Personal information

Netherlands

Biography

Patrick Kemmeren obtained his PhD in 2005 from Utrecht University for his work on analyzing and integrating genome-scale data. During his PhD, he also spent time at the European Bioinformatics Institute as a visiting scientist. A postdoctoral fellowship allowed him to work at the University of California, San Francisco. Under the supervision of Dr. Nevan Krogan, he worked on the definition of an accurate and comprehensive map of stable protein-protein interactions. After returning to University Medical Center Utrecht (UMC Utrecht), he obtained a VENI grant from the Dutch Science Foundation (NWO) in 2007. After starting his own research group, Patrick received an NWO VIDI award in 2012 to further investigate the molecular mechanisms underlying genetic interactions. In 2013, Patrick became an Assistant Professor at the Center for Molecular Medicine, UMC Utrecht.
Patrick joined the Princess Máxima Center for Pediatric Oncology as a principal investigator in 2016, where he exploits cancer genomics data through a combination of bioinformatics and systems biology approaches with the goal to improve our understanding of childhood cancer initiation and progression as well as improve patient care for children with cancer. Examples include driving bioinformatics research for precision oncology and diagnostics, improving structural variation detection and investigating biological mechanisms of genetic interactions in childhood cancer. In 2020 he also became head of the Big Data Core, a research facility within the Máxima initiated by Patrick that coordinates several institute-wide activities concerning data stewardship as well as data and computational infrastructures for data intensive childhood cancer research and care. Since October 2021 he has also been appointed as associate professor at the Center for Molecular Medicine, UMC Utrecht to foster further collaboration between the Máxima and the strategic program Cancer at UMC Utrecht.
In addition to these research activities, Patrick has been the coordinator of the High-Performance Computing facility for Life Sciences at Utrecht Science Park between 2012 and 2017, executive committee member of the Utrecht Bioinformatics Center since 2014 and board member of the Netherlands Bioinformatics and Systems Biology research school since 2017.

Activities

Employment (2)

Universitair Medisch Centrum Utrecht: Utrecht, NL

2021-10 to present | Associate Professor (Center for Molecular Medicine)
Employment
Source: Self-asserted source
Patrick Kemmeren

Prinses Máxima Centrum voor Kinderoncologie: Utrecht, Utrecht, NL

2016-01-01 to present | Principal Investigator & head Big Data Core
Employment
Source: Self-asserted source
Patrick Kemmeren

Works (50 of 64)

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Page 1 of 2

Data from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Data from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Figure S1 from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Figure S1 from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Supplementary Methods from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Supplementary Methods from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Table S1 from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Table S1 from DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

2023-03-31 | Preprint
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Trecode: A FAIR Eco-System for the Analysis and Archiving of Omics Data in a Combined Diagnostic and Research Setting

BioMedInformatics
2022-12 | Journal article | Author
Contributors: Hindrik Kerstens; Jayne Y Hehir-Kwa; Ellen van de Geer; Chris van Run; Shashi Badloe; Alex Janse; John Baker-Hernandez; Sam de Vos; Douwe van der Leest; Eugène Verwiel et al.
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Multidisciplinary Digital Publishing Institute

Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program ‘iTHER’

European Journal of Cancer
2022-11 | Journal article
Part of ISSN: 0959-8049
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

Molecular Characterization Reveals Subclasses of 1q Gain in Intermediate Risk Wilms Tumors

Cancers
2022-10-05 | Journal article
Part of ISSN: 2072-6694
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren
grade
Preferred source (of 2)‎

Mesenchymal tumor organoid models recapitulate rhabdomyosarcoma subtypes

EMBO Molecular Medicine
2022-08-02 | Journal article
Part of ISSN: 1757-4676
Part of ISSN: 1757-4684
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

Improved Gene Fusion Detection in Childhood Cancer Diagnostics Using RNA Sequencing

JCO Precision Oncology
2022-05 | Journal article
Part of ISSN: 2473-4284
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

A systematic analysis of genetic interactions and their underlying biology in childhood cancer

Communications Biology
2021-10-06 | Journal article
Contributors: Josephine T. Daub; Saman Amini; Denise J. E. Kersjes; Xiaotu Ma; Natalie Jäger; Jinghui Zhang; Stefan M. Pfister; Frank C. P. Holstege; Patrick Kemmeren
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Crossref

Suboptimal Global Transcriptional Response Increases the Harmful Effects of Loss-of-Function Mutations

