Scientific publications


Charles Hoyt. PyBEL: a Computational Framework for Biological Expression Language". Oxford University Press Bioinformatics Online.

Mufassra Naz. Systematic Analysis of GWAS Data Reveals Genomic Hotspots for Shared Mechanisms between Neurodegenerative Diseases. Journal of Alzheimer Disease & Parkinsonism.

Reagon Karki. Comorbidity analysis between Alzheimer's disease and Type 2 Diabetes Mellitus based on shared pathways and the role of T2DM drugs. IOS Press.

Alpha Tom Kodamullil. Of mice and men: comparative analysis of neuro-inflammatory mechanisms in human and mouse using cause-and-effect models. IOS Press.

Anandhi Iyappan. Neuroimaging Feature Terminology (NIFT): a controlled terminology for the annotation of brain imaging features. IOS Press.

Daniel Dominog-Fernandez. Multimodal Mechanistic Diseases (NeuroMMSig): a web server for mechanism enrichment. Oxford University Press Bioinformatics Online.

Alpha Tom Kodamullil. Tracing investment in drug development for Alzheimer disease. Nature.


Naz, M., Kodamullil, A.T., & Hofmann-Apitius, M. (2016). Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. Briefings in bioinformatics, 17(3), 505-516.

Iyappan, A., Kawalia, S. B., Raschka, T., Hofmann-Apitius, M., & Senger, P. (2016). NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. Journal of Biomedical Semantics, 7(1), 45.

Iyappan, A., Gündel, M., Shahid, M., Wang, J., Li, H., Mevissen, H. T., ... & Younesi, E. (2016). Toward a Pathway Inventory of the Human Brain for Modeling Disease Mechanisms Underlying Neurodegeneration. Journal of Alzheimer's Disease, (Preprint), 1-18.

Wüllner U, Kaut O, deBoni L, Piston D, Schmitt I. (2016).
DNA methylation in Parkinson’s disease
More: Accepted for publication in Journal of Neurochemistry


Hofmann-Apitius, M. (2015). Is dementia research ready for big data approaches?. BMC medicine, 13(1), 1.

Hofmann-Apitius, M., Alarcón-Riquelme, M. E., Chamberlain, C., & McHale, D. (2015). Towards the taxonomy of human disease. Nature Reviews Drug Discovery, 14(2).

Malhotra, A., Younesi, E., Sahadevan, S., Zimmermann, J., & Hofmann-Apitius, M. (2015). Exploring novel mechanistic insights in Alzheimer’s disease by assessing reliability of protein interactions. Scientific reports, 5.

Younesi, E., Malhotra, A., Gündel, M., Scordis, P., Page, M., Müller, B., ... & Hofmann-Apitius, M. (2015). PDON: Parkinson’s disease ontology for representation and modeling of the Parkinson’s disease knowledge domain. Theoretical Biology and Medical Modelling, 12(1), 1.

Kodamullil, A. T., Younesi, E., Naz, M., Bagewadi, S., & Hofmann-Apitius, M. (2015). Computable cause-and-effect models of healthy and Alzheimer's disease states and their mechanistic differential analysis. Alzheimer's & Dementia, 11(11), 1329-1339.

Martin Hofmann-Apitius, Marta E. Alarcón-Riquelme, Chris Chamberlain and Duncan McHale (2015).
Towards reforming the taxonomy of human disease. In Nature Reviews - Drug Discovery, Vol. 14, 75 - 76.


Hunter, P. J.; de Bono, B. (2014). Biophysical constraints on the evolution of tissue structure and function.
In: The Journal of Physiology, Vol. 592, Issue 11.

Molinuevo et al., Neurobiol Aging. White matter changes in preclinical Alzheimer's disease: a magnetic resonance imaging-diffusion tensor imaging study on cognitively normal older people with positive amyloid b protein 42 levels, 2014 Dec;
35(12):2671-80. doi: 10.1016/j.neurobiolaging.2014.05.027.
Epub 2014 Jun 6.

