Publikationen

Renner C, Reimer N, Christoph J, Busch H, Metzger P, Boerries M, Ustjanzew A, Boehm D, Unberath P.
Extending cBioPortal for Therapy Recommendation Documentation in Molecular Tumor Boards: Development and Usability Study.
JMIR Med Inform. 2023 Dec 11;11:e50017. doi: 10.2196/50017. PMID: 38079196; PMCID: PMC10750236.

Henke E, Peng Y, Reinecke I, Zoch M, Sedlmayr M, Bathelt F. An Extract-Transform-Load Process Design for the Incremental Loading of German Real-World Data Based on FHIR and OMOP CDM: Algorithm Development and Validation. JMIR Med Inform 2023; 11:e47310. DOI: 10.2196/47310.

Wolfien M, Ahmadi N, Fitzer K, Grummt S, Heine KL, Jung IC,  Krefting DK, Kühn A, Peng Y, Reinecke I, Scheel J, Schmidt T, Schmücker P, Schüttler C, Waltemath D, Zoch M, Sedlmayr M. Ten Topics to Get Started in Medical Informatics Research. J Med Internet Res 2023; 25:e45948. DOI: 10.2196/45948.

Schmid K, Sehring J, Németh A, Harter PN, Weber KJ, Vengadeswaran A, Storf H, Seidemann C, Karki K, Fischer P, Dohmen H, Selignow C, von Deimling A, Grau S, Schröder U, Plate KH, Stein M, Uhl E, Acker T, Amsel D.
DistSNE: Distributed computing and online visualization of DNA methylation-based central nervous system tumor classification.
Brain Patho 2023; e13228. DOI: 10.1111/bpa.13228. Epub ahead of print.

Scheible R, Thomczyk F, Blum M, Rautenberg M, Prunotto A, Yazijy S, Boeker M.
Integrating row level security in i2b2: segregation of medical records into data marts without data replication and synchronization.
JAMIA Open 2023; 6:ooad068. DOI: 10.1093/jamiaopen/ooad068.

Sehring J, Dohmen H, Selignow C, Schmid K, Grau S, Stein M, Uhl E, Mukhopadhyay A, Németh A, Amsel D, Acker T.
Leveraging Attention-Based Convolutional Neural Networks for Meningioma Classification in Computational Histopathology.
Cancers 2023; 15:5190. DOI: 10.3390/cancers15215190.

Metzger P, Hess ME, Blaumeiser A, Pauli T, Schipperges V, Mertes R, Christoph J, Unberath P, Reimer N, Scheible R, Illert AL, Busch H, Andrieux G, Boerries M.
MIRACUM-Pipe: An Adaptable Pipeline for Next-Generation Sequencing Analysis, Reporting, and Visualization for Clinical Decision Making.
Cancers 2023; 15:3456. DOI: 10.3390/cancers15133456.

Mang JM, Prokosch HU, Kapsner L.
Reproducibility in 2023 – An End-to-End Template for Analysis and Manuscript Writing
Stud Health Technol Inform 2023; 18;302:58-62. DOI: 10.3233/SHTI230064.

Peng Y, Henke E, Reinecke I, Zoch M, Sedlmayr M, Bathelt F.
An ETL-process design for data harmonization to participate in international research with German real-world data based on FHIR and OMOP CDM.
Int J Med Inform 2023; 169:104925. DOI: 10.1016/j.ijmedinf.2022.104925.

Vass A, Reinecke I, Boeker M, Prokosch HU, Gulden C.
Availability of Structured Data Elements in Electronic Health Records for Supporting Patient Recruitment in Clinical Trials.
Stud Health Technol Inform 2022; 290:130-134. DOI: 10.3233/SHTI220046. PMID: 35672985.

Scheible R, Caliskan D, Fischer P, Thomczyk F, Zabka S, Schneider H, Boeker M, Schulz S, Prokosch HU, Gulden C.
AHD2FHIR: A Tool for Mapping of Natural Language Annotations to Fast Healthcare Interoperability Resources – A Technical Case Report.
Stud Health Technol Inform 2022; 290:32-36. DOI: 10.3233/SHTI220026. PMID: 35672965.

Bialke M, Geidel L, Hampf C, Blumentritt A, Penndorf P, Schuldt R, Moser F, Lang S, Werner P, Stäubert S, Hund H, Albashiti F, Gührer J, Prokosch H, Bahls T, Hoffmann W.
A FHIR has been lit on gICS: facilitating the standardised exchange of informed consent in a large network of university medicine.
BMC Med Inform Decis Mak 2022; 22:335. DOI: https://doi.org/10.1186/s12911-022-02081-4.

Ahmadi N, Peng Y, Wolfien M, Zoch M, Sedlmayr M.
OMOP CDM Can Facilitate Data-Driven Studies for Cancer Prediction: A Systematic Review.
Int. J. Mol. Sci 2022; 23:11834. DOI: https://doi.org/10.3390/ijms231911834.

Scheer J, Volkert A, Brich N, Weinert L, Santhanam N, Krone M, Ganslandt T, Boeker M, Nagel T.
Visualization Techniques of Time-Oriented Data for the Comparison of Single Patients With Multiple Patients or Cohorts: Scoping Review.
J Med Internet Res 2022; 24:e38041. DOI: 10.2196/38041.

Schoenthaler M, Fichtner UA;  Boeker M; Zoeller D, Binder B, Prokosch HU, Praus P, Walther T, Glienke M, Horki P. Gratzke C; Farin-Glattacker E.
A nationwide registry for recurrent urolithiasis in the upper urinary tract – The RECUR study protocol.
BMC Health Serv Res 2022; 22:1060. DOI: 10.1186/s12913-022-08375-7.

