Hendrik Marks


Embryonic stem cells (ESCs) are derived from the inner cell mass (ICM) of the early embryo and are widely used as in vitro model to study pluripotency and embryonic development. Recent advances in stem cell technology enabled the derivation of mouse ESCs in defined serum-free medium containing 2 kinase inhibitors (2i), so-called “ground state” pluripotent ESCs. The inhibitors are thought to maintain stemness by blocking the signalling activity of Erk and Gsk3. Information on signal transduction, transcriptional networks and epigenetic mechanisms acting in ground state pluripotent cells is scarce.

The aim of my research group is to further define the ground state and to decipher regulatory mechanisms that maintain ESCs in the ground state. Current projects include: i) unravel the mode of action of the 2 kinase inhibitors in ground state pluripotency by state-of-the-art (phospho)proteomics on signaling pathways and nuclear factors; ii) decipher regulatory transcription factor networks and epigenetic mechanisms acting to maintain and to exit the ground state by genome-wide bisulfite sequencing and ChIP-seq; iii) use single cell RNA-Seq profiling to determine the role of (transcriptional) heterogeneity.


Hendrik Marks obtained his PhD from Wageningen University in genomics and transcriptomics of White Spot Syndrome Virus. In 2006 he joined the department of Molecular Biology at Radboud University Nijmegen to initiate epigenetic profiling of mouse embryonic stem cells. Recently he obtained the prestigious NWO VIDI grant to establish his own research group.

(Inter)national Personal Prizes & Awards

• Van Gogh grant: 15K euro together with Alice Jouneau (INRA, Fr) (2018-2019)
• Hypatia talent development career track for young groupleaders (2014-2015)
• VIDI personal grant: 800k euro personal grant to investigate pluripotency (2013-2018)
• Nomination Radboud Science Award (2013)
• Best paper of RIMLS institute (2013)
• Educational PhD certificate (2005)
• Travel Grants: Stichting LEB Fonds 2.5k euro for meetings in USA/ Canada (2002-2005)
• Various of my publications were accompanied by extensive editorials, and highlighted in national newspapers

Other relevant experience and professional memberships

• Supervision of a large number (international) PhD and MSc students (>30 students)
• Lecturing/ Coordination range of courses at Radboud University (since 2006)
• Examination committee of (Medical) Biology at Radboud University (since 2016)
• Co-coordination of master Medical Epigenomics at Radboud University (since 2015)
• Coordination master courses EHD (3EC) & TiMBII (3EC) at Radboud University (since 2013)
• Invited member study group NWO: “Nucleic Acids” (since 2013)
• Advisory Board, Oxford Global NGS & Single Cell Analysis, London, UK (since 2010)
• Coordination of 2-day scientific lab retreat Molecular Biology (75+ people; 2013-2015)
• Presented seminars at >40 conferences/meetings in Europe/ US over the last 10 years
• Highschool Biology teaching materials (“Biology for you”) (2017)
• Expert for various (inter)national media such as the Dutch newspapers Bionieuws & NRC Handelsblad

Selection of my research in the media

• Dutch major newspaper Algemeen Dagblad (AD) (2015)
• European Pharmaceutical Review (2014)
• Analist (2014)
• Dutch major newspaper NRC Handelsblad (2013)
• Dutch National Radio 5 Hoe?Zo! (2012)
• Dutch newspaper Gelderlander/ other regional newspapers (2005 & 2015)
• Popular science magazine EOS (2005, 2012 & 2015)
• Popular science magazine Bionieuws (2012, 2013 & 2015)
• Popular science magazine C2W (2012 & 2015)
• Kennislink (2012, 2013 & 2015)
• Noorderlicht (2012)
• NWT-Online (2012)
• ScienceOmega.com (2012)
• Epigenie (2012)

(Ad-hoc) Reviewer

• Scientific journals
Nature, Science, Nature Genetics, Cell Stem Cell, Developmental Cell, Nature Biotechnology, Nature Structural & Molecular Biology, Nucleic Acids Research, Genome Research, PLoS Biology, Genome Biology, Cell Reports, EMBO Journal, PLoS One, Molecular Biology Reports, Journal of General Virology, Virus Research, Gene, Epigenetics, Stem Cell Reviews & Reports, Journal of Stem Cells Research, Development & Therapy, Human Genetics, Diseases of Aquatic Organisms, International Journal of Bioinformatics Research and Applications, BMC Bioinformatics, Molecular Genetics and Genomics, Computer Methods and Programs in Biomedicine, BBA Proteins and Proteomics, Clinical Epigenetics, Current Genomics

• Granting agencies
NWO, European Commission (Horizon 2020), MRC, INSERM, French National Research Agency, Israel Science Foundation, Royal Society New Zealand