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  1. Book: miRNomics

    Allmer, Jens / Yousef, Malik

    MicroRNA biology and computational analysis

    (Methods in molecular biology ; 2257 ; Springer protocols)

    2021  

    Author's details edited by Jens Allmer, Malik Yousef
    Series title Methods in molecular biology ; 2257
    Springer protocols
    Collection
    Keywords miRNS
    Subject microRNS ; Mikro-RNS ; miRNA ; microRNA
    Language English
    Size x, 507 Seiten, Illustrationen
    Edition Second edition
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT020884622
    ISBN 978-1-0716-1169-2 ; 9781071611708 ; 1-0716-1169-0 ; 1071611704
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -2257- verfügbar in Königswinter Königswinter

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  2. Article ; Online: Noncoding RNA Databases.

    Allmer, Jens

    Current pharmaceutical biotechnology

    2022  Volume 24, Issue 7, Page(s) 825–831

    Abstract: Diseases such as cancer are often defined by dysregulation of gene expression. Noncoding RNAs (ncRNA) such as microRNAs are involved in gene expression and cell-cell communication. Many other ncRNAs exist, such as circular RNAs and small nucleolar RNAs. ... ...

    Abstract Diseases such as cancer are often defined by dysregulation of gene expression. Noncoding RNAs (ncRNA) such as microRNAs are involved in gene expression and cell-cell communication. Many other ncRNAs exist, such as circular RNAs and small nucleolar RNAs. A wealth of knowledge is available for many ncRNAs, but the information is federated in many databases. A small number of highly complementary ncRNA databases are discussed in this work. Their relevance for cancer research is highlighted, and some of the current problems and limitations are revealed. A central or shared database enforcing community reporting and quality standards is needed in the future. • RNA-seq • Noncoding RNAs • Databases • Data repositories.
    MeSH term(s) Humans ; RNA, Long Noncoding/genetics ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Neoplasms/genetics
    Chemical Substances RNA, Long Noncoding ; RNA, Untranslated ; MicroRNAs
    Language English
    Publishing date 2022-05-24
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2132197-8
    ISSN 1873-4316 ; 1389-2010
    ISSN (online) 1873-4316
    ISSN 1389-2010
    DOI 10.2174/1570180819666220520124511
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6212: 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)

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  3. Book: miRNomics

    Yousef, Malik / Allmer, Jens

    microRNA biology and computational analysis

    (Methods in molecular biology ; 1107 ; Springer protocols)

    2014  

    Author's details ed. by Malik Yousef ; Jens Allmer
    Series title Methods in molecular biology ; 1107
    Springer protocols
    Collection
    Keywords miRNS
    Subject microRNS ; Mikro-RNS ; miRNA ; microRNA
    Language English
    Size XII, 333 S. : Ill., graph. Darst.
    Publisher Humana Press
    Publishing place New York, NY u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT018099341
    ISBN 978-1-62703-747-1 ; 9781627037488 ; 1-62703-747-0 ; 1627037489
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2013 A 4272 available for loan (reading room) Lesesaal EG

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  4. Article ; Online: Special issue on COVID-19 data integration opportunities and vaccine development strategies.

    Allmer, Jens

    Journal of integrative bioinformatics

    2021  Volume 18, Issue 1, Page(s) 1–2

    MeSH term(s) Biomedical Research ; COVID-19 ; COVID-19 Vaccines ; Humans ; SARS-CoV-2 ; Viral Vaccines
    Chemical Substances COVID-19 Vaccines ; Viral Vaccines
    Language English
    Publishing date 2021-03-22
    Publishing country Germany
    Document type Editorial
    ZDB-ID 2147212-9
    ISSN 1613-4516 ; 1432-4385
    ISSN (online) 1613-4516
    ISSN 1432-4385
    DOI 10.1515/jib-2021-0006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Conference proceedings: Transcriptomics to Combat the Coronavirus

    Allmer, Jens

    2021  , Page(s) Abstr. 146

    Event/congress 65th Annual Meeting of the German Association for Medical Informatics, Biometry and Epidemiology (GMDS), Meeting of the Central European Network (CEN: German Region, Austro-Swiss Region and Polish Region) of the International Biometric Society (IBS); Berlin; Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie; 2020
    Keywords Medizin, Gesundheit ; transcriptomics ; microRNA ; miRNA mimics ; Coronavirus ; medication
    Publishing date 2021-02-26
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Conference proceedings
    DOI 10.3205/20gmds083
    Database German Medical Science

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Community-wide collaboration is a must to reinstall trust in bioinformatics solutions and biomedical interpretation.

    Takan, Savaş / Allmer, Jens

    Journal of integrative bioinformatics

    2023  Volume 20, Issue 1

    Abstract: Science has become a highly competitive undertaking concerning, for example, resources, positions, students, and publications. At the same time, the number of journals presenting scientific findings skyrockets while the knowledge increase per manuscript ... ...