Mang JM, Seuchter S, Gulden C, Schild S, Kraska D, Prokosch HU, Kapsner LA.
DQAgui: a graphical user interface for the MIRACUM data quality assessment tool.
BMC Med Inform Decis Mak 2022; 22:213. DOI: 10.1186/s12911-022-01961-z.

Roschka S, Leddig T, Bullerjahn M, Richter G, Liedtke W, Martin M and Hoffmann W.
Secondary use of health care data and left-over biosamples within the ‘Medical Informatics Initiative’ (MII): a quasi-randomized controlled evaluation of patient perceptions and preferences regarding the consent process.
BMC Med Inform Decis Mak 2022; 22:184. DOI: 10.1186/s12911-022-01922-6.

Schüttler C, Jahns R, Prokosch HU, Wach S, Wullich B.
Biobanken, translationale Forschung und Medizininformatik.
Urologie 2022; DOI: 10.1007/s00120-022-01850-3.

Zenker S, Strech D, Ihrig K, Jahns R, Müller G, Schickhardt C, Schmidt G, Speer R, Winkler E, Graf von Kielmansegg S, Drepper J.
Data protection-compliant broad consent for secondary use of health care data and human biosamples for (bio)medical research: towards a new German national standard
Journal of Biomedical Informatics Available online 25 May 2022, 104096

Schulz S, Boeker M, Prunotto A.
Validation of Multiple Path Translation for SNOMED CT Localisation.
Stud Health Technol Inform 2022; 294:961-962. DOI: 10.3233/SHTI220641.

Bathelt F, Reinecke I, Peng Y, Henke E, Weidner J, Bartos M, Gött R, Waltemath D, Engelmann K, Schwarz PEH, Sedlmayr M.
Opportunities of Digital Infrastructures for Disease Management—Exemplified on COVID-19-Related Change in Diagnosis Counts for Diabetes-Related Eye Diseases
Nutrients 2022; 14,2016. DOI: 10.3390/nu14102016.

Mariño J, Kasbohm E, Struckmann S, Kapsner LA, Schmidt CO.
R Packages for Data Quality Assessments and Data Monitoring: A Software Scoping Review with Recommendations for Future Developments
Applied Scieneces 2022; 26. DOI: 10.3390/app12094238.

Fitzer K, Häuslschmid R, Blasini R, Altun FB, Hampf C, Freiesleben S, Macho P, Prokosch H, Gulden C.
Patient Recruitment System for Clinical Trials: A Mixed-Methods Study about Requirements at 10 University Hospitals
JMIR Med Inf 2022. 10:e28696. DOI: 10.2196/28696.

Unberath P, Mahlmeister L, Reimer N, Busch H, Boerries M, Christoph J.
Searching of Clinical Trials Made Easier in cBioPortal Using Patients‘ Genetic and Clinical Profiles.
Appl Clin Inform 2022; 13:363-369. DOI: 10.1055/s-0042-1743560.

Medenwald D, Brunner T, Christiansen H, Kisser U, Mansoorian S, Vordermark D, Prokosch HU, Seuchter SA, Kapsner LA on behalf of our MII research group.
Shift of radiotherapy use during the first wave of the COVID-19 pandemic? An analysis of German inpatient data
Strahlenther Onkol 2022. DOI: 10.1007/s00066-021-01883-1.

Spohr C, Poggio T, Andrieux G, Schönberger K, Cabezas-Wallscheid N, Boerries M, Halbach S, Illert AL, Brummer T.
Gab2 deficiency prevents Flt3-ITD driven acute myeloid leukemia in vivo
Leukemia 2022; 36:970-982. DOI: 10.1038/s41375-021-01490-0.

Frey P, Devisme A, Rose K, Schrempp M, Freihen V, Andrieux G, Boerries M, Hecht A.
SMAD4 mutations do not preclude epithelial-mesenchymal transition in colorectal cancer
Oncogene 2022; 41:824-837. DOI: 10.1038/s41388-021-02128-2.

Härzschel A, Li L, Krenn PW, Szenes-Nagy E, Andrieux G, Bayer E, Pfeifer D, Polcik L, Denk U, Höpner JP, Karabatak E, Danner DJ, Tangermann S, Kenner L, Jumaa H, Greil R, Börries M, Ruppert R, Maity PC, Hartmann TN.
Kindlin-3 maintains marginal zone B cells but confines follicular B cell activation and differentiation
J Leukoc Biol 2022; 111:745-758. DOI: 10.1002/JLB.1HI0621-313R.

Scheible R, Strecker P, Yazijy S, Talpa R, Puhl A, Boeker M.
A Multilingual Browser Platform for Medical Subject Headings
Stud Health Technol Inform 2022; 289:384-387. DOI: 10.3233/SHTI210939.

Strecker P, Boeker M, Buechner S, Scheible R.
Usability Evaluation of a Modern Multilingual MeSH Browser
Stud Health Technol Inform 2022; 295:37-40. DOI: 10.3233/SHTI220653.

