Thomas (Tom) H.A. Ederveen, PhD

I'm a biomedical senior scientist c.q. bioinformatician at the Radboudumc Nijmegen, currently active in the CMBI Computational Biology department, and in strong collaboration with many other disciplines within our institute, most notably the departments of Dermatology and Medical Microbiology. Here, we focus mainly on the analysis of genomes of bacteria, on human and animal microbiota (i.e. microbiome studies) and on bacterial strain tracking. My work further extends to also other types of (multi)omics and molecular data analysis, all mostly in context of biomedical and clinical research.

I see myself a biologist applying public bioinformatics tools and approaches in order to make sense out of microbial samples from various biological sources, in the field of (medical) biology and food and nutrition. Much of my own work relates to the analysis of the human microbiome in both healthy and disease status, in order to identify desirable and undesirable bacteria, respectively. In the end, by understanding these processes we hope to come up with interventions to cure diseases underlying an imbalance (dysbiosis) in the human microbiome.

As of 2020, I'm also partly involved in research efforts and development related to FAIR, i.e. to make scientific data Findable Accessible Interoperable and Reusable. Here, I'm working on FAIR schema's, data standards and systems such as FAIR data points, in order to make (multi)omics study data available to the world in a human- and machine readable fashion.

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Curriculum Vitae (CV) Thomas (Tom) H.A. Ederveen   Dissertation (PhD) Thomas (Tom) H.A. Ederveen

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# 2022
Link to Open Access Location Agamah F.E., Bayjanov J.R., Niehues A., Njoku K.F., Skelton M., Mazandu G.K., Ederveen T.H.A., Mulder N., Chimusa E.R., 't Hoen P.A.C., Computational approaches for network-based integrative multi-omics analysis. Front Mol Biosci, Nov;9:967205

Link to Open Access Location Niehues H.*, van der Krieken D.A.*, Ederveen T.H.A.*, Jansen P.A.M., van Niftrik L., Mesman R., Netea M.G., Smits J.P.H., Schalkwijk J., van den Bogaard E.H., Zeeuwen P.L.J.M., Antimicrobial Late Cornified Envelope Proteins: The Psoriasis Risk Factor Deletion of LCE3B/C Genes Affects Microbiota Composition. J Invest Dermatol, Jul;142(7):1947-1955

Link to Open Access Location Guzzardi M.A.*, Ederveen T.H.A.*, Rizzo F., Weisz A., Collado M.C., Muratori F., Gross G., Alkema W., Iozzo P., Maternal pre-pregnancy overweight and neonatal gut bacterial colonization are associated with cognitive development and gut microbiota composition in pre-school-age offspring. Brain Behav Immun, Feb;100:311-320

# 2021
Link to Open Access Location Andralojc K.M., Molina M.A., Qiu M., Spruijtenburg B., Rasing M., Pater B., Huynen M.A., Dutilh B.E., Ederveen T.H.A., Elmelik D., Siebers A.G., Loopik D., Bekkers R.L.M., Leenders W.P.J., Melchers W.J.G., Novel high-resolution targeted sequencing of the cervicovaginal microbiome. BMC Biol, Dec;19(1):267

Link to Open Access Location Hartog G.D.*, Ederveen T.H.A.*, Venkatasubramanian P.B.*, Ferwerda G., van den Kieboom C.H., van der Gaast-de Jongh C.E., Vissers M., Zoll J., Melchers W.J.G., Huynen M.A., Rots N., Rahamat-Langendoen J., de Jonge M.I., Chemokine profiling in children and adults with symptomatic and asymptomatic respiratory viral infections. J Infect, Dec;83(6):709-737

Link to Open Access Location Voorberg A.N., Niehues H., Oosterhaven J.A.F., Romeijn G.L.E., van Vlijmen-Willems I.M.J.J., van Erp P.E.J., Ederveen T.H.A., Zeeuwen P.L.J.M., Schuttelaar M.L.A., Vesicular hand eczema transcriptome analysis provides insights into its pathophysiology. Exp Dermatol, Dec;30(12):1775-1786