    Abstract Science has become a highly competitive undertaking concerning, for example, resources, positions, students, and publications. At the same time, the number of journals presenting scientific findings skyrockets while the knowledge increase per manuscript seems to be diminishing. Science has also become ever more dependent on computational analyses. For example, virtually all biomedical applications involve computational data analysis. The science community develops many computational tools, and there are numerous alternatives for many computational tasks. The same is true for workflow management systems, leading to a tremendous duplication of efforts. Software quality is often of low concern, and typically, a small dataset is used as a proof of principle to support rapid publication. Installation and usage of such tools are complicated, so virtual machine images, containers, and package managers are employed more frequently. These simplify installation and ease of use but do not solve the software quality issue and duplication of effort. We believe that a community-wide collaboration is needed to (a) ensure software quality, (b) increase reuse of code, (c) force proper software review, (c) increase testing, and (d) make interoperability more seamless. Such a science software ecosystem will overcome current issues and increase trust in current data analyses.
    MeSH term(s) Humans ; Ecosystem ; Trust ; Computational Biology/methods ; Software ; Workflow
    Language English
    Publishing date 2023-02-23
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2147212-9
    ISSN 1613-4516 ; 1613-4516
    ISSN (online) 1613-4516
    ISSN 1613-4516
    DOI 10.1515/jib-2022-0028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Conference proceedings: Big Data Requires Big Caution – OMICS Data Are No Exception

    Allmer, Jens

    2021  , Page(s) Abstr. 145

    Event/congress 65th Annual Meeting of the German Association for Medical Informatics, Biometry and Epidemiology (GMDS), Meeting of the Central European Network (CEN: German Region, Austro-Swiss Region and Polish Region) of the International Biometric Society (IBS); Berlin; Deutsche Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie; 2020
    Keywords Medizin, Gesundheit ; OMICS ; big data ; microRNA ; regulation ; RNA-seq ; transcriptomics
    Publishing date 2021-02-26
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Conference proceedings
    DOI 10.3205/20gmds012
    Database German Medical Science

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Towards an Internet of Science.

    Allmer, Jens

    Journal of integrative bioinformatics

    2019  Volume 16, Issue 3

    Abstract: Big data and complex analysis workflows (pipelines) are common issues in data driven science such as bioinformatics. Large amounts of computational tools are available for data analysis. Additionally, many workflow management systems to piece together ... ...

    Abstract Big data and complex analysis workflows (pipelines) are common issues in data driven science such as bioinformatics. Large amounts of computational tools are available for data analysis. Additionally, many workflow management systems to piece together such tools into data analysis pipelines have been developed. For example, more than 50 computational tools for read mapping are available representing a large amount of duplicated effort. Furthermore, it is unclear whether these tools are correct and only a few have a user base large enough to have encountered and reported most of the potential problems. Bringing together many largely untested tools in a computational pipeline must lead to unpredictable results. Yet, this is the current state. While presently data analysis is performed on personal computers/workstations/clusters, the future will see development and analysis shift to the cloud. None of the workflow management systems is ready for this transition. This presents the opportunity to build a new system, which will overcome current duplications of effort, introduce proper testing, allow for development and analysis in public and private clouds, and include reporting features leading to interactive documents.
    MeSH term(s) Computational Biology ; Internet ; Software ; User-Computer Interface ; Workflow
    Language English
    Publishing date 2019-05-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2147212-9
    ISSN 1613-4516 ; 1432-4385
    ISSN (online) 1613-4516
    ISSN 1432-4385
    DOI 10.1515/jib-2019-0024
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Medical Omics

    Allmer, Jens / Hofestädt, Ralf

    GMS Medizinische Informatik, Biometrie und Epidemiologie

    2023  Volume 19, Page(s) 7

    Title translation Medizinische Omik
    Keywords Medizin, Gesundheit ; Medical Omics ; Medizinische Omik
    Publishing date 2023-07-04
    Publisher German Medical Science GMS Publishing House; Düsseldorf
    Document type Article ; Online
    ISSN 1860-9171
    ISSN (online) 1860-9171
    DOI 10.3205/mibe000246
    Database German Medical Science

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  10. Article ; Online: Challenges for the development of automated RNA-seq analyses pipelines

    Beukers, Matthieu / Allmer, Jens

    Deutsche Gesellschaft fur Medizinische Informatik, Biometrie und Epidemiologie e.V. (GMDS)

    2023  Volume 19

    Abstract: Background: Transcriptional changes are hallmarks of development and disease. RNA sequencing (RNA-seq) allows qualitative and quantitative RNA expression analysis. Raw RNA-seq data passes through a multi-step computational pipeline to derive meaning from ...

    Abstract Background: Transcriptional changes are hallmarks of development and disease. RNA sequencing (RNA-seq) allows qualitative and quantitative RNA expression analysis. Raw RNA-seq data passes through a multi-step computational pipeline to derive meaning from such measurements. Often ad hoc scripts are used for such analyses. However, the use of workflow management systems (WFMS) should be encouraged in order to enhance result reproducibility, to establish best data analysis practices, and to share such data analysis workflows. In this work, we created RNA-seq data analysis workflows in three WFMS, namely Galaxy (free, open-source), KNIME (free, commercial, and partially open source), and CLC (commercial, closed source). Methods: These tools were compared using a variety of criteria ranging from installation to workflow execution and sharing. Four different workflows (WFs) performing RNA-seq data analysis were successfully constructed in all three WFMS. In summary, Galaxy currently provides the most significant number of analysis tools for RNA-seq, while CLC offers the most intuitive visualization. KNIME lags behind in these two aspects but excels at other levels, such as machine learning. Results: Since we already decided on the three WMFS, many of the criteria we suggest for WFMS evaluation do not apply to our situation and we focus on the WF creation here. While it was possible to construct RNA-seq analysis WFs with all three WFMS tools, the constructed WFs are different. These differences entailed disparate results, which were further sensitive to processing settings leading to different biological interpretations in the worst case. We further performed an in-depth analysis of challenges using the three WFMS and provide decision support for which WFMS to use in RNA-seq analysis. In short, RNA-seq is currently best performed using Galaxy, followed by CLC, and KNIME. The level of expertise with these WFMS should be taken into account during the WFMS selection. Finally, we share the WFs in the hope of reducing the ...
    Keywords RNA sequencing ; RNA-seq ; data analysis workflow ; workflow management system
    Subject code 020
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2187776-2
    ISSN 1860-9171 ; 1860-8779
    ISSN (online) 1860-9171
    ISSN 1860-8779
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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