Molecular Biology and Evolution
2021-03-09 | Journal article
Part of ISSN: 1537-1719
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology

npj Precision Oncology
2021-03-02 | Journal article
Contributors: Ianthe A. E. M. van Belzen; Alexander Schönhuth; Patrick Kemmeren; Jayne Y. Hehir-Kwa
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Crossref

An organoid biobank for childhood kidney cancers that captures disease and tissue heterogeneity

Nature Communications
2020-12 | Journal article
Part of ISSN: 2041-1723
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

A comprehensive map of genetic interactions in childhood cancer reveals multiple underlying biological mechanisms

2020-11-18 | Preprint
Contributors: Josephine T. Daub; Saman Amini; Denise J.E. Kersjes; Xiaotu Ma; Natalie Jäger; Jinghui Zhang; Stefan M. Pfister; Frank C.P. Holstege; Patrick Kemmeren
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Crossref

Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function

Molecular Systems Biology
2020-10 | Journal article
Contributors: Wim J de Jonge; Mariël Brok; Philip Lijnzaad; Patrick Kemmeren; Frank CP Holstege
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Crossref

An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions

STAR Protocols
2020-06 | Journal article
Part of ISSN: 2666-1667
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

A framework for exhaustive modelling of genetic interaction patterns using Petri nets

Bioinformatics
2020-04-01 | Journal article
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

Kaposiform hemangioendothelioma and tufted angioma – (epi)genetic analysis including genome-wide methylation profiling

Annals of Diagnostic Pathology
2020-02 | Journal article
Part of ISSN: 1092-9134
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

DNA Methylation Profiling Identifies Distinct Clusters in Angiosarcomas

Clinical Cancer Research
2020-01-01 | Journal article
Contributors: Marije E. Weidema; Ellen van de Geer; Christian Koelsche; Ingrid M.E. Desar; Patrick Kemmeren; Melissa H.S. Hillebrandt-Roeffen; Vincent K.Y. Ho; Winette T.A. van der Graaf; Yvonne M.H. Versleijen-Jonkers; Andreas von Deimling et al.
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Crossref

Next-generation phenotyping using computer vision algorithms in rare genomic neurodevelopmental disorders

Genetics in Medicine
2019-08 | Journal article
Part of ISSN: 1098-3600
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

The 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 Computational Biology
2019-05-13 | Journal article
Contributors: Saman Amini; Donna K. Slonim; Annika Jacobsen; Olga Ivanova; Philip Lijnzaad; Jaap Heringa; Frank C. P. Holstege; K. Anton Feenstra; Patrick Kemmeren
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Crossref

The clinical implementation of copy number detection in the age of next-generation sequencing

Expert Review of Molecular Diagnostics
2018-10-03 | Journal article
Part of ISSN: 1473-7159
Part of ISSN: 1744-8352
Contributors: Patrick Kemmeren
Source: Self-asserted source
Patrick Kemmeren

Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation

PLOS ONE
2017-03-03 | Journal article
Contributors: Saman Amini; Michael Polymenis; Frank C. P. Holstege; Patrick Kemmeren
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Crossref

An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation.

2016 | Journal article
Contributors: Ma S; Kemmeren P; Aliferis CF; Statnikov A
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions.

2015 | Journal article
Contributors: Sameith K; Amini S; Groot Koerkamp MJ; van Leenen D; Brok M; Brabers N; Lijnzaad P; van Hooff SR; Benschop JJ; Lenstra TL et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Cell cycle population effects in perturbation studies.

2014 | Journal article
Contributors: O'Duibhir E; Lijnzaad P; Benschop JJ; Lenstra TL; van Leenen D; Groot Koerkamp MJ; Margaritis T; Brok MO; Kemmeren P; Holstege FC
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

De-novo learning of genome-scale regulatory networks in S. cerevisiae.

2014 | Journal article
Contributors: Ma S; Kemmeren P; Gresham D; Statnikov A
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

The genomic landscape of compensatory evolution.

2014-08 | Journal article
Contributors: Szamecz B; Boross G; Kalapis D; Kovács K; Fekete G; Farkas Z; Lázár V; Hrtyan M; Kemmeren P; Groot Koerkamp MJ et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

2014-04 | Journal article
Contributors: Kemmeren P; Sameith K; van de Pasch LA; Benschop JJ; Lenstra TL; Margaritis T; O'Duibhir E; Apweiler E; van Wageningen S; Ko CW et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

The role of Ctk1 kinase in termination of small non-coding RNAs.