Link to Open Access Location Arends D.W., Miellet W.R., Langereis J.D., Ederveen T.H.A., van der Gaast-de Jongh C.E., van Scherpenzeel M., Knol M.J., van Sorge N.M., Lefeber D.J., Trzciński K., Sanders E.A.M., Dorfmueller H.C., Bootsma H.J., de Jonge M.I., Examining the distribution and impact of single nucleotide polymorphisms in the capsular locus of Streptococcus pneumoniae serotype 19A. Infect Immun, Oct;89(11):e0024621

# 2020
Link to Open Access Location van Beek L.F., Surmann K., van den Berg van Saparoea H.B., Houben D., Jong W.S.P., Hentschker C., Ederveen T.H.A., Mitsi E., Ferreira D.M., van Opzeeland F., van der Gaast-de Jongh C.E., Joosten I., Völker U., Schmidt F., Luirink J., Diavatopoulos D.A., de Jonge M.I., Exploring metal availability in the natural niche of Streptococcus pneumoniae to discover potential vaccine antigens. Virulence, Dec;11(1):1310-1328

Link to Open Access Location Ederveen T.H.A.*, Smits J.P.H.*, Boekhorst J., Schalkwijk J., van den Bogaard E.H., Zeeuwen P.L.J.M., Skin microbiota in health and disease: From sequencing to biology. J Dermatol, Oct;47(10):1110-1118

Link to Open Access Location Voß F., van Beek L.F., Schwudke D., Ederveen T.H.A., van Opzeeland F.J., Thalheim D., Werner S., de Jonge M.I., Hammerschmidt S., Lipidation of Pneumococcal Antigens Leads to Improved Immunogenicity and Protection. Vaccines, Jun;8(2):310

Link to Open Access Location Smits J.P.H.*, Ederveen T.H.A.*, Rikken G., van den Brink N.J.M., van Vlijmen-Willems I.M.J.J., Boekhorst J., Kamsteeg M., Schalkwijk J., van Hijum S.A.F.T., Zeeuwen P.L.J.M., van den Bogaard E.H., TARgeting the cutaneous microbiota in atopic dermatitis by coal tar via AHR-dependent induction of antimicrobial peptides. J Invest Dermatol, Feb;140(2):415-424

# 2019
Link to Open Access Location Ederveen T.H.A., Smits J.P.H., Hajo K., van Schalkwijk S., Kouwenhoven T.A., Lukovac S., Wels M., van den Bogaard E.H., Schalkwijk J., Boekhorst J., Zeeuwen P.L.J.M., van Hijum S.A.F.T., A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota. Sci Rep, Dec;9(1):19834

Link to Open Access Location Gommers L.M.M., Ederveen T.H.A., van der Wijst J., Overmars-Bos C., Kortman G.A.M., Boekhorst J., Bindels R.J.M., de Baaij J.H.F., Hoenderop J.G.J., Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia. FASEB J, Oct;33(10):11235-11246

Link to Open Access Location Rogier R., Ederveen T.H.A., Wopereis H., Hartog A., Boekhorst J., van Hijum S.A.F.T., Knol J., Garssen J., Walgreen B., Helsen M.M., van der Kraan P.M., van Lent P.L.E.M., van de Loo F.A.J., Abdollahi-Roodsaz S., Koenders M.I., Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice. PLoS One, Jul;14(7):e0219366

Link to Open Access Location Chermprapai S., Ederveen T.H.A., Broere F., Broens E.M., Schlotter Y.M., van Schalkwijk S., Boekhorst J., van Hijum S.A.F.T., Rutten V.P.M.G., The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study. Vet Microbiol, Feb;229:90-99

# 2018
Link to Open Access Location Ederveen T.H.A.*, Ferwerda G.*, Ahout I.M., Vissers M., de Groot R., Boekhorst J., Timmerman H.M., Huynen M.A., van Hijum S.A.F.T.*, de Jonge M.I.*, Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. Microbiome, Jan;6(1):10

