Author Archive:Christian Knell

ByChristian Knell

Scoping review on clinical decision support systems accepted for publication

The integration of clinical decision support systems for pharmacogenomic testing into clinical routine has been investigated by the MIRACUM consortium over the last nine months. This joint effort has now resulted in a scoping literature review accepted by BMC Medical Informatics and Decision Making. A total of 12 authors from nine MIRACUM sites provide an overview of the designs of user-system interactions in recent system developments. The final analysis comprises the essence of 32 articles that were identified in a PubMed search. As the most widespread tool, alerts have been identified, next to pharmacogenomic reports, inbox messages, and several more. The authors conclude that i) further evaluation efforts of developed prototypes will be necessary and ii) in the future clinical decision support systems will include prediction models to identify eligible patients for pre-emptive genotyping.

Hinderer M, Boeker M, Wagner SA, Lablans M, Newe S, Hülsemann JL, Neumaier M, Binder H, Renz H, Acker T, Prokosch HU, Sedlmayr M.
Integrating clinical decision support systems for pharmacogenomic testing into clinical routine – a scoping review of designs of user-system interactions in recent system development.
BMC Med Inform Decis Mak. 2017 Jun 6;17(1):81. DOI: 10.1186/s12911-017-0480-y.

ByChristian Knell

Two new professorships in Magdeburg

The Medical Faculty of the Otto-von-Guericke-University Magdeburg aims at promoting its digital infrastructure in the fields of Medical Informatics and announces two new professorships: one W2 Professor for Biostatistics and one W3 Professor in Epidemiology and Health System Research. The latter will hold the position of Director of the Institute for Epidemiology and Health System Research. Please refer to the linked documents for more details.

ByChristian Knell

Second MIRACUM research article accepted for publication in Pharmacogenomics

The second joint project results of the MIRACUM consortium got accepted for publication in Pharmacogenomics. A project team of 11 of our MIRACUM partners has performed a survey among the clinicians of eight German university hospitals to assess the physicians’ attitude, their knowledge and their experience in pharmacogenomic clinical decision support. Overall, 564 physicians of 13 different medical specialties participated. The authors concluded that physicians in German hospitals require additional education of both genetics and pharmacogenomics. Furthermore, the physicians are mostly inexperienced in pharmacogenomic clinical decision support systems (CDSS) but need to be provided with access to relevant pharmacogenomic CDSS.


Hinderer M, Boeker M, Wagner SA, Binder H, Ückert F, Hülsemann JL, Neumaier M, Schade-Brittinger C, Acker T, Prokosch HU, Sedlmayr B. The experience of physicians in pharmacogenomic clinical decision support within eight German University Hospitals. Pharmacogenomics 2017.

ByChristian Knell

MIRACUM 0.9 released

After nine month of intense work with more than 100 MIRACUM team members contributing to the various pilot projects and to the MIRACUM grant proposal for the BMBF MI-I networking and developing phase MIRACUM version 0.9 has just been released.


We are proud that we have already achieved two joint MIRACUM publications and implemented a Version 0.9 data sharing infrastructure based on eight DIC implementation. In the last three weeks we could even extend this data sharing network in a cross-consortia cooperation with HD4CR, resulting in distributed proof-of-concept analysis based on 11 i2b2 and OMOP research data repository instances.

We thank all our MIRACUM team members for their tremendous engagement in the last nine month – you are a great team!

We are looking forward to leverage the value of our eight DIC data together in future research projects

Stefanie Knöpfel, Ulli Prokosch and the Erlangen MIRACUM team

ByChristian Knell

MIRACUM workshop at the conhIT 2017 in Berlin

Six members of our MIRACUM consortium held a workshop on the 25th of April 2017 at the conhIT 2017 in Berlin. They presented the current BMBF funding scheme “medical informatics” as well as the most recent areas of research activities of the MIRACUM consortium. As head of the workshop, Paul Schmücker introduced the current BMBF funding scheme “medical informatics” and lead through the workshop session. Martin Lablans provided the audience with an insight into medical data sharing and its tremendous importance for the German healthcare. Following this, Thomas Ganslandt illustrated both the development and the implementation of data repositories for data sharing. The fourth speaker was Jan Christoph describing both how to integrate omics data into clinical data and what might be most challanging to achieve this. Last but not least, Marc Hinderer presented the latest research results of the MIRACUM consortium regarding clinical decision support for molecular tumor boards.

