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  1. Book: Medizininformatik

    Dugas, Martin

    ein Kompendium für Studium und Praxis

    2017  

    Author's details Martin Dugas
    Keywords Medizininformatik ; Informationssysteme im Gesundheitswesen ; Elektronische Patientenakte ; Medizinische Terminologien ; Medizinische Bildverarbeitung ; Medizinische Informatik
    Subject Medizininformatik
    Subject code 610
    Language German
    Size X, 259 Seiten, Illustrationen, 24 cm x 16.8 cm
    Publisher Springer Vieweg
    Publishing place Berlin
    Publishing country Germany
    Document type Book
    HBZ-ID HT019289316
    ISBN 978-3-662-53327-7 ; 9783662533284 ; 3-662-53327-8 ; 3662533286
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2017 A 957 available for loan (reading room) Lesesaal EG

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  2. Article ; Online: Cogito: automated and generic comparison of annotated genomic intervals.

    Bürger, Annika / Dugas, Martin

    BMC bioinformatics

    2022  Volume 23, Issue 1, Page(s) 315

    Abstract: Background: Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While the corresponding raw and processed data are made available through specialized public databases, the processed files are ... ...

    Abstract Background: Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While the corresponding raw and processed data are made available through specialized public databases, the processed files are usually limited to a specific research question. Hence, they are unsuitable for an unbiased, systematic overview of a complex dataset. However, possible combinations of different sample types and conditions grow exponentially with the amount of sample types and conditions. Therefore the risk to miss a correlation or to overrate an identified correlation should be mitigated in a complex dataset. Since reanalysis of a full study is rarely a viable option, new methods are needed to address these issues systematically, reliably, reproducibly and efficiently.
    Results: Cogito "COmpare annotated Genomic Intervals TOol" provides a workflow for an unbiased, structured overview and systematic analysis of complex genomic datasets consisting of different data types (e.g. RNA-seq, ChIP-seq) and conditions. Cogito is able to visualize valuable key information of genomic or epigenomic interval-based data, thereby providing a straightforward analysis approach for comparing different conditions. It supports getting an unbiased impression of a dataset and developing an appropriate analysis strategy for it. In addition to a text-based report, Cogito offers a fully customizable report as a starting point for further in-depth investigation.
    Conclusions: Cogito implements a novel approach to facilitate high-level overview analyses of complex datasets, and offers additional insights into the data without the need for a full, time-consuming reanalysis. The R/Bioconductor package is freely available at https://bioconductor.org/packages/release/bioc/html/Cogito.html , a comprehensive documentation with detailed descriptions and reproducible examples is included.
    MeSH term(s) Chromatin Immunoprecipitation Sequencing ; Epigenomics ; Genome ; Genomics ; Software
    Language English
    Publishing date 2022-08-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-022-04853-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Portal of Medical Data Models: Application in Federated Data Capture.

    Ganzinger, Matthias / Blumenstock, Max / Niklas, Christian / Dugas, Martin

    Studies in health technology and informatics

    2023  Volume 302, Page(s) 137–138

    Abstract: So far, the portal for medical data models allows its users to download medical forms in a standardized format. Importing data models into electronic data capture software involved a manual step of downloading and importing the files. Now, the portal was ...

    Abstract So far, the portal for medical data models allows its users to download medical forms in a standardized format. Importing data models into electronic data capture software involved a manual step of downloading and importing the files. Now, the portal was enhanced with a web services interface to allow electronic data capture systems to automatically download the forms. This mechanism can be used in federated studies to ensure that all partners are working with identical definitions of study forms.
    MeSH term(s) User-Computer Interface ; Software ; Records
    Language English
    Publishing date 2023-05-19
    Publishing country Netherlands
    Document type Journal Article
    ISSN 1879-8365
    ISSN (online) 1879-8365
    DOI 10.3233/SHTI230084
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Sharing clinical trial data.

    Dugas, Martin

    Lancet (London, England)

    2016  Volume 387, Issue 10035, Page(s) 2287

    MeSH term(s) Advisory Committees ; Clinical Trials as Topic ; Editorial Policies ; Humans ; Information Dissemination/methods
    Language English
    Publishing date 2016-06-04
    Publishing country England
    Document type Comment ; Letter
    ZDB-ID 3306-6
    ISSN 1474-547X ; 0023-7507 ; 0140-6736
    ISSN (online) 1474-547X
    ISSN 0023-7507 ; 0140-6736
    DOI 10.1016/S0140-6736(16)30683-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ua VI Zs.5: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 94: Show issues

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  5. Article ; Online: Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle.

