering
Co-authored papers 5
Eva Apweiler
University Medical Centre Utrecht, Universiteitsweg
Co-authored papers 5
Jan J Molenaar
Co-authored papers 4
Jaak Vilo
Institute of Computer Science, University of Tartu
Co-authored papers 4
Alvis Brazma
European Bioinformatics Institute
Co-authored papers 4
Sake van Wageningen
Oncode Institute, The Netherlands Cancer Institute
Co-authored papers 4
Loes A L van de Pasch
University Medical Centre Utrecht, Universiteitsweg
Co-authored papers 4
Linda V Bakker
Wageningen University and Research
Co-authored papers 4
Hindrik H D Kerstens
Co-authored papers 4
Han G Brunner
Maastricht University Medical Centre
Co-authored papers 3
Jonathan S Weissman
Whitehead Institute for Biomedical Research
Co-authored papers 3
Antony J Miles
University Medical Centre Utrecht, Universiteitsweg
Co-authored papers 3
Ugis Sarkans
Co-authored papers 3
Berend Snel
Utrecht University
Co-authored papers 3
Cheuk W Ko
University Medical Centre Utrecht, Universiteitsweg
Co-authored papers 3
Sean R Collins
University of California davis
Co-authored papers 3
Dorothea Fiedler
Leibniz Forschungsinstitut fur Molekulare Pharmakologie (FMP)
Co-authored papers 2
Marcel Kool
Hopp Children's Cancer Center (KiTZ)
Co-authored papers 2
Release 1.2