ByChristian Knell

MIRACUM professorships expand

Mannheim University of Applied Sciences : Dr. Ulrike Kutscha starts her work in September

image of Dr. Ulrike Kutscha, a woman with short brown hair and glasses

In autumn 2016 the University of Applied Sciences Mannheim has issued a W2 professorship for “Medical Data Science”. Dr. Ulrike Kutscha (Heidelberg) accepted the call on April 10th, 2017. She will start her work at Mannheim University of Applied Sciences on September 1st, 2017.



Establishment of a new professorship in Mainz

We can also announce the next W2 professorship that has been released by the University Medical Center of the Johannes-Gutenberg-University Mainz. The new professor will lead the group of Medical Informatics at the Institute for Medical Biometry, Epidemiology and Informatics (IMBEI). A major focus will be the conceptual design and implementation of a data integration centre. Based on data from patient care and health insurances, research on health services as well as clinical and translational research shall be pursued.

ByChristian Knell

Back from New York City

Jan Christoph and Marc Hinderer of the MIRACUM team spent 10 days in New York City for an intense research visit and have just returned with lots of input for some of our use cases. They also opened the door for future cooperations with three distinguished U.S. biomedical informatics and cancer research centers.

First they had the chance to visit the Memorial Sloan Kettering Cancer Center (MSKCC) for several days to join the molecular oncology and bioinformatics groups of Dr. Michael F. Berger (developer of the powerful and new MSK-IMPACT genome-sequencing test) and Dr. Ahmet Zehir. Especially the interviews with key scientists as well as the participation in the  sign-out meetings of the MSKCC team and the quality control meetings provided valuable input for the MIRACUM use case on precision medicine. Together with our MIRACUM members, Michael Berger illustrated the opportunities of identifing actionable targets with a large gene panel rather than performing whole-exome-sequencing or even whole-genome-sequencing. In several meetings with Ahmet Zehir (Director of Clinical Bioinformatics at MSKCC) they learned about the “Clinical Variation and Result” database which is extensively used for moleculargenetic diagnostics within MSKCC. He invited our MIRACUM members to join him for several sign-out meetings of the MSKCC team and for quality control meetings in order to learn about the advantages of this database. Furthermore, he described how to modify and integrate such a database within the MIRACUM consortium. Moreover, our MIRACUM members met Dr. Sumit Middha and his team in order to understand and analyze the omics pipeline of MSKCC. This pipeline comprises automated and streamlined workflows for DNA sequencing, which has the chance to help taking genomic sequencing in Germany to the next level. Since the development and integration of a pharmacogenomic clinical decision support system is one of MIRACUM’s main goals for the upcoming phase, our MIRACUM members met Dr. Debyani Chakravarty and Dr. Jianjiong Gao, two of the leading scientists for knowledge bases at MSKCC and the main developers of two powerful and well-known tools regarding cancer genomics data. They offered our MIRACUM members a comprehensive insight into OncoKB and cBioPortal. OncoKB is the precision oncology knowledge base of MSKCC, which also comprises a pharmacogenomic clinical decision support system. cBioPortal is a “web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data” (Gao et al. 2016). In addition to that, next steps in order to design and implement both OncoKB and cBioPortal into a German clinical environment were discussed and determined.

MarcA photo showing Hinderer and Jan Christoph in front of the building of the "Memorial Sloan-Kettering Cancer Center"

A photo showing Ahmet Zehir, Michael F. Berger, Jan Christoph and Marc Hinderer (standing in front of the office door)

At the Department of Biomedical Informatics of the Columbia University, our MIRACUM members met the two leading scientists in biomedical informatics – Dr. George Hripcsak and Dr. Noemie Elhadad. George Hripcsak is Professor and Chair of the Department of Biomedical Informatics of Columbia University and Director of Medical Informatics Services at the Presbyterian Hospital/Columbia Campus in New York. Our MIRACUM members discussed with him both the cooperation with the OHDSI consortium and possible approaches to apply the OMOP common data model within MIRACUM. A presentation of the newest version of the Achilles and Atlas tools illustrated the potential of these particular tools for the analysis of cross-network data both within the MIRACUM project and for Germany. Noemie Elhadad is an Associate Professor of Biomedical Informatics at Columbia University and the main developer of the HARVEST tool. She offered the MIRACUM members a comprehensive insight into HARVEST – an innovative tool for the summarization and visualization of care processes. Moreover, she showed potential ways in which HARVEST could support the MIRACUM consortium in its project regarding the visualization of patient timelines.