Devane J, Ott E, Olinger EG, Epting D, Decker E, Friedrich A, Bachmann N, Renschler G, Eisenberger T, Briem-Richter A, Grabhorn EF, Powell L, Wilson IJ, Rice SJ, Miles CG, Wood K; Genomics England Research Consortium; Trivedi P, Hirschfield G, Pietrobattista A, Wohler E, Mezina A, Sobreira N, Agolini E, Maggiore G, Dahmer-Heath M, Yilmaz A, Boerries M, Metzger P, Schell C, Grünewald I, Konrad M, König J, Schlevogt B, Sayer JA, Bergmann C.
Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations – PMC (nih.gov)
Am J Hum Genet 2022; 109: 928–943. DOI: 10.1016/j.ajhg.2022.03.015.

Ustjanzew A, Desuki A, Ritzel C, Dolezilek AC, Wagner DC, Christoph J, Unberath P, Kindler T, Faber J, Marini F, Panholzer T, Paret C.
cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board
BMC Med Inform Dec Mak 2021, 21:358. DOI: 110.1186/s12911-021-01719-z.

Reimer N, Unberath P, Busch H, Börries M, Metzger P, Ustjanzew A, Renner C, Prokosch HU, Christoph J.
Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform
Stud Health Technol Inform 2021; 287: 139-143. DOI: 10.3233/SHTI210833.

Walther T, Farin E, Boeker M, Prokosch HU, Binder B, Praus F, Ploner N, Fichtner UA, Horki P, Haeuslschmid R, Seuchter S, Gratzke C, Schoenthaler M.
RECUR – Aufbau eines automatisierten digitalen Registers für Patient*innen mit rezidivierenden Steinen des oberen Harntraktes
Gesundheitswesen 2021; 83: S27-S32. DOI: 10.1055/a-1651-0311.

Reinecke I, Zoch M, Reich C, Sedlmayr M, Bathelt F.
The usage of OHDSI OMOP – A Scoping Review.
Stud Health Technol Inform 2021; 283:95-103. DOI: 10.3233/SHTI210546.

Kapsner LA, Mang JM, Mate S, Seuchter SA, Vengadeswaran A, Bathelt F, Deppenwiese N, Kadioglu D, Kraska D, Prokosch HU.
Linking a Consortium-Wide Data Quality Assessment Tool with the MIRACUM Metadata Repository
Appl Clin Inform 2021; 12:826-835. DOI: 10.1055/s-0041-1733847.

Schüttler C, Prokosch HU, Sedlmayr M, Sedlmayr B.
Evaluation of Three Feasibility Tools for Identifying Patient Data and Biospecimen Availability: Comparative Usability Study
JMIR Med Inform 2021;9(7):e25531, DOI: 10.2196/25531.

Reimer N, Unberath P, Busch H, Ingenerf J.
FhirSpark – Implementing a Mediation Layer to Bring FHIR to the cBioPortal for Cancer Genomics
Stud Health Technol Inform 2021; 281:303-307. DOI: 10.3233/SHTI210169

Zoch M, Gierschner C, Peng Y, Gruhl M, Leutner LA, Sedlmayr M, Bathelt F.
Adaption of the OMOP CDM for Rare Diseases
Stud Health Technol Inform 2021; 281:138-142. DOI: 10.3233/SHTI210136.

Sass J, Zabka S, Essenwanger A, Schepers J, Boeker M, Thun S.
Fast Healthcare Interoperability Resources (FHIR®) Representation of Medication Data Derived from German Procedure Classification Codes (OPS) Using Identification of Medicinal Products (IDMP) Compliant Terminology
Stud Health Technol Inform 2021; 278:231-236. DOI: 10.3233/SHTI210074.

Mate S, Seuchter SA, Ehrenberg K, Deppenwiese N, Zierk J, Prokosch HU, Kraska D, Kapsner LA.
A Multi-User Terminology Mapping Toolbox
Stud Health Technol Inform 2021; 278:217-223. DOI: 10.3233/SHTI210072.

Schaaf J, Sedlmayr M, Prokosch HU, Tegtbauer N, Kadioglu D, Schaefer J, Boeker M, Storf H.
Visualization of Similar Patients in a Clinical Decision Support System for Rare Diseases – A Focus Group Study
Stud Health Technol Inform 2021; 278:49-57. DOI: 10.3233/SHTI210050.

Caliskan D, Zierk J, Kraska D, Schulz S, Daumke P, Prokosch HU, Kapsner LA.
First Steps to Evaluate an NLP Tool’s Medication Extraction Accuracy from Discharge Letters
Stud Health Technol Inform 2021; 278:224-230. DOI: 10.3233/SHTI210073.

Kapsner LA, Zavgorodnij MG, Majorova SP, Hotz‐Wagenblatt A, Kolychev OV, Lebedev IN, Hoheisel JD, Hartmann A, Bauer A, Mate S, Prokosch H, Haller F, and Moskalev EA.
BiasCorrector: fast and accurate correction of all types of experimental biases in quantitative DNA methylation data derived by different technologies
Int. J. Cancer 2021; ijc.33681. DOI: 10.1002/ijc.33681.

Maier C,  Kapsner LA, Mate S, Prokosch HU, Kraus S.
Patient Cohort Identification on Time Series Data Using the OMOP Common Data Model
Appl Clin Inform 2021; 12: 057-064. DOI: 10.1055/s-0040-1721481.

Lenz S, Hess M, Binder H.
Deep generative models in DataSHIELD
BMC Med Res Methodol 2021; 21: 64. DOI: 10.1186/s12874-021-01237-6.

Gruendner J, Gulden C, Kampf MO, Mate S, Prokosch HU, Zierck J.
A Framework for Criteria-Based Selection and Processing of Fast Healthcare Interoperability Resources (FHIR) Data for Statistical Analysis: Design and Implementation Study
JMIR Med Inform 2021; 9: e25645. DOI: 10.2196/25645.