2013 | Journal article
Contributors: Lenstra TL; Tudek A; Clauder S; Xu Z; Pachis ST; van Leenen D; Kemmeren P; Steinmetz LM; Libri D; Holstege FC
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis.

2012 | Journal article
Contributors: Apweiler E; Sameith K; Margaritis T; Brabers N; van de Pasch L; Bakker LV; van Leenen D; Holstege FC; Kemmeren P
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

The specificity and topology of chromatin interaction pathways in yeast.

2011-05 | Journal article
Contributors: Lenstra TL; Benschop JJ; Kim T; Schulze JM; Brabers NA; Margaritis T; van de Pasch LA; van Heesch SA; Brok MO; Groot Koerkamp MJ et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Functional overlap and regulatory links shape genetic interactions between signaling pathways.

2010-12 | Journal article
Contributors: van Wageningen S; Kemmeren P; Lijnzaad P; Margaritis T; Benschop JJ; de Castro IJ; van Leenen D; Groot Koerkamp MJ; Ko CW; Miles AJ et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Epistatic relationships reveal the functional organization of yeast transcription factors.

2010-10 | Journal article
Contributors: Zheng J; Benschop JJ; Shales M; Kemmeren P; Greenblatt J; Cagney G; Holstege F; Li H; Krogan NJ
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

A consensus of core protein complex compositions for Saccharomyces cerevisiae.

2010-06 | Journal article
Contributors: Benschop JJ; Brabers N; van Leenen D; Bakker LV; van Deutekom HW; van Berkum NL; Apweiler E; Lijnzaad P; Holstege FC; Kemmeren P
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system.

2009 | Journal article
Contributors: van Wijk SJ; de Vries SJ; Kemmeren P; Huang A; Boelens R; Bonvin AM; Timmers HT
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system.

2009 | Journal article
Contributors: van Wijk SJL; de Vries SJ; Kemmeren P; Huang A; Boelens R; Bonvin AMJJ; Timmers HTM
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Adaptable gene-specific dye bias correction for two-channel DNA microarrays.

2009 | Journal article
Contributors: Margaritis T; Lijnzaad P; van Leenen D; Bouwmeester D; Kemmeren P; van Hooff SR; Holstege FC
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Cotranslational assembly of the yeast SET1C histone methyltransferase complex.

2009-10 | Journal article
Contributors: Halbach A; Zhang H; Wengi A; Jablonska Z; Gruber IM; Halbeisen RE; Dehé PM; Kemmeren P; Holstege F; Géli V et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Functional organization of the S. cerevisiae phosphorylation network.

2009-03 | Journal article
Contributors: Fiedler D; Braberg H; Mehta M; Chechik G; Cagney G; Mukherjee P; Silva AC; Shales M; Collins SR; van Wageningen S et al.
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

CCR4/NOT complex associates with the proteasome and regulates histone methylation.

2007-04 | Journal article
Contributors: Laribee RN; Shibata Y; Mersman DP; Collins SR; Kemmeren P; Roguev A; Weissman JS; Briggs SD; Krogan NJ; Strahl BD
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.

2007-03 | Journal article
Contributors: Collins SR; Kemmeren P; Zhao XC; Greenblatt JF; Spencer F; Holstege FC; Weissman JS; Krogan NJ
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Transcriptome-based identification of pro- and antioxidative gene expression in kidney cortex of nitric oxide-depleted rats.

2007-01 | Journal article
Contributors: Wesseling S; Joles JA; van Goor H; Bluyssen HA; Kemmeren P; Holstege FC; Koomans HA; Braam B
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Multiple robust signatures for detecting lymph node metastasis in head and neck cancer.

2006-02 | Journal article
Contributors: Roepman P; Kemmeren P; Wessels LF; Slootweg PJ; Holstege FC
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases.

2005-07 | Journal article
Contributors: van Driel MA; Cuelenaere K; Kemmeren PP; Leunissen JA; Brunner HG; Vriend G
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central

Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.

2005-04 | Journal article
Contributors: Radonjic M; Andrau JC; Lijnzaad P; Kemmeren P; Kockelkorn TT; van Leenen D; van Berkum NL; Holstege FC
Source: Self-asserted source
Patrick Kemmeren via Europe PubMed Central
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Peer review (1 review for 1 publication/grant)

Review activity for Genome medicine. (1)