A photo showing Jan Christoph, George Hripsak and Marc Hinderer standing on the roof deck of the Presbyterian Building

At last, Jan and Marc met leading scientists in clinical health informatics of the Weil Cornell Medical College: Dr. Jyotishman Pathak, Dr. Thomas CampionDr. David R. Artz and Dr. Olivier Elemento. They gave our MIRACUM members an insight into their omics pipeline and discussed potential options for the implementation of their Precision Medicine Knowledgebase (PMKB) into the MIRACUM infrastructure. Since the Weil Cornell Medical College extensively uses i2b2 and OMOP for data integration, the scientists outlined the purpose of the application both within their clinical and their research environment. Furthermore, they described their current pharmacogenomic Clinical Decision Support System and explained the technical mechanisms behind this system.

During all these visits the architecture of the MIRACUM data integration center and the interoperability between similar US initiatives/projects was extensively discussed and opportunities for future cooperations have been outlined.



ByChristian Knell

7th new Medical Informatics/Medical Data Science Professorship announced from MIRACUM members

We are happy to announce the seventh  newly established professorship in the context of the MIRACUM consortium. The Faculty of Medicine Mannheim of Heidelberg University invites applicants for a W3 Professorship for Medical Informatics Detailed information is provided in the job advertisement in English and German. We are looking forward to receiving your applications and a future cooperation in the MIRACUM consortium!

ByChristian Knell

3rd MIRACUM Steering Board Meeting in Frankfurt

The MIRACUM Steering Board, together with the University hospital´s CIOs and team members from the participating medical informatics, biometrics and bioinformatics groups met for two days (29th/30th of March) at Frankfurt University Hospital for rounding up their grant proposal for the development and networking phase. The status of pilot projects was demonstrated and workplans for the future defined. While two members of the Erlangen Medical Informatics department in parallel pursued a 10 day research visit at three research groups in New York City, the input from those international cooperation partners and scientific advisors was directly transferred into the concepts for use case implementation.

The MIRACUM Steering Board congratulated the Medical Faculty of Gießen Universities and the Medical Faculty Mannheim of Heidelberg University for their recent announcement of new professorships in Medical Informatics. Finally the MIRACUM Steering Board initiated the planning of their first Scientific Symposium in February 2018.

ByChristian Knell

Erlangen´s tranSMART projects at the eHealth Summit 2017

For many years now Erlangen´s Chair of Medical Informatics has committed itself to the support of translational research. Since the i2b2 Toolkit has been successfully deployed in various projects for more than five years now, Erlangen´s section of medical informatics also faced the challenge of supporting the integration and -with it- the evaluation of molecular and genomic analysis data by providing clinical data. To this end the platform tranSMART, which evolved from i2b2 and was developed further by the Transmart Foundation, has been established at the medical faculty of the FAU Erlangen-Nürnberg. It has been refined and evaluated both for its application in medical teaching and for its usability regarding its use by basic researchers in medicine. Two of these projects have now been accepted for a presentation at the eHealth Summit 2017 in Vienna (23th/24th May 2017). The detailed results of the project will soon be published in the conference proceedings of the IOS series “Studies in Health Technologies and Informatics” as well.

  • Christoph Jan, Knell Christian, Nachberger Elisabeth, Stürzl Michael, Maier Christian, Prokosch Hans-Ulrich, Sedlmayr Martin. Two Years of tranSMART in a University Hospital for Translational Research and Education.
  • Knell Christian, Sedlmayr Martin, Christoph Jan. Developing interactive plug-ins for for tranSMART using the SmartR fram ework workwork: The case of survival analysis.
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