Schüttler J, Mang JM, Kapsner LA, Seuchter SA, Binder H, Zöller D, Kohlbacher O, Boeker M, Zacharowski K, Rohde G, Balig J, Kampf MO, Röhrig R, Prokosch HU
Letalität von Patienten mit COVID-19: Untersuchungen zu Ursachen und Dynamik an deutschen Universitätsklinika
Anästh Intensivmed 2021; 62: 244–257. DOI: 10.19224/ai2021.244.

Hampf C, Bialke M, Geidel L, Vass A, Bahls T, Blasini R, Blumentritt A, Boeker M, Bruns C, Jandrig B, Fünfgeld M, Heinrich P, Leddig T, Michel-Backofen A, Pirkl A, Rautenberg M, Simons F, Stahl D, Prokosch HU, Hoffmann W.
A survey on the current status and future perspective of informed consent management in the MIRACUM consortium of the German Medical Informatics Initiative
BMC transl med commun 2021; 6:7. DOI: 10.1186/s41231-021-00086-1.

Schaaf J, Sedlmayr M, Sedlmayr B, Prokosch HU, Storf H.
Evaluation of a clinical decision support system for rare diseases: a qualitative study
BMC Med Inform Decis Mak 2021; 21:6. DOI: 10.1186/s12911-021-01435-8.

Klann JG et al.
Validation of an Internationally Derived Patient Severity Phenotype to Support COVID-19 Analytics from Electronic Health Record Data
J Am Med Inform Assoc 2021; ocab018.  DOI: 10.1093/jamia/ocab018.

Kapsner LA, Kampf MO, Seuchter SA, Gruendner J, Gulden C, Mate S, Mang JM, Schüttler C, Deppenwiese N, Krause L, Zöller D, Balig J, Fuchs T, Fischer P, Haverkamp C, Holderried M, Mayer G, Stenzhorn H, Stolnicu A, Storck M, Storf H, Zohner J, Kohlbacher O, Strzelczyk A, Schüttler J, Acker T, Boeker M, Kaisers UX, Kestler HA, Prokosch HU on behalf of our MII-Research Group.
Reduced Rate of Inpatient Hospital Admissions in 18 German University Hospitals During the COVID-19 Lockdown
Front. Public Health 2021; 8:594117. DOI: 10.3389/fpubh.2020.594117.

Melzer G, Maiwald T, Prokosch HU, Ganslandt T.
Leveraging Real-World Data for the Selection of Relevant Eligibility Criteria for the Implementation of Electronic Recruitment Support in Clinical Trials
Appl Clin Inform 2021; 12:017-026. DOI: 10.1055/s-0040-1721010.

Gulden C, Blasini R, Nassirian A, Stein A, Altun F, Kirchner M, Prokosch HU, Boeker M.
Prototypical Clinical Trial Registry Based on Fast Healthcare Interoperability Resources (FHIR): Design and Implementation Study
JMIR Med Inform 2021; 9:e20470. DOI: 10.2196/20470.

Grünwald BT, Devisme A, Andrieux G, Vyas F, Aliar K, McCloskey CW, Macklin A, Jang GH, Denroche R, Romero JM, Bavi P, Bronsert P, Notta F, O’Kane G, Wilson J, Knox J, Tamblyn L, Udaskin M, Radulovich N, Fischer SE, Boerries M, Gallinger S, Kislinger T, Khokha R.
Spatially confined sub-tumor microenvironments in pancreatic cancer
Cell 2021; 184:5577-5592.e18. DOI: 10.1016/j.cell.2021.09.022.

Sicklinger F, Meyer IS, Li X, Radtke D, Dicks S, Kornadt MP, Mertens C, Meier JK, Lavine KJ, Zhang Y, Kuhn TC, Terzer T, Patel J, Boerries M, Schramm G, Frey N, Katus HA, Voehringer D, Leuschner F.
Basophils balance healing after myocardial infarction via IL-4/IL-13
J Clin Invest 2021; 131:e136778. DOI: 10.1172/JCI136778.

Haring E, Andrieux G, Uhl FM, Krausz M, Proietti M, Sauer B, Esser PR, Martin SF, Pfeifer D, Schmitt-Graeff A, Duyster J, Köhler N, Grimbacher B, Boerries M, Aumann K, Zeiser R, Apostolova P.
Therapeutic targeting of endoplasmic reticulum stress in acute graft-versus-host disease
Haematologica 2021;  DOI: 10.3324/haematol.2021.278387. Online ahead of print.

Kläsener K, Jellusova J, Andrieux G, Salzer U, Böhler C, Steiner SN, Albinus JB, Cavallari M, Süß B, Voll RE, Boerries M, Wollscheid B, Reth M.
CD20 as a gatekeeper of the resting state of human B cells
Proc Natl Acad Sci U S A 2021; 118:e2021342118. DOI: 10.1073/pnas.2021342118.

Corrales E, Levit-Zerdoun E, Metzger P, Kowar S, Ku M, Brummer T, Boerries M.
Dynamic transcriptome analysis reveals signatures of paradoxical effect of vemurafenib on human dermal fibroblasts
Cell Commun Signal 2021; 19:123. DOI: 10.1186/s12964-021-00801-3.

Osswald L, Hamarsheh S, Uhl FM, Andrieux G, Klein C, Dierks C, Duquesne S, Braun LM, Schmitt-Graeff A, Duyster J, Boerries M, Brummer T, Zeiser R.
Oncogenic KrasG12D Activation in the Nonhematopoietic Bone Marrow Microenvironment Causes Myelodysplastic Syndrome in Mice
Mol Cancer Res 2021; 19:1596-1608. DOI: 10.1158/1541-7786.MCR-20-0275.