# 2017
Link to Open Access Location Aarts E.*, Ederveen T.H.A.*, Naaijen J., Zwiers M.P., Boekhorst J., Timmerman H.M., Smeekens S.P., Netea M.G., Buitelaar J.K., Franke B., van Hijum S.A.F.T.*, Arias Vasquez A.*, Gut microbiome in ADHD and its relation to neural reward anticipation. PLoS One, Sep;12(9):e0183509

Link to Open Access Location Rogier R.*, Ederveen T.H.A.*, Boekhorst J., Wopereis H., Scher J.U., Manasson J., Frambach S.J.C.M., Knol J., Garssen J., van der Kraan P.M., Koenders M.I., van den Berg W.B., van Hijum S.A.F.T., Abdollahi-Roodsaz S., Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. Microbiome, Jun;5(1):63

Link to Open Access Location Zeeuwen P.L., Boekhorst J., Ederveen T.H.A., Kleerebezem M., Schalkwijk J., van Hijum S.A.F.T., Timmerman H.M., Reply to Meisel et al. : Skin microbiome surveys are strongly influenced by experimental design. J Invest Dermatol, Apr;137(4):961-962

Link to Open Access Location Zeeuwen P.L.*, Ederveen T.H.A.*, van der Krieken D.A.*, Niehues H.*, Boekhorst J., Kezic S., Hanssen D.A., Otero M.E., van Vlijmen-Willems I.M., Rodijk-Olthuis D., Falcone D., van den Bogaard E.H., Kamsteeg M., de Koning H.D., Zeeuwen-Franssen M.E., van Steensel M.A., Kleerebezem M., Timmerman H.M., van Hijum S.A.F.T., Schalkwijk J., Gram-Positive Anaerobe Cocci (GPAC) are Underrepresented in the Microbiome of Filaggrin-Deficient Human Skin. J Allergy Clin Immunol, Apr;139(4):1368-1371

# 2016
Link to Open Access Location van der Krieken D.A.*, Ederveen T.H.A.*, van Hijum S.A.F.T., Jansen P.A., Melchers W.J., Scheepers P.T., Schalkwijk J., Zeeuwen P.L.,
An In vitro Model for Bacterial Growth on Human Stratum Corneum.
Acta Derm Venereol, Nov;96(7):873-879

# 2013
Link to Open Access Location Ederveen T.H.A., Overmars L., van Hijum S.A.F.T., Reduce Manual Curation by Combining Gene Predictions from Multiple Annotation Engines, a Case Study of Start Codon Prediction. PLoS One, May;8(5):e63523

# 2011
Link to Open Access Location Ederveen T.H.A., Mandemaker I.K., Logie C., The Human Histone H3 Complement Anno 2011. Biochim Biophys Acta, Oct;1809(10):577-86

Dissertation (PhD)

# 2019
Link to Open Access Location Ederveen T.H.A., Co-Promoters: van Hijum S.A.F.T., Boekhorst J., Zeeuwen P.L., Promotor: Schalkwijk J., On the role of host microbiota associated with health and disease - a metagenomics survey through marker-gene sequencing and genomics approaches. Radboud University, Nijmegen, March 28, 2019


Bioinformatics Tools and Software:

COMPANION   for Comparative Genome Annotation   ( Ederveen et al., PLoS One, 2013 )
TaxPhlAn   for Taxonomy Phylogenetic Analysis   ( Ederveen et al., Sci Rep., 2019 )

DockerHub   GitHub


Click here for my Radboudumc webpage.

E-mail address:

Tom [dot] Ederveen [at]

Visiting address:

Radboud University Medical Center
CMBI department (room 0.08)
RIMLS Research Tower (ground floor)
Geert Grooteplein Zuid 28, route 260
6525 GA, Nijmegen, The Netherlands

Phone number:

+31 (0)24 36 19390 (office)