    Tekath, Tobias / Dugas, Martin

    Bioinformatics (Oxford, England)

    2021  Volume 37, Issue 21, Page(s) 3781–3787

    Abstract: Motivation: Each year, the number of published bulk and single-cell RNA-seq datasets is growing exponentially. Studies analyzing such data are commonly looking at gene-level differences, while the collected RNA-seq data inherently represents reads of ... ...

    Abstract Motivation: Each year, the number of published bulk and single-cell RNA-seq datasets is growing exponentially. Studies analyzing such data are commonly looking at gene-level differences, while the collected RNA-seq data inherently represents reads of transcript isoform sequences. Utilizing transcriptomic quantifiers, RNA-seq reads can be attributed to specific isoforms, allowing for analysis of transcript-level differences. A differential transcript usage (DTU) analysis is testing for proportional differences in a gene's transcript composition, and has been of rising interest for many research questions, such as analysis of differential splicing or cell-type identification.
    Results: We present the R package DTUrtle, the first DTU analysis workflow for both bulk and single-cell RNA-seq datasets, and the first package to conduct a 'classical' DTU analysis in a single-cell context. DTUrtle extends established statistical frameworks, offers various result aggregation and visualization options and a novel detection probability score for tagged-end data. It has been successfully applied to bulk and single-cell RNA-seq data of human and mouse, confirming and extending key results. In addition, we present novel potential DTU applications like the identification of cell-type specific transcript isoforms as biomarkers.
    Availability and implementation: The R package DTUrtle is available at https://github.com/TobiTekath/DTUrtle with extensive vignettes and documentation at https://tobitekath.github.io/DTUrtle/.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Humans ; Animals ; Mice ; Single-Cell Gene Expression Analysis ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; Transcriptome ; Protein Isoforms
    Chemical Substances Protein Isoforms
    Language English
    Publishing date 2021-06-13
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btab629
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Cogito

    Annika Bürger / Martin Dugas

    BMC Bioinformatics, Vol 23, Iss 1, Pp 1-

    automated and generic comparison of annotated genomic intervals

    2022  Volume 16

    Abstract: Abstract Background Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While the corresponding raw and processed data are made available through specialized public databases, the processed ... ...

    Abstract Abstract Background Genetic and epigenetic biological studies often combine different types of experiments and multiple conditions. While the corresponding raw and processed data are made available through specialized public databases, the processed files are usually limited to a specific research question. Hence, they are unsuitable for an unbiased, systematic overview of a complex dataset. However, possible combinations of different sample types and conditions grow exponentially with the amount of sample types and conditions. Therefore the risk to miss a correlation or to overrate an identified correlation should be mitigated in a complex dataset. Since reanalysis of a full study is rarely a viable option, new methods are needed to address these issues systematically, reliably, reproducibly and efficiently. Results Cogito “COmpare annotated Genomic Intervals TOol” provides a workflow for an unbiased, structured overview and systematic analysis of complex genomic datasets consisting of different data types (e.g. RNA-seq, ChIP-seq) and conditions. Cogito is able to visualize valuable key information of genomic or epigenomic interval-based data, thereby providing a straightforward analysis approach for comparing different conditions. It supports getting an unbiased impression of a dataset and developing an appropriate analysis strategy for it. In addition to a text-based report, Cogito offers a fully customizable report as a starting point for further in-depth investigation. Conclusions Cogito implements a novel approach to facilitate high-level overview analyses of complex datasets, and offers additional insights into the data without the need for a full, time-consuming reanalysis. The R/Bioconductor package is freely available at https://bioconductor.org/packages/release/bioc/html/Cogito.html , a comprehensive documentation with detailed descriptions and reproducible examples is included.
    Keywords Correlation ; Statistics ; Genomic interval ; Reproducible data analysis ; Data integration ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  7. Article ; Online: Design of case report forms based on a public metadata registry: re-use of data elements to improve compatibility of data.

    Dugas, Martin

    Trials

    2016  Volume 17, Issue 1, Page(s) 566

    Abstract: Background: Clinical trials use many case report forms (CRFs) per patient. Because of the astronomical number of potential CRFs, data element re-use at the design stage is attractive to foster compatibility of data from different trials. The objective ... ...

    Abstract Background: Clinical trials use many case report forms (CRFs) per patient. Because of the astronomical number of potential CRFs, data element re-use at the design stage is attractive to foster compatibility of data from different trials. The objective of this work is to assess the technical feasibility of a CRF editor with connection to a public metadata registry (MDR) to support data element re-use.
    Results: Based on the Medical Data Models portal, an ISO/IEC 11179-compliant MDR was implemented and connected to a web-based CRF editor. Three use cases were implemented: re-use at the form, item group and data element levels.
    Conclusions: CRF design with data element re-use from a public MDR is feasible. A prototypic system is available. The main limitation of the system is the amount of available MDR content.
    Language English
    Publishing date 2016-11-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2040523-6
    ISSN 1745-6215 ; 1468-6694 ; 1468-6708
    ISSN (online) 1745-6215 ; 1468-6694
    ISSN 1468-6708
    DOI 10.1186/s13063-016-1691-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Integration of Patient-Reported Outcome Data Collected Via Web Applications and Mobile Apps Into a Nation-Wide COVID-19 Research Platform Using Fast Healthcare Interoperability Resources: Development Study.