Hoefflin R, Harlander S, Abhari BA, Peighambari A, Adlesic M, Seidel P, Zodel K, Haug S, Göcmen B, Li Y, Lahrmann B, Grabe N, Heide D, Boerries M, Köttgen A, Heikenwalder M, Frew IJ.
Therapeutic Effects of Inhibition of Sphingosine-1-Phosphate Signaling in HIF-2α Inhibitor-Resistant Clear Cell Renal Cell Carcinoma
Cancers (Basel) 2021; 13:4801. DOI: 10.3390/cancers13194801.

Bauer C, Quante M, Breunis WB, Regina C, Schneider M, Andrieux G, Gorka O, Groß O, Boerries M, Kammerer B, Hettmer S.
Lack of Electron Acceptors Contributes to Redox Stress and Growth Arrest in Asparagine-Starved Sarcoma Cells
Cancers (Basel) 2021; 13:412. DOI: 10.3390/cancers13030412.

Haring E, Uhl FM, Andrieux G, Proietti M, Bulashevska A, Sauer B, Braun LM, de Vega Gomez E, Esser PR, Martin SF, Pfeifer D, Follo M, Schmitt-Graeff A, Buescher J, Duyster J, Grimbacher B, Boerries M, Pearce EL, Zeiser R, Apostolova P.
Bile acids regulate intestinal antigen presentation and reduce graft-versus-host disease without impairing the graft-versus-leukemia effect
Haematologica 2021; 106:2131-2146. DOI: 10.3324/haematol.2019.242990.

Hoefflin R, Lazarou A, Hess ME, Reiser M, Wehrle J, Metzger P, Frey AV, Becker H, Aumann K, Berner K, Boeker M, Buettner N, Dierks C, Duque-Afonso J, Eisenblaetter M, Erbes T, Fritsch R, Ge IX, Geißler AL, Grabbert M, Heeg S, Heiland DH, Hettmer S, Kayser G, Keller A, Kleiber A, Kutilina A, Mehmed L, Meiss F, Poxleitner P, Rawluk J, Ruf J, Schäfer H, Scherer F, Shoumariyeh K, Tzschach A, Peters C, Brummer T, Werner M, Duyster J, Lassmann S, Miething C, Boerries M, Illert AL, von Bubnoff N.
Transitioning the Molecular Tumor Board from Proof of Concept to Clinical Routine: A German Single-Center Analysis
Cancers (Basel) 2021; 13:1151. DOI: 10.3390/cancers13051151.

Kind F, Fassbender TF, Andrieux G, Boerries M, Meyer PT, Ruf J.
Early PSA Change after [177Lu]PSMA-617 Radioligand Therapy as a Predicator of Biochemical Response and Overall Survival
Cancers (Basel) 2021; 14:149. DOI: 10.3390/cancers14010149.

Hussung S, Akhoundova D, Hipp J, Follo M, Klar RFU, Philipp U, Scherer F, von Bubnoff N, Duyster J, Boerries M, Wittel U, Fritsch RM.
Longitudinal analysis of cell-free mutated KRAS and CA 19-9 predicts survival following curative resection of pancreatic cancer
BMC Cancer 2021; 21:49. DOI: 10.1186/s12885-020-07736-x.

Pugliese P, Knell C, Christoph J.
Exchange of Clinical and Omics Data According to FAIR Principles: A Review of Open Source Solutions
Methods Inf Med 2020; 59:e13-e20. DOI: 10.1055/s-0040-1712968.

Gruendner J, Wolf N, Tögel L, Haller F, Prokosch HU, Christoph J.
Integrating Genomics and Clinical Data for Statistical Analysis by Using GEnome MINIng (GEMINI) and Fast Healthcare Interoperability Resources (FHIR): System Design and Implementation
JMIR 2020; 22:e19879. DOI: 10.2196/19879.

Schaaf J, Prokosch HU,  Boeker M, Schaefer J, Vasseur J, Storf H, Sedlmayr M.
Interviews with experts in rare diseases for the development of clinical decision support system software – a qualitative study
BMC Med Inform Decis Mak 2020; 20, 230. DOI: 10.1186/s12911-020-01254-3.

Jaravine V, Balmford J, Metzger P, Boerries M, Binder H, Boeker M.
Annotation of Human Exome Gene Variants with Consensus Pathogenicity
Genes 2020; 11 (9), 1076. DOI: 10.3390/genes11091076.

Brat GA, Weber GM, Gehlenborg N et al.
International electronic health record-derived COVID-19 clinical course profiles: the 4CE consortium
npj Digi. Med 2020; 3, 109. DOI: 10.1038/s41746-020-00308-0.

Rau H, Geidel L, Bialke M, Blumentritt A, Langanke M, Liedtke W, Pasewald S, Stahl D, Bahls T, Maier C, Prokosch HU, Hoffmann W.
The generic Informed Consent Service gICS^®: implementation and benefits of a modular consent software tool to master the challenge of electronic consent management in research
J Transl Med 2020; 18, 287. DOI: 10.1186/s12967-020-02457-y.

Fuchs M, Kreutzer FP, Kapsner L.A, Mitzka S, Just A, Perbellini F, Terracciano CM, Xiao K, Geffers R, Bogdan C, Prokosch, HU, Fiedler J, Thum T, Kunz M.
Integrative Bioinformatic Analyses of Global Transcriptome Data Decipher Novel Molecular Insights into Cardiac Anti-Fibrotic Therapies
Int J Mol Sci 2020; 21, 4727. DOI: 10.3390/ijms21134727.

