In recent years he developed tools to detect, quantify and identify as many as possible metabolites in mammalian biofluids, tissues and cells. His research aims at improving sample preparation and multi-dimensional chromatographic and electro-driven separation methods, improving the interfacing to mass spectrometry, miniaturizing analytical methods using micro/nano-technology and developing methods for the identification of metabolites. He has developed several innovative technologies for miniaturized and high throughput metabolomics, for which he also holds a few patents.

In collaboration with clinicians, biomedical researchers, biostatisticians and other –omics researchers he works on better (early) diagnosis and interventions for (cardio)vascular and metabolic diseases and neurological diseases.

He is initiator and Scientific Director of the Netherlands Metabolomics Centre. He is one of the four PIs of the recently funded Netherlands X-omics Initiative (2018-2027, 40M€; www.x-omics.nl), building a truly integrated x-omics infrastructure; Hankemeier leads the metabolomics programme and builds a high throughput metabolomics facility in his lab.

He has developed a microfluidic 3D cell culture platform allowing to have 40 and more individual cell cultures with organotypic functionality. For example, he has established blood vessels, neuronal co-cultures, gut tubes in that platform, and used metabolomics to study disease mechanisms and the mechanism of action of drugs using patient-derived human cells. 

His ultimate goal is to identify early disease pathways and network changes that can be modulated by interventions to prevent or treat diseases, and support the development of novel intervention strategies to prevent or treat diseases.

He is Medical Delta Professor of Translational Epidemiology at the Department of Epidemiology at Erasmus University Medical Centre. He is the Scientific Director of the Netherlands Metabolomics Centre (www.metabolomicscentre.nl). He is co-founder of  MIMETAS (https://mimetas.com/), the worldwide first organ-on-a-chip company. He has a MSc in chemistry and a PhD in analytical chemistry.  From 1996 to 2004 he was responsible as a scientific Product Manager at the department of Analytical Sciences at TNO for research in the fields of food safety, food quality and metabolomics.