Previous publications


Bagewadi, S., Adhikari, S., Dhrangadhariya, A., Irin, A. K., Ebeling, C., Namasivayam, A. A., ... & Senger, P. (2015). NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. Database, 2015, bav099


Malhotra, Ashutosh; Younesi, Erfan; Bagewadi, Shweta; Hofmann-Apitius, Martin (2014). Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease. In: GenomeMedicine

Malhotra, A., Younesi, E., Gündel, M., Müller, B., Heneka, M. T., & Hofmann-Apitius, M. (2014). ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease. Alzheimer's & Dementia, 10(2), 238-246.

Younesi, E. (2014). A Knowledge-based Integrative Modeling Approach for In-Silico Identification of Mechanistic Targets in Neurodegeneration with Focus on Alzheimer’s Disease (Doctoral dissertation, Universitäts- und Landesbibliothek Bonn).

Fluck, J., & Hofmann-Apitius, M. (2014). Text mining for systems biology. Drug discovery today, 19(2), 140-144.


Malhotra, A., Younesi, E., Gurulingappa, H., & Hofmann-Apitius, M. (2013). ‘HypothesisFinder: ’A Strategy for the Detection of Speculative Statements in Scientific Text. PLoS computational biology, 9(7), e1003117.

Shahid, M., Shahzad Cheema, M., Klenner, A., Younesi, E., & Hofmann‐Apitius, M. (2013). SVM based descriptor selection and classification of neurodegenerative disease drugs for pharmacological modeling. Molecular Informatics, 32(3), 241-249.

Younesi, E., & Hofmann-Apitius, M. (2013). A network model of genomic hormone interactions underlying dementia and its translational validation through serendipitous off-target effect. J Transl Med, 11, 177.

Younesi, E., & Hofmann-Apitius, M. (2013). Biomarker-guided translation of brain imaging into disease pathway models. Scientific reports, 3.


Kola, I.; Bell, J (2011). A call to reform the taxonomy of human disease, In: Nature Reviews Drug Discovery 10, 641-642 (September 2011) | doi:10.1038/nrd3534

Articles in magazines


Malhotra, Ashutosh; Younesi, Erfan; Bagewadi, Shweta; Hofmann-Apitius, Martin (2014). Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease. In: GenomeMedicine

McHale, D.; Hofmann-Apitius, M. (2014). AETIONOMY: Reclassifying Alzheimer‘s disease to find new drug targets. In: Dementia in Europe, Issue 17.

Press release 2015

Innovative Medicines Initiative Alzheimer’s disease projects launch joint platform

  • IMI Alzheimer’s disease projects AETIONOMY, EMIF and EPAD have a combined budget of €138 million and jointly address many key challenges for medicines research and development.
  • Collaboration via IMI Alzheimer’s Disease Research Platform will enable faster progress.
  • The platform will have a global reach through a Memorandum of Understanding between IMI and the Global Alzheimer’s Platform (GAP).
  • Announcement comes at 12th International Conference on Alzheimer's and Parkinson's Diseases and Related Neurological Disorders (AD/PD 2015) and in wake of major WHO conference on dementia.

Brussels, Belgium, 19 March 2015 – Today, the Innovative Medicines Initiative (IMI) and its AETIONOMY, EMIF and EPAD projects are proud to announce the creation of the IMI Alzheimer’s Disease Research Platform. The platform will facilitate collaboration between the three projects, helping them to deliver results faster. At the same time, IMI and the Global Alzheimer’s Platform (GAP) are announcing their plans to sign a Memorandum of Understanding to accelerate Alzheimer’s drug development by building a global, standing, trial-ready platform for Alzheimer’s drug development.

The announcements come during a symposium held at the 12th International Conference on Alzheimer's and Parkinson's Diseases and Related Neurological Disorders (AD/PD 2015), and in the wake of a major World Health Organization (WHO) conference on dementia.

Dementia already affects over 35 million people globally, and as populations age, this figure is set to rise to over 115 million by 2050. The disease places a huge and growing burden on health and social care systems and on the families and carers of those affected. Yet despite decades of research, there is still neither treatment nor cure for the disease.

The challenge of developing new, effective treatments for dementia is simply too great for any organisation to tackle alone, and so IMI has launched a number of projects that bring together leading experts from the pharmaceutical industry, universities, small biotechs, and patient organisations from across Europe and beyond. The three projects in the new IMI Alzheimer’s Disease Research Platform have a combined budget of €138 million and address complementary areas of Alzheimer’s disease research.