Schaaf J, Sedlmayr M, Prokosch HU, Ganslandt T, Schade-Brittinger C, von Wagner M, Kadioglu D, Schubert K, Lee-Kirsch MA, K. Kraemer BK, Winner B, Mueller T,  Schaefer JR, Wagner TOF, Bruckner-Tuderman L, Tuescher O, Boeker M, Storf H.
The Status Quo of Rare Diseases Centres for the Development of a Clinical Decision Support System – A Cross-Sectional Study
Stud Health Technol Inform 2020; 271:176-183. DOI: 10.3233/SHTI200094.

Ploner N, Prokosch HU.
Integrating a Secure and Generic Mobile App for Patient Reported Outcome Acquisition into an EHR Infrastructure Based on FHIR Resources
Stud Health Technol Inform 2020; 270:991-995. DOI: 10.3233/SHTI200310.

Gruhl M, Reinecke I, Sedlmayr M.
Specification and Distribution of Vocabularies Among Consortial Partners
Stud Health Technol Inform 2020; 270:1393-1394. DOI: 10.3233/SHTI200458.

Reinecke I, Gulden C, Kümmel M, Nassirian A, Blasini R, Sedlmayr M.
Design for a Modular Clinical Trial Recruitment Support System Based on FHIR and OMOP
Stud Health Technol Inform 2020; 270:158-162. DOI: 10.3233/SHTI200142.

Bild R, Bialke M, Buckow K, Ganslandt T, Ihrig K, Jahns R, Merzweiler A, Roschka S, Schreiweis B, Stäubert S, Zenker S, Prasser F.
Towards a comprehensive and interoperable representation of consent-based data usage permissions in the German medical informatics initiative
BMC Med Inform Decis Mak 2020; 20, 103.  DOI: 10.1186/s12911-020-01138-6.

Becker L, Ganslandt T, Prokosch HU, Newe A.
Applied practice and possible leverage points for information technology support for the screening for clinical trials: A qualitative study
JMIR Med Inform 2020; 8:e15749. DOI: 10.2196/15749.

Zierk J, Krebs A, Rauh M, Metzler M, Löscher A, Strasser E, Krause SW.
Blood counts in adult and elderly individuals: defining the norms over eight decades of life
Br J Haematol 2020; 189:777-789. DOI: 10.1111/bjh.16430.

Zierk J, Arzideh F, Kapsner LA, Prokosch HU, Metzler M, Rauh M.
Reference Interval Estimation from Mixed Distributions using Truncation Points and the Kolmogorov-Smirnov Distance (kosmic)
Sci Rep 2020; 10, 1704. DOI: 10.1038/s41598-020-58749-2.

Buechner P, Hinderer M, Unberath P, Metzger P, Boeker M, Acker T, Haller F, Mack E, Nowak D, Paret C, Schanze D, von Bubnoff N, Wagner S, Busch H, Boerries M, Christoph J.
Requirements Analysis and Specification for a Molecular Tumor Board Platform Based on cBioPortal
Diagnostics 2020; 10, 93. DOI:10.3390/diagnostics10020093.

Zabka S, Schulz S, Brunner O, Boeker M.
How versioning of terminology systems can be supported by ontological models – a case study on TNM tumor classification.
Applied Ontology 2020; 15:41-60. DOI: 10.3233/AO-190220.

Scheible R, Kadioglu D, Ehl S, Blum M, Boeker M, Folz M, Grimbacher B, Göbel J, Klein C, Nieters A, Rusch S, Kindle G, Storf H.
Enabling External Inquiries to an Existing Patient Registry by Using the Open Source Registry System for Rare Diseases: Demonstration of the System Using the European Society for Immunodeficiencies Registry.
JMIR Med Inform 2020; 8:e17420. DOI: 10.2196/17420.

Zabka S, Ammon D, Ganslandt T, Gewehr J, Haverkamp C , Kiefer S, Lautenbacher H, Löbe M, Thun S, Boeker M.
Towards a Medication Core Data Set for the Medical Informatics Initiative (MII): Initial Mapping Experience between the German Procedure Classification (OPS) and the Identification of Medicinal Products (IDMP)
Proceedings of the Joint Ontology Workshops 2019, Episode V: The Styrian Autumn of Ontology, Graz, Austria, September 23-25, 2019. Edited by Adrien Barton, Selja Seppälä, Daniele Porello, Vol-2518.

Lenz S, Hess M, Binder H.
Unsupervised deep learning on biomedical data with BoltzmannMachines.jl
Preprint Server bioRxiv.

Hampf C, Bahls T, Hund H, Drepper J, Lablans M, Speer R.
Record Linkage: Optionen für standortübergreifende Datenzusammenführung
mdi – Forum der Medizin_Dokumentation und Medizin_Informatik 4_2019.

Mate S, Bürkle T, Kapsner LA, Toddenroth D, Kampf M, Sedlmayr M, Castellanos I, Prokosch HU, Kraus S.
A Method for the Graphical Modeling of Relative Temporal Constraints
J Biomed Inform 2019, 100. DOI: 10.1016/j.jbi.2019.103314.

Vey J, Kapsner LA, Fuchs M, Unberath P, Veronesi G, Kunz M.
A Toolbox for Functional Analysis and the Systematic Identification of Diagnostic and Prognostic Gene Expression Signatures Combining Meta-Analysis and Machine Learning
Cancers 2019, 11, 1606. DOI:10.3390/cancers11101606.