    Oehm, Johannes Benedict / Riepenhausen, Sarah Luise / Storck, Michael / Dugas, Martin / Pryss, Rüdiger / Varghese, Julian

    Journal of medical Internet research

    2024  Volume 26, Page(s) e47846

    Abstract: Background: The Network University Medicine projects are an important part of the German COVID-19 research infrastructure. They comprise 2 subprojects: COVID-19 Data Exchange (CODEX) and Coordination on Mobile Pandemic Apps Best Practice and Solution ... ...

    Abstract Background: The Network University Medicine projects are an important part of the German COVID-19 research infrastructure. They comprise 2 subprojects: COVID-19 Data Exchange (CODEX) and Coordination on Mobile Pandemic Apps Best Practice and Solution Sharing (COMPASS). CODEX provides a centralized and secure data storage platform for research data, whereas in COMPASS, expert panels were gathered to develop a reference app framework for capturing patient-reported outcomes (PROs) that can be used by any researcher.
    Objective: Our study aims to integrate the data collected with the COMPASS reference app framework into the central CODEX platform, so that they can be used by secondary researchers. Although both projects used the Fast Healthcare Interoperability Resources (FHIR) standard, it was not used in a way that data could be shared directly. Given the short time frame and the parallel developments within the CODEX platform, a pragmatic and robust solution for an interface component was required.
    Methods: We have developed a means to facilitate and promote the use of the German Corona Consensus (GECCO) data set, a core data set for COVID-19 research in Germany. In this way, we ensured semantic interoperability for the app-collected PRO data with the COMPASS app. We also developed an interface component to sustain syntactic interoperability.
    Results: The use of different FHIR types by the COMPASS reference app framework (the general-purpose FHIR Questionnaire) and the CODEX platform (eg, Patient, Condition, and Observation) was found to be the most significant obstacle. Therefore, we developed an interface component that realigns the Questionnaire items with the corresponding items in the GECCO data set and provides the correct resources for the CODEX platform. We extended the existing COMPASS questionnaire editor with an import function for GECCO items, which also tags them for the interface component. This ensures syntactic interoperability and eases the reuse of the GECCO data set for researchers.
    Conclusions: This paper shows how PRO data, which are collected across various studies conducted by different researchers, can be captured in a research-compatible way. This means that the data can be shared with a central research infrastructure and be reused by other researchers to gain more insights about COVID-19 and its sequelae.
    MeSH term(s) Humans ; Mobile Applications ; COVID-19/epidemiology ; Consensus ; Data Collection ; Patient Reported Outcome Measures
    Language English
    Publishing date 2024-02-27
    Publishing country Canada
    Document type Journal Article
    ZDB-ID 2028830-X
    ISSN 1438-8871 ; 1438-8871
    ISSN (online) 1438-8871
    ISSN 1438-8871
    DOI 10.2196/47846
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Conference proceedings: A step toward anonymized medical image pipeline

    Naderi Boldaji, Hamidreza / Fritz-Kebede, Fleur / Dugas, Martin

    2023  , Page(s) Abstr. 119

    Event/congress 68. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie e. V. (GMDS); Heilbronn; Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie; 2023
    Keywords Medizin, Gesundheit ; anonymization ; DICOM ; pipeline
    Publishing date 2023-09-15
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Conference proceedings
    DOI 10.3205/23gmds166
    Database German Medical Science

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  10. Book: Medizinische Informatik und Bioinformatik

    Dugas, Martin / Schmidt, Karin

    ein Kompendium für Studium und Praxis ; mit 21 Tabellen

    (Springer-Lehrbuch)

    2003  

    Author's details Martin Dugas ; Karin Schmidt
    Series title Springer-Lehrbuch
    Keywords Medizinische Informatik ; Bioinformatik
    Subject Medizininformatik
    Language German
    Size VIII, 229 S. : Ill., graph. Darst.
    Publisher Springer
    Publishing place Berlin u.a.
    Publishing country Germany
    Document type Book
    HBZ-ID HT013428691
    ISBN 3-540-42568-3 ; 978-3-540-42568-7
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2002 A 5175 order for loan Magazin

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