AETIONOMY is paving the way towards a new approach to the classification of neurodegenerative diseases, particularly Alzheimer’s and Parkinson’s diseases, thereby improving drug development and increasing patients’ chances of receiving a treatment that works for them.

EMIF is developing a common information framework of patient-level data that will link up and facilitate access to diverse medical and research data sources, opening up new avenues of research, particularly in the fields of Alzheimer’s disease and obesity.

EPAD is pioneering a new, more flexible approach to clinical trials of innovative Alzheimer’s disease treatments designed for people who have the disease but have not yet developed dementia.

‘The European Union has a long tradition of fostering research collaboration,’ said Jean Georges, Executive Director of Alzheimer Europe, which is a partner in all three projects. ‘The creation of the IMI Alzheimer’s Disease Research Platform is another great example of European research projects working together to improve our understanding of dementia and to give hope to the 8.4 million Europeans affected by dementia of a cure of the condition in the future. Alzheimer Europe is delighted to support all three projects by representing the views of people with dementia and their carers in the research consortia and by making the research results available to the wider general public.’

The projects are keen to collaborate more closely with other Alzheimer’s research projects around the world. The global reach of the platform will be aided by the signature of a Memorandum of Understanding between IMI and the Global Alzheimer’s Platform (GAP). In addition, international collaboration is already built into the IMI projects. For example, EPAD, EMIF and the Medical Research Council’s Dementias Platform UK are already linked and a number of EPAD partners are directly involved in other initiatives such as GAP.

Irene Norstedt, IMI Acting Executive Director commented: ‘Alzheimer’s disease is a global challenge that requires a global solution, and it is in this spirit that the IMI Alzheimer’s Disease Research Platform is reaching out to other initiatives on Alzheimer’s disease around the world. Everyone working on Alzheimer’s disease needs to pull together if we want to deliver results that will help us to end the suffering caused by this terrible disease.’

Find out more:

Press release 2014

AETIONOMY organizes knowledge about dementia to develop new drugs and therapies

Thursday, February 06, 2014

BRUSSELS. In January the AETIONOMY consortium started a project aiming to develop a new way to classify Alzheimer’s and Parkinson’s disease. The 5-year-project is funded by the Innovative Medicines Initiative (IMI), a joint undertaking between the European Union and the pharmaceutical industry association EFPIA. The new classification will be generated using data derived from a wide range of new biological approaches and will be based on the underlying causes of the disease. Currently, Alzheimer’s disease and Parkinson’s disease are classified by their symptoms and severity but it is clear that this does not represent the many different causes of these diseases. It has been widely recognised that within these broad disease groups there are sub-groups where the different causes result in the symptoms of memory loss or movement disorder.

The AETIONOMY project will involve the collection of all available data including clinical data, imaging and genetic data and will create a new way to combine all the data together to look for patterns which could identify sub-groups of patients with similar causes of their disease. The project will run for the next 5 years and will include a Clinical Study, which aims at a validation of the “mechanism-based taxonomy” generated in the course of the first years.

AETIONOMY is a collaboration of 17 partners across 11 countries and is led by Professor Duncan McHale from UCB Pharma and Professor Martin Hofmann-Apitius from the Fraunhofer Institute for Algorithms and Scientific Computing (SCAI). The collaboration is funded as part of the IMI Taxonomy Call (Call 8) which aims at improving the way we classify diseases to ensure patients get the right drugs and to improve how we find new drugs. The collaboration includes 4 EFPIA Pharmaceutical companies (UCB, Novartis, Sanofi-Aventis and Boehringer Ingelheim), 2 SMEs, 9 Academic institutions and 2 patient advocacy groups.

Project info *
Start date: 01/01/2014, Duration: 5 years, IMI funding: € 8.0 million, EFPIA in-kind: €8.0 million, Other: €1.8 million, Total cost: €17.8 million

The research leading to these results has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreement n° [115568], resources of which are composed of financial contribution from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in kind contribution.

Find out more: 8th Call for proposals topic text:

(p. 45 onwards)