Gruendner J, Schwachhofer T, Sippl P, Wolf N, Erpenbeck M, Gulden C, Kapsner LA, Zierk J, Mate S, Stürzl M, Croner R, Prokosch HU, Toddenroth D.
KETOS: Clinical decision support and machine learning as a service – A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services
PLoS ONE 2019; 14(10): e0223010. DOI: 10.1371/journal.pone.0223010.

Öfelein M, Reichold M, Maier C, Prokosch HU.
Designing a Framework of Components to Support Patient Engagement in Research
Stud Health Technol Inform 2019; 267:20-27. DOI: 10.3233/SHTI190800.

Vengadeswaran A, Neuhaus P, Hegselmann S, Storf H, Kadioglu D.
Semantically annotated Metadata: Interconnecting Samply.MDR and MDM-Portal
Stud Health Technol Inform 2019; 267:86-92. DOI: 10.3233/SHTI190810.

Kapsner LA, Kampf MO, Seuchter SA, Kamdje-Wabo G, Gradinger T, Ganslandt T, Mate S, Guendner J, Kraska D, Prokosch HU.
Moving Towards an EHR Data Quality Framework: The MIRACUM Approach
Stud Health Technol Inform 2019; 267:247-253. DOI: 10.3233/SHTI190834.

Schneiderheinze H, Prokosch HU, Apel H, Bellut L, Wullich B, Trollmann R, Schüttler C.
Development and usability analysis of a multimedia eConsent solution
Stud Health Technol Inform 2019; 267:297-303. DOI: 10.3233/SHTI190841.

Gulden C, Kirchner M, Schüttler C, Hinderer M, Kampf M, Prokosch HUP, Toddenroth D.
Extractive summarization of clinical trial descriptions
Int J Med Inform 2019; 129:114-121. DOI: 10.1016/j.ijmedinf.2019.05.019.

Bild R, Ganslandt T, Ihrig K, Jahns R, Merzweiler A, Schreiweis B , Stäubert S, Zenker S, Bialke M, Prasser F.
Erster Schritt: Im Rahmen der Medizininformatik-Initiative des Bundesforschungsministeriums ist eine elektronische Abbildung von Informationen aus Patienten-Einwilligungserklärungen entwickelt worden
E-HEALTH-COM 2019; 2_3:50-53.

Gruendner J, Prokosch HU, Schindler S, Lenz S, Binder H.
A Queue-Poll Extension and DataSHIELD: Standardised, Monitored, Indirect and Secure Access to Sensitive Data
Stud Health Technol Inform 2019; 258:115-119. DOI: 10.3233/978-1-61499-959-1-115.

Gulden C, Landerer I, Nassirian A, Altun FB, Andrae J.
Extraction and Prevalence of Structured Data Elements in Free-Text Clinical Trial Eligibility Criteria
Stud Health Technol Inform 2019; 258:226-230. DOI: 10.3233/978-1-61499-959-1-226.

Hasselblatt H, Andrae J, Tassoni A, Fitzer K, Bahls T, Prokosch HU, Boeker M.
Establishing an Interoperable Clinical Trial Information System Within MIRACUM
Stud Health Technol Inform 2019; 258:216-220. DOI: 10.3233/978-1-61499-959-1-216.

Walther D, Paret C, Ritzel C, Büchner P, Unberath P, Maier W, Metzger P, Christoph J, Storf H, Boerries M, Wagner S.
Definition of an annotation pipeline for a molecular tumor board focused on the processing of the result and oncological drugs in terms of usability and approval status
GMS Publishing House; 2019. DocAbstr. 283. DOI: 10.3205/19gmds179.

Kampf MO, Kraska D, Prokosch HU.
An Analysis of Erlangen University Hospital’s Billing Data on Utility-Based De-Identification
Stud Health Technol Inform 2019;258:70-74. DOI: 10.3233/978-1-61499-959-1-70.

Sommer M, Kirchner M, Gulden C, Egloffstein S, Lux MP, Beckmann MW, Mackensen A, Prokosch HU.
Design and Implementation of a Single Source Multipurpose Hospital-Wide Clinical Trial Registry
Stud Health Technol Inform 2019; 258:164-168. DOI: 10.3233/978-1-61499-959-1-164.

Unberath P, Knell C, Prokosch HU, Christoph J.
Developing New Analysis Functions for a Translational Research Platform: Extending the cBioPortal for Cancer Genomics
Stud Health Technol Inform 2019; 258:46-50. DOI: 10.3233/978-1-61499-959-1-46.

Daumke P, Heitmann KU, Heckmann S, Martínez-Costa C, Schulz S.
Clinical Text Mining on FHIR
Stud Health Technol Inform 2019 ;264:83-87. DOI: 10.3233/SHTI190188.

Ganslandt T, Neumaier M.
Digital networks for laboratory data: potentials, barriers and current initiatives
Clin Chem Lab Med 2019 ;57:336-342. DOI: 10.1515/cclm-2018-1131.

Schoenthaler M, Boeker M, Horki P.
How to compete with Google and Co.: big data and artificial intelligence in stones
Curr Opin Urol 2018; 29:135-143 DOI: 10.1097/MOU.0000000000000578.

Bietenbeck A, Boeker M, Schulz S.
NPU, LOINC, and SNOMED CT: a comparison of terminologies for laboratory results reveals individual advantages and a lack of possibilities to encode interpretive comments
Journal of Laboratory Medicine 2018; 42: 267-275. DOI: 10.1515/labmed-2018-0103.

Lenz S, Zöller D, Hess M, Binder H.
Architectures for distributed privacy-preserving deep learning
Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie. 63. Jahrestagung der GMDS, Osnabrück, 02.-06.09.2018. Düsseldorf: German Medical Science GMS Publishing House; 2018. DocAbstr. 207. DOI: 10.3205/18gmds097.

Treppner M, Lenz S, Binder H, Zöller D.
Modeling Activity Tracker Data Using Deep Boltzmann Machines
Stud Health Technol Inform 2018; 253:155-159. DOI: 10.3233/978-1-61499-896-9-155.

Kadioglu D, Breil B, Knell C, Lablans M, Mate S, Schlue D, Serve H, Storf H,  Ückert F,  Wagner T, Weingardt P, Prokosch HU.
Samply.MDR – A Metadata Repository and Its Application in Various Research Networks
Stud Health Technol Inform 2018; 253:50-54. DOI: 10.3233/978-1-61499-896-9-50.

Gulden C, Mate S, Prokosch HU, Kraus S.
Investigating the Capabilities of FHIR Search for Clinical Trial Phenotyping
Stud Health Technol Inform 2018; 253:3-7. DOI: 10.3233/978-1-61499-896-9-3.

Prokosch HU, Acker T, Bernarding J, Binder H, Boeker M, Boerries M, Daumke P, Ganslandt T, Hesser J, Höning G, Neumaier M, Marquardt K, Renz H, Rothkötter HJ, Schade-Brittinger C, Schmücker P, Schüttler J, Sedlmayr M, Serve H, Sohrabi K, Storf H.
MIRACUM: Medical Informatics in Research and Care in University Medicine – A Large Data Sharing Network to Enhance Translational Research and Medical Care
Methods Inf Med 2018; 57:e82– e91, DOI: 3414/ME17–02–0025.

Sedlmayr M, Prokosch HU.
Datenaustausch in der Forschung via OMOP/OHDSI
EHEALTHCOM 4/18, COMPLEX|Medizininformatik 34-37, Juni 2018.

Knaup P, M. Deserno TM, Prokosch HU, Sax U.
Implementation of a National Framework to Promote Health Data Sharing
CC-BY-NC-ND 4.0 · Yearb Med Inform, April 2018, DOI: 10.1055/s-0038-1641210.

Hinderer M, Boerries M, Boeker M, Neumaier M, Loubal FP, Acker T, Brunner M, Prokosch HU, Christoph J.
Implementing Pharmacogenomic Clinical Decision Support into German Hospitals
Stud Health Technol Inform 2018; 247:870-874. DOI: 10.3233/978-1-61499-852-5-870.

Maier C, Lang L, Storf H, Vormstein P, Bieber R, Bernarding J, Herrmann T, Haverkamp C, Horki P, Laufer J, Berger F, Höning G, Fritsch HW, Schüttler J, Ganslandt T, Prokosch HU, Sedlmayr M.
Towards Implementation of OMOP in a German University Hospital Consortium
Appl Clin Inform 2018; 9:54-61. DOI: 10.1055/s-0037-1617452 .

Haverkamp C, Ganslandt T, Horki P, Boeker M, Dörfler A, Schwab S, Berkefeld J, Pfeilschifter W, Niesen WD, Egger K, Kaps M, Brockmann MA, Neumaier-Probst E, Szabo K, Skalej M, Bien S, Best C, Prokosch HU, Urbach H.
Regional Differences in Thrombectomy Rates: Secondary use of Billing Codes in the MIRACUM (Medical Informatics for Research and Care in University Medicine) Consortium
Clin Neuroradiol 2018; 28:225-234.8. DOI: 10.1007/s00062-017-0656-y.

Christoph J, Knell C, Bosserhoff A, Naschberger E, Stürzl M, Rübner M, Seuss H, Ruh M, Prokosch HU, Sedlmayr B.
Usability and Suitability of the Omics-Integrating Analysis Platform tranSMART for Translational Research and Education
ACI 2017; 8:1173-1183. DOI: 10.4338/ACI-2017-05-RA-0085.

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; 17:81. DOI: 10.1186/s12911-017-0480-y.

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 18:773-785. DOI: 10.2217/pgs-2017-0027.

Hinderer M, Boerries M, Haller F, Wagner S, Sollfranke S, Acker T, Prokosch HU. Christoph J.
Supporting Molecular Tumor Boards in Molecular-guided Decision-making – the Current Status of Five German University Hospitals
Stud Health Technol Inform 2017; 236:48-54. DOI: 10.3233/978-1-61499-759-7-48.

Christoph J, Knell C, Naschberger E, Stürzl M, Maier C, Prokosch HU, Sedlmayr M.
Two Years of tranSMART in a University Hospital for Translational Research and Education
Stud Health Technol Inform. 2017 ;236:70-79. DOI: 10.3233/978-1-61499-759-7-70.

Knell C, Sedlmayr M, Christoph J.
Developing Interactive Plug-ins for tranSMART Using the SmartR Framework: The Case of Survival Analysis
Stud Health Technol Inform. 2017; 236:375-382. DOI: 10.3233/978-1-61499-759-7-375.

Prabhune, A, Stotzka, Gertz, M., Hesser, J.
Managing Provenance for Medical Datasets An Example Case for Documenting the Workflow for Image Processing
HEALTHINF 2017:236-243. DOI: 10.5220